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Adamoski D, M Dos Reis L, Mafra ACP, Corrêa-da-Silva F, Moraes-Vieira PMMD, Berindan-Neagoe I, Calin GA, Dias SMG. HuR controls glutaminase RNA metabolism. Nat Commun 2024; 15:5620. [PMID: 38965208 PMCID: PMC11224379 DOI: 10.1038/s41467-024-49874-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 06/21/2024] [Indexed: 07/06/2024] Open
Abstract
Glutaminase (GLS) is directly related to cell growth and tumor progression, making it a target for cancer treatment. The RNA-binding protein HuR (encoded by the ELAVL1 gene) influences mRNA stability and alternative splicing. Overexpression of ELAVL1 is common in several cancers, including breast cancer. Here we show that HuR regulates GLS mRNA alternative splicing and isoform translation/stability in breast cancer. Elevated ELAVL1 expression correlates with high levels of the glutaminase isoforms C (GAC) and kidney-type (KGA), which are associated with poor patient prognosis. Knocking down ELAVL1 reduces KGA and increases GAC levels, enhances glutamine anaplerosis into the TCA cycle, and drives cells towards glutamine dependence. Furthermore, we show that combining chemical inhibition of GLS with ELAVL1 silencing synergistically decreases breast cancer cell growth and invasion. These findings suggest that dual inhibition of GLS and HuR offers a therapeutic strategy for breast cancer treatment.
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Affiliation(s)
- Douglas Adamoski
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo, Brazil
- Graduate Program in Genetics and Molecular Biology, Institute of Biology University of Campinas (UNICAMP), Campinas, Sao Paulo, Brazil
| | - Larissa M Dos Reis
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo, Brazil
- Graduate Program in Genetics and Molecular Biology, Institute of Biology University of Campinas (UNICAMP), Campinas, Sao Paulo, Brazil
- Department of Genetics, Evolution, Microbiology, and Immunology, Laboratory of Immunometabolism, Institute of Biology, University of Campinas-UNICAMP, Campinas, SP, Brazil
| | - Ana Carolina Paschoalini Mafra
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo, Brazil
- Graduate Program in Genetics and Molecular Biology, Institute of Biology University of Campinas (UNICAMP), Campinas, Sao Paulo, Brazil
- Department of Radiation Oncology, Washington University School of Medicine, S. Louis, MO, USA
| | - Felipe Corrêa-da-Silva
- Graduate Program in Genetics and Molecular Biology, Institute of Biology University of Campinas (UNICAMP), Campinas, Sao Paulo, Brazil
- Department of Genetics, Evolution, Microbiology, and Immunology, Laboratory of Immunometabolism, Institute of Biology, University of Campinas-UNICAMP, Campinas, SP, Brazil
| | - Pedro Manoel Mendes de Moraes-Vieira
- Department of Genetics, Evolution, Microbiology, and Immunology, Laboratory of Immunometabolism, Institute of Biology, University of Campinas-UNICAMP, Campinas, SP, Brazil
| | - Ioana Berindan-Neagoe
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, University of Medicine and Pharmacy "Iuliu-Hatieganu", Cluj-Napoca, Romania
| | - George A Calin
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Center for RNA Inference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sandra Martha Gomes Dias
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo, Brazil.
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2
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Acharya P, Parkins S, Tranter M. RNA binding proteins as mediators of pathological cardiac remodeling. Front Cell Dev Biol 2024; 12:1368097. [PMID: 38818408 PMCID: PMC11137256 DOI: 10.3389/fcell.2024.1368097] [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: 01/09/2024] [Accepted: 05/01/2024] [Indexed: 06/01/2024] Open
Abstract
RNA binding proteins (RBPs) play a central in the post-transcriptional regulation of gene expression, which can account for up to 50% of all variations in protein expression within a cell. Following their binding to target RNAs, RBPs most typically confer changes in gene expression through modulation of alternative spicing, RNA stabilization/degradation, or ribosome loading/translation rate. All of these post-transcriptional regulatory processes have been shown to play a functional role in pathological cardiac remodeling, and a growing body of evidence is beginning to identify the mechanistic contribution of individual RBPs and their cardiac RNA targets. This review highlights the mechanisms of RBP-dependent post-transcriptional gene regulation in cardiomyocytes and fibroblasts and our current understanding of how RNA binding proteins functionally contribute to pathological cardiac remodeling.
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Affiliation(s)
- Pooja Acharya
- Department of Molecular Medicine and Therapeutics, The Ohio State University Wexner Medical Center, Columbus, OH, United States
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, Columbus, OH, United States
| | - Sharon Parkins
- Department of Molecular Medicine and Therapeutics, The Ohio State University Wexner Medical Center, Columbus, OH, United States
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, Columbus, OH, United States
- Department of Internal Medicine, Division of Cardiovascular Health and Disease, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Michael Tranter
- Department of Molecular Medicine and Therapeutics, The Ohio State University Wexner Medical Center, Columbus, OH, United States
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, Columbus, OH, United States
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3
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Wu J, Niu L, Yang K, Xu J, Zhang D, Ling J, Xia P, Wu Y, Liu X, Liu J, Zhang J, Yu P. The role and mechanism of RNA-binding proteins in bone metabolism and osteoporosis. Ageing Res Rev 2024; 96:102234. [PMID: 38367813 DOI: 10.1016/j.arr.2024.102234] [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: 10/11/2023] [Revised: 02/06/2024] [Accepted: 02/13/2024] [Indexed: 02/19/2024]
Abstract
Osteoporosis is a prevalent chronic metabolic bone disease that poses a significant risk of fractures or mortality in elderly individuals. Its pathophysiological basis is often attributed to postmenopausal estrogen deficiency and natural aging, making the progression of primary osteoporosis among elderly people, especially older women, seemingly inevitable. The treatment and prevention of osteoporosis progression have been extensively discussed. Recently, as researchers delve deeper into the molecular biological mechanisms of bone remodeling, they have come to realize the crucial role of posttranscriptional gene control in bone metabolism homeostasis. RNA-binding proteins, as essential actors in posttranscriptional activities, may exert influence on osteoporosis progression by regulating the RNA life cycle. This review compiles recent findings on the involvement of RNA-binding proteins in abnormal bone metabolism in osteoporosis and describes the impact of some key RNA-binding proteins on bone metabolism regulation. Additionally, we explore the potential and rationale for modulating RNA-binding proteins as a means of treating osteoporosis, with an overview of drugs that target these proteins.
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Affiliation(s)
- Jiaqiang Wu
- Jiujiang Clinical Precision Medicine Research Center, Jiujiang, Jiangxi, 332000, China; The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, China; Department of General Surgery, First Medical Center of the Chinese PLA General Hospital, Beijing, China
| | - Liyan Niu
- HuanKui College of Nanchang University, Nanchang 330006, China
| | - Kangping Yang
- The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
| | - Jingdong Xu
- Queen Mary College of Nanchang University, Nanchang 330006, China
| | - Deju Zhang
- Food and Nutritional Sciences, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, 999077, Hong Kong, China
| | - Jitao Ling
- Department of Endocrinology and Metabolism, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, No. 1, Minde Road, Donghu District, Nanchang 330006, China; Institute for the Study of Endocrinology and Metabolism in Jiangxi Province, Nanchang 330006, China
| | - Panpan Xia
- Department of Endocrinology and Metabolism, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, No. 1, Minde Road, Donghu District, Nanchang 330006, China; Institute for the Study of Endocrinology and Metabolism in Jiangxi Province, Nanchang 330006, China
| | - Yuting Wu
- Department of Endocrinology and Metabolism, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, No. 1, Minde Road, Donghu District, Nanchang 330006, China; Institute for the Study of Endocrinology and Metabolism in Jiangxi Province, Nanchang 330006, China
| | - Xiao Liu
- Department of Cardiology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
| | - Jianping Liu
- Department of Endocrinology and Metabolism, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, No. 1, Minde Road, Donghu District, Nanchang 330006, China; Institute for the Study of Endocrinology and Metabolism in Jiangxi Province, Nanchang 330006, China
| | - Jing Zhang
- Jiujiang Clinical Precision Medicine Research Center, Jiujiang, Jiangxi, 332000, China; Department of Anesthesiology, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, 330006, China.
| | - Peng Yu
- Jiujiang Clinical Precision Medicine Research Center, Jiujiang, Jiangxi, 332000, China; Department of Endocrinology and Metabolism, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, No. 1, Minde Road, Donghu District, Nanchang 330006, China; Institute for the Study of Endocrinology and Metabolism in Jiangxi Province, Nanchang 330006, China.
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4
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Cao J, Wei Z, Nie Y, Chen HZ. Therapeutic potential of alternative splicing in cardiovascular diseases. EBioMedicine 2024; 101:104995. [PMID: 38350330 PMCID: PMC10874720 DOI: 10.1016/j.ebiom.2024.104995] [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: 09/24/2023] [Revised: 01/19/2024] [Accepted: 01/21/2024] [Indexed: 02/15/2024] Open
Abstract
RNA splicing is an important RNA processing step required by multiexon protein-coding mRNAs and some noncoding RNAs. Precise RNA splicing is required for maintaining gene and cell function; however, mis-spliced RNA transcripts can lead to loss- or gain-of-function effects in human diseases. Mis-spliced RNAs induced by gene mutations or the dysregulation of splicing regulators may result in frameshifts, nonsense-mediated decay (NMD), or inclusion/exclusion of exons. Genetic animal models have characterised multiple splicing factors required for cardiac development or function. Moreover, sarcomeric and ion channel genes, which are closely associated with cardiovascular function and disease, are hotspots for AS. Here, we summarise splicing factors and their targets that are associated with cardiovascular diseases, introduce some therapies potentially related to pathological AS targets, and raise outstanding questions and future directions in this field.
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Affiliation(s)
- Jun Cao
- College of Chemistry and Life Science, Beijing University of Technology, Beijing, 100124, PR China; University of Texas Medical Branch at Galveston, TX, 77555, USA
| | - Ziyu Wei
- Department of Biochemistry & Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Yu Nie
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100037, China.
| | - Hou-Zao Chen
- Department of Biochemistry & Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China; Medical Epigenetics Research Center, Chinese Academy of Medical Sciences, Beijing, China.
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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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6
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Podszywalow-Bartnicka P, Neugebauer KM. Multiple roles for AU-rich RNA binding proteins in the development of haematologic malignancies and their resistance to chemotherapy. RNA Biol 2024; 21:1-17. [PMID: 38798162 PMCID: PMC11135835 DOI: 10.1080/15476286.2024.2346688] [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] [Accepted: 04/08/2024] [Indexed: 05/29/2024] Open
Abstract
Post-transcriptional regulation by RNA binding proteins can determine gene expression levels and drive changes in cancer cell proteomes. Identifying mechanisms of protein-RNA binding, including preferred sequence motifs bound in vivo, provides insights into protein-RNA networks and how they impact mRNA structure, function, and stability. In this review, we will focus on proteins that bind to AU-rich elements (AREs) in nascent or mature mRNA where they play roles in response to stresses encountered by cancer cells. ARE-binding proteins (ARE-BPs) specifically impact alternative splicing, stability, decay and translation, and formation of RNA-rich biomolecular condensates like cytoplasmic stress granules (SGs). For example, recent findings highlight the role of ARE-BPs - like TIAR and HUR - in chemotherapy resistance and in translational regulation of mRNAs encoding pro-inflammatory cytokines. We will discuss emerging evidence that different modes of ARE-BP activity impact leukaemia and lymphoma development, progression, adaptation to microenvironment and chemotherapy resistance.
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Affiliation(s)
- Paulina Podszywalow-Bartnicka
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, CT, USA
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Karla M. Neugebauer
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, CT, USA
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7
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Finan JM, Sutton TL, Dixon DA, Brody JR. Targeting the RNA-Binding Protein HuR in Cancer. Cancer Res 2023; 83:3507-3516. [PMID: 37683260 DOI: 10.1158/0008-5472.can-23-0972] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 07/12/2023] [Accepted: 09/06/2023] [Indexed: 09/10/2023]
Abstract
The RNA-binding protein human antigen R (HuR) is a well-established regulator of gene expression at the posttranscriptional level. Its dysregulation has been implicated in various human diseases, particularly cancer. In cancer, HuR is considered "active" when it shows increased subcellular localization in the cytoplasm, in addition to its normal nuclear localization. Cytoplasmic HuR plays a crucial role in stabilizing and enhancing the translation of prosurvival mRNAs that are involved in stress responses relevant to cancer progression, such as hypoxia, radiotherapy, and chemotherapy. In general, due to HuR's abundance and function in cancer cells compared with normal cells, it is an appealing target for oncology research. Exploiting the principles underlying HuR's role in tumorigenesis and resistance to stressors, targeting HuR has the potential for synergy with existing and novel oncologic therapies. This review aims to explore HuR's role in homeostasis and cancer pathophysiology, as well as current targeting strategies, which include silencing HuR expression, preventing its translocation and dimerization from the nucleus to the cytoplasm, and inhibiting mRNA binding. Furthermore, this review will discuss recent studies investigating the potential synergy between HuR inhibition and traditional chemotherapeutics.
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Affiliation(s)
- Jennifer M Finan
- Department of Surgery, Oregon Health & Science University, Portland, Oregon
| | - Thomas L Sutton
- Department of Surgery, Oregon Health & Science University, Portland, Oregon
| | - Dan A Dixon
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas
| | - Jonathan R Brody
- Department of Surgery, Oregon Health & Science University, Portland, Oregon
- Brenden-Colson Center for Pancreatic Care, Oregon Health & Science University, Portland, Oregon
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Choi S, Cho N, Kim EM, Kim KK. The role of alternative pre-mRNA splicing in cancer progression. Cancer Cell Int 2023; 23:249. [PMID: 37875914 PMCID: PMC10594706 DOI: 10.1186/s12935-023-03094-3] [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: 09/06/2023] [Accepted: 10/06/2023] [Indexed: 10/26/2023] Open
Abstract
Alternative pre-mRNA splicing is a critical mechanism that generates multiple mRNA from a single gene, thereby increasing the diversity of the proteome. Recent research has highlighted the significance of specific splicing isoforms in cellular processes, particularly in regulating cell numbers. In this review, we examine the current understanding of the role of alternative splicing in controlling cancer cell growth and discuss specific splicing factors and isoforms and their molecular mechanisms in cancer progression. These isoforms have been found to intricately control signaling pathways crucial for cell cycle progression, proliferation, and apoptosis. Furthermore, studies have elucidated the characteristics and functional importance of splicing factors that influence cell numbers. Abnormal expression of oncogenic splicing isoforms and splicing factors, as well as disruptions in splicing caused by genetic mutations, have been implicated in the development and progression of tumors. Collectively, these findings provide valuable insights into the complex interplay between alternative splicing and cell proliferation, thereby suggesting the potential of alternative splicing as a therapeutic target for cancer.
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Affiliation(s)
- Sunkyung Choi
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Namjoon Cho
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Eun-Mi Kim
- Department of Predictive Toxicology, Korea Institute of Toxicology, Daejeon, 34114, Republic of Korea.
| | - Kee K Kim
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea.
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9
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Banerjee S, Galarza-Muñoz G, Garcia-Blanco MA. Role of RNA Alternative Splicing in T Cell Function and Disease. Genes (Basel) 2023; 14:1896. [PMID: 37895245 PMCID: PMC10606310 DOI: 10.3390/genes14101896] [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: 09/12/2023] [Revised: 09/24/2023] [Accepted: 09/26/2023] [Indexed: 10/29/2023] Open
Abstract
Alternative RNA splicing, a ubiquitous mechanism of gene regulation in eukaryotes, expands genome coding capacity and proteomic diversity. It has essential roles in all aspects of human physiology, including immunity. This review highlights the importance of RNA alternative splicing in regulating immune T cell function. We discuss how mutations that affect the alternative splicing of T cell factors can contribute to abnormal T cell function and ultimately lead to autoimmune diseases. We also explore the potential applications of strategies that target the alternative splicing changes of T cell factors. These strategies could help design therapeutic approaches to treat autoimmune disorders and improve immunotherapy.
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Affiliation(s)
- Shefali Banerjee
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA 22903, USA;
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77550, USA
| | | | - Mariano A. Garcia-Blanco
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA 22903, USA;
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77550, USA
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10
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Vujovic A, de Rooij L, Chahi AK, Chen HT, Yee BA, Loganathan SK, Liu L, Chan DC, Tajik A, Tsao E, Moreira S, Joshi P, Xu J, Wong N, Balde Z, Jahangiri S, Zandi S, Aigner S, Dick JE, Minden MD, Schramek D, Yeo GW, Hope KJ. In Vivo Screening Unveils Pervasive RNA-Binding Protein Dependencies in Leukemic Stem Cells and Identifies ELAVL1 as a Therapeutic Target. Blood Cancer Discov 2023; 4:180-207. [PMID: 36763002 PMCID: PMC10150294 DOI: 10.1158/2643-3230.bcd-22-0086] [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: 05/17/2022] [Revised: 11/30/2022] [Accepted: 02/06/2023] [Indexed: 02/11/2023] Open
Abstract
Acute myeloid leukemia (AML) is fueled by leukemic stem cells (LSC) whose determinants are challenging to discern from hematopoietic stem cells (HSC) or uncover by approaches focused on general cell properties. We have identified a set of RNA-binding proteins (RBP) selectively enriched in human AML LSCs. Using an in vivo two-step CRISPR-Cas9 screen to assay stem cell functionality, we found 32 RBPs essential for LSCs in MLL-AF9;NrasG12D AML. Loss-of-function approaches targeting key hit RBP ELAVL1 compromised LSC-driven in vivo leukemic reconstitution, and selectively depleted primitive malignant versus healthy cells. Integrative multiomics revealed differentiation, splicing, and mitochondrial metabolism as key features defining the leukemic ELAVL1-mRNA interactome with mitochondrial import protein, TOMM34, being a direct ELAVL1-stabilized target whose repression impairs AML propagation. Altogether, using a stem cell-adapted in vivo CRISPR screen, this work demonstrates pervasive reliance on RBPs as regulators of LSCs and highlights their potential as therapeutic targets in AML. SIGNIFICANCE LSC-targeted therapies remain a significant unmet need in AML. We developed a stem-cell-adapted in vivo CRISPR screen to identify key LSC drivers. We uncover widespread RNA-binding protein dependencies in LSCs, including ELAVL1, which we identify as a novel therapeutic vulnerability through its regulation of mitochondrial metabolism. This article is highlighted in the In This Issue feature, p. 171.
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Affiliation(s)
- Ana Vujovic
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Laura de Rooij
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Ava Keyvani Chahi
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - He Tian Chen
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Brian A. Yee
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California
| | - Sampath K. Loganathan
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada
| | - Lina Liu
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Derek C.H. Chan
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Amanda Tajik
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Emily Tsao
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Steven Moreira
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Pratik Joshi
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Joshua Xu
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Nicholas Wong
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Zaldy Balde
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Soheil Jahangiri
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Sasan Zandi
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Stefan Aigner
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California
| | - John E. Dick
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Mark D. Minden
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- Faculty of Medicine, University of Toronto, Toronto, Canada
| | - Daniel Schramek
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Gene W. Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California
| | - Kristin J. Hope
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
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11
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Zhou Y, Chen L, Ni S. Identification and functional characterization of zebrafish ELAVL1b as a new member of antimicrobial protein. FISH & SHELLFISH IMMUNOLOGY 2023; 135:108671. [PMID: 36893928 DOI: 10.1016/j.fsi.2023.108671] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 02/21/2023] [Accepted: 03/07/2023] [Indexed: 06/18/2023]
Abstract
Previous studies have shown that ELAVL1 play multiple roles and may be associated with immune response. However, it remains largely unknown about the direct roles of ELAVL1 during a bacterial infection. After reporting the zebrafish ELAVL1a is a maternal immune factor that can protect zebrafish embryos from bacterial infection, here we studied the immune function of zebrafish ELAVL1b. In this study, we showed that zebrafish elavl1b was markedly up-regulated by LTA and LPS treatment, suggesting it may be involved in anti-infectious responses. We also showed that zebrafish recombinant ELAVL1b (rELAVL1b) could bind to both the Gram-positive and negative bacteria M. luteus and S. aureus, E. coli and A. hydrophila as well as their signature molecules LTA and LPS, hinting it may act as a pattern recognition receptor, capable of identifying pathogens. In addition, rELAVL1b could directly kill the Gram-positive and negative bacteria tested via inducing membrane depolarization and intracellular ROS production. Collectively, our results indicate that zebrafish ELAVL1b plays an immune-relevant role as a newly-characterized antimicrobial protein. This work also provides further information to understand the biological roles of ELAVL family and the innate immunity in vertebrates.
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Affiliation(s)
- Yang Zhou
- School of bioscience and technology, Weifang medical university, Weifang, 261053, Shandong Province, China
| | - Lu Chen
- School of pharmacy, Weifang medical university, Weifang, 261053, Shandong Province, China
| | - Shousheng Ni
- School of bioscience and technology, Weifang medical university, Weifang, 261053, Shandong Province, China.
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12
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Ma Q, Lu Q, Lei X, Zhao J, Sun W, Huang D, Zhu Q, Xu Q. Relationship between HuR and tumor drug resistance. Clin Transl Oncol 2023:10.1007/s12094-023-03109-5. [PMID: 36947360 DOI: 10.1007/s12094-023-03109-5] [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: 08/21/2022] [Accepted: 01/31/2023] [Indexed: 03/23/2023]
Abstract
Human resistance protein R (HuR), also known as embryonic lethal abnormal visual-like protein (ELAVL1), is an RNA-binding protein widely expressed in vivo that affects the mRNA stability of targeted and is involved in post-transcriptional regulation. Recent studies have shown that HuR is aberrantly expressed in different human cancers and is an essential factor in poor clinical prognosis. The role of HuR in numerous tumors suggests that it could be a new target for tumor therapy and as a marker for efficacy and prognostic assessment. This review focuses on the relationship between HuR and drug resistance in different tumors and briefly describes the structure, function, and inhibitors of HuR. We summarize the mechanisms by which HuR causes tumor resistance and the molecular targets affected.
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Affiliation(s)
- Qiancheng Ma
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Qiliang Lu
- Qingdao Medical College, Qingdao University, Qingdao, 266000, China
| | | | - Jie Zhao
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Wen Sun
- Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Dongsheng Huang
- The Key Laboratory of Tumor Molecular Diagnosis, and Individualized Medicine of Zhejiang Province, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, 310014, China.
| | - Qing Zhu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Qiuran Xu
- The Key Laboratory of Tumor Molecular Diagnosis, and Individualized Medicine of Zhejiang Province, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, 310014, China.
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13
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Sheta M, Yoshida K, Kanemoto H, Calderwood SK, Eguchi T. Stress-Inducible SCAND Factors Suppress the Stress Response and Are Biomarkers for Enhanced Prognosis in Cancers. Int J Mol Sci 2023; 24:ijms24065168. [PMID: 36982267 PMCID: PMC10049278 DOI: 10.3390/ijms24065168] [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: 01/24/2023] [Revised: 03/02/2023] [Accepted: 03/06/2023] [Indexed: 03/11/2023] Open
Abstract
The cell stress response is an essential system present in every cell for responding and adapting to environmental stimulations. A major program for stress response is the heat shock factor (HSF)–heat shock protein (HSP) system that maintains proteostasis in cells and promotes cancer progression. However, less is known about how the cell stress response is regulated by alternative transcription factors. Here, we show that the SCAN domain (SCAND)-containing transcription factors (SCAN-TFs) are involved in repressing the stress response in cancer. SCAND1 and SCAND2 are SCAND-only proteins that can hetero-oligomerize with SCAN-zinc finger transcription factors, such as MZF1(ZSCAN6), for accessing DNA and transcriptionally co-repressing target genes. We found that heat stress induced the expression of SCAND1, SCAND2, and MZF1 bound to HSP90 gene promoter regions in prostate cancer cells. Moreover, heat stress switched the transcript variants’ expression from long noncoding RNA (lncRNA-SCAND2P) to protein-coding mRNA of SCAND2, potentially by regulating alternative splicing. High expression of HSP90AA1 correlated with poorer prognoses in several cancer types, although SCAND1 and MZF1 blocked the heat shock responsiveness of HSP90AA1 in prostate cancer cells. Consistent with this, gene expression of SCAND2, SCAND1, and MZF1 was negatively correlated with HSP90 gene expression in prostate adenocarcinoma. By searching databases of patient-derived tumor samples, we found that MZF1 and SCAND2 RNA were more highly expressed in normal tissues than in tumor tissues in several cancer types. Of note, high RNA expression of SCAND2, SCAND1, and MZF1 correlated with enhanced prognoses of pancreatic cancer and head and neck cancers. Additionally, high expression of SCAND2 RNA was correlated with better prognoses of lung adenocarcinoma and sarcoma. These data suggest that the stress-inducible SCAN-TFs can function as a feedback system, suppressing excessive stress response and inhibiting cancers.
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Affiliation(s)
- Mona Sheta
- Department of Dental Pharmacology, Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8525, Japan
- Department of Cancer Biology, National Cancer Institute, Cairo University, Cairo 11796, Egypt
| | - Kunihiro Yoshida
- Department of Dental Pharmacology, Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8525, Japan
- Department of Oral and Maxillofacial Surgery, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8525, Japan
| | - Hideka Kanemoto
- Department of Oral and Maxillofacial Surgery, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8525, Japan
| | - Stuart K. Calderwood
- Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Takanori Eguchi
- Department of Dental Pharmacology, Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8525, Japan
- Correspondence: ; Tel.: +81-86-235-6661
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14
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Wang L, Ji Y, Chen Y, Bai J, Gao P, Feng P. A splicing silencer in SMN2 intron 6 is critical in spinal muscular atrophy. Hum Mol Genet 2023; 32:971-983. [PMID: 36255739 DOI: 10.1093/hmg/ddac260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 10/10/2022] [Accepted: 10/14/2022] [Indexed: 11/14/2022] Open
Abstract
Spinal muscular atrophy (SMA) is a fatal neuromuscular disease caused by homozygous deletions or mutations of the SMN1 gene. SMN2 is a paralogous gene of SMN1 and a modifying gene of SMA. A better understanding of how SMN2 exon 7 splicing is regulated helps discover new therapeutic targets for SMA therapy. Based on an antisense walk method to map exonic and intronic splicing silencers (ESSs and ISSs) in SMN2 exon 7 and the proximal regions of its flanking introns, we identified one ISS (ISS6-KH) at upstream of the branch point site in intron 6. By using mutagenesis-coupled RT-PCR with SMN1/2 minigenes, immunochromatography, overexpression and siRNA-knockdown, we found this ISS consists of a bipartite hnRNP A1 binding cis-element and a poly-U sequence located between the proximal hnRNP A1 binding site (UAGCUA) and the branch site. Both HuR and hnRNP C1 proteins promote exon 7 skipping through the poly-U stretch. Mutations or deletions of these motifs lead to efficient SMN2 exon 7 inclusion comparable to SMN1 gene. Furthermore, we identified an optimal antisense oligonucleotide that binds the intron six ISS and causes striking exon 7 inclusion in the SMN2 gene in patient fibroblasts and SMA mouse model. Our findings demonstrate that this novel ISS plays an important role in SMN2 exon 7 skipping and highlight a new therapeutic target for SMA therapy.
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Affiliation(s)
- Li Wang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Yinfeng Ji
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Yuqing Chen
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Jialin Bai
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Peng Gao
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Pengchao Feng
- Nanjing Antisense Biopharmaceutical Co., Ltd, Nanjing 210046, China
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15
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Ghram M, Morris G, Culjkovic-Kraljacic B, Mars JC, Gendron P, Skrabanek L, Revuelta MV, Cerchietti L, Guzman ML, Borden KLB. The eukaryotic translation initiation factor eIF4E reprograms alternative splicing. EMBO J 2023; 42:e110496. [PMID: 36843541 PMCID: PMC10068332 DOI: 10.15252/embj.2021110496] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/28/2023] Open
Abstract
Aberrant splicing is typically attributed to splice-factor (SF) mutation and contributes to malignancies including acute myeloid leukemia (AML). Here, we discovered a mutation-independent means to extensively reprogram alternative splicing (AS). We showed that the dysregulated expression of eukaryotic translation initiation factor eIF4E elevated selective splice-factor production, thereby impacting multiple spliceosome complexes, including factors mutated in AML such as SF3B1 and U2AF1. These changes generated a splicing landscape that predominantly supported altered splice-site selection for ~800 transcripts in cell lines and ~4,600 transcripts in specimens from high-eIF4E AML patients otherwise harboring no known SF mutations. Nuclear RNA immunoprecipitations, export assays, polysome analyses, and mutational studies together revealed that eIF4E primarily increased SF production via its nuclear RNA export activity. By contrast, eIF4E dysregulation did not induce known SF mutations or alter spliceosome number. eIF4E interacted with the spliceosome and some pre-mRNAs, suggesting its direct involvement in specific splicing events. eIF4E induced simultaneous effects on numerous SF proteins, resulting in a much larger range of splicing alterations than in the case of mutation or dysregulation of individual SFs and providing a novel paradigm for splicing control and dysregulation.
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Affiliation(s)
- Mehdi Ghram
- Department of Pathology and Cell Biology, Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC, Canada.,Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, Canada
| | - Gavin Morris
- Department of Pathology and Cell Biology, Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC, Canada.,Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, Canada
| | - Biljana Culjkovic-Kraljacic
- Department of Pathology and Cell Biology, Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC, Canada.,Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, Canada
| | - Jean-Clement Mars
- Department of Pathology and Cell Biology, Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC, Canada.,Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, Canada
| | - Patrick Gendron
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, Canada
| | - Lucy Skrabanek
- Department of Physiology and Biophysics, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA.,Applied Bioinformatics Core, Weill Cornell Medicine, New York, NY, USA
| | - Maria Victoria Revuelta
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Leandro Cerchietti
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Monica L Guzman
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Katherine L B Borden
- Department of Pathology and Cell Biology, Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC, Canada.,Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, Canada
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16
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Fisher E, Feng J. RNA splicing regulators play critical roles in neurogenesis. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1728. [PMID: 35388651 DOI: 10.1002/wrna.1728] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/07/2022] [Accepted: 03/09/2022] [Indexed: 06/14/2023]
Abstract
Alternative RNA splicing increases transcript diversity in different cell types and under varying conditions. It is executed with the help of RNA splicing regulators (RSRs), which are operationally defined as RNA-binding proteins (RBPs) that regulate alternative splicing, but not directly catalyzing the chemical reactions of splicing. By systematically searching for RBPs and manually identifying those that regulate splicing, we curated 305 RSRs in the human genome. Surprisingly, most of the RSRs are involved in neurogenesis. Among these RSRs, we focus on nine families (PTBP, NOVA, RBFOX, ELAVL, CELF, DBHS, MSI, PCBP, and MBNL) that play essential roles in the neurogenic pathway. A better understanding of their functions will provide novel insights into the role of splicing in brain development, health, and disease. This comprehensive review serves as a stepping-stone to explore the diverse and complex set of RSRs as fundamental regulators of neural development. This article is categorized under: RNA-Based Catalysis > RNA Catalysis in Splicing and Translation RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
- Emily Fisher
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, New York, USA
- Veterans Affairs Western New York Healthcare System, Buffalo, New York, USA
| | - Jian Feng
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, New York, USA
- Veterans Affairs Western New York Healthcare System, Buffalo, New York, USA
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17
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Imbriano C, Belluti S. Histone Marks-Dependent Effect on Alternative Splicing: New Perspectives for Targeted Splicing Modulation in Cancer? Int J Mol Sci 2022; 23:ijms23158304. [PMID: 35955433 PMCID: PMC9368390 DOI: 10.3390/ijms23158304] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/23/2022] [Accepted: 07/25/2022] [Indexed: 11/16/2022] Open
Abstract
Alternative splicing (AS) is a tightly regulated mechanism that generates the complex human proteome from a small number of genes. Cis-regulatory RNA motifs in exons and introns control AS, recruiting positive and negative trans-acting splicing regulators. At a higher level, chromatin affects splicing events. Growing evidence indicates that the popular histone code hypothesis can be extended to RNA-level processes, such as AS. In addition to nucleosome positioning, which can generate transcriptional barriers to shape the final splicing outcome, histone post-translational modifications can contribute to the detailed regulation of single exon inclusion/exclusion. A histone-based system can identify alternatively spliced chromatin stretches, affecting RNAPII elongation locally or recruiting splicing components via adaptor complexes. In tumor cells, several mechanisms trigger misregulated AS events and produce cancer-associated transcripts. On a genome-wide level, aberrant AS can be the consequence of dysfunctional epigenetic splicing code, including altered enrichment in histone post-translational modifications. This review describes the main findings related to the effect of histone modifications and variants on splicing outcome and how a dysfunctional epigenetic splicing code triggers aberrant AS in cancer. In addition, it highlights recent advances in programmable DNA-targeting technologies and their possible application for AS targeted epigenetic modulation.
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18
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Hu Antigen R (HuR) Protein Structure, Function and Regulation in Hepatobiliary Tumors. Cancers (Basel) 2022; 14:cancers14112666. [PMID: 35681645 PMCID: PMC9179498 DOI: 10.3390/cancers14112666] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/19/2022] [Accepted: 05/23/2022] [Indexed: 12/10/2022] Open
Abstract
Simple Summary Hepatobiliary tumors are a group of primary malignancies encompassing the liver, the intra- and extra-hepatic biliary tracts, and the gall bladder. Within the liver, hepatocellular carcinoma (HCC) is the most common type of primary cancer, which is, also, representing the third-most recurrent cause of cancer-associated death and the sixth-most prevalent type of tumor worldwide, nowadays. Although less frequent, cholangiocarcinoma (CCA) is, currently, a fatal cancer with limited therapeutic options. Here, we review the regulatory role of Hu antigen R (HuR), a ubiquitous member of the ELAV/Hu family of RNA-binding proteins (RBPs), in the pathogenesis, progression, and treatment of HCC and CCA. Overall, HuR is proposed as a valuable diagnostic and prognostic marker, as well as a therapeutic target in hepatobiliary cancers. Therefore, novel therapeutic approaches that can selectively modulate HuR function appear to be highly attractive for the clinical management of these types of tumors. Abstract Hu antigen R (HuR) is a 36-kDa ubiquitous member of the ELAV/Hu family of RNA-binding proteins (RBPs), which plays an important role as a post-transcriptional regulator of specific RNAs under physiological and pathological conditions, including cancer. Herein, we review HuR protein structure, function, and its regulation, as well as its implications in the pathogenesis, progression, and treatment of hepatobiliary cancers. In particular, we focus on hepatocellular carcinoma (HCC) and cholangiocarcinoma (CCA), tumors where the increased cytoplasmic localization of HuR and activity are proposed, as valuable diagnostic and prognostic markers. An overview of the main regulatory axes involving HuR, which are associated with cell proliferation, invasion, metastasis, apoptosis, and autophagy in HCC, is provided. These include the transcriptional, post-transcriptional, and post-translational modulators of HuR function, in addition to HuR target transcripts. Finally, whereas studies addressing the relevance of targeting HuR in CCA are limited, in the past few years, HuR has emerged as a potential therapeutic target in HCC. In fact, the therapeutic efficacy of some pharmacological inhibitors of HuR has been evaluated, in early experimental models of HCC. We, further, discuss the major findings and future perspectives of therapeutic approaches that specifically block HuR interactions, either with post-translational modifiers or cognate transcripts in hepatobiliary cancers.
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19
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SRSF6 Regulates the Alternative Splicing of the Apoptotic Fas Gene by Targeting a Novel RNA Sequence. Cancers (Basel) 2022; 14:cancers14081990. [PMID: 35454897 PMCID: PMC9025165 DOI: 10.3390/cancers14081990] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 04/08/2022] [Accepted: 04/12/2022] [Indexed: 12/20/2022] Open
Abstract
Simple Summary Alternative splicing (AS) produces multiple mRNA isoforms from a gene to make a large number of proteins. Fas (Apo-1/CD95) pre-mRNA, a member of TNF receptor family that mediates apoptosis, can generate pro-apoptotic and anti-apoptotic proteins through AS. Here, we identified SRSF6 as an essential regulator protein in Fas AS. We further located a new functional target sequence of SRSF6 in Fas splicing. In addition, our large-scale RNA-seq analysis using GTEX and TCGA indicated that while SRSF6 expression was correlated with Fas expression in normal tissues, the correlation was disrupted in tumors. Our results suggest a novel regulatory mechanisms of Fas AS. Abstract Alternative splicing (AS) is a procedure during gene expression that allows the production of multiple mRNAs from a single gene, leading to a larger number of proteins with various functions. The alternative splicing (AS) of Fas (Apo-1/CD95) pre-mRNA can generate membrane-bound or soluble isoforms with pro-apoptotic and anti-apoptotic functions. SRSF6, a member of the Serine/Arginine-rich protein family, plays essential roles in both constitutive and alternative splicing. Here, we identified SRSF6 as an important regulatory protein in Fas AS. The cassette exon inclusion of Fas was decreased by SRSF6-targeting shRNA treatment, but increased by SRSF6 overexpression. The deletion and substitution mutagenesis of the Fas minigene demonstrated that the UGCCAA sequence in the cassette exon of the Fas gene causes the functional disruption of SRSF6, indicating that these sequences are essential for SRSF6 function in Fas splicing. In addition, biotin-labeled RNA-pulldown and immunoblotting analysis showed that SRSF6 interacted with these RNA sequences. Mutagenesis in the splice-site strength alteration demonstrated that the 5′ splice-site, but not the 3′ splice-site, was required for the SRSF6 regulation of Fas pre-mRNA. In addition, a large-scale RNA-seq analysis using GTEX and TCGA indicated that while SRSF6 expression was correlated with Fas expression in normal tissues, the correlation was disrupted in tumors. Furthermore, high SRSF6 expression was linked to the high expression of pro-apoptotic and immune activation genes. Therefore, we identified a novel RNA target with 5′ splice-site dependence of SRSF6 in Fas pre-mRNA splicing, and a correlation between SRSF6 and Fas expression.
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20
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Jain A, McCoy M, Coats C, Brown SZ, Addya S, Pelz C, Sears RC, Yeo CJ, Brody JR. HuR Plays a Role in Double-Strand Break Repair in Pancreatic Cancer Cells and Regulates Functional BRCA1-Associated-Ring-Domain-1(BARD1) Isoforms. Cancers (Basel) 2022; 14:cancers14071848. [PMID: 35406624 PMCID: PMC8997573 DOI: 10.3390/cancers14071848] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 03/07/2022] [Accepted: 04/02/2022] [Indexed: 02/06/2023] Open
Abstract
Human Antigen R (HuR/ELAVL1) is known to regulate stability of mRNAs involved in pancreatic ductal adenocarcinoma (PDAC) cell survival. Although several HuR targets are established, it is likely that many remain currently unknown. Here, we identified BARD1 mRNA as a novel target of HuR. Silencing HuR caused a >70% decrease in homologous recombination repair (HRR) efficiency as measured by the double-strand break repair (pDR-GFP reporter) assay. HuR-bound mRNAs extracted from RNP-immunoprecipitation and probed on a microarray, revealed a subset of HRR genes as putative HuR targets, including the BRCA1-Associated-Ring-Domain-1 (BARD1) (p < 0.005). BARD1 genetic alterations are infrequent in PDAC, and its context-dependent upregulation is poorly understood. Genetic silencing (siRNA and CRISPR knock-out) and pharmacological targeting of HuR inhibited both full length (FL) BARD1 and its functional isoforms (α, δ, Φ). Silencing BARD1 sensitized cells to olaparib and oxaliplatin; caused G2-M cell cycle arrest; and increased DNA-damage while decreasing HRR efficiency in cells. Exogenous overexpression of BARD1 in HuR-deficient cells partially rescued the HRR dysfunction, independent of an HuR pro-oncogenic function. Collectively, our findings demonstrate for the first time that BARD1 is a bona fide HuR target, which serves as an important regulatory point of the transient DNA-repair response in PDAC cells.
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Affiliation(s)
- Aditi Jain
- The Jefferson Pancreas, Biliary and Related Cancer Center, Department of Surgery, Thomas Jefferson University, Philadelphia, PA 19107, USA; (C.C.); (S.Z.B.); (C.J.Y.)
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA;
- Correspondence: (A.J.); (J.R.B.); Tel.: +1-215-955-2693 (A.J.); +1-443-812-1852 (J.R.B.)
| | - Matthew McCoy
- Department of Oncology, Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC 20007, USA;
| | - Carolyn Coats
- The Jefferson Pancreas, Biliary and Related Cancer Center, Department of Surgery, Thomas Jefferson University, Philadelphia, PA 19107, USA; (C.C.); (S.Z.B.); (C.J.Y.)
| | - Samantha Z. Brown
- The Jefferson Pancreas, Biliary and Related Cancer Center, Department of Surgery, Thomas Jefferson University, Philadelphia, PA 19107, USA; (C.C.); (S.Z.B.); (C.J.Y.)
- The Department of Surgery, Brenden-Colson Center for Pancreatic Care, The Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97201, USA
| | - Sankar Addya
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA;
| | - Carl Pelz
- The Department of Molecular and Medical Genetics, Brenden-Colson Center for Pancreatic Care, The Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97201, USA; (C.P.); (R.C.S.)
| | - Rosalie C. Sears
- The Department of Molecular and Medical Genetics, Brenden-Colson Center for Pancreatic Care, The Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97201, USA; (C.P.); (R.C.S.)
| | - Charles J. Yeo
- The Jefferson Pancreas, Biliary and Related Cancer Center, Department of Surgery, Thomas Jefferson University, Philadelphia, PA 19107, USA; (C.C.); (S.Z.B.); (C.J.Y.)
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA;
| | - Jonathan R. Brody
- The Department of Surgery, Brenden-Colson Center for Pancreatic Care, The Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97201, USA
- Correspondence: (A.J.); (J.R.B.); Tel.: +1-215-955-2693 (A.J.); +1-443-812-1852 (J.R.B.)
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21
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Wei L, Lai EC. Regulation of the Alternative Neural Transcriptome by ELAV/Hu RNA Binding Proteins. Front Genet 2022; 13:848626. [PMID: 35281806 PMCID: PMC8904962 DOI: 10.3389/fgene.2022.848626] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 02/01/2022] [Indexed: 11/30/2022] Open
Abstract
The process of alternative polyadenylation (APA) generates multiple 3' UTR isoforms for a given locus, which can alter regulatory capacity and on occasion change coding potential. APA was initially characterized for a few genes, but in the past decade, has been found to be the rule for metazoan genes. While numerous differences in APA profiles have been catalogued across genetic conditions, perturbations, and diseases, our knowledge of APA mechanisms and biology is far from complete. In this review, we highlight recent findings regarding the role of the conserved ELAV/Hu family of RNA binding proteins (RBPs) in generating the broad landscape of lengthened 3' UTRs that is characteristic of neurons. We relate this to their established roles in alternative splicing, and summarize ongoing directions that will further elucidate the molecular strategies for neural APA, the in vivo functions of ELAV/Hu RBPs, and the phenotypic consequences of these regulatory paradigms in neurons.
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Affiliation(s)
- Lu Wei
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Eric C. Lai
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, United States
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22
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Zhang W, Liu L, Zhao S, Chen L, Wei Y, Chen W, Ge F. Research progress on RNA‑binding proteins in breast cancer (Review). Oncol Lett 2022; 23:121. [PMID: 35261635 PMCID: PMC8867207 DOI: 10.3892/ol.2022.13241] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 02/03/2022] [Indexed: 11/28/2022] Open
Abstract
Breast cancer is the most common malignancy among women, and the abnormal regulation of gene expression serves an important role in its occurrence and development. However, the molecular mechanisms underlying gene expression are highly complex and heterogeneous, and RNA-binding proteins (RBPs) are among the key regulatory factors. RBPs bind targets in an environment-dependent or environment-independent manner to influence mRNA stability and the translation of genes involved in the formation, progression, metastasis and treatment of breast cancer. Due to the growing interest in these regulators, the present review summarizes the most influential studies concerning RBPs associated with breast cancer to elucidate the role of RBPs in breast cancer and to assess how they interact with other key pathways to provide new molecular targets for the diagnosis and treatment of breast cancer.
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Affiliation(s)
- Wenzhu Zhang
- Department of Breast Surgery, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, P.R. China
| | - Linlin Liu
- School of Forensic Medicine, Kunming Medical University, Kunming, Yunnan 650500, P.R. China
| | - Shengdi Zhao
- Department of Breast Surgery, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, P.R. China
| | - Liang Chen
- Department of Breast Surgery, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, P.R. China
| | - Yuxian Wei
- Department of Endocrine Breast Surgery, First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
| | - Wenlin Chen
- Third Department of Breast Surgery, The Third Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650118, P.R. China
| | - Fei Ge
- Department of Breast Surgery, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, P.R. China
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23
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Assoni G, La Pietra V, Digilio R, Ciani C, Licata NV, Micaelli M, Facen E, Tomaszewska W, Cerofolini L, Pérez-Ràfols A, Varela Rey M, Fragai M, Woodhoo A, Marinelli L, Arosio D, Bonomo I, Provenzani A, Seneci P. HuR-targeted agents: An insight into medicinal chemistry, biophysical, computational studies and pharmacological effects on cancer models. Adv Drug Deliv Rev 2022; 181:114088. [PMID: 34942276 DOI: 10.1016/j.addr.2021.114088] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 10/07/2021] [Accepted: 12/16/2021] [Indexed: 12/13/2022]
Abstract
The Human antigen R (HuR) protein is an RNA-binding protein, ubiquitously expressed in human tissues, that orchestrates target RNA maturation and processing both in the nucleus and in the cytoplasm. A survey of known modulators of the RNA-HuR interactions is followed by a description of its structure and molecular mechanism of action - RRM domains, interactions with RNA, dimerization, binding modes with naturally occurring and synthetic HuR inhibitors. Then, the review focuses on HuR as a validated molecular target in oncology and briefly describes its role in inflammation. Namely, we show ample evidence for the involvement of HuR in the hallmarks and enabling characteristics of cancer, reporting findings from in vitro and in vivo studies; and we provide abundant experimental proofs of a beneficial role for the inhibition of HuR-mRNA interactions through silencing (CRISPR, siRNA) or pharmacological inhibition (small molecule HuR inhibitors).
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Affiliation(s)
- Giulia Assoni
- Chemistry Department, University of Milan, Via Golgi 19, I-20133 Milan, Italy; Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, via Sommarive 9, 38123 Trento, Italy
| | - Valeria La Pietra
- Department of Pharmacy, University of Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy
| | - Rosangela Digilio
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, via Sommarive 9, 38123 Trento, Italy
| | - Caterina Ciani
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, via Sommarive 9, 38123 Trento, Italy
| | - Nausicaa Valentina Licata
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, via Sommarive 9, 38123 Trento, Italy
| | - Mariachiara Micaelli
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, via Sommarive 9, 38123 Trento, Italy
| | - Elisa Facen
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, via Sommarive 9, 38123 Trento, Italy
| | - Weronika Tomaszewska
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, via Sommarive 9, 38123 Trento, Italy
| | - Linda Cerofolini
- Magnetic Resonance Center (CERM), University of Florence and Interuniversity Consortium for Magnetic Resonance of Metalloproteins (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy
| | - Anna Pérez-Ràfols
- Giotto Biotech S.R.L., Via Madonna del Piano 6, 50019 Sesto Fiorentino (FI), Italy
| | - Marta Varela Rey
- Gene Regulatory Control in Disease Group, Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Health Research Institute of Santiago de Compostela (IDIS), University of Santiago de Compostela, 15706 Santiago de Compostela, Spain
| | - Marco Fragai
- Magnetic Resonance Center (CERM), University of Florence and Interuniversity Consortium for Magnetic Resonance of Metalloproteins (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy
| | - Ashwin Woodhoo
- Gene Regulatory Control in Disease Group, Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Health Research Institute of Santiago de Compostela (IDIS), University of Santiago de Compostela, 15706 Santiago de Compostela, Spain; Department of Functional Biology, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain; Galician Agency of Innovation (GAIN), Xunta de Galicia, Santiago de Compostela, Spain; Center for Cooperative Research in Biosciences (CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao 48013, Spain
| | - Luciana Marinelli
- Department of Pharmacy, University of Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy
| | - Daniela Arosio
- Istituto di Scienze e Tecnologie Chimiche "G. Natta" (SCITEC), National Research Council (CNR), Via C. Golgi 19, I-20133 Milan, Italy
| | - Isabelle Bonomo
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, via Sommarive 9, 38123 Trento, Italy
| | - Alessandro Provenzani
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, via Sommarive 9, 38123 Trento, Italy.
| | - Pierfausto Seneci
- Chemistry Department, University of Milan, Via Golgi 19, I-20133 Milan, Italy.
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24
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Backlund M, Kulozik AE. Differential Analysis of the Nuclear and the Cytoplasmic RNA Interactomes in Living Cells. Methods Mol Biol 2022; 2428:291-304. [PMID: 35171487 DOI: 10.1007/978-1-0716-1975-9_18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
RNA-binding proteins are key mediators of many of the RNA-regulatory functions throughout the RNA life cycle in the nucleus and in the cytoplasm. The invention and the recent refinement of the RNA-interactome capture technology has now enabled the analysis of the global RNA-interactome in living cells in the nucleus and in the cytoplasm separately. This technology thus allows an unprecedented differential view on the function of RNA-binding proteins in these compartments. Here we describe a method combining nucleo-cytoplasmic fractionation and enhanced RNA-interactome capture (eRIC) for studying RBPs binding to polyadenylated RNAs separately in the cytoplasmic and in the nuclear compartments.
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Affiliation(s)
- Michael Backlund
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University, Heidelberg, Germany
- Hopp Children's Cancer Center, National Center for Tumor Diseases (NCT), Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University, Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Andreas E Kulozik
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University, Heidelberg, Germany.
- Hopp Children's Cancer Center, National Center for Tumor Diseases (NCT), Heidelberg, Germany.
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University, Heidelberg, Germany.
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
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25
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Role of Human Antigen R (HuR) in the Regulation of Pulmonary ACE2 Expression. Cells 2021; 11:cells11010022. [PMID: 35011584 PMCID: PMC8750694 DOI: 10.3390/cells11010022] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 12/13/2021] [Accepted: 12/19/2021] [Indexed: 12/12/2022] Open
Abstract
Patients with COPD may be at an increased risk for severe illness from COVID-19 because of ACE2 upregulation, the entry receptor for SARS-CoV-2. Chronic exposure to cigarette smoke, the main risk factor for COPD, increases pulmonary ACE2. How ACE2 expression is controlled is not known but may involve HuR, an RNA binding protein that increases protein expression by stabilizing mRNA. We hypothesized that HuR would increase ACE2 protein expression. We analyzed scRNA-seq data to profile ELAVL1 expression in distinct respiratory cell populations in COVID-19 and COPD patients. HuR expression and cellular localization was evaluated in COPD lung tissue by multiplex immunohistochemistry and in human lung cells by imaging flow cytometry. The regulation of ACE2 expression was evaluated using siRNA-mediated knockdown of HuR. There is a significant positive correlation between ELAVL1 and ACE2 in COPD cells. HuR cytoplasmic localization is higher in smoker and COPD lung tissue; there were also higher levels of cleaved HuR (CP-1). HuR binds to ACE2 mRNA but knockdown of HuR does not change ACE2 protein levels in primary human lung fibroblasts (HLFs). Our work is the first to investigate the association between ACE2 and HuR. Further investigation is needed to understand the mechanistic underpinning behind the regulation of ACE2 expression.
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26
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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: 1.3] [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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27
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Daks A, Petukhov A, Fedorova O, Shuvalov O, Kizenko A, Tananykina E, Vasileva E, Semenov O, Bottrill A, Barlev N. The RNA-binding protein HuR is a novel target of Pirh2 E3 ubiquitin ligase. Cell Death Dis 2021; 12:581. [PMID: 34091597 PMCID: PMC8179929 DOI: 10.1038/s41419-021-03871-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 05/18/2021] [Accepted: 05/24/2021] [Indexed: 11/24/2022]
Abstract
The RING-finger protein Pirh2 is a p53 family-specific E3 ubiquitin ligase. Pirh2 also ubiquitinates several other important cellular factors and is involved in carcinogenesis. However, its functional role in other cellular processes is poorly understood. To address this question, we performed a proteomic search for novel interacting partners of Pirh2. Using the GST-pulldown approach combined with LC-MS/MS, we revealed 225 proteins that interacted with Pirh2. We found that, according to the GO description, a large group of Pirh2-associated proteins belonged to the RNA metabolism group. Importantly, one of the identified proteins from that group was an RNA-binding protein ELAVL1 (HuR), which is involved in the regulation of splicing and protein stability of several oncogenic proteins. We demonstrated that Pirh2 ubiquitinated the HuR protein facilitating its proteasome-mediated degradation in cells. Importantly, the Pirh2-mediated degradation of HuR occurred in response to heat shock, thereby affecting the survival rate of HeLa cells under elevated temperature. Functionally, Pirh2-mediated degradation of HuR augmented the level of c-Myc expression, whose RNA level is otherwise attenuated by HuR. Taken together, our data indicate that HuR is a new target of Pirh2 and this functional interaction contributes to the heat-shock response of cancer cells affecting their survival.
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Affiliation(s)
- Alexandra Daks
- Institute of Cytology, Russian Academy of Sciences, 194064, St Petersburg, Russian Federation.
| | - Alexey Petukhov
- Institute of Cytology, Russian Academy of Sciences, 194064, St Petersburg, Russian Federation.,Almazov National Medical Research Centre, Institute of Hematology, 197341, St Petersburg, Russian Federation
| | - Olga Fedorova
- Institute of Cytology, Russian Academy of Sciences, 194064, St Petersburg, Russian Federation
| | - Oleg Shuvalov
- Institute of Cytology, Russian Academy of Sciences, 194064, St Petersburg, Russian Federation
| | - Alena Kizenko
- Institute of Cytology, Russian Academy of Sciences, 194064, St Petersburg, Russian Federation
| | - Elizaveta Tananykina
- Institute of Cytology, Russian Academy of Sciences, 194064, St Petersburg, Russian Federation
| | - Elena Vasileva
- Institute of Cytology, Russian Academy of Sciences, 194064, St Petersburg, Russian Federation
| | - Oleg Semenov
- Institute of Cytology, Russian Academy of Sciences, 194064, St Petersburg, Russian Federation
| | - Andrew Bottrill
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Nickolai Barlev
- Institute of Cytology, Russian Academy of Sciences, 194064, St Petersburg, Russian Federation. .,Moscow Institute of Physics and Technology, 141700, Dolgoprudny, Moscow Region, Russian Federation.
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28
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Lee S, Wei L, Zhang B, Goering R, Majumdar S, Wen J, Taliaferro JM, Lai EC. ELAV/Hu RNA binding proteins determine multiple programs of neural alternative splicing. PLoS Genet 2021; 17:e1009439. [PMID: 33826609 PMCID: PMC8055025 DOI: 10.1371/journal.pgen.1009439] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 04/19/2021] [Accepted: 02/22/2021] [Indexed: 12/15/2022] Open
Abstract
ELAV/Hu factors are conserved RNA binding proteins (RBPs) that play diverse roles in mRNA processing and regulation. The founding member, Drosophila Elav, was recognized as a vital neural factor 35 years ago. Nevertheless, little was known about its impacts on the transcriptome, and potential functional overlap with its paralogs. Building on our recent findings that neural-specific lengthened 3' UTR isoforms are co-determined by ELAV/Hu factors, we address their impacts on splicing. While only a few splicing targets of Drosophila are known, ectopic expression of each of the three family members (Elav, Fne and Rbp9) alters hundreds of cassette exon and alternative last exon (ALE) splicing choices. Reciprocally, double mutants of elav/fne, but not elav alone, exhibit opposite effects on both classes of regulated mRNA processing events in larval CNS. While manipulation of Drosophila ELAV/Hu RBPs induces both exon skipping and inclusion, characteristic ELAV/Hu motifs are enriched only within introns flanking exons that are suppressed by ELAV/Hu factors. Moreover, the roles of ELAV/Hu factors in global promotion of distal ALE splicing are mechanistically linked to terminal 3' UTR extensions in neurons, since both processes involve bypass of proximal polyadenylation signals linked to ELAV/Hu motifs downstream of cleavage sites. We corroborate the direct action of Elav in diverse modes of mRNA processing using RRM-dependent Elav-CLIP data from S2 cells. Finally, we provide evidence for conservation in mammalian neurons, which undergo broad programs of distal ALE and APA lengthening, linked to ELAV/Hu motifs downstream of regulated polyadenylation sites. Overall, ELAV/Hu RBPs orchestrate multiple broad programs of neuronal mRNA processing and isoform diversification in Drosophila and mammalian neurons.
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Affiliation(s)
- Seungjae Lee
- Developmental Biology Program, Sloan Kettering Institute, New York City, New York, United States of America
| | - Lu Wei
- Developmental Biology Program, Sloan Kettering Institute, New York City, New York, United States of America
| | - Binglong Zhang
- Developmental Biology Program, Sloan Kettering Institute, New York City, New York, United States of America
| | - Raeann Goering
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
- RNA Bioscience Initiative University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Sonali Majumdar
- Developmental Biology Program, Sloan Kettering Institute, New York City, New York, United States of America
| | - Jiayu Wen
- Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - J. Matthew Taliaferro
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
- RNA Bioscience Initiative University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Eric C. Lai
- Developmental Biology Program, Sloan Kettering Institute, New York City, New York, United States of America
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29
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Abstract
Posttranscriptional control of mRNA regulates various biological processes, including inflammatory and immune responses. RNA-binding proteins (RBPs) bind cis-regulatory elements in the 3' untranslated regions (UTRs) of mRNA and regulate mRNA turnover and translation. In particular, eight RBPs (TTP, AUF1, KSRP, TIA-1/TIAR, Roquin, Regnase, HuR, and Arid5a) have been extensively studied and are key posttranscriptional regulators of inflammation and immune responses. These RBPs sometimes collaboratively or competitively bind the same target mRNA to enhance or dampen regulatory activities. These RBPs can also bind their own 3' UTRs to negatively or positively regulate their expression. Both upstream signaling pathways and microRNA regulation shape the interactions between RBPs and target RNA. Dysregulation of RBPs results in chronic inflammation and autoimmunity. Here, we summarize the functional roles of these eight RBPs in immunity and their associated diseases.
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Affiliation(s)
- Shizuo Akira
- Laboratory of Host Defense, WPI Immunology Frontier Research Center (IFReC), Osaka University, Osaka 565-0874, Japan.,Department of Host Defense, Division of Host Defense, Research Institute for Microbial Diseases (RIMD), Osaka University, Osaka 565-0874, Japan;
| | - Kazuhiko Maeda
- Laboratory of Host Defense, WPI Immunology Frontier Research Center (IFReC), Osaka University, Osaka 565-0874, Japan.,Department of Host Defense, Division of Host Defense, Research Institute for Microbial Diseases (RIMD), Osaka University, Osaka 565-0874, Japan;
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30
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Vilys L, Peciuliene I, Jakubauskiene E, Zinkeviciute R, Makino Y, Kanopka A. U2AF - Hypoxia-induced fas alternative splicing regulator. Exp Cell Res 2020; 399:112444. [PMID: 33347855 DOI: 10.1016/j.yexcr.2020.112444] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 12/01/2020] [Accepted: 12/15/2020] [Indexed: 01/21/2023]
Abstract
The splicing machinery heavily contributes to biological complexity and especially to the ability of cells to adapt to altered cellular conditions. Hypoxia also plays a key role in the pathophysiology of many disease states. Recent studies have revealed that tumorigenesis and hypoxia are involved in large-scale alterations in alternative pre-mRNA splicing. Fas pre-mRNA is alternatively spliced by excluding exon 6 to produce soluble Fas (sFas) protein that lacks a transmembrane domain and acts by inhibiting Fas mediated apoptosis. In the present study we show that U2AF is involved in hypoxia dependent anti-apoptotic Fas mRNA isoform formation. Our performed studies show that U2AF-RNA interaction is reduced in hypoxic cells, leading to reduction of Fas and increased sFas mRNAs formation. Efficient U2AF-RNA interactions of both subunits are important for Fas exon 6 inclusion into forming mRNA in normoxic and hypoxic cells.
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Affiliation(s)
- Laurynas Vilys
- Department of Immunology and Cell Biology, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Inga Peciuliene
- Department of Immunology and Cell Biology, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Egle Jakubauskiene
- Department of Immunology and Cell Biology, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Ruta Zinkeviciute
- Department of Eukaryote Gene Engineering, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Yuichi Makino
- Division of Metabolism and Biosystemic Science, Department of Medicine, Asahikawa Medical College, Asahikawa, Hokkaido, Japan
| | - Arvydas Kanopka
- Department of Immunology and Cell Biology, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania.
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31
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Du JX, Zhu GQ, Cai JL, Wang B, Luo YH, Chen C, Cai CZ, Zhang SJ, Zhou J, Fan J, Zhu W, Dai Z. Splicing factors: Insights into their regulatory network in alternative splicing in cancer. Cancer Lett 2020; 501:83-104. [PMID: 33309781 DOI: 10.1016/j.canlet.2020.11.043] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/24/2020] [Accepted: 11/26/2020] [Indexed: 12/18/2022]
Abstract
More than 95% of all human genes are alternatively spliced after transcription, which enriches the diversity of proteins and regulates transcript and/or protein levels. The splicing isoforms produced from the same gene can manifest distinctly, even exerting opposite effects. Mounting evidence indicates that the alternative splicing (AS) mechanism is ubiquitous in various cancers and drives the generation and maintenance of various hallmarks of cancer, such as enhanced proliferation, inhibited apoptosis, invasion and metastasis, and angiogenesis. Splicing factors (SFs) play pivotal roles in the recognition of splice sites and the assembly of spliceosomes during AS. In this review, we mainly discuss the similarities and differences of SF domains, the details of SF function in AS, the effect of SF-driven pathological AS on different hallmarks of cancer, and the main drivers of SF expression level and subcellular localization. In addition, we briefly introduce the application prospects of targeted therapeutic strategies, including small-molecule inhibitors, siRNAs and splice-switching oligonucleotides (SSOs), from three perspectives (drivers, SFs and pathological AS). Finally, we share our insights into the potential direction of research on SF-centric AS-related regulatory networks.
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Affiliation(s)
- Jun-Xian Du
- Department of General Surgery, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Gui-Qi Zhu
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China; Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, 200032, China
| | - Jia-Liang Cai
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China; Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, 200032, China
| | - Biao Wang
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China; Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, 200032, China
| | - Yi-Hong Luo
- Department of General Surgery, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Cong Chen
- Department of General Surgery, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Cheng-Zhe Cai
- Department of General Surgery, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Si-Jia Zhang
- Department of General Surgery, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Jian Zhou
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China; Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, 200032, China
| | - Jia Fan
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China; Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, 200032, China
| | - Wei Zhu
- Department of General Surgery, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China.
| | - Zhi Dai
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China; Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, 200032, China.
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32
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Simion V, Zhou H, Haemmig S, Pierce JB, Mendes S, Tesmenitsky Y, Pérez-Cremades D, Lee JF, Chen AF, Ronda N, Papotti B, Marto JA, Feinberg MW. A macrophage-specific lncRNA regulates apoptosis and atherosclerosis by tethering HuR in the nucleus. Nat Commun 2020; 11:6135. [PMID: 33262333 PMCID: PMC7708640 DOI: 10.1038/s41467-020-19664-2] [Citation(s) in RCA: 105] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Accepted: 10/26/2020] [Indexed: 01/10/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are emerging regulators of pathophysiological processes including atherosclerosis. Using RNA-seq profiling of the intima of lesions, here we identify a macrophage-specific lncRNA MAARS (Macrophage-Associated Atherosclerosis lncRNA Sequence). Aortic intima expression of MAARS increases by 270-fold with atherosclerotic progression and decreases with regression by 60%. MAARS knockdown reduces atherosclerotic lesion formation by 52% in LDLR-/- mice, largely independent of effects on lipid profile and inflammation, but rather by decreasing macrophage apoptosis and increasing efferocytosis in the vessel wall. MAARS interacts with HuR/ELAVL1, an RNA-binding protein and important regulator of apoptosis. Overexpression and knockdown studies verified MAARS as a critical regulator of macrophage apoptosis and efferocytosis in vitro, in an HuR-dependent manner. Mechanistically, MAARS knockdown alters HuR cytosolic shuttling, regulating HuR targets such as p53, p27, Caspase-9, and BCL2. These findings establish a mechanism by which a macrophage-specific lncRNA interacting with HuR regulates apoptosis, with implications for a broad range of vascular disease states.
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Affiliation(s)
- Viorel Simion
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Haoyang Zhou
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Cardiology, The Third Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Stefan Haemmig
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jacob B Pierce
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Shanelle Mendes
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Yevgenia Tesmenitsky
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Daniel Pérez-Cremades
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - James F Lee
- The Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Alex F Chen
- Department of Cardiology, The Third Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Nicoletta Ronda
- Department of Food and Drug, University of Parma, Parma, Italy
| | - Bianca Papotti
- Department of Food and Drug, University of Parma, Parma, Italy
| | - Jarrod A Marto
- The Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA, USA
- Departments of Cancer Biology and Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Mark W Feinberg
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
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Li J, Durose WW, Ito J, Kakita A, Iguchi Y, Katsuno M, Kunisawa K, Shimizu T, Ikenaka K. Exploring the factors underlying remyelination arrest by studying the post-transcriptional regulatory mechanisms of cystatin F gene. J Neurochem 2020; 157:2070-2090. [PMID: 32947653 DOI: 10.1111/jnc.15190] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 08/11/2020] [Accepted: 09/07/2020] [Indexed: 12/20/2022]
Abstract
Remyelination plays an important role in determining the fate of demyelinating disorders. However, it is arrested during chronic disease states. Cystatin F, a papain-like lysosomal cysteine proteinase inhibitor, is a crucial regulator of demyelination and remyelination. Using hemizygous proteolipid protein transgenic 4e (PLP4e/- ) mice, an animal model of chronic demyelination, we found that cystatin F mRNA expression was induced at 2.5 months of age and up-regulated in the early phase of demyelination, but significantly decreased in the chronic phase. We next investigated cystatin F regulatory factors as potential mechanisms of remyelination arrest in chronic demyelinating disorders. We used the CysF-STOP-tetO::Iba-mtTA mouse model, in which cystatin F gene expression is driven by the tetracycline operator. Interestingly, we found that forced cystatin F mRNA over-expression was eventually decreased. Our findings show that cystatin F expression is modulated post-transcriptionally. We next identified embryonic lethal, abnormal vision, drosophila like RNA-binding protein 1 (ELAVL-1), and miR29a as cystatin F mRNA stabilizing and destabilizing factors, respectively. These roles were confirmed in vitro in NIH3T3 cells. Using postmortem plaque samples from human multiple sclerosis patients, we also confirmed that ELAVL-1 expression was highly correlated with the previously reported expression pattern of cystatin F. These data indicate the important roles of ELAVL-1 and miR29a in regulating cystatin F expression. Furthermore, they provide new insights into potential therapeutic targets for demyelinating disorders.
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Affiliation(s)
- Jiayi Li
- Division of Neurobiology and Bioinformatics, National Institute for Physiological Sciences, Okazaki, Japan.,Department of Physiological Sciences, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Okazaki, Japan.,Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Wilaiwan Wisessmith Durose
- Division of Neurobiology and Bioinformatics, National Institute for Physiological Sciences, Okazaki, Japan.,Department of Physiological Sciences, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Okazaki, Japan.,Research Center for Neuroscience, Institute of Molecular Biosciences, Mahidol University, Salaya, Nakhonpathom, Thailand.,Department of Pediatrics, Hematology University of Minnesota, Minneapolis, MN, USA
| | - Junko Ito
- Department of Pathology, Brain Research Institute, Niigata University, Niigata, Japan
| | - Akiyoshi Kakita
- Department of Pathology, Brain Research Institute, Niigata University, Niigata, Japan
| | - Yohei Iguchi
- Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Masahisa Katsuno
- Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kazuo Kunisawa
- Division of Neurobiology and Bioinformatics, National Institute for Physiological Sciences, Okazaki, Japan.,Department of Physiological Sciences, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Okazaki, Japan.,Research Division of Advanced Diagnostic System, Graduate School of Health Sciences, Fujita Health University, Toyoake, Japan
| | - Takeshi Shimizu
- Division of Neurobiology and Bioinformatics, National Institute for Physiological Sciences, Okazaki, Japan.,Department of Physiological Sciences, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Okazaki, Japan.,Department of Neurophysiology and Brain Science, Graduate School of Medical Sciences, Nagoya City University, Nagoya, Aichi, Japan
| | - Kazuhiro Ikenaka
- Division of Neurobiology and Bioinformatics, National Institute for Physiological Sciences, Okazaki, Japan.,Department of Physiological Sciences, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Okazaki, Japan
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Cao J, Cowan DB, Wang DZ. tRNA-Derived Small RNAs and Their Potential Roles in Cardiac Hypertrophy. Front Pharmacol 2020; 11:572941. [PMID: 33041815 PMCID: PMC7527594 DOI: 10.3389/fphar.2020.572941] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 08/28/2020] [Indexed: 12/21/2022] Open
Abstract
Transfer RNAs (tRNAs) are abundantly expressed, small non-coding RNAs that have long been recognized as essential components of the protein translation machinery. The tRNA-derived small RNAs (tsRNAs), including tRNA halves (tiRNAs), and tRNA fragments (tRFs), were unexpectedly discovered and have been implicated in a variety of important biological functions such as cell proliferation, cell differentiation, and apoptosis. Mechanistically, tsRNAs regulate mRNA destabilization and translation, as well as retro-element reverse transcriptional and post-transcriptional processes. Emerging evidence has shown that tsRNAs are expressed in the heart, and their expression can be induced by pathological stress, such as hypertrophy. Interestingly, cardiac pathophysiological conditions, such as oxidative stress, aging, and metabolic disorders can be viewed as inducers of tsRNA biogenesis, which further highlights the potential involvement of tsRNAs in these conditions. There is increasing enthusiasm for investigating the molecular and biological functions of tsRNAs in the heart and their role in cardiovascular disease. It is anticipated that this new class of small non-coding RNAs will offer new perspectives in understanding disease mechanisms and may provide new therapeutic targets to treat cardiovascular disease.
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Affiliation(s)
- Jun Cao
- Department of Cardiology, Boston Children's Hospital, Harvard Medical School, Boston, MA, United States
| | - Douglas B Cowan
- Department of Cardiology, Boston Children's Hospital, Harvard Medical School, Boston, MA, United States
| | - Da-Zhi Wang
- Department of Cardiology, Boston Children's Hospital, Harvard Medical School, Boston, MA, United States
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35
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Nilsson K, Abdurahman S, Schwartz S. Influenza virus natural sequence heterogeneity in segment 8 affects interactions with cellular RNA-binding proteins and splicing efficiency. Virology 2020; 549:39-50. [PMID: 32829114 DOI: 10.1016/j.virol.2020.08.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 08/11/2020] [Accepted: 08/12/2020] [Indexed: 11/18/2022]
Abstract
Segment 8 mRNAs of influenza virus A/Brevig Misson/1918/1 (H1N1) are poorly spliced compared to segment 8 mRNAs of influenza virus A/Netherlands/178/95 (H3N2). Using oligonucleotide-mediated protein pull down with oligos spanning the entire length of segment 8 of either influenza virus H1N1 or influenza virus H3N2 we identified cellular RNA binding proteins that interacted with oligonucleotides derived from either H1N1 or H3N2 sequences. When the identified hot spots for RNA binding proteins in H1N1 segment 8 mRNAs were replaced by H3N2 sequences, splicing efficiency increased significantly. Replacing as few as three nucleotides of the H1N1 mRNA with sequences from H3N2 mRNA, enhanced splicing of the H1N1 mRNAs. Cellular proteins U2AF65 and HuR interacted preferentially with the 3'-splice site of H3N2 and overexpression of HuR reduced the levels of unspliced H1N1 mRNAs, suggesting that U2AF65 and HuR contribute to control of influenza virus mRNA splicing.
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MESH Headings
- A549 Cells
- Alternative Splicing
- ELAV-Like Protein 1/genetics
- ELAV-Like Protein 1/metabolism
- Genetic Variation
- HeLa Cells
- Host-Pathogen Interactions/genetics
- Humans
- Influenza A Virus, H1N1 Subtype/genetics
- Influenza A Virus, H1N1 Subtype/metabolism
- Influenza A Virus, H3N2 Subtype/genetics
- Influenza A Virus, H3N2 Subtype/metabolism
- Oligonucleotides/chemistry
- Oligonucleotides/metabolism
- Plasmids/chemistry
- Plasmids/metabolism
- Protein Binding
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Viral/chemistry
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Splicing Factor U2AF/genetics
- Splicing Factor U2AF/metabolism
- Transfection
- Viral Nonstructural Proteins/genetics
- Viral Nonstructural Proteins/metabolism
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Affiliation(s)
- Kersti Nilsson
- Department of Laboratory Medicine, BMC-B13, Lund University, 221 84, Lund, Sweden
| | - Samir Abdurahman
- Department of Science and Technology, Örebro University, 701 82, Örebro, Sweden
| | - Stefan Schwartz
- Department of Laboratory Medicine, BMC-B13, Lund University, 221 84, Lund, Sweden.
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36
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Wu M, Tong CWS, Yan W, To KKW, Cho WCS. The RNA Binding Protein HuR: A Promising Drug Target for Anticancer Therapy. Curr Cancer Drug Targets 2020; 19:382-399. [PMID: 30381077 DOI: 10.2174/1568009618666181031145953] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Revised: 08/24/2018] [Accepted: 10/18/2018] [Indexed: 02/07/2023]
Abstract
The stability of mRNA is one of the key factors governing the regulation of eukaryotic gene expression and function. Human antigen R (HuR) is an RNA-binding protein that regulates the stability, translation, and nucleus-to-cytoplasm shuttling of its target mRNAs. While HuR is normally localized within the nucleus, it has been shown that HuR binds mRNAs in the nucleus and then escorts the mRNAs to the cytoplasm where HuR protects them from degradation. It contains several RNA recognition motifs, which specifically bind to adenylate and uridylate-rich regions within the 3'-untranslated region of the target mRNA to mediate its effect. Many of the HuR target mRNAs encode proteins important for cell growth, tumorigenesis, angiogenesis, tumor inflammation, invasion and metastasis. HuR overexpression is known to correlate well with high-grade malignancy and poor prognosis in many tumor types. Thus, HuR has emerged as an attractive drug target for cancer therapy. Novel small molecule HuR inhibitors have been identified by high throughput screening and new formulations for targeted delivery of HuR siRNA to tumor cells have been developed with promising anticancer activity. This review summarizes the significant role of HuR in cancer development, progression, and poor treatment response. We will discuss the potential and challenges of targeting HuR therapeutically.
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Affiliation(s)
- Mingxia Wu
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong
| | - Christy W S Tong
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong
| | - Wei Yan
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong
| | - Kenneth K W To
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong
| | - William C S Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Hong Kong
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37
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Wu KE, Parker KR, Fazal FM, Chang HY, Zou J. RNA-GPS predicts high-resolution RNA subcellular localization and highlights the role of splicing. RNA (NEW YORK, N.Y.) 2020; 26:851-865. [PMID: 32220894 PMCID: PMC7297119 DOI: 10.1261/rna.074161.119] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 03/19/2020] [Indexed: 06/10/2023]
Abstract
Subcellular localization is essential to RNA biogenesis, processing, and function across the gene expression life cycle. However, the specific nucleotide sequence motifs that direct RNA localization are incompletely understood. Fortunately, new sequencing technologies have provided transcriptome-wide atlases of RNA localization, creating an opportunity to leverage computational modeling. Here we present RNA-GPS, a new machine learning model that uses nucleotide-level features to predict RNA localization across eight different subcellular locations-the first to provide such a wide range of predictions. RNA-GPS's design enables high-throughput sequence ablation and feature importance analyses to probe the sequence motifs that drive localization prediction. We find localization informative motifs to be concentrated on 3'-UTRs and scattered along the coding sequence, and motifs related to splicing to be important drivers of predicted localization, even for cytotopic distinctions for membraneless bodies within the nucleus or for organelles within the cytoplasm. Overall, our results suggest transcript splicing is one of many elements influencing RNA subcellular localization.
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Affiliation(s)
- Kevin E Wu
- Department of Computer Science, Stanford University, Stanford, California 94305, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, California 94305, USA
- Center for Personal and Dynamic Regulomes, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Kevin R Parker
- Center for Personal and Dynamic Regulomes, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Furqan M Fazal
- Center for Personal and Dynamic Regulomes, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Howard Y Chang
- Center for Personal and Dynamic Regulomes, Stanford University School of Medicine, Stanford, California 94305, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California 94305, USA
| | - James Zou
- Department of Computer Science, Stanford University, Stanford, California 94305, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, California 94305, USA
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38
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Asian Zika Virus Isolate Significantly Changes the Transcriptional Profile and Alternative RNA Splicing Events in a Neuroblastoma Cell Line. Viruses 2020; 12:v12050510. [PMID: 32380717 PMCID: PMC7290316 DOI: 10.3390/v12050510] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 04/27/2020] [Indexed: 12/18/2022] Open
Abstract
The alternative splicing of pre-mRNAs expands a single genetic blueprint to encode multiple, functionally diverse protein isoforms. Viruses have previously been shown to interact with, depend on, and alter host splicing machinery. The consequences, however, incited by viral infection on the global alternative slicing (AS) landscape are under-appreciated. Here, we investigated the transcriptional and alternative splicing profile of neuronal cells infected with a contemporary Puerto Rican Zika virus (ZIKVPR) isolate, an isolate of the prototypical Ugandan ZIKV (ZIKVMR), and dengue virus 2 (DENV2). Our analyses revealed that ZIKVPR induced significantly more differential changes in expressed genes compared to ZIKVMR or DENV2, despite all three viruses showing equivalent infectivity and viral RNA levels. Consistent with the transcriptional profile, ZIKVPR induced a higher number of alternative splicing events compared to ZIKVMR or DENV2, and gene ontology analyses highlighted alternative splicing changes in genes associated with mRNA splicing. In summary, we show that ZIKV affects cellular RNA homeostasis not only at the transcriptional levels but also through the alternative splicing of cellular transcripts. These findings could provide new molecular insights into the neuropathologies associated with this virus.
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39
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Schultz CW, Preet R, Dhir T, Dixon DA, Brody JR. Understanding and targeting the disease-related RNA binding protein human antigen R (HuR). WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 11:e1581. [PMID: 31970930 DOI: 10.1002/wrna.1581] [Citation(s) in RCA: 121] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 12/02/2019] [Accepted: 12/07/2019] [Indexed: 02/06/2023]
Abstract
Altered gene expression is a characteristic feature of many disease states such as tumorigenesis, and in most cancers, it facilitates cancer cell survival and adaptation. Alterations in global gene expression are strongly impacted by post-transcriptional gene regulation. The RNA binding protein (RBP) HuR (ELAVL1) is an established regulator of post-transcriptional gene regulation and is overexpressed in most human cancers. In many cancerous settings, HuR is not only overexpressed, but it is "overactive" as denoted by increased subcellular localization within the cytoplasm. This dysregulation of HuR expression and cytoplasmic localization allows HuR to stabilize and increase the translation of various prosurvival messenger RNA (mRNAs) involved in the pathogenesis of numerous cancers and various diseases. Based on almost 20 years of work, HuR is now recognized as a therapeutic target. Herein, we will review the role HuR plays in the pathophysiology of different diseases and ongoing therapeutic strategies to target HuR. We will focus on three ongoing-targeted strategies: (1) inhibiting HuR's translocation from the nucleus to the cytoplasm; (2) inhibiting the ability of HuR to bind target RNA; and (3) silencing HuR expression levels. In an oncologic setting, HuR has been demonstrated to be critical for a cancer cell's ability to survive a variety of cancer relevant stressors (including drugs and elements of the tumor microenvironment) and targeting this protein has been shown to sensitize cancer cells further to insult. We strongly believe that targeting HuR could be a powerful therapeutic target to treat different diseases, particularly cancer, in the near future. This article is categorized under: RNA in Disease and Development > RNA in Disease NRA Turnover and Surveillance > Regulation of RNA Stability Translation > Translation Regulation.
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Affiliation(s)
- Christopher W Schultz
- Department of Surgery, Jefferson Pancreas, Biliary and Related Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Ranjan Preet
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas
| | - Teena Dhir
- Department of Surgery, Jefferson Pancreas, Biliary and Related Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Dan A Dixon
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas
| | - Jonathan R Brody
- Department of Surgery, Jefferson Pancreas, Biliary and Related Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
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40
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Poganik JR, Long MJC, Disare MT, Liu X, Chang SH, Hla T, Aye Y. Post-transcriptional regulation of Nrf2-mRNA by the mRNA-binding proteins HuR and AUF1. FASEB J 2019; 33:14636-14652. [PMID: 31665914 DOI: 10.1096/fj.201901930r] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The nuclear factor erythroid 2-related factor 2 (Nrf2) signaling axis is a target of covalent drugs and bioactive native electrophiles. However, much of our understanding of Nrf2 regulation has been focused at the protein level. Here we report a post-transcriptional modality to directly regulate Nrf2-mRNA. Our initial studies focused on the effects of the key mRNA-binding protein (mRBP) HuR on global transcriptomic changes incurred upon oxidant or electrophile stimulation. These RNA-sequencing data and subsequent mechanistic analyses led us to discover a novel role of HuR in regulating Nrf2 activity, and in the process, we further identified the related mRBP AUF1 as an additional novel Nrf2 regulator. Both mRBPs regulate Nrf2 activity by direct interaction with the Nrf2 transcript. Our data showed that HuR enhances Nrf2-mRNA maturation and promotes its nuclear export, whereas AUF1 stabilizes Nrf2-mRNA. Both mRBPs target the 3'-UTR of Nrf2-mRNA. Using a Nrf2 activity-reporter zebrafish strain, we document that this post-transcriptional control of Nrf2 activity is conserved at the whole-vertebrate level.-Poganik, J. R., Long, M. J. C., Disare, M. T., Liu, X., Chang, S.-H., Hla, T., Aye, Y. Post-transcriptional regulation of Nrf2-mRNA by the mRNA-binding proteins HuR and AUF1.
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Affiliation(s)
- Jesse R Poganik
- Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland.,Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA
| | - Marcus J C Long
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA
| | - Michael T Disare
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA
| | - Xuyu Liu
- Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Sung-Hee Chang
- Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Timothy Hla
- Department of Surgery, Harvard Medical School, Boston, Massachusetts, USA; and.,Vascular Biology Program, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Yimon Aye
- Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
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41
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Abstract
Most human genes have multiple sites at which RNA 3' end cleavage and polyadenylation can occur, enabling the expression of distinct transcript isoforms under different conditions. Novel methods to sequence RNA 3' ends have generated comprehensive catalogues of polyadenylation (poly(A)) sites; their analysis using innovative computational methods has revealed how poly(A) site choice is regulated by core RNA 3' end processing factors, such as cleavage factor I and cleavage and polyadenylation specificity factor, as well as by other RNA-binding proteins, particularly splicing factors. Here, we review the experimental and computational methods that have enabled the global mapping of mRNA and of long non-coding RNA 3' ends, quantification of the resulting isoforms and the discovery of regulators of alternative cleavage and polyadenylation (APA). We highlight the different types of APA-derived isoforms and their functional differences, and illustrate how APA contributes to human diseases, including cancer and haematological, immunological and neurological diseases.
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42
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Peciuliene I, Vilys L, Jakubauskiene E, Zaliauskiene L, Kanopka A. Hypoxia alters splicing of the cancer associated Fas gene. Exp Cell Res 2019; 380:29-35. [PMID: 31002816 DOI: 10.1016/j.yexcr.2019.04.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 04/08/2019] [Accepted: 04/14/2019] [Indexed: 02/02/2023]
Abstract
The removal of introns from mRNA precursors (pre-mRNAs) is an essential step in eukaryotic gene expression. The splicing machinery heavily contributes to biological complexity and especially to the ability of cells to adapt to altered cellular conditions. Hypoxia also plays a key role in the pathophysiology of many disease states. Recent studies have revealed that tumorigenesis and hypoxia involve large-scale alterations in alternative pre-mRNA splicing. Cancer associated Fas protein plays a central role in the physiological regulation of programmed cell death and has been implicated in the pathogenesis of various malignancies and diseases of the immune system. Fas pre-mRNA is alternatively spliced by excluding exon 6 to produce soluble Fas (sFas) protein that lacks a transmembrane domain and acts by inhibiting Fas mediated apoptosis. Another cancer related protein Rac1 plays an important regulatory role specifically in cells' motility, growth and survival. Rac pre-mRNA is alternatively spliced to produce Rac1b protein, which is upregulated in metastatic diseases. In the present study we, for the first time, show that anti-apoptotic Fas mRNA isoform formation is regulated by cellular microenvironment - hypoxia. Hypoxic microenvironment, however, does not influence Rac1 pre-mRNAs alternative splicing. Also our presented results indicate that splicing factors hnRNP A1 and SPF45, previously shown to regulate Fas alternative splicing in normoxic cells, are not involved in hypoxia dependent alternative Fas pre-mRNA splicing regulation in an amount dependent manner. Our observations on hypoxia dependent alternative Fas pre-mRNA splicing regulation indicate a probable involvement of other, yet unidentified splicing factors. Presented data also shows the contribution of pre-mRNA splicing to cell survival under unfavorable conditions.
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Affiliation(s)
- Inga Peciuliene
- Department of Immunology and Cell Biology, Vilnius University, Institute of Biotechnology, Vilnius, Lithuania
| | - Laurynas Vilys
- Department of Immunology and Cell Biology, Vilnius University, Institute of Biotechnology, Vilnius, Lithuania
| | - Egle Jakubauskiene
- Department of Immunology and Cell Biology, Vilnius University, Institute of Biotechnology, Vilnius, Lithuania
| | | | - Arvydas Kanopka
- Department of Immunology and Cell Biology, Vilnius University, Institute of Biotechnology, Vilnius, Lithuania.
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43
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Karginov FV. HuR controls apoptosis and activation response without effects on cytokine 3' UTRs. RNA Biol 2019; 16:686-695. [PMID: 30777501 DOI: 10.1080/15476286.2019.1582954] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
RNA binding proteins regulate gene expression through several post-transcriptional mechanisms. The broadly expressed HuR/ELAVL1 is important for proper function of multiple immune cell types, and has been proposed to regulate cytokine and other mRNA 3' UTRs upon activation. However, this mechanism has not been previously dissected in stable cellular settings. In this study, HuR demonstrated strong anti-apoptotic and activation roles in Jurkat T cells. Detailed transcriptomic analysis of HuR knockout cells revealed a substantial negative impact on the activation program, coordinately preventing the expression of immune response gene categories, including all cytokines. Knockout cells showed a significant defect in IL-2 production, which was rescued upon reintroduction of HuR. Interestingly, the mechanism of HuR regulation did not involve control of the cytokine 3' UTRs: HuR knockout did not affect the activity of 3' UTR reporters in 293 cells, and had no effect on IL-2 and TNF 3' UTRs in resting or activated Jurkats. Instead, impaired cytokine production corresponded with defective induction of the IL-2 promoter upon activation. Accordingly, upregulation of NFATC1 was also impaired, without 3' UTR effects. Together, these results indicate that HuR controls cytokine production through coordinated upstream pathways, and that additional mechanisms must be considered in investigating its function.
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Affiliation(s)
- Fedor V Karginov
- a Department of Molecular, Cell, and Systems Biology , Institute for Integrative Genome Biology, University of California , Riverside , CA , USA
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44
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D'Agostino VG, Sighel D, Zucal C, Bonomo I, Micaelli M, Lolli G, Provenzani A, Quattrone A, Adami V. Screening Approaches for Targeting Ribonucleoprotein Complexes: A New Dimension for Drug Discovery. SLAS DISCOVERY 2019; 24:314-331. [PMID: 30616427 DOI: 10.1177/2472555218818065] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
RNA-binding proteins (RBPs) are pleiotropic factors that control the processing and functional compartmentalization of transcripts by binding primarily to mRNA untranslated regions (UTRs). The competitive and/or cooperative interplay between RBPs and an array of coding and noncoding RNAs (ncRNAs) determines the posttranscriptional control of gene expression, influencing protein production. Recently, a variety of well-recognized and noncanonical RBP domains have been revealed by modern system-wide analyses, underlying an evolving classification of ribonucleoproteins (RNPs) and their importance in governing physiological RNA metabolism. The possibility of targeting selected RNA-protein interactions with small molecules is now expanding the concept of protein "druggability," with new implications for medicinal chemistry and for a deeper characterization of the mechanism of action of bioactive compounds. Here, taking SF3B1, HuR, LIN28, and Musashi proteins as paradigmatic case studies, we review the strategies applied for targeting RBPs, with emphasis on the technological advancements to study protein-RNA interactions and on the requirements of appropriate validation strategies to parallel high-throughput screening (HTS) efforts.
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Affiliation(s)
- Vito Giuseppe D'Agostino
- 1 University of Trento, Department of Cellular, Computational and Integrative Biology (CIBIO), Trento, Italy
| | - Denise Sighel
- 1 University of Trento, Department of Cellular, Computational and Integrative Biology (CIBIO), Trento, Italy
| | - Chiara Zucal
- 1 University of Trento, Department of Cellular, Computational and Integrative Biology (CIBIO), Trento, Italy
| | - Isabelle Bonomo
- 1 University of Trento, Department of Cellular, Computational and Integrative Biology (CIBIO), Trento, Italy
| | - Mariachiara Micaelli
- 1 University of Trento, Department of Cellular, Computational and Integrative Biology (CIBIO), Trento, Italy
| | - Graziano Lolli
- 1 University of Trento, Department of Cellular, Computational and Integrative Biology (CIBIO), Trento, Italy
| | - Alessandro Provenzani
- 1 University of Trento, Department of Cellular, Computational and Integrative Biology (CIBIO), Trento, Italy
| | - Alessandro Quattrone
- 1 University of Trento, Department of Cellular, Computational and Integrative Biology (CIBIO), Trento, Italy
| | - Valentina Adami
- 2 University of Trento, HTS Core Facility, Department of Cellular, Computational and Integrative Biology (CIBIO), Trento, Italy
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45
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Carrascoso I, Alcalde J, Tabas-Madrid D, Oliveros JC, Izquierdo JM. Transcriptome-wide analysis links the short-term expression of the b isoforms of TIA proteins to protective proteostasis-mediated cell quiescence response. PLoS One 2018; 13:e0208526. [PMID: 30533021 PMCID: PMC6289441 DOI: 10.1371/journal.pone.0208526] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 11/19/2018] [Indexed: 12/20/2022] Open
Abstract
Control of gene expression depends on genetics and environmental factors. The T-cell intracellular antigens T-cell intracellular antigen 1 (TIA1), TIA1-like/related protein (TIAL1/TIAR) and human antigen R (HuR/ELAVL1) are RNA-binding proteins that play crucial roles in regulating gene expression in both situations. This study used massive sequencing analysis to uncover molecular and functional mechanisms resulting from the short-time expression of the b isoforms of TIA1 and TIAR, and of HuR in HEK293 cells. Our gene profiling analysis identified several hundred differentially expressed genes (DEGs) and tens of alternative splicing events associated with TIA1b, TIARb and HuR overexpression. Gene ontology analysis revealed that the controlled expression of these proteins strongly influences the patterns of DEGs and RNA variants preferentially associated with development, reproduction, cell cycle, metabolism, autophagy and apoptosis. Mechanistically, TIA1b and TIARb isoforms display both common and differential effects on the regulation of gene expression, involving systematic perturbations of cell biosynthetic machineries (splicing and translation). The transcriptome outputs were validated using functional assays of the targeted cellular processes as well as expression analysis for selected genes. Collectively, our observations suggest that early TIA1b and TIARb expression operates to connect the regulatory crossroads to protective proteostasis responses associated with a survival quiescence phenotype.
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Affiliation(s)
- Isabel Carrascoso
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid (CSIC/UAM), C/ Nicolás Cabrera, Madrid, Spain
| | - José Alcalde
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid (CSIC/UAM), C/ Nicolás Cabrera, Madrid, Spain
| | - Daniel Tabas-Madrid
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, C/ Darwin, Madrid, Spain
| | - Juan Carlos Oliveros
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, C/ Darwin, Madrid, Spain
| | - José M. Izquierdo
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid (CSIC/UAM), C/ Nicolás Cabrera, Madrid, Spain
- * E-mail:
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46
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Lixa C, Mujo A, de Magalhães MTQ, Almeida FCL, Lima LMTR, Pinheiro AS. Oligomeric transition and dynamics of RNA binding by the HuR RRM1 domain in solution. JOURNAL OF BIOMOLECULAR NMR 2018; 72:179-192. [PMID: 30535889 DOI: 10.1007/s10858-018-0217-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 12/04/2018] [Indexed: 06/09/2023]
Abstract
Human antigen R (HuR) functions as a major post-transcriptional regulator of gene expression through its RNA-binding activity. HuR is composed by three RNA recognition motifs, namely RRM1, RRM2, and RRM3. The two N-terminal RRM domains are disposed in tandem and contribute mostly to HuR interaction with adenine and uracil-rich elements (ARE) in mRNA. Here, we used a combination of NMR and electrospray ionization-ion mobility spectrometry-mass spectrometry (ESI-IMS-MS) to characterize the structure, dynamics, RNA recognition, and dimerization of HuR RRM1. Our solution structure reveals a canonical RRM fold containing a 19-residue, intrinsically disordered N-terminal extension, which is not involved in RNA binding. NMR titration results confirm the primary RNA-binding site to the two central β-strands, β1 and β3, for a cyclooxygenase 2 (Cox2) ARE I-derived, 7-nucleotide RNA ligand. We show by 15N relaxation that, in addition to the N- and C-termini, the β2-β3 loop undergoes fast backbone dynamics (ps-ns) both in the free and RNA-bound state, indicating that no structural ordering happens upon RNA interaction. ESI-IMS-MS reveals that HuR RRM1 dimerizes, however dimer population represents a minority. Dimerization occurs via the α-helical surface, which is oppositely orientated to the RNA-binding β-sheet. By using a DNA analog of the Cox2 ARE I, we show that DNA binding stabilizes HuR RRM1 monomer and shifts the monomer-dimer equilibrium toward the monomeric species. Altogether, our results deepen the current understanding of the mechanism of RNA recognition employed by HuR.
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Affiliation(s)
- Carolina Lixa
- Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-909, Brazil
| | - Amanda Mujo
- Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-909, Brazil
| | - Mariana T Q de Magalhães
- Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Fabio C L Almeida
- National Center for Nuclear Magnetic Resonance Jiri Jonas, Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Luis Mauricio T R Lima
- Faculty of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-590, Brazil
| | - Anderson S Pinheiro
- Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-909, Brazil.
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47
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Jang HN, Liu Y, Choi N, Oh J, Ha J, Zheng X, Shen H. Binding of SRSF4 to a novel enhancer modulates splicing of exon 6 of Fas pre-mRNA. Biochem Biophys Res Commun 2018; 506:703-708. [PMID: 30376989 DOI: 10.1016/j.bbrc.2018.10.123] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 10/20/2018] [Indexed: 11/29/2022]
Abstract
Alternative splicing of exon 6 in Fas pre-mRNA generates a membrane bound pro-apoptotic isoform or soluble anti-apoptotic isoform. SRSF4 is a member of Arginine-Serine rich (SR) protein family. Here we demonstrate that increased SRSF4 expression stimulates exon 6 inclusion, and that reduced SRSF4 expression promotes exon 6 exclusion. We also show that weaker but not stronger 5' splice-site strength of exon 6 abolishes the SRSF4 effects on exon 6 splicing. Furthermore, we identified a novel enhancer on exon 6, on which SRSF4 interacts functionally and physically. Our results illustrate a novel regulatory mechanism of Fas pre-mRNA splicing.
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Affiliation(s)
- Ha Na Jang
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, 500-712, South Korea
| | - Yongchao Liu
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, 500-712, South Korea
| | - Namjeong Choi
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, 500-712, South Korea
| | - Jagyeong Oh
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, 500-712, South Korea
| | - Jiyeon Ha
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, 500-712, South Korea
| | - Xuexiu Zheng
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, 500-712, South Korea.
| | - Haihong Shen
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, 500-712, South Korea.
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48
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Sutandy FXR, Ebersberger S, Huang L, Busch A, Bach M, Kang HS, Fallmann J, Maticzka D, Backofen R, Stadler PF, Zarnack K, Sattler M, Legewie S, König J. In vitro iCLIP-based modeling uncovers how the splicing factor U2AF2 relies on regulation by cofactors. Genome Res 2018; 28:699-713. [PMID: 29643205 PMCID: PMC5932610 DOI: 10.1101/gr.229757.117] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 02/09/2018] [Indexed: 01/26/2023]
Abstract
Alternative splicing generates distinct mRNA isoforms and is crucial for proteome diversity in eukaryotes. The RNA-binding protein (RBP) U2AF2 is central to splicing decisions, as it recognizes 3′ splice sites and recruits the spliceosome. We establish “in vitro iCLIP” experiments, in which recombinant RBPs are incubated with long transcripts, to study how U2AF2 recognizes RNA sequences and how this is modulated by trans-acting RBPs. We measure U2AF2 affinities at hundreds of binding sites and compare in vitro and in vivo binding landscapes by mathematical modeling. We find that trans-acting RBPs extensively regulate U2AF2 binding in vivo, including enhanced recruitment to 3′ splice sites and clearance of introns. Using machine learning, we identify and experimentally validate novel trans-acting RBPs (including FUBP1, CELF6, and PCBP1) that modulate U2AF2 binding and affect splicing outcomes. Our study offers a blueprint for the high-throughput characterization of in vitro mRNP assembly and in vivo splicing regulation.
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Affiliation(s)
| | | | - Lu Huang
- Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany
| | - Anke Busch
- Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany
| | - Maximilian Bach
- Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany
| | - Hyun-Seo Kang
- Institute of Structural Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany.,Biomolecular NMR and Center for Integrated Protein Science Munich at Department of Chemistry, Technical University of Munich, 85747 Garching, Germany
| | - Jörg Fallmann
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, 04107 Leipzig, Germany
| | - Daniel Maticzka
- Bioinformatics Group, Department of Computer Science, University of Freiburg, 79110 Freiburg, Germany
| | - Rolf Backofen
- Bioinformatics Group, Department of Computer Science, University of Freiburg, 79110 Freiburg, Germany.,Centre for Biological Signalling Studies (BIOSS), University of Freiburg, 79104 Freiburg, Germany
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, 04107 Leipzig, Germany
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, 60438 Frankfurt a.M., Germany
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany.,Biomolecular NMR and Center for Integrated Protein Science Munich at Department of Chemistry, Technical University of Munich, 85747 Garching, Germany
| | - Stefan Legewie
- Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany
| | - Julian König
- Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany
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49
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Suess B, Kemmerer K, Weigand JE. Splicing and Alternative Splicing Impact on Gene Design. Synth Biol (Oxf) 2018. [DOI: 10.1002/9783527688104.ch7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Beatrix Suess
- Department of Biology; Technische Universität Darmstadt; Schnittspahnstraße 10 64287 Darmstadt Germany
| | - Katrin Kemmerer
- Department of Biology; Technische Universität Darmstadt; Schnittspahnstraße 10 64287 Darmstadt Germany
| | - Julia E. Weigand
- Department of Biology; Technische Universität Darmstadt; Schnittspahnstraße 10 64287 Darmstadt Germany
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50
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Manzoni L, Zucal C, Maio DD, D’Agostino VG, Thongon N, Bonomo I, Lal P, Miceli M, Baj V, Brambilla M, Cerofolini L, Elezgarai S, Biasini E, Luchinat C, Novellino E, Fragai M, Marinelli L, Provenzani A, Seneci P. Interfering with HuR–RNA Interaction: Design, Synthesis and Biological Characterization of Tanshinone Mimics as Novel, Effective HuR Inhibitors. J Med Chem 2018; 61:1483-1498. [DOI: 10.1021/acs.jmedchem.7b01176] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Leonardo Manzoni
- Institute of Molecular Science and Technology (ISTM), CNR, Via Golgi 19, 20133 Milan, Italy
| | - Chiara Zucal
- Centre
for Integrative Biology (CIBIO), University of Trento, Via Sommarive
9, 38123 Povo, Trento, Italy
| | - Danilo Di Maio
- Scuola Normale Superiore, Piazza
dei Cavalieri 7, I-56126 Pisa, Italy
| | - Vito G. D’Agostino
- Centre
for Integrative Biology (CIBIO), University of Trento, Via Sommarive
9, 38123 Povo, Trento, Italy
| | - Natthakan Thongon
- Centre
for Integrative Biology (CIBIO), University of Trento, Via Sommarive
9, 38123 Povo, Trento, Italy
| | - Isabelle Bonomo
- Centre
for Integrative Biology (CIBIO), University of Trento, Via Sommarive
9, 38123 Povo, Trento, Italy
| | - Preet Lal
- Centre
for Integrative Biology (CIBIO), University of Trento, Via Sommarive
9, 38123 Povo, Trento, Italy
| | - Marco Miceli
- Chemistry
Department, University of Milan, Via Golgi 19, 20133 Milan, Italy
| | - Vanessa Baj
- Chemistry
Department, University of Milan, Via Golgi 19, 20133 Milan, Italy
| | - Marta Brambilla
- Chemistry
Department, University of Milan, Via Golgi 19, 20133 Milan, Italy
| | - Linda Cerofolini
- Consorzio Interuniversitario di Risonanze Magnetiche di Metallo Proteine (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
- CERM and
Chemistry Department, University of Florence, Via della Lastruccia 3-13, 50019 Sesto Fiorentino, Florence, Italy
| | - Saioa Elezgarai
- Istituto di Ricerche Farmacologiche Mario Negri, Milan, 20156, Italy
| | - Emiliano Biasini
- Centre
for Integrative Biology (CIBIO), University of Trento, Via Sommarive
9, 38123 Povo, Trento, Italy
- Istituto di Ricerche Farmacologiche Mario Negri, Milan, 20156, Italy
| | - Claudio Luchinat
- CERM and
Chemistry Department, University of Florence, Via della Lastruccia 3-13, 50019 Sesto Fiorentino, Florence, Italy
| | - Ettore Novellino
- Pharmacy
Department, University of Naples, Via Montesano 49, 80131 Naples, Italy
| | - Marco Fragai
- Consorzio Interuniversitario di Risonanze Magnetiche di Metallo Proteine (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
- CERM and
Chemistry Department, University of Florence, Via della Lastruccia 3-13, 50019 Sesto Fiorentino, Florence, Italy
| | - Luciana Marinelli
- Pharmacy
Department, University of Naples, Via Montesano 49, 80131 Naples, Italy
| | - Alessandro Provenzani
- Centre
for Integrative Biology (CIBIO), University of Trento, Via Sommarive
9, 38123 Povo, Trento, Italy
| | - Pierfausto Seneci
- Chemistry
Department, University of Milan, Via Golgi 19, 20133 Milan, Italy
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