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Ashour K, Sali S, Aldoukhi AH, Hall D, Mubaid S, Busque S, Lian XJ, Gagné JP, Khattak S, Di Marco S, Poirier GG, Gallouzi IE. pADP-ribosylation regulates the cytoplasmic localization, cleavage, and pro-apoptotic function of HuR. Life Sci Alliance 2024; 7:e202302316. [PMID: 38538092 PMCID: PMC10972696 DOI: 10.26508/lsa.202302316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 04/05/2024] Open
Abstract
HuR (ElavL1) is one of the main post-transcriptional regulators that determines cell fate. Although the role of HuR in apoptosis is well established, the post-translational modifications that govern this function remain elusive. In this study, we show that PARP1/2-mediated poly(ADP)-ribosylation (PARylation) is instrumental in the pro-apoptotic function of HuR. During apoptosis, a substantial reduction in HuR PARylation is observed. This results in the cytoplasmic accumulation and the cleavage of HuR, both of which are essential events for apoptosis. These effects are mediated by a pADP-ribose-binding motif within the HuR-HNS region (HuR PAR-binding site). Under normal conditions, the association of the HuR PAR-binding site with pADP-ribose is responsible for the nuclear retention of HuR. Mutations within this motif prevent the binding of HuR to its import factor TRN2, leading to its cytoplasmic accumulation and cleavage. Collectively, our findings underscore the role of PARylation in controlling the pro-apoptotic function of HuR, offering insight into the mechanism by which PARP1/2 enzymes regulate cell fate and adaptation to various assaults.
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Affiliation(s)
- Kholoud Ashour
- Department of Biochemistry, McGill University, Montreal, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Canada
- Faculty of Applied Medical Sciences, Medical Laboratory Technology, Taibah University, Medina, Saudi Arabia
| | - Sujitha Sali
- https://ror.org/01q3tbs38 KAUST Smart-Health Initiative (KSHI) and Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Jeddah, Saudi Arabia
| | - Ali H Aldoukhi
- https://ror.org/01q3tbs38 KAUST Smart-Health Initiative (KSHI) and Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Jeddah, Saudi Arabia
| | - Derek Hall
- Department of Biochemistry, McGill University, Montreal, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Canada
| | - Souad Mubaid
- Department of Biochemistry, McGill University, Montreal, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Canada
| | - Sandrine Busque
- Department of Biochemistry, McGill University, Montreal, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Canada
| | - Xian Jin Lian
- Department of Biochemistry, McGill University, Montreal, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Canada
| | - Jean-Philippe Gagné
- Centre de recherche du CHU de Québec-Pavillon CHUL, Faculté de Médecine, Université Laval, Québec, Canada
| | - Shahryar Khattak
- https://ror.org/01q3tbs38 KAUST Smart-Health Initiative (KSHI) and Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Jeddah, Saudi Arabia
| | - Sergio Di Marco
- https://ror.org/01q3tbs38 KAUST Smart-Health Initiative (KSHI) and Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Jeddah, Saudi Arabia
- Department of Biochemistry, McGill University, Montreal, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Canada
| | - Guy G Poirier
- Centre de recherche du CHU de Québec-Pavillon CHUL, Faculté de Médecine, Université Laval, Québec, Canada
| | - Imed-Eddine Gallouzi
- https://ror.org/01q3tbs38 KAUST Smart-Health Initiative (KSHI) and Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Jeddah, Saudi Arabia
- Department of Biochemistry, McGill University, Montreal, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Canada
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Shatat AAS, Mahgoup EM, Rashed MH, Saleh IG, Akool ES. Molecular mechanisms of extracellular-ATP-mediated colorectal cancer progression: Implication of purinergic receptors-mediated nucleocytoplasmic shuttling of HuR. Purinergic Signal 2024:10.1007/s11302-024-10021-2. [PMID: 38801618 DOI: 10.1007/s11302-024-10021-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 05/09/2024] [Indexed: 05/29/2024] Open
Abstract
One of the leading causes of cancer-related deaths worldwide is colorectal cancer (CRC). Extracellular ATP (e-ATP) and purinergic receptors (P2R) play a central role in CRC proliferation and progression. Human antigen R (HuR) is becoming more and more understood to be essential for the expression of genes linked to cancer. The current study demonstrates that ATP can mediate CRC (Caco-2 cells) progression via induction of HuR nucleocytoplasmic shuttling and subsequent expression of cancer-related genes, a consequence mostly mediated via the P2R receptor. It was also noted that suppression of HuR activity by using dihydrotanshinone I (DHTS) prevents cancer-related gene expression and subsequent CRC (Caco-2 cells) progression induced by ATP. The expression of cyclin A2/cyclin-dependent kinase 2 (CDK2), Bcl-2, ProT-α, hypoxia-inducible factor1-α (HIF1-α), vascular endothelial growth factor A (VEGF-A), transforming growth factor-β (TGF-β) and matrix metallopeptidase 9 (MMP-9) induced by ATP were highly reduced in the presence of either PPADS (non-selective P2R antagonist) or DHTS. In addition, e-ATP-induced Caco-2 cell proliferation as well as cell survival were highly reduced in the presence of either PPADS or DHTS or selective CDK-2 inhibitor (Roscovitine) or selective Bcl-2 inhibitor (ABT-263). Furthermore, it was found that MMP-9 is critical for Caco-2 cells migration induced by e-ATP as demonstrated by a clear reduction in cells migration in the presence of a selective MMP-9 inhibitor (Marimastat). Collectively, these data demonstrate that ATP through P2R activation can induce HuR nucleocytoplasmic shuttling that could be translated into an increase in cancer-related genes expression and subsequent, cell proliferation and progression.
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Affiliation(s)
- Abdel-Aziz S Shatat
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Al-Azhar University, Cairo, Egypt
| | - Elsayed M Mahgoup
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Al-Azhar University, Cairo, Egypt
| | - Mohammed H Rashed
- Department of Clinical Pharmacy, Faculty of Pharmacy, Al-Azhar University, Cairo, Egypt
| | - Ibrahim G Saleh
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Al-Azhar University, Cairo, Egypt
- Department of Clinical Pharmacy and Pharmacy Practice, Faculty of Pharmacy, Sinai University, Kantra, Ismailia, Egypt
| | - El-Sayed Akool
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Al-Azhar University, Cairo, Egypt.
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Deng B, Wang J, Yang T, Deng Z, Yuan J, Zhang B, Zhou Z, Chen F, Fang L, Liang C, Yan B, Ai Y. TNF and IFNγ-induced cell death requires IRF1 and ELAVL1 to promote CASP8 expression. J Cell Biol 2024; 223:e202305026. [PMID: 38319288 PMCID: PMC10847335 DOI: 10.1083/jcb.202305026] [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: 05/06/2023] [Revised: 10/23/2023] [Accepted: 12/15/2023] [Indexed: 02/07/2024] Open
Abstract
TNFα and IFNγ (TNF/IFNγ) synergistically induce caspase-8 activation and cancer cell death. However, the mechanism of IFNγ in promoting TNF-initiated caspase-8 activation in cancer cells is poorly understood. Here, we found that in addition to CASP8, CYLD is transcriptionally upregulated by IFNγ-induced transcription factor IRF1. IRF1-mediated CASP8 and CYLD upregulation additively mediates TNF/IFNγ-induced cancer cell death. Clinically, the expression levels of TNF, IFNγ, CYLD, and CASP8 in melanoma tumors are increased in patients responsive to immune checkpoint blockade (ICB) therapy after anti-PD-1 treatment. Accordingly, our genetic screen revealed that ELAVL1 (HuR) is required for TNF/IFNγ-induced caspase-8 activation. Mechanistically, ELAVL1 binds CASP8 mRNA and extends its stability to sustain caspase-8 expression both in IFNγ-stimulated and in basal conditions. Consequently, ELAVL1 determines death receptors-initiated caspase-8-dependent cell death triggered from stimuli including TNF and TRAIL by regulating basal/stimulated caspase-8 levels. As caspase-8 is a master regulator in cell death and inflammation, these results provide valuable clues for tumor immunotherapy and inflammatory diseases.
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Affiliation(s)
- Buhao Deng
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Jingyi Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Tingyun Yang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Zhao Deng
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Jiafan Yuan
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Bohan Zhang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Zhen Zhou
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Fang Chen
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Lu Fang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Chengzhi Liang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Bo Yan
- Department of Neurology, Institute of Neuroimmunology, Tianjin Medical University General Hospital, Tianjin, China
| | - Youwei Ai
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
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Čižmáriková M, Michalková R, Mirossay L, Mojžišová G, Zigová M, Bardelčíková A, Mojžiš J. Ellagic Acid and Cancer Hallmarks: Insights from Experimental Evidence. Biomolecules 2023; 13:1653. [PMID: 38002335 PMCID: PMC10669545 DOI: 10.3390/biom13111653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 11/10/2023] [Accepted: 11/12/2023] [Indexed: 11/26/2023] Open
Abstract
Cancer is a complex and multifaceted disease with a high global incidence and mortality rate. Although cancer therapy has evolved significantly over the years, numerous challenges persist on the path to effectively combating this multifaceted disease. Natural compounds derived from plants, fungi, or marine organisms have garnered considerable attention as potential therapeutic agents in the field of cancer research. Ellagic acid (EA), a natural polyphenolic compound found in various fruits and nuts, has emerged as a potential cancer prevention and treatment agent. This review summarizes the experimental evidence supporting the role of EA in targeting key hallmarks of cancer, including proliferation, angiogenesis, apoptosis evasion, immune evasion, inflammation, genomic instability, and more. We discuss the molecular mechanisms by which EA modulates signaling pathways and molecular targets involved in these cancer hallmarks, based on in vitro and in vivo studies. The multifaceted actions of EA make it a promising candidate for cancer prevention and therapy. Understanding its impact on cancer biology can pave the way for developing novel strategies to combat this complex disease.
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Affiliation(s)
- Martina Čižmáriková
- Department of Pharmacology, Faculty of Medicine, Pavol Jozef Šafárik University, 040 01 Košice, Slovakia; (M.Č.); (R.M.); (M.Z.); (A.B.)
| | - Radka Michalková
- Department of Pharmacology, Faculty of Medicine, Pavol Jozef Šafárik University, 040 01 Košice, Slovakia; (M.Č.); (R.M.); (M.Z.); (A.B.)
| | - Ladislav Mirossay
- Department of Pharmacology, Faculty of Medicine, Pavol Jozef Šafárik University, 040 01 Košice, Slovakia; (M.Č.); (R.M.); (M.Z.); (A.B.)
| | - Gabriela Mojžišová
- Center of Clinical and Preclinical Research MEDIPARK, Faculty of Medicine, Pavol Jozef Šafárik University, 040 01 Košice, Slovakia;
| | - Martina Zigová
- Department of Pharmacology, Faculty of Medicine, Pavol Jozef Šafárik University, 040 01 Košice, Slovakia; (M.Č.); (R.M.); (M.Z.); (A.B.)
| | - Annamária Bardelčíková
- Department of Pharmacology, Faculty of Medicine, Pavol Jozef Šafárik University, 040 01 Košice, Slovakia; (M.Č.); (R.M.); (M.Z.); (A.B.)
| | - Ján Mojžiš
- Department of Pharmacology, Faculty of Medicine, Pavol Jozef Šafárik University, 040 01 Košice, Slovakia; (M.Č.); (R.M.); (M.Z.); (A.B.)
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Huang Z, Liu S, Tang A, Wu X, Aube J, Xu L, Huang Y. Targeting RNA-binding protein HuR to inhibit the progression of renal tubular fibrosis. J Transl Med 2023; 21:428. [PMID: 37391777 PMCID: PMC10311833 DOI: 10.1186/s12967-023-04298-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 06/23/2023] [Indexed: 07/02/2023] Open
Abstract
BACKGROUND Upregulation of an RNA-binding protein HuR has been implicated in glomerular diseases. Herein, we evaluated whether it is involved in renal tubular fibrosis. METHODS HuR was firstly examined in human kidney biopsy tissue with tubular disease. Second, its expression and the effect of HuR inhibition with KH3 on tubular injury were further assessed in a mouse model induced by a unilateral renal ischemia/reperfusion (IR). KH3 (50 mg kg-1) was given daily via intraperitoneal injection from day 3 to 14 after IR. Last, one of HuR-targeted pathways was examined in cultured proximal tubular cells. RESULTS HuR significantly increases at the site of tubular injury both in progressive CKD in patients and in IR-injured kidneys in mice, accompanied by upregulation of HuR targets that are involved in inflammation, profibrotic cytokines, oxidative stress, proliferation, apoptosis, tubular EMT process, matrix remodeling and fibrosis in renal tubulointerstitial fibrosis. KH3 treatment reduces the IR-induced tubular injury and fibrosis, accompanied by the remarkable amelioration in those involved pathways. A panel of mRNA array further revealed that 519 molecules in mouse kidney following IR injury changed their expression and 71.3% of them that are involved in 50 profibrotic pathways, were ameliorated when treated with KH3. In vitro, TGFβ1 induced tubular HuR cytoplasmic translocation and subsequent tubular EMT, which were abrogated by KH3 administration in cultured HK-2 cells. CONCLUSIONS These results suggest that excessive upregulation of HuR contributes to renal tubulointerstitial fibrosis by dysregulating genes involved in multiple profibrotic pathways and activating the TGFß1/HuR feedback circuit in tubular cells. Inhibition of HuR may have therapeutic potential for renal tubular fibrosis.
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Affiliation(s)
- Zhimin Huang
- Division of Nephrology & Hypertension, Department of Internal Medicine, University of Utah Health Science, Wintrobe Rm 403, 26 N Medical Dr., Salt Lake City, UT, 84132, USA
| | - Simeng Liu
- Division of Nephrology & Hypertension, Department of Internal Medicine, University of Utah Health Science, Wintrobe Rm 403, 26 N Medical Dr., Salt Lake City, UT, 84132, USA
| | - Anna Tang
- Division of Nephrology & Hypertension, Department of Internal Medicine, University of Utah Health Science, Wintrobe Rm 403, 26 N Medical Dr., Salt Lake City, UT, 84132, USA
| | - Xiaoqing Wu
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, USA
| | - Jeffrey Aube
- Department of Chemical Biology and Medical Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
| | - Liang Xu
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, USA
| | - Yufeng Huang
- Division of Nephrology & Hypertension, Department of Internal Medicine, University of Utah Health Science, Wintrobe Rm 403, 26 N Medical Dr., Salt Lake City, UT, 84132, USA.
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Mehta M, Raguraman R, Ramesh R, Munshi A. RNA binding proteins (RBPs) and their role in DNA damage and radiation response in cancer. Adv Drug Deliv Rev 2022; 191:114569. [PMID: 36252617 PMCID: PMC10411638 DOI: 10.1016/j.addr.2022.114569] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 09/27/2022] [Accepted: 09/29/2022] [Indexed: 01/24/2023]
Abstract
Traditionally majority of eukaryotic gene expression is influenced by transcriptional and post-transcriptional events. Alterations in the expression of proteins that act post-transcriptionally can affect cellular signaling and homeostasis. RNA binding proteins (RBPs) are a family of proteins that specifically bind to RNAs and are involved in post-transcriptional regulation of gene expression and important cellular processes such as cell differentiation and metabolism. Deregulation of RNA-RBP interactions and any changes in RBP expression or function can lead to various diseases including cancer. In cancer cells, RBPs play an important role in regulating the expression of tumor suppressors and oncoproteins involved in various cell-signaling pathways. Several RBPs such as HuR, AUF1, RBM38, LIN28, RBM24, tristetrapolin family and Musashi play critical roles in various types of cancers and their aberrant expression in cancer cells makes them an attractive therapeutic target for cancer treatment. In this review we provide an overview of i). RBPs involved in cancer progression and their mechanism of action ii). the role of RBPs, including HuR, in breast cancer progression and DNA damage response and iii). explore RBPs with emphasis on HuR as therapeutic target for breast cancer therapy.
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Affiliation(s)
- Meghna Mehta
- Department of Radiation Oncology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73013, USA; Stephenson Cancer Center, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73013, USA
| | - Rajeswari Raguraman
- Department of Pathology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73013, USA; Stephenson Cancer Center, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73013, USA
| | - Rajagopal Ramesh
- Department of Pathology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73013, USA; Stephenson Cancer Center, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73013, USA
| | - Anupama Munshi
- Department of Radiation Oncology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73013, USA; Stephenson Cancer Center, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73013, USA.
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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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Lunin SM, Novoselova EG, Glushkova OV, Parfenyuk SB, Novoselova TV, Khrenov MO. Cell Senescence and Central Regulators of Immune Response. Int J Mol Sci 2022; 23:ijms23084109. [PMID: 35456927 PMCID: PMC9028919 DOI: 10.3390/ijms23084109] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 04/04/2022] [Accepted: 04/06/2022] [Indexed: 12/13/2022] Open
Abstract
Pathways regulating cell senescence and cell cycle underlie many processes associated with ageing and age-related pathologies, and they also mediate cellular responses to exposure to stressors. Meanwhile, there are central mechanisms of the regulation of stress responses that induce/enhance or weaken the response of the whole organism, such as hormones of the hypothalamic-pituitary-adrenal (HPA) axis, sympathetic and parasympathetic systems, thymic hormones, and the pineal hormone melatonin. Although there are many analyses considering relationships between the HPA axis and organism ageing, we found no systematic analyses of relationships between the neuroendocrine regulators of stress and inflammation and intracellular mechanisms controlling cell cycle, senescence, and apoptosis. Here, we provide a review of the effects of neuroendocrine regulators on these mechanisms. Our analysis allowed us to postulate a multilevel system of central regulators involving neurotransmitters, glucocorticoids, melatonin, and the thymic hormones. This system finely regulates the cell cycle and metabolic/catabolic processes depending on the level of systemic stress, stage of stress response, and energy capabilities of the body, shifting the balance between cell cycle progression, cell cycle stopping, senescence, and apoptosis. These processes and levels of regulation should be considered when studying the mechanisms of ageing and the proliferation on the level of the whole organism.
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Adachi Y, Masuda M, Sakakibara I, Uchida T, Niida Y, Mori Y, Kamei Y, Okumura Y, Ohminami H, Ohnishi K, Yamanaka-Okumura H, Nikawa T, Taketani Y. All-trans retinoic acid changes muscle fiber type via increasing GADD34 dependent on MAPK signal. Life Sci Alliance 2022; 5:5/7/e202101345. [PMID: 35318262 PMCID: PMC8960774 DOI: 10.26508/lsa.202101345] [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: 12/21/2021] [Revised: 03/09/2022] [Accepted: 03/11/2022] [Indexed: 11/25/2022] Open
Abstract
ATRA increases GADD34 expression by decreasing the expression of Six1, which down-regulates the transcriptional activity with TLE3 and increasing mRNA stability through blocking the interaction between TTP and ARE on GADD34 mRNA, resulting in muscle fiber type change. All-trans retinoic acid (ATRA) increases the sensitivity to unfolded protein response in differentiating leukemic blasts. The downstream transcriptional factor of PERK, a major arm of unfolded protein response, regulates muscle differentiation. However, the role of growth arrest and DNA damage-inducible protein 34 (GADD34), one of the downstream factors of PERK, and the effects of ATRA on GADD34 expression in muscle remain unclear. In this study, we identified ATRA increased the GADD34 expression independent of the PERK signal in the gastrocnemius muscle of mice. ATRA up-regulated GADD34 expression through the transcriptional activation of GADD34 gene via inhibiting the interaction of homeobox Six1 and transcription co-repressor TLE3 with the MEF3-binding site on the GADD34 gene promoter in skeletal muscle. ATRA also inhibited the interaction of TTP, which induces mRNA degradation, with AU-rich element on GADD34 mRNA via p-38 MAPK, resulting in the instability of GADD34 mRNA. Overexpressed GADD34 in C2C12 cells changes the type of myosin heavy chain in myotubes. These results suggest ATRA increases GADD34 expression via transcriptional and post-transcriptional regulation, which changes muscle fiber type.
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Affiliation(s)
- Yuichiro Adachi
- Department of Clinical Nutrition and Food Management, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Masashi Masuda
- Department of Clinical Nutrition and Food Management, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Iori Sakakibara
- Department of Nutritional Physiology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Takayuki Uchida
- Department of Nutritional Physiology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Yuki Niida
- Department of Clinical Nutrition and Food Management, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Yuki Mori
- Department of Clinical Nutrition and Food Management, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Yuki Kamei
- Department of Clinical Nutrition and Food Management, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Yosuke Okumura
- Department of Clinical Nutrition and Food Management, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Hirokazu Ohminami
- Department of Clinical Nutrition and Food Management, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Kohta Ohnishi
- Department of Clinical Nutrition and Food Management, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Hisami Yamanaka-Okumura
- Department of Clinical Nutrition and Food Management, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Takeshi Nikawa
- Department of Nutritional Physiology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Yutaka Taketani
- Department of Clinical Nutrition and Food Management, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
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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: 1] [Impact Index Per Article: 0.3] [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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11
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Borgonetti V, Coppi E, Galeotti N. Targeting the RNA-Binding Protein HuR as Potential Thera-Peutic Approach for Neurological Disorders: Focus on Amyo-Trophic Lateral Sclerosis (ALS), Spinal Muscle Atrophy (SMA) and Multiple Sclerosis. Int J Mol Sci 2021; 22:ijms221910394. [PMID: 34638733 PMCID: PMC8508990 DOI: 10.3390/ijms221910394] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 01/03/2023] Open
Abstract
The importance of precise co- and post-transcriptional processing of RNA in the regulation of gene expression has become increasingly clear. RNA-binding proteins (RBPs) are a class of proteins that bind single- or double-chain RNA, with different affinities and selectivity, thus regulating the various functions of RNA and the fate of the cells themselves. ELAV (embryonic lethal/abnormal visual system)/Hu proteins represent an important family of RBPs and play a key role in the fate of newly transcribed mRNA. ELAV proteins bind AU-rich element (ARE)-containing transcripts, which are usually present on the mRNA of proteins such as cytokines, growth factors, and other proteins involved in neuronal differentiation and maintenance. In this review, we focused on a member of ELAV/Hu proteins, HuR, and its role in the development of neurodegenerative disorders, with a particular focus on demyelinating diseases.
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12
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Ma Y, Yin S, Liu XF, Hu J, Cai N, Zhang XB, Fu L, Cao XC, Yu Y. Comprehensive Analysis of the Functions and Prognostic Value of RNA-Binding Proteins in Thyroid Cancer. Front Oncol 2021; 11:625007. [PMID: 33816259 PMCID: PMC8010172 DOI: 10.3389/fonc.2021.625007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 01/25/2021] [Indexed: 12/24/2022] Open
Abstract
RNA binding proteins (RBPs) have been proved to play pivotal roles in a variety types of tumors. However, there is no convincible evidence disclosing the functions of RBPs in thyroid cancer (THCA) thoroughly and systematically. Integrated analysis of the functional and prognostic effect of RBPs help better understanding tumorigenesis and development in thyroid and may provide a novel therapeutic method for THCA. In this study, we obtained a list of human RBPs from Gerstberger database, which covered 1,542 genes encoding RBPs. Gene expression data of THCA was downloaded from The Cancer Genome Atlas (TCGA, n = 567), from which we extracted 1,491 RBPs' gene expression data. We analyzed differentially expressed RBPs using R package "limma". Based on differentially expressed RBPs, we constructed protein-protein interaction network and the GO and KEGG pathway enrichment analyses were carried out. We found six RBPs (AZGP1, IGF2BP2, MEX3A, NUDT16, NUP153, USB1) independently associated with prognosis of patients with thyroid cancer according to univariate and multivariate Cox proportional hazards regression models. The survival analysis and risk score analysis achieved good performances from this six-gene prognostic model. Nomogram was constructed to guide clinical decision in practice. Finally, biological experiments disclosed that NUP153 and USB1 can significantly impact cancer cell proliferation and migration. In conclusion, our research provided a new insight of thyroid tumorigenesis and development based on analyses of RBPs. More importantly, the six-gene model may play an important role in clinical practice in the future.
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Affiliation(s)
- Yue Ma
- The First Department of Breast Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Tianjin’s Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
| | - Shi Yin
- The First Department of Breast Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Tianjin’s Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
| | - Xiao-feng Liu
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Tianjin’s Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
| | - Jing Hu
- The First Department of Breast Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Tianjin’s Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
| | - Ning Cai
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiao-bei Zhang
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Tianjin’s Clinical Research Center for Cancer, Tianjin, China
- Department of Anesthesiology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
| | - Li Fu
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Tianjin’s Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
| | - Xu-chen Cao
- The First Department of Breast Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Tianjin’s Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
| | - Yue Yu
- The First Department of Breast Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Tianjin’s Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
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13
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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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14
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Kang D, Lee Y, Lee JS. RNA-Binding Proteins in Cancer: Functional and Therapeutic Perspectives. Cancers (Basel) 2020; 12:cancers12092699. [PMID: 32967226 PMCID: PMC7563379 DOI: 10.3390/cancers12092699] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/17/2020] [Accepted: 09/18/2020] [Indexed: 12/12/2022] Open
Abstract
Simple Summary RNA-binding proteins (RBPs) play central roles in regulating posttranscriptional expression of genes. Many of them are known to be deregulated in a wide variety of cancers. Dysregulated RBPs influence the expression levels of target RNAs related to cancer phenotypes, such as proliferation, apoptosis, angiogenesis, senescence, and EMT/invasion/metastasis. Thus, understanding the molecular functions of RBPs and their roles in cancer-related phenotypes can lead to improved therapeutic strategies. Abstract RNA-binding proteins (RBPs) crucially regulate gene expression through post-transcriptional regulation, such as by modulating microRNA (miRNA) processing and the alternative splicing, alternative polyadenylation, subcellular localization, stability, and translation of RNAs. More than 1500 RBPs have been identified to date, and many of them are known to be deregulated in cancer. Alterations in the expression and localization of RBPs can influence the expression levels of oncogenes, tumor-suppressor genes, and genome stability-related genes. RBP-mediated gene regulation can lead to diverse cancer-related cellular phenotypes, such as proliferation, apoptosis, angiogenesis, senescence, and epithelial-mesenchymal transition (EMT)/invasion/metastasis. This regulation can also be associated with cancer prognosis. Thus, RBPs can be potential targets for the development of therapeutics for the cancer treatment. In this review, we describe the molecular functions of RBPs, their roles in cancer-related cellular phenotypes, and various approaches that may be used to target RBPs for cancer treatment.
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Affiliation(s)
- Donghee Kang
- Medical Research Center, College of Medicine, Inha University, Incheon 22212, Korea; (D.K.); (Y.L.)
- Department of Molecular Medicine, College of Medicine, Inha University, Incheon 22212, Korea
- Program in Biomedical Science & Engineering, Inha University Graduate School, Incheon 22212, Korea
| | - Yerim Lee
- Medical Research Center, College of Medicine, Inha University, Incheon 22212, Korea; (D.K.); (Y.L.)
- Department of Molecular Medicine, College of Medicine, Inha University, Incheon 22212, Korea
| | - Jae-Seon Lee
- Medical Research Center, College of Medicine, Inha University, Incheon 22212, Korea; (D.K.); (Y.L.)
- Department of Molecular Medicine, College of Medicine, Inha University, Incheon 22212, Korea
- Program in Biomedical Science & Engineering, Inha University Graduate School, Incheon 22212, Korea
- Correspondence: ; Tel.: +82-32-860-9832
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15
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Dong R, Chen P, Polireddy K, Wu X, Wang T, Ramesh R, Dixon DA, Xu L, Aubé J, Chen Q. An RNA-Binding Protein, Hu-antigen R, in Pancreatic Cancer Epithelial to Mesenchymal Transition, Metastasis, and Cancer Stem Cells. Mol Cancer Ther 2020; 19:2267-2277. [PMID: 32879054 DOI: 10.1158/1535-7163.mct-19-0822] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Revised: 04/17/2020] [Accepted: 08/21/2020] [Indexed: 01/04/2023]
Abstract
Pancreatic cancer has poor prognosis and treatment outcomes due to its highly metastatic nature and resistance to current treatments. The RNA-binding protein (RBP) Hu-antigen R (HuR) is a central player in posttranscriptional regulation of cancer-related gene expression, and contributes to tumorigenesis, tumor growth, metastasis, and drug resistance. HuR has been suggested to regulate pancreatic cancer epithelial-to-mesenchymal transition (EMT), but the mechanism was not well understood. Here, we further elucidated the role HuR plays in pancreatic cancer cell EMT, and developed a novel inhibitor specifically interrupting HuR-RNA binding. The data showed that HuR binds to the 3'-UTR of the mRNA of the transcription factor Snail, resulting in stabilization of Snail mRNA and enhanced Snail protein expression, thus promoted EMT, metastasis, and formation of stem-like cancer cells (CSC) in pancreatic cancer cells. siRNA silencing or CRISPR/Cas9 gene deletion of HuR inhibited pancreatic cancer cell EMT, migration, invasion, and inhibited CSCs. HuR knockout cells had dampened tumorigenicity in immunocompromised mice. A novel compound KH-3 interrupted HuR-RNA binding, and KH-3 inhibited pancreatic cancer cell viability, EMT, migration/invasion in vitro KH-3 showed HuR-dependent activity and inhibited HuR-positive tumor growth and metastasis in vivo.
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Affiliation(s)
- Ruochen Dong
- Department of Pharmacology, Toxicology and Therapeutics, the University of Kansas Medical Center, Kansas City, Kansas
| | - Ping Chen
- Department of Pharmacology, Toxicology and Therapeutics, the University of Kansas Medical Center, Kansas City, Kansas
| | - Kishore Polireddy
- Department of Pharmacology, Toxicology and Therapeutics, the University of Kansas Medical Center, Kansas City, Kansas
| | - Xiaoqing Wu
- Department of Molecular Biosciences, The University of Kansas, Lawrence, Kansas
| | - Tao Wang
- Department of Pharmacology, Toxicology and Therapeutics, the University of Kansas Medical Center, Kansas City, Kansas
| | - Remya Ramesh
- Department of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, The University of North Carolina, Chapel Hill, North Carolina
| | - Dan A Dixon
- Department of Molecular Biosciences, The University of Kansas, Lawrence, Kansas
| | - Liang Xu
- Department of Molecular Biosciences, The University of Kansas, Lawrence, Kansas
| | - Jeffrey Aubé
- Department of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, The University of North Carolina, Chapel Hill, North Carolina
| | - Qi Chen
- Department of Pharmacology, Toxicology and Therapeutics, the University of Kansas Medical Center, Kansas City, Kansas.
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16
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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: 118] [Impact Index Per Article: 29.5] [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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17
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Pabis M, Popowicz GM, Stehle R, Fernández-Ramos D, Asami S, Warner L, García-Mauriño SM, Schlundt A, Martínez-Chantar ML, Díaz-Moreno I, Sattler M. HuR biological function involves RRM3-mediated dimerization and RNA binding by all three RRMs. Nucleic Acids Res 2019; 47:1011-1029. [PMID: 30418581 PMCID: PMC6344896 DOI: 10.1093/nar/gky1138] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 10/28/2018] [Indexed: 12/22/2022] Open
Abstract
HuR/ELAVL1 is an RNA-binding protein involved in differentiation and stress response that acts primarily by stabilizing messenger RNA (mRNA) targets. HuR comprises three RNA recognition motifs (RRMs) where the structure and RNA binding of RRM3 and of full-length HuR remain poorly understood. Here, we report crystal structures of RRM3 free and bound to cognate RNAs. Our structural, NMR and biochemical data show that RRM3 mediates canonical RNA interactions and reveal molecular details of a dimerization interface localized on the α-helical face of RRM3. NMR and SAXS analyses indicate that the three RRMs in full-length HuR are flexibly connected in the absence of RNA, while they adopt a more compact arrangement when bound to RNA. Based on these data and crystal structures of tandem RRM1,2-RNA and our RRM3-RNA complexes, we present a structural model of RNA recognition involving all three RRM domains of full-length HuR. Mutational analysis demonstrates that RRM3 dimerization and RNA binding is required for functional activity of full-length HuR in vitro and to regulate target mRNAs levels in human cells, thus providing a fine-tuning for HuR activity in vivo.
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Affiliation(s)
- Marta Pabis
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany.,Center for Integrated Protein Science Munich at Chair Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany.,Max Planck Research Group hosted by the Malopolska Centre of Biotechnology of the Jagiellonian University, Krakow, Poland
| | - Grzegorz M Popowicz
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany.,Center for Integrated Protein Science Munich at Chair Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
| | - Ralf Stehle
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany.,Center for Integrated Protein Science Munich at Chair Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
| | - David Fernández-Ramos
- CIC bioGUNE, Centro de Investigación Cooperativa en Biociencias. Technology Park of Bizkaia, 48160 Derio, Bizkaia, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Sam Asami
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany.,Center for Integrated Protein Science Munich at Chair Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
| | - Lisa Warner
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany.,Center for Integrated Protein Science Munich at Chair Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
| | - Sofía M García-Mauriño
- Instituto de Investigaciones Químicas (IIQ)-Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla - Consejo Superior de Investigaciones Científicas (CSIC), Avda. Americo Vespucio 49, 41092 Sevilla, Spain
| | - Andreas Schlundt
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany.,Center for Integrated Protein Science Munich at Chair Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
| | - María L Martínez-Chantar
- CIC bioGUNE, Centro de Investigación Cooperativa en Biociencias. Technology Park of Bizkaia, 48160 Derio, Bizkaia, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Irene Díaz-Moreno
- Instituto de Investigaciones Químicas (IIQ)-Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla - Consejo Superior de Investigaciones Científicas (CSIC), Avda. Americo Vespucio 49, 41092 Sevilla, Spain
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany.,Center for Integrated Protein Science Munich at Chair Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
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18
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Inhibition of Caspase-2 Translation by the mRNA Binding Protein HuR: A Novel Path of Therapy Resistance in Colon Carcinoma Cells? Cells 2019; 8:cells8080797. [PMID: 31366165 PMCID: PMC6721497 DOI: 10.3390/cells8080797] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 07/26/2019] [Accepted: 07/29/2019] [Indexed: 12/28/2022] Open
Abstract
An increased expression and cytoplasmic abundance of the ubiquitous RNA binding protein human antigen R (HuR) is critically implicated in the dysregulated control of post- transcriptional gene expression during colorectal cancer development and is frequently associated with a high grade of malignancy and therapy resistance. Regardless of the fact that HuR elicits a broad cell survival program by increasing the stability of mRNAs coding for prominent anti-apoptotic factors, recent data suggest that HuR is critically involved in the regulation of translation, particularly, in the internal ribosome entry site (IRES) controlled translation of cell death regulatory proteins. Accordingly, data from human colon carcinoma cells revealed that HuR maintains constitutively reduced protein and activity levels of caspase-2 through negative interference with IRES-mediated translation. This review covers recent advances in the understanding of mechanisms underlying HuR's modulatory activity on IRES-triggered translation. With respect to the unique regulatory features of caspase-2 and its multiple roles (e.g., in DNA-damage-induced apoptosis, cell cycle regulation and maintenance of genomic stability), the pathophysiological consequences of negative caspase-2 regulation by HuR and its impact on therapy resistance of colorectal cancers will be discussed in detail. The negative HuR-caspase-2 axis may offer a novel target for tumor sensitizing therapies.
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19
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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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20
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Li XL, Subramanian M, Jones MF, Chaudhary R, Singh DK, Zong X, Gryder B, Sindri S, Mo M, Schetter A, Wen X, Parvathaneni S, Kazandjian D, Jenkins LM, Tang W, Elloumi F, Martindale JL, Huarte M, Zhu Y, Robles AI, Frier SM, Rigo F, Cam M, Ambs S, Sharma S, Harris CC, Dasso M, Prasanth KV, Lal A. Long Noncoding RNA PURPL Suppresses Basal p53 Levels and Promotes Tumorigenicity in Colorectal Cancer. Cell Rep 2018; 20:2408-2423. [PMID: 28877474 DOI: 10.1016/j.celrep.2017.08.041] [Citation(s) in RCA: 115] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 07/21/2017] [Accepted: 08/09/2017] [Indexed: 12/13/2022] Open
Abstract
Basal p53 levels are tightly suppressed under normal conditions. Disrupting this regulation results in elevated p53 levels to induce cell cycle arrest, apoptosis, and tumor suppression. Here, we report the suppression of basal p53 levels by a nuclear, p53-regulated long noncoding RNA that we termed PURPL (p53 upregulated regulator of p53 levels). Targeted depletion of PURPL in colorectal cancer cells results in elevated basal p53 levels and induces growth defects in cell culture and in mouse xenografts. PURPL associates with MYBBP1A, a protein that binds to and stabilizes p53, and inhibits the formation of the p53-MYBBP1A complex. In the absence of PURPL, MYBBP1A interacts with and stabilizes p53. Silencing MYBBP1A significantly rescues basal p53 levels and proliferation in PURPL-deficient cells, suggesting that MYBBP1A mediates the effect of PURPL in regulating p53. These results reveal a p53-PURPL auto-regulatory feedback loop and demonstrate a role for PURPL in maintaining basal p53 levels.
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Affiliation(s)
- Xiao Ling Li
- Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), NIH, Bethesda, MD 20892, USA
| | - Murugan Subramanian
- Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), NIH, Bethesda, MD 20892, USA
| | - Matthew F Jones
- Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), NIH, Bethesda, MD 20892, USA
| | - Ritu Chaudhary
- Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), NIH, Bethesda, MD 20892, USA
| | - Deepak K Singh
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Xinying Zong
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Berkley Gryder
- Oncogenomics Section, Genetics Branch, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | - Sivasish Sindri
- Oncogenomics Section, Genetics Branch, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | - Min Mo
- Laboratory of Gene Regulation and Development, National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | - Aaron Schetter
- Molecular Genetics and Carcinogenesis Section, Laboratory of Human Carcinogenesis, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | - Xinyu Wen
- Oncogenomics Section, Genetics Branch, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | - Swetha Parvathaneni
- Department of Biochemistry and Molecular Biology, College of Medicine, Howard University, Washington, DC 20059, USA
| | - Dickran Kazandjian
- Molecular Genetics and Carcinogenesis Section, Laboratory of Human Carcinogenesis, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | - Lisa M Jenkins
- Laboratory of Cell Biology, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | - Wei Tang
- Molecular Epidemiology Section, Laboratory of Human Carcinogenesis, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | - Fathi Elloumi
- Office of Science and Technology Resources, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | - Jennifer L Martindale
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, NIH, Baltimore, MD 21224, USA
| | - Maite Huarte
- Center for Applied Medical Research, Department of Gene Therapy and Regulation of Gene Expression, University of Navarra, 31008 Pamplona, Spain
| | - Yuelin Zhu
- Molecular Genetics Section, Genetics Branch, CCR, NCI, NIH, Bethesda, MD 28092, USA
| | - Ana I Robles
- Molecular Genetics and Carcinogenesis Section, Laboratory of Human Carcinogenesis, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | | | - Frank Rigo
- Ionis Pharmaceuticals, Carlsbad, CA 92010, USA
| | - Maggie Cam
- Office of Science and Technology Resources, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | - Stefan Ambs
- Molecular Epidemiology Section, Laboratory of Human Carcinogenesis, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | - Sudha Sharma
- Department of Biochemistry and Molecular Biology, College of Medicine, Howard University, Washington, DC 20059, USA
| | - Curtis C Harris
- Molecular Genetics and Carcinogenesis Section, Laboratory of Human Carcinogenesis, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | - Mary Dasso
- Laboratory of Gene Regulation and Development, National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | - Kannanganattu V Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Ashish Lal
- Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), NIH, Bethesda, MD 20892, USA.
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Blagden S, Abdel Mouti M, Chettle J. Ancient and modern: hints of a core post-transcriptional network driving chemotherapy resistance in ovarian cancer. WILEY INTERDISCIPLINARY REVIEWS. RNA 2018; 9:e1432. [PMID: 28762650 PMCID: PMC5763387 DOI: 10.1002/wrna.1432] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 06/12/2017] [Accepted: 06/12/2017] [Indexed: 01/04/2023]
Abstract
RNA-binding proteins (RBPs) and noncoding (nc)RNAs (such as microRNAs, long ncRNAs, and others) cooperate within a post-transcriptional network to regulate the expression of genes required for many aspects of cancer behavior including its sensitivity to chemotherapy. Here, using an RBP-centric approach, we explore the current knowledge surrounding contributers to post-transcriptional gene regulation (PTGR) in ovarian cancer and identify commonalities that hint at the existence of an evolutionarily conserved core PTGR network. This network regulates survival and chemotherapy resistance in the contemporary context of the cancer cell. There is emerging evidence that cancers become dependent on PTGR factors for their survival. Further understanding of this network may identify innovative therapeutic targets as well as yield crucial insights into the hard-wiring of many malignancies, including ovarian cancer. WIREs RNA 2018, 9:e1432. doi: 10.1002/wrna.1432 This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications Translation > Translation Mechanisms RNA in Disease and Development > RNA in Disease.
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Hong S. RNA Binding Protein as an Emerging Therapeutic Target for Cancer Prevention and Treatment. J Cancer Prev 2017; 22:203-210. [PMID: 29302577 PMCID: PMC5751837 DOI: 10.15430/jcp.2017.22.4.203] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 11/17/2017] [Accepted: 11/21/2017] [Indexed: 12/13/2022] Open
Abstract
After transcription, RNAs are always associated with RNA binding proteins (RBPs) to perform biological activities. RBPs can interact with target RNAs in sequence- and structure-dependent manner through their unique RNA binding domains. In development and progression of carcinogenesis, RBPs are aberrantly dysregulated in many human cancers with various mechanisms, such as genetic alteration, epigenetic change, noncoding RNA-mediated regulation, and post-translational modifications. Upon deregulation in cancers, RBPs influence every step in the development and progression of cancer, including sustained cell proliferation, evasion of apoptosis, avoiding immune surveillance, inducing angiogenesis, and activating metastasis. To develop therapeutic strategies targeting RBPs, RNA interference-based oligonucleotides or small molecule inhibitors have been screened based on reduced RBP-RNA interaction and changed level of target RNAs. Identification of binding RNAs with high-throughput techniques and integral analysis of multiple datasets will help us develop new therapeutic drugs or prognostic biomarkers for human cancers.
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Affiliation(s)
- Suntaek Hong
- Department of Biochemistry, College of Medicine, Gachon University, Incheon, Korea
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23
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Pereira B, Billaud M, Almeida R. RNA-Binding Proteins in Cancer: Old Players and New Actors. Trends Cancer 2017; 3:506-528. [PMID: 28718405 DOI: 10.1016/j.trecan.2017.05.003] [Citation(s) in RCA: 461] [Impact Index Per Article: 65.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 05/04/2017] [Accepted: 05/05/2017] [Indexed: 12/15/2022]
Abstract
RNA-binding proteins (RBPs) are key players in post-transcriptional events. The combination of versatility of their RNA-binding domains with structural flexibility enables RBPs to control the metabolism of a large array of transcripts. Perturbations in RBP-RNA networks activity have been causally associated with cancer development, but the rational framework describing these contributions remains fragmented. We review here the evidence that RBPs modulate multiple cancer traits, emphasize their functional diversity, and assess future trends in the study of RBPs in cancer.
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Affiliation(s)
- Bruno Pereira
- i3S - Institute for Research and Innovation in Health, University of Porto, 4200-135 Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-465 Porto, Portugal.
| | - Marc Billaud
- Clinical and Experimental Model of Lymphomagenesis, Institut National de la Santé et de la Recherche Médicale (INSERM) Unité 1052, Centre National de la Recherche Scientifique (CNRS) Unité 5286, Centre Léon Bérard, Université Claude Bernard Lyon 1, Centre de Recherche en Cancérologie de Lyon, Lyon, France
| | - Raquel Almeida
- i3S - Institute for Research and Innovation in Health, University of Porto, 4200-135 Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-465 Porto, Portugal; Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal; Biology Department, Faculty of Sciences of the University of Porto, 4169-007 Porto, Portugal
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24
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Patrucco L, Peano C, Chiesa A, Guida F, Luisi I, Boria I, Mignone F, De Bellis G, Zucchelli S, Gustincich S, Santoro C, Sblattero D, Cotella D. Identification of novel proteins binding the AU-rich element of α-prothymosin mRNA through the selection of open reading frames (RIDome). RNA Biol 2016; 12:1289-300. [PMID: 26512911 DOI: 10.1080/15476286.2015.1107702] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
We describe here a platform for high-throughput protein expression and interaction analysis aimed at identifying the RNA-interacting domainome. This approach combines the selection of a phage library displaying "filtered" open reading frames with next-generation DNA sequencing. The method was validated using an RNA bait corresponding to the AU-rich element of α-prothymosin, an RNA motif that promotes mRNA stability and translation through its interaction with the RNA-binding protein ELAVL1. With this strategy, we not only confirmed known RNA-binding proteins that specifically interact with the target RNA (such as ELAVL1/HuR and RBM38) but also identified proteins not previously known to be ARE-binding (R3HDM2 and RALY). We propose this technology as a novel approach for studying the RNA-binding proteome.
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Affiliation(s)
- Laura Patrucco
- a Department of Health Sciences and Interdisciplinary Research Center on Autoimmune Diseases (IRCAD) ; Università del Piemonte Orientale ; Novara , Italy
| | - Clelia Peano
- b Institute of Biomedical Technologies; National Research Council (ITB CNR) ; Milan , Italy
| | - Andrea Chiesa
- a Department of Health Sciences and Interdisciplinary Research Center on Autoimmune Diseases (IRCAD) ; Università del Piemonte Orientale ; Novara , Italy
| | - Filomena Guida
- c Department of Life Sciences ; University of Trieste ; Italy
| | - Imma Luisi
- c Department of Life Sciences ; University of Trieste ; Italy
| | - Ilenia Boria
- d Department of Chemistry ; University of Milan ; Italy
| | - Flavio Mignone
- e Department of Sciences and Innovation ; Università del Piemonte Orientale ; Alessandria , Italy
| | - Gianluca De Bellis
- b Institute of Biomedical Technologies; National Research Council (ITB CNR) ; Milan , Italy
| | - Silvia Zucchelli
- a Department of Health Sciences and Interdisciplinary Research Center on Autoimmune Diseases (IRCAD) ; Università del Piemonte Orientale ; Novara , Italy.,f Area of Neuroscience; SISSA ; Trieste , Italy
| | | | - Claudio Santoro
- a Department of Health Sciences and Interdisciplinary Research Center on Autoimmune Diseases (IRCAD) ; Università del Piemonte Orientale ; Novara , Italy
| | - Daniele Sblattero
- a Department of Health Sciences and Interdisciplinary Research Center on Autoimmune Diseases (IRCAD) ; Università del Piemonte Orientale ; Novara , Italy.,c Department of Life Sciences ; University of Trieste ; Italy
| | - Diego Cotella
- a Department of Health Sciences and Interdisciplinary Research Center on Autoimmune Diseases (IRCAD) ; Università del Piemonte Orientale ; Novara , Italy
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25
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Dysregulation of TTP and HuR plays an important role in cancers. Tumour Biol 2016; 37:14451-14461. [DOI: 10.1007/s13277-016-5397-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 09/09/2016] [Indexed: 12/16/2022] Open
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26
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The RNA binding protein HuR determines the differential translation of autism-associated FoxP subfamily members in the developing neocortex. Sci Rep 2016; 6:28998. [PMID: 27383233 PMCID: PMC4935837 DOI: 10.1038/srep28998] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 06/13/2016] [Indexed: 12/21/2022] Open
Abstract
Forkhead-box domain (Fox) containing family members are known to play a role in neocorticogenesis and have also been associated with disorders on the autism spectrum. Here we show that a single RNA-binding protein, Hu antigen R (HuR), dictates translation specificity of bound mRNAs and is sufficient to define distinct Foxp-characterized subpopulations of neocortical projection neurons. Furthermore, distinct phosphorylation states of HuR differentially regulate translation of Foxp mRNAs in vitro. This demonstrates the importance of RNA binding proteins within the framework of the developing brain and further confirms the role of mRNA translation in autism pathogenesis.
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27
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Radulovic M, Baqader NO, Stoeber K, Godovac-Zimmermann J. Spatial Cross-Talk between Oxidative Stress and DNA Replication in Human Fibroblasts. J Proteome Res 2016; 15:1907-38. [PMID: 27142241 DOI: 10.1021/acs.jproteome.6b00101] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
MS-based proteomics has been applied to a differential network analysis of the nuclear-cytoplasmic subcellular distribution of proteins between cell-cycle arrest: (a) at the origin activation checkpoint for DNA replication, or (b) in response to oxidative stress. Significant changes were identified for 401 proteins. Cellular response combines changes in trafficking and in total abundance to vary the local compartmental abundances that are the basis of cellular response. Appreciable changes for both perturbations were observed for 245 proteins, but cross-talk between oxidative stress and DNA replication is dominated by 49 proteins that show strong changes for both. Many nuclear processes are influenced by a spatial switch involving the proteins {KPNA2, KPNB1, PCNA, PTMA, SET} and heme/iron proteins HMOX1 and FTH1. Dynamic spatial distribution data are presented for proteins involved in caveolae, extracellular matrix remodelling, TGFβ signaling, IGF pathways, emerin complexes, mitochondrial protein import complexes, spliceosomes, proteasomes, and so on. The data indicate that for spatially heterogeneous cells cross-compartmental communication is integral to their system biology, that coordinated spatial redistribution for crucial protein networks underlies many functional changes, and that information on dynamic spatial redistribution of proteins is essential to obtain comprehensive pictures of cellular function. We describe how spatial data of the type presented here can provide priorities for further investigation of crucial features of high-level spatial coordination across cells. We suggest that the present data are related to increasing indications that much of subcellular protein transport is constitutive and that perturbation of these constitutive transport processes may be related to cancer and other diseases. A quantitative, spatially resolved nucleus-cytoplasm interaction network is provided for further investigations.
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Affiliation(s)
- Marko Radulovic
- Division of Medicine, University College London, Center for Nephrology , Royal Free Campus, Rowland Hill Street, London NW3 2PF, United Kingdom.,Insitute of Oncology and Radiology , Pasterova 14, 11000 Belgrade, Serbia
| | - Noor O Baqader
- Division of Medicine, University College London, Center for Nephrology , Royal Free Campus, Rowland Hill Street, London NW3 2PF, United Kingdom
| | - Kai Stoeber
- Research Department of Pathology and UCL Cancer Institute, Rockefeller Building, University College London , University Street, London WC1E 6JJ, United Kingdom
| | - Jasminka Godovac-Zimmermann
- Division of Medicine, University College London, Center for Nephrology , Royal Free Campus, Rowland Hill Street, London NW3 2PF, United Kingdom
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28
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Zurla C, Jung J, Santangelo PJ. Can we observe changes in mRNA "state"? Overview of methods to study mRNA interactions with regulatory proteins relevant in cancer related processes. Analyst 2016; 141:548-62. [PMID: 26605378 PMCID: PMC4701657 DOI: 10.1039/c5an01959a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
RNA binding proteins (RBP) regulate the editing, localization, stabilization, translation, and degradation of ribonucleic acids (RNA) through their interactions with specific cis-acting elements within target RNAs. Post-transcriptional regulatory mechanisms are directly involved in the control of the immune response and stress response and their alterations play a crucial role in cancer related processes. In this review, we discuss mRNAs and RNA binding proteins relevant to tumorigenesis, current methodologies for detecting RNA interactions, and last, we describe a novel method to detect such interactions, which combines peptide modified, RNA imaging probes (FMTRIPs) with proximity ligation (PLA) and rolling circle amplification (RCA). This assay detects native RNA in a sequence specific and single RNA sensitive manner, and PLA allows for the quantification and localization of protein-mRNA interactions with single-interaction sensitivity in situ.
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Affiliation(s)
- C Zurla
- Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 313 Ferst Drive, UA Whitaker Blgd, Atlanta, GA 30332, USA.
| | - J Jung
- Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 313 Ferst Drive, UA Whitaker Blgd, Atlanta, GA 30332, USA.
| | - P J Santangelo
- Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 313 Ferst Drive, UA Whitaker Blgd, Atlanta, GA 30332, USA.
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29
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Post-Translational Modifications and RNA-Binding Proteins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 907:297-317. [PMID: 27256391 DOI: 10.1007/978-3-319-29073-7_12] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
RNA-binding proteins affect cellular metabolic programs through development and in response to cellular stimuli. Though much work has been done to elucidate the roles of a handful of RNA-binding proteins and their effect on RNA metabolism, the progress of studies to understand the effects of post-translational modifications of this class of proteins is far from complete. This chapter summarizes the work that has been done to identify the consequence of post-translational modifications to some RNA-binding proteins. The effects of these modifications have been shown to increase the panoply of functions that a given RNA-binding protein can assume. We will survey the experimental methods that are used to identify the presence of several protein modifications and methods that attempt to discern the consequence of these modifications.
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30
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Mori T, Yanagisawa Y, Kitani Y, Sugiyama M, Kishida O, Nishimura K. Gene expression profiles in Rana pirica tadpoles following exposure to a predation threat. BMC Genomics 2015; 16:258. [PMID: 25886855 PMCID: PMC4403775 DOI: 10.1186/s12864-015-1389-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 02/24/2015] [Indexed: 11/22/2022] Open
Abstract
Background Rana pirica tadpoles show morphological changes in response to a predation threat: larvae of the dragonfly Aeshna nigroflava induce heightened tail depth, whereas larval salamander Hynobius retardatus induce a bulgy morphology with heightened tail depth. Although both predators induce similar tail morphologies, it is possible that there are functional differences between these tail morphs. Results Here, we performed a discriminant microarray analysis using Xenopus laevis genome arrays to compare tail tissues of control and predator-exposed tadpoles. We identified 9 genes showing large-scale changes in their expression profile: ELAV-like1, methyltransferase like 7A, dolichyl-phosphate mannosyltransferase, laminin subunit beta-1, gremlin 1, BCL6 corepressor-like 1, and three genes of unknown identity. A further 80 genes showed greater than 5 fold differences in expression after exposure to dragonfly larvae and 81 genes showed altered expression after exposure to larval salamanders. Predation-threat responsive genes were identified by selecting genes that reverted to control levels of expression following removal of the predator. Thirteen genes were induced specifically by dragonfly larvae, nine others were salamander-specific, and sixteen were induced by both. Functional analyses indicated that some of the genes induced by dragonfly larvae caused an increase in laminins necessary for cell adhesion in the extracellular matrix. The higher expression of gremlin 1 and HIF1a genes after exposure to dragonfly larvae indicated an in vivo hypoxic reaction, while down-regulation of syndecan-2 may indicate impairment of angiogenesis. Exposure to larval salamanders caused down-regulation of XCIRP-1, which is known to inhibit expression of adhesion molecules; the tadpoles showed reduced expression of cα(E)-catenin, small muscle protein, dystrophin, and myosin light chain genes. Conclusion The connective tissue of tadpoles exposed to larval salamanders may be looser. The differences in gene expression profiles induced by the two predators suggest that there are functional differences between the altered tail tissues of the two groups of tadpoles. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1389-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tsukasa Mori
- Department of Marine Science and Resources, Nihon University College of Bioresource Sciences, Kameino 1866, Fujisawa, 252-0880, Japan.
| | - Yukio Yanagisawa
- Department of Liberal Art, Nihon University College of Bioresource Sciences, Kameino 1866, Fujisawa, 252-0880, Japan.
| | - Yoichiro Kitani
- Department of Marine Science and Resources, Nihon University College of Bioresource Sciences, Kameino 1866, Fujisawa, 252-0880, Japan.
| | - Manabu Sugiyama
- Department of Marine Science and Resources, Nihon University College of Bioresource Sciences, Kameino 1866, Fujisawa, 252-0880, Japan.
| | - Osamu Kishida
- Teshio Experimental Forest, Field Science Center for Northern Biosphere, Hokkaido University, Horonobe, Hokkaido, 098-2943, Japan.
| | - Kinya Nishimura
- Graduate School of Fisheries Sciences, Hokkaido University, Hakodate, 041-8611, Japan.
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31
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Wigington CP, Jung J, Rye EA, Belauret SL, Philpot AM, Feng Y, Santangelo PJ, Corbett AH. Post-transcriptional regulation of programmed cell death 4 (PDCD4) mRNA by the RNA-binding proteins human antigen R (HuR) and T-cell intracellular antigen 1 (TIA1). J Biol Chem 2014; 290:3468-87. [PMID: 25519906 DOI: 10.1074/jbc.m114.631937] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Post-transcriptional processing of mRNA transcripts plays a critical role in establishing the gene expression profile of a cell. Such processing events are mediated by a host of factors, including RNA-binding proteins and microRNAs. A number of critical cellular pathways are subject to regulation at multiple levels that allow fine-tuning of key biological responses. Programmed cell death 4 (PDCD4) is a tumor suppressor and an important modulator of mRNA translation that is regulated by a number of mechanisms, most notably as a target of the oncomiR, miR-21. Here, we provide evidence for post-transcriptional regulation of PDCD4 by the RNA-binding proteins, HuR and TIA1. Complementary approaches reveal binding of both HuR and TIA1 to the PDCD4 transcript. Consistent with a model where RNA-binding proteins modulate the PDCD4 transcript, knockdown of HuR and/or TIA1 results in a significant decrease in steady-state PDCD4 mRNA and protein levels. However, fractionation experiments suggest that the mode of regulation of the PDCD4 transcript likely differs in the cytoplasm and the nucleus as the pool of PDCD4 mRNA present in the cytoplasm is more stable than the nuclear pool of PDCD4 transcript. We observe a competitive mode of binding between HuR and TIA1 on the PDCD4 transcript in the cytoplasm, suggesting that these two factors dynamically interact with one another as well as the PDCD4 transcript to maintain tight control of PDCD4 levels. Overall, this study reveals an additional set of regulatory interactions that modulate the expression of PDCD4, a key pro-apoptotic factor, and also reveals new insights into how HuR and TIA1 functions are integrated to achieve such regulation.
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Affiliation(s)
- Callie P Wigington
- From the Department of Biochemistry and Graduate Program in Biochemistry, Cell and Developmental Biology, Emory University, Atlanta, Georgia 30322
| | - Jeenah Jung
- the Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, and Emory University, Atlanta, Georgia 30332
| | - Emily A Rye
- From the Department of Biochemistry and Graduate Program in Biochemistry, Cell and Developmental Biology, Emory University, Atlanta, Georgia 30322
| | - Sara L Belauret
- the School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30322
| | - Akahne M Philpot
- From the Department of Biochemistry and the Summer Scholars Research Program, Winship Cancer Institute, Atlanta, Georgia 30332, and
| | - Yue Feng
- the Department of Pharmacology, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Philip J Santangelo
- the Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, and Emory University, Atlanta, Georgia 30332
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32
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Durie D, Hatzoglou M, Chakraborty P, Holcik M. HuR controls mitochondrial morphology through the regulation of Bcl xL translation. ACTA ACUST UNITED AC 2014; 1. [PMID: 25328858 PMCID: PMC4199323 DOI: 10.4161/trla.23980] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
BclxL is a key prosurvival factor that in addition to controlling mitochondrial membrane permeability regulates mitochondrial network dynamics. The expression of BclxL is regulated at the level of transcription, splicing and selective translation. In this study, we show that the RNA-binding protein HuR, which is known to orchestrate an anti-apoptotic cellular program, functions as a translational repressor of BclxL. We show that HuR binds directly to the 5`UTR of BclxL, and represses BclxL translation through the inhibition of its internal ribosome entry site (IRES). Reduction of HuR levels leads to the derepression of BclxL translation and subsequent rearrangement of the mitochondrial network. Our results place BclxL into the HuR-regulated operon and provide further insight into the regulation of cellular stress response by HuR.
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Affiliation(s)
- Danielle Durie
- Apoptosis Research Center, Children's Hospital of Eastern Ontario Research Institute
| | - Maria Hatzoglou
- Department of Nutrition, Case Western Reserve University, School of Medicine, Cleveland, Ohio, U.S.A
| | - Pranesh Chakraborty
- Department of Pediatrics, University of Ottawa ; Newborn Screening Ontario, Children's Hospital of Eastern Ontario, 401 Smyth Road, Ottawa, K1H 8L1, Canada
| | - Martin Holcik
- Apoptosis Research Center, Children's Hospital of Eastern Ontario Research Institute ; Department of Pediatrics, University of Ottawa
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Wurth L, Gebauer F. RNA-binding proteins, multifaceted translational regulators in cancer. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1849:881-6. [PMID: 25316157 DOI: 10.1016/j.bbagrm.2014.10.001] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 10/01/2014] [Accepted: 10/04/2014] [Indexed: 12/21/2022]
Abstract
RNA-binding proteins (RBPs) orchestrate transcript fate and function. Even though alterations in post-transcriptional events contribute to key steps of tumor initiation and progression, RBP-mediated control has remained relatively unexplored in cancer. Here, we discuss examples of this promising field focusing on translation regulation, and highlight the variety of molecular mechanisms by which RBPs impinge on translation with consequences for tumorigenesis. This article is part of a Special Issue entitled: Translation and Cancer.
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Affiliation(s)
- Laurence Wurth
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Fátima Gebauer
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003 Barcelona, Spain.
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Campos-Melo D, Droppelmann CA, Volkening K, Strong MJ. RNA-binding proteins as molecular links between cancer and neurodegeneration. Biogerontology 2014; 15:587-610. [PMID: 25231915 DOI: 10.1007/s10522-014-9531-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 09/11/2014] [Indexed: 12/12/2022]
Abstract
For many years, epidemiological studies have suggested an association between cancer and neurodegenerative disorders-two disease processes that seemingly have little in common. Although these two disease processes share disruptions in a wide range of cellular pathways, including cell survival, cell death and the cell cycle, the end result is very divergent: uncontrolled cell survival and proliferation in cancer and progressive neuronal cell death in neurodegeneration. Despite the clinical data connecting these two disease processes, little is known about the molecular links between them. Among the mechanisms affected in cancer and neurodegenerative diseases, alterations in RNA metabolism are obtaining significant attention given the critical role for RNA transcription, maturation, transport, stability, degradation and translation in normal cellular function. RNA-binding proteins (RBPs) are integral to each stage of RNA metabolism through their participation in the formation of ribonucleoprotein complexes (RNPs). RBPs have a broad range of functions including posttranscriptional regulation of mRNA stability, splicing, editing and translation, mRNA export and localization, mRNA polyadenylation and miRNA biogenesis, ultimately impacting the expression of every single gene in the cell. In this review, we examine the evidence for RBPs as being key a molecular linkages between cancer and neurodegeneration.
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Affiliation(s)
- Danae Campos-Melo
- Molecular Medicine Group, Robarts Research Institute, Western University, London, ON, Canada
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López de Silanes I, Graña O, De Bonis ML, Dominguez O, Pisano DG, Blasco MA. Identification of TERRA locus unveils a telomere protection role through association to nearly all chromosomes. Nat Commun 2014; 5:4723. [PMID: 25182072 PMCID: PMC4164772 DOI: 10.1038/ncomms5723] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Accepted: 07/17/2014] [Indexed: 12/13/2022] Open
Abstract
Telomeric RNAs (TERRAs) are UUAGGG repeat-containing RNAs that are transcribed from the subtelomere towards the telomere. The precise genomic origin of TERRA has remained elusive. Using a whole-genome RNA-sequencing approach, we identify novel mouse transcripts arising mainly from the subtelomere of chromosome 18, and to a lesser extend chromosome 9, that resemble TERRA in several key aspects. Those transcripts contain UUAGGG-repeats and are heterogeneous in size, fluctuate in abundance in a TERRA-like manner during the cell cycle, are bound by TERRA RNA-binding proteins and are regulated in a manner similar to TERRA in response to stress and the induction of pluripotency. These transcripts are also found to associate with nearly all chromosome ends and downregulation of the transcripts that originate from chromosome 18 causes a reduction in TERRA abundance. Interestingly, downregulation of either chromosome 18 transcripts or TERRA results in increased number of telomere dysfunction-induced foci, suggesting a protective role at telomeres. Telomeric RNAs (TERRAs) are known to be transcribed towards the telomere from subtelomeric regions, however, their precise genomic origins are unclear. Here López de Silanes et al. identify novel transcripts that originate from the subtelomeric region of mouse chromosome 18 and behave as bona fide TERRAs.
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Affiliation(s)
- Isabel López de Silanes
- Telomeres and Telomerase Group, Spanish National Cancer Research Centre (CNIO), C/Melchor Fernández Almagro, 3, 28029 Madrid, Spain
| | - Osvaldo Graña
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), C/Melchor Fernández Almagro, 3, 28029 Madrid, Spain
| | - Maria Luigia De Bonis
- Telomeres and Telomerase Group, Spanish National Cancer Research Centre (CNIO), C/Melchor Fernández Almagro, 3, 28029 Madrid, Spain
| | - Orlando Dominguez
- Genomics Unit, Spanish National Cancer Research Centre (CNIO), C/Melchor Fernández Almagro, 3, 28029 Madrid, Spain
| | - David G Pisano
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), C/Melchor Fernández Almagro, 3, 28029 Madrid, Spain
| | - Maria A Blasco
- Telomeres and Telomerase Group, Spanish National Cancer Research Centre (CNIO), C/Melchor Fernández Almagro, 3, 28029 Madrid, Spain
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Kotta-Loizou I, Giaginis C, Theocharis S. Clinical significance of HuR expression in human malignancy. Med Oncol 2014; 31:161. [PMID: 25112469 DOI: 10.1007/s12032-014-0161-y] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 08/01/2014] [Indexed: 12/28/2022]
Abstract
Hu-antigen R (HuR) is an RNA-binding protein that regulates the stability, translation, and nucleus-to-cytoplasm translocation of target mRNAs. The aim of the present review was to summarize and present the currently available information in the English literature on HuR expression in various human tumors, verifying its possible clinical significance. HuR function is directly linked to its subcellular localization. In normal cells, HuR is mostly localized in the nucleus, while in malignant cells, an increase in cytoplasmic HuR levels has been noted, in both cell lines and tissue samples. Moreover, in malignancy, elevated HuR expression levels and cytoplasmic immunohistochemical pattern have been correlated with advanced clinicopathological parameters and altered expression levels of proteins implicated in neoplasia. Additionally, elevated HuR expression levels and mainly cytoplasmic immunohistochemical pattern were correlated with decreased patients' survival rate in various human tumors. HuR is a putative drug target for cancer therapy, since it is expressed ubiquitously in malignant clinical samples and has an apparently consistent role in tumor formation and progression.
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Affiliation(s)
- Ioly Kotta-Loizou
- Division of Cell and Molecular Biology, Imperial College London, London, UK
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Mechanisms of miRNA-Mediated Gene Regulation from Common Downregulation to mRNA-Specific Upregulation. Int J Genomics 2014; 2014:970607. [PMID: 25180174 PMCID: PMC4142390 DOI: 10.1155/2014/970607] [Citation(s) in RCA: 351] [Impact Index Per Article: 35.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Revised: 07/09/2014] [Accepted: 07/17/2014] [Indexed: 12/12/2022] Open
Abstract
Discovered in 1993, micoRNAs (miRNAs) are now recognized as one of the major regulatory gene families in eukaryotes. To date, 24521 microRNAs have been discovered and there are certainly more to come. It was primarily acknowledged that miRNAs result in gene expression repression at both the level of mRNA stability by conducting mRNA degradation and the level of translation (at initiation and after initiation) by inhibiting protein translation or degrading the polypeptides through binding complementarily to 3′UTR of the target mRNAs. Nevertheless, some studies revealed that miRNAs have the capability of activating gene expression directly or indirectly in respond to different cell types and conditions and in the presence of distinct cofactors. This reversibility in their posttranslational gene regulatory natures enables the bearing cells to rapidly response to different cell conditions and consequently block unnecessary energy wastage or maintain the cell state. This paper provides an overview of the current understandings of the miRNA characteristics including their genes and biogenesis, as well as their mediated downregulation. We also review up-to-date knowledge of miRNA-mediated gene upregulation through highlighting some notable examples and discuss the emerging concepts of their associations with other posttranscriptional gene regulation processes.
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Attenuation of the ELAV1-like protein HuR sensitizes adenocarcinoma cells to the intrinsic apoptotic pathway by increasing the translation of caspase-2L. Cell Death Dis 2014; 5:e1321. [PMID: 25010987 PMCID: PMC4123073 DOI: 10.1038/cddis.2014.279] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 05/16/2014] [Accepted: 05/20/2014] [Indexed: 12/22/2022]
Abstract
Caspase-2 represents the most conserved member of the caspase family, which exhibits features of both initiator and effector caspases. Using ribonucleoprotein (RNP)-immunoprecipitation assay, we identified the proapoptotic caspase-2L encoding mRNA as a novel target of the ubiquitous RNA-binding protein HuR in DLD-1 colon carcinoma cells. Unexpectedly, crosslinking-RNP and RNA probe pull-down experiments revealed that HuR binds exclusively to the caspase-2-5' untranslated region (UTR) despite that the 3' UTR of the mRNA bears several adenylate- and uridylate-rich elements representing the prototypical HuR binding sites. By using RNAi-mediated loss-of-function approach, we observed that HuR regulates the mRNA and in turn the protein levels of caspase-2 in a negative manner. Silencing of HuR did not affect the stability of caspase-2 mRNA but resulted in an increased redistribution of caspase-2 transcripts from RNP particles to translational active polysomes implicating that HuR exerts a direct repressive effect on caspase-2 translation. Consistently, in vitro translation of a luciferase reporter gene under the control of an upstream caspase-2-5'UTR was strongly impaired after the addition of recombinant HuR, whereas translation of caspase-2 coding region without the 5'UTR is not affected by HuR confirming the functional role of the caspase-2-5'UTR. Functionally, an elevation in caspase-2 level by HuR knockdown correlated with an increased sensitivity of cells to apoptosis induced by staurosporine- and pore-forming toxins as implicated by their significant accumulation in the sub G1 phase and an increase in caspase-2, -3 and poly ADP-ribose polymerase cleavage, respectively. Importantly, HuR knockdown cells remained insensitive toward STS-induced apoptosis if cells were additionally transfected with caspase-2-specific siRNAs. Collectively, our findings support the hypothesis that HuR by acting as an endogenous inhibitor of caspase-2-driven apoptosis may essentially contribute to the antiapoptotic program of adenocarcinoma cells by HuR.
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HuR regulates alternative splicing of the TRA2β gene in human colon cancer cells under oxidative stress. Mol Cell Biol 2014; 34:2857-73. [PMID: 24865968 DOI: 10.1128/mcb.00333-14] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Hu antigen R (HuR) regulates stress responses through stabilizing and/or facilitating the translation of target mRNAs. The human TRA2β gene encodes splicing factor transformer 2β (Tra2β) and generates 5 mRNA isoforms (TRA2β1 to -5) through alternative splicing. Exposure of HCT116 colon cancer cells to sodium arsenite stimulated checkpoint kinase 2 (Chk2)- and mitogen-activated protein kinase p38 (p38(MAPK))-mediated phosphorylation of HuR at positions S88 and T118. This induced an association between HuR and the 39-nucleotide (nt) proximal region of TRA2β exon 2, generating a TRA2β4 mRNA that includes exon 2, which has multiple premature stop codons. HuR knockdown or Chk2/p38(MAPK) double knockdown inhibited the arsenite-stimulated production of TRA2β4 and increased Tra2β protein, facilitating Tra2β-dependent inclusion of exons in target pre-mRNAs. The effects of HuR knockdown or Chk2/p38(MAPK) double knockdown were also confirmed using a TRA2β minigene spanning exons 1 to 4, and the effects disappeared when the 39-nt region was deleted from the minigene. In endogenous HuR knockdown cells, the overexpression of a HuR mutant that could not be phosphorylated (with changes of serine to alanine at position 88 [S88A], S100A, and T118A) blocked the associated TRA2β4 interaction and TRA2β4 generation, while the overexpression of a phosphomimetic HuR (with mutations S88D, S100D, and T118D) restored the TRA2β4-related activities. Our findings revealed the potential role of nuclear HuR in the regulation of alternative splicing programs under oxidative stress.
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Ramírez CM, Lin CS, Abdelmohsen K, Goedeke L, Yoon JH, Madrigal-Matute J, Martin-Ventura JL, Vo DT, Uren PJ, Penalva LO, Gorospe M, Fernández-Hernando C. RNA binding protein HuR regulates the expression of ABCA1. J Lipid Res 2014; 55:1066-76. [PMID: 24729624 DOI: 10.1194/jlr.m044925] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Indexed: 12/31/2022] Open
Abstract
ABCA1 is a major regulator of cellular cholesterol efflux and plasma HDL biogenesis. Even though the transcriptional activation of ABCA1 is well established, the posttranscriptional regulation of ABCA1 expression is poorly understood. Here, we investigate the potential contribution of the RNA binding protein (RBP) human antigen R (HuR) on the posttranscriptional regulation of ABCA1 expression. RNA immunoprecipitation assays demonstrate a direct interaction between HuR and ABCA1 mRNA. We found that HuR binds to the 3' untranslated region of ABCA1 and increases ABCA1 translation, while HuR silencing reduces ABCA1 expression and cholesterol efflux to ApoA1 in human hepatic (Huh-7) and monocytic (THP-1) cells. Interestingly, cellular cholesterol levels regulate the expression, intracellular localization, and interaction between HuR and ABCA1 mRNA. Finally, we found that HuR expression was significantly increased in macrophages from human atherosclerotic plaques, suggesting an important role for this RBP in controlling macrophage cholesterol metabolism in vivo. In summary, we have identified HuR as a novel posttranscriptional regulator of ABCA1 expression and cellular cholesterol homeostasis, thereby opening new avenues for increasing cholesterol efflux from atherosclerotic foam macrophages and raising circulat-ing HDL cholesterol levels.
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Affiliation(s)
- Cristina M Ramírez
- Vascular Biology and Therapeutics Program, Department of Comparative Medicine, Yale University School of Medicine, New Haven, CT 06520 Departments of Medicine and Cell Biology, New York University School of Medicine, New York, NY 10016
| | - Chin Sheng Lin
- Departments of Medicine and Cell Biology, New York University School of Medicine, New York, NY 10016 Division of Cardiology, Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, Republic of China
| | - Kotb Abdelmohsen
- Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224
| | - Leigh Goedeke
- Vascular Biology and Therapeutics Program, Department of Comparative Medicine, Yale University School of Medicine, New Haven, CT 06520 Departments of Medicine and Cell Biology, New York University School of Medicine, New York, NY 10016
| | - Je-Hyun Yoon
- Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224
| | - Julio Madrigal-Matute
- Departments of Medicine and Cell Biology, New York University School of Medicine, New York, NY 10016
| | - Jose L Martin-Ventura
- Vascular Research Lab, IIS-Fundación Jimenez Díaz, Autónoma University, Madrid 28040, Spain
| | - Dat T Vo
- Children's Cancer Research Institute, Department of Cellular and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229
| | - Philip J Uren
- Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089
| | - Luiz O Penalva
- Children's Cancer Research Institute, Department of Cellular and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229
| | - Myriam Gorospe
- Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224
| | - Carlos Fernández-Hernando
- Vascular Biology and Therapeutics Program, Department of Comparative Medicine, Yale University School of Medicine, New Haven, CT 06520 Departments of Medicine and Cell Biology, New York University School of Medicine, New York, NY 10016
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Talwar S, House R, Sundaramurthy S, Balasubramanian S, Yu H, Palanisamy V. Inhibition of caspases protects mice from radiation-induced oral mucositis and abolishes the cleavage of RNA-binding protein HuR. J Biol Chem 2013; 289:3487-500. [PMID: 24362034 DOI: 10.1074/jbc.m113.504951] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The oral mucosal epithelium is typically insulted during chemotherapy and ionizing radiation (IR) therapy and disposed to mucositis, which creates painful inflammation and ulceration in the oral cavity. Oral mucositis alters gene expression patterns, inhibits cellular growth, and initiates cell death in the oral epithelial compartments. Such alterations are governed by several different factors, including transcription factors, RNA-binding proteins, and microRNAs. IR-induced post-transcriptional regulation of RNA-binding proteins exists but is poorly studied in clinically relevant settings. We herein report that the RNA-binding protein human antigen R (HuR) undergoes cleavage modification by caspase-3 following IR-induced oral mucositis and subsequently promotes the expression of the pro-apoptotic factor BAX (Bcl-2-associated X protein), as well as cell death. Further analyses revealed that the HuR cleavage product-1 (HuR-CP1) directly associates and stabilizes the BAX mRNA and concurrently activates the apoptotic pathway. On the other hand, a noncleavable isoform of HuR promotes the clonogenic capacity of primary oral keratinocytes and decreases the effect of IR-induced cell death. Additionally, specific inhibition of caspase-3 by a compound, NSC321205, increases the clonogenic capacity of primary oral keratinocytes and causes increased basal layer cellularity, thickened mucosa, and elevated epithelial cell growth in the tongues of mice with oral mucositis. This protective effect of NSC321205 is mediated by a decrease in caspase-3 activity and the consequent inhibition of HuR cleavage, which reduces the expression of BAX in mice with IR-induced oral mucositis. Thus, we have identified a new molecular mechanism of HuR in the regulation of mRNA turnover and apoptosis in oral mucositis, and our data suggest that blocking the cleavage of HuR enhances cellular growth in the oral epithelial compartment.
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Affiliation(s)
- Sudha Talwar
- From the Department of Craniofacial Biology and Center for Oral Health Research, College of Dental Medicine, and
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Pang L, Tian H, Chang N, Yi J, Xue L, Jiang B, Gorospe M, Zhang X, Wang W. Loss of CARM1 is linked to reduced HuR function in replicative senescence. BMC Mol Biol 2013; 14:15. [PMID: 23837869 PMCID: PMC3718661 DOI: 10.1186/1471-2199-14-15] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Accepted: 07/02/2013] [Indexed: 11/15/2022] Open
Abstract
Background The co-activator-associated arginine methyltransferase 1 (CARM1) catalyzes the methylation of HuR. However, the functional impact of this modification is not fully understood. Here, we investigated the influence of HuR methylation by CARM1 upon the turnover of HuR target mRNAs encoding senescence-regulatory proteins. Results Changing the methylation status of HuR in HeLa cells by either silencing CARM1 or mutating the major methylation site (R217K) greatly diminished the effect of HuR in regulating the turnover of mRNAs encoding cyclin A, cyclin B1, c-fos, SIRT1, and p16. Although knockdown of CARM1 or HuR individually influenced the expression of cyclin A, cyclin B1, c-fos, SIRT1, and p16, joint knockdown of both CARM1 and HuR did not show further effect. Methylation by CARM1 enhanced the association of HuR with the 3′UTR of p16 mRNA, but not with the 3′UTR of cyclin A, cyclin B1, c-fos, or SIRT1 mRNAs. In senescent human diploid fibroblasts (HDFs), reduced CARM1 was accompanied by reduced HuR methylation. In addition, knockdown of CARM1 or mutation of the major methylation site of HuR in HDF markedly impaired the ability of HuR to regulate the expression of cyclin A, cyclin B1, c-fos, SIRT1, and p16 as well to maintain a proliferative phenotype. Conclusion CARM1 represses replicative senescence by methylating HuR and thereby enhancing HuR’s ability to regulate the turnover of cyclin A, cyclin B1, c-fos, SIRT1, and p16 mRNAs.
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Affiliation(s)
- Lijun Pang
- Department of Biochemistry and Molecular Biology, Peking University health Science Center, 38 Xueyuan Road, Beijing 100191, P. R. China
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Burkhart RA, Pineda DM, Chand SN, Romeo C, Londin ER, Karoly ED, Cozzitorto JA, Rigoutsos I, Yeo CJ, Brody JR, Winter JM. HuR is a post-transcriptional regulator of core metabolic enzymes in pancreatic cancer. RNA Biol 2013; 10:1312-23. [PMID: 23807417 DOI: 10.4161/rna.25274] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Cancer cell metabolism differs from normal cells, yet the regulatory mechanisms responsible for these differences are incompletely understood, particularly in response to acute changes in the tumor microenvironment. HuR, an RNA-binding protein, acts under acute stress to regulate core signaling pathways in cancer through post-transcriptional regulation of mRNA targets. We demonstrate that HuR regulates the metabolic phenotype in pancreatic cancer cells and is critical for survival under acute glucose deprivation. Using three pancreatic cancer cell line models, HuR-proficient cells demonstrated superior survival under glucose deprivation when compared with isogenic cells with siRNA-silencing of HuR expression (HuR-deficient cells). We found that HuR-proficient cells utilized less glucose, but produced greater lactate, as compared with HuR-deficient cells. Acute glucose deprivation was found to act as a potent stimulus for HuR translocation from the nucleus to the cytoplasm, where HuR stabilizes its mRNA targets. We performed a gene expression array on ribonucleoprotein-immunoprecipitated mRNAs bound to HuR and identified 11 novel HuR target transcripts that encode enzymes central to glucose metabolism. Three (GPI, PRPS2 and IDH1) were selected for validation studies, and confirmed as bona fide HuR targets. These findings establish HuR as a critical regulator of pancreatic cancer cell metabolism and survival under acute glucose deprivation. Further explorations into HuR's role in cancer cell metabolism should uncover novel therapeutic targets that are critical for cancer cell survival in a metabolically compromised tumor microenvironment.
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Affiliation(s)
- Richard A Burkhart
- Department of Surgery; Jefferson Pancreas, Biliary and Related Cancer Center; Philadelphia, PA USA
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Aparicio LA, Abella V, Valladares M, Figueroa A. Posttranscriptional regulation by RNA-binding proteins during epithelial-to-mesenchymal transition. Cell Mol Life Sci 2013; 70:4463-77. [PMID: 23715860 PMCID: PMC3827902 DOI: 10.1007/s00018-013-1379-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Revised: 05/10/2013] [Accepted: 05/16/2013] [Indexed: 12/22/2022]
Abstract
Epithelial-to-mesenchymal transition (EMT), one of the crucial steps for carcinoma cells to acquire invasive capacity, results from the disruption of cell–cell contacts and the acquisition of a motile mesenchymal phenotype. Although the transcriptional events controlling EMT have been extensively studied, in recent years, several posttranscriptional mechanisms have emerged as critical in the regulation of EMT during tumor progression. In this review, we highlight the regulation of posttranscriptional events in EMT by RNA-binding proteins (RBPs). RBPs are responsible for controlling pre-mRNA splicing, capping, and polyadenylation, as well as mRNA export, turnover, localization, and translation. We discuss the most relevant aspects of RBPs controlling the metabolism of EMT-related mRNAs, and describe the implication of novel posttranscriptional mechanisms regulating EMT in response to different signaling pathways. Novel insight into posttranscriptional regulation of EMT by RBPs is uncovering new therapeutic targets in cancer invasion and metastasis.
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Affiliation(s)
- Luis A Aparicio
- Servizo de Oncología Médica, Complejo Hospitalario Universitario A Coruña (CHUAC), SERGAS, A Coruña, Spain
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Halder SK, Sugimoto J, Matsunaga H, Ueda H. Therapeutic benefits of 9-amino acid peptide derived from prothymosin alpha against ischemic damages. Peptides 2013; 43:68-75. [PMID: 23499560 DOI: 10.1016/j.peptides.2013.02.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2013] [Revised: 02/27/2013] [Accepted: 02/27/2013] [Indexed: 12/11/2022]
Abstract
Prothymosin alpha (ProTα), a nuclear protein, plays multiple functions including cell survival. Most recently, we demonstrated that the active 30-amino acid peptide sequence/P30 (amino acids 49-78) in ProTα retains its substantial activity in neuroprotection in vitro and in vivo as well as in the inhibition of cerebral blood vessel damages by the ischemic stress in retina and brain. But, it has remained to identify the minimum peptide sequence in ProTα that retains neuroprotective activity. The present study using the experiments of alanine scanning suggested that any amino acid in 9-amino acid peptide sequence/P9 (amino acids 52-60) of P30 peptide is necessary for its survival activity of cultured rat cortical neurons against the ischemic stress. In the retinal ischemia-perfusion model, intravitreous injection of P9 24h after ischemia significantly inhibited the cellular and functional damages at day 7. On the other hand, 2,3,5-triphenyltetrazolium chloride (TTC) staining and electroretinogram assessment showed that systemic delivery with P9 1h after the cerebral ischemia (1h tMCAO) significantly blocks the ischemia-induced brain damages. In addition, systemic P9 delivery markedly inhibited the cerebral ischemia (tMCAO)-induced disruption of blood vessels in brain. Taken together, the present study provides a therapeutic importance of 9-amino acid peptide sequence against ischemic damages.
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Affiliation(s)
- Sebok Kumar Halder
- Department of Molecular Pharmacology and Neuroscience, Nagasaki University Graduate School of Biomedical Sciences, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
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Abstract
Gene expression patterns change dramatically in aging and age-related events. The DNA microarray is now recognized as a useful device in molecular biology and widely used to identify the molecular mechanisms of aging and the biological effects of drugs for therapeutic purpose in age-related diseases. Recently, numerous technological advantages have led to the evolution of DNA microarrays and microarray-based techniques, revealing the genomic modification and all transcriptional activity. Here, we show the step-by-step methods currently used in our lab to handling the oligonucleotide microarray and miRNA microarray. Moreover, we introduce the protocols of ribonucleoprotein [RNP] immunoprecipitation followed by microarray analysis (RIP-chip) which reveal the target mRNA of age-related RNA-binding proteins.
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St Laurent G, Shtokalo D, Heydarian M, Palyanov A, Babiy D, Zhou J, Kumar A, Urcuqui-Inchima S. Insights from the HuR-interacting transcriptome: ncRNAs, ubiquitin pathways, and patterns of secondary structure dependent RNA interactions. Mol Genet Genomics 2012; 287:867-79. [PMID: 23052832 DOI: 10.1007/s00438-012-0722-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Accepted: 09/17/2012] [Indexed: 12/22/2022]
Abstract
The HuR protein regulates the expression of thousands of cellular transcripts by modulating mRNA splicing, trafficking, translation, and stability. Although it serves as a model of RNA-protein interactions, many features of HuR's interactions with RNAs remain unknown. In this report, we deployed the cryogenic RNA immunoprecipitation technique to analyze HuR-interacting RNAs with the Affymetrix all-exon microarray platform. We revealed several thousand novel HuR-interacting RNAs, including hundreds of non-coding RNAs such as natural antisense transcripts from stress responsive loci. To gain insight into the mechanisms of specificity and sensitivity of HuR's interaction with its target RNAs, we searched HuR-interacting RNAs for composite patterns of primary sequence and secondary structure. We provide evidence that secondary structures of 66-75 nucleotides enhance HuR's recognition of its specific RNA targets composed of short primary sequence patterns. We validated thousands of these RNAs by analysis of overlap with recently published findings, including HuR's interaction with RNAs in the pathways of RNA splicing and stability. Finally, we observed a striking enrichment for members of ubiquitin ligase pathways among the HuR-interacting mRNAs, suggesting a new role for HuR in the regulation of protein degradation to mirror its known function in protein translation.
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Affiliation(s)
- Georges St Laurent
- Grupo de Inmunovirologia, Universidad de Antioquia, Calle 67 Número 53-108, Medellin, Antioquia, Colombia.
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Plateroti M, de Araujo PR, da Silva AE, Penalva LOF. The RNA-Binding Protein Musashi1: A Major Player in Intestinal Epithelium Renewal and Colon Cancer Development. CURRENT COLORECTAL CANCER REPORTS 2012; 8:290-297. [PMID: 23914149 DOI: 10.1007/s11888-012-0141-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Aberrant gene expression is the cause and the consequence of tumorigenesis. A major component of gene expression is translation regulation; a process whose main players are RNA-binding-proteins (RBPs). More than 800 RBPs have been identified in the human genome and several of them have been shown to control gene networks associated with relevant cancer processes. A more systematic characterization of RBPs starts to reveal that similar to transcription factors, they can function as tumor suppressors or oncogenes. A relevant example is Musashi1 (Msi1), which is emerging as a critical regulator of tumorigenesis in multiple cancer types, including colon cancer. Msi1 is a stem marker in several tissues and is critical in maintaining the balance between self-renewal and differentiation. However, a boost in Msi1 expression can most likely lead cells towards an oncogenic pathway. In this article, we discuss the parallels between Msi1 function in normal renewal of intestinal epithelium and in colon cancer.
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Affiliation(s)
- Michelina Plateroti
- Centre de Génétique et de Physiologie Moléculaire et Cellulaire, Université Claude Bernard Lyon 1, France. 16 Rue Raphael Dubois, 69622 Villeurbanne, Cedex France
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von Roretz C, Lian XJ, Macri AM, Punjani N, Clair E, Drouin O, Dormoy-Raclet V, Ma JF, Gallouzi IE. Apoptotic-induced cleavage shifts HuR from being a promoter of survival to an activator of caspase-mediated apoptosis. Cell Death Differ 2012; 20:154-68. [PMID: 22955946 DOI: 10.1038/cdd.2012.111] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Little is known about the cellular mechanisms modulating the shift in balance from a state of survival to cell death by caspase-mediated apoptosis in response to a lethal stress. Here we show that the RNA-binding protein HuR has an important function in mediating this switch. During caspase-mediated apoptosis, HuR is cleaved to generate two cleavage products (CPs). Our data demonstrate that the cleavage of HuR switches its function from being a prosurvival factor under normal conditions to becoming a promoter of apoptosis in response to a lethal stress. In the absence of an apoptotic stimuli, HuR associates with and promotes the expression of caspase-9 and prothymosin α (ProT) mRNAs, and pro- and antiapoptotic factors, respectively, both of which have been characterized as important players in determining cell fate. During the early steps of caspase-mediated apoptosis, however, the level of caspase-9 protein increases, while ProT remains unchanged. Under these conditions, the two HuR-CPs selectively bind to and stabilize caspase-9 mRNA, but do not bind to ProT. Hence, taken together, our data show that by maintaining a threshold of expression of proapoptotic factors such as caspase-9 in response to a lethal stress, the HuR-CPs help a cell to switch from resisting death to undergoing apoptosis.
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Affiliation(s)
- C von Roretz
- Department of Biochemistry, Rosalind and Morris Goodman Cancer Center, McGill University, Montreal, Quebec, Canada
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Jung J, Lifland AW, Zurla C, Alonas EJ, Santangelo PJ. Quantifying RNA-protein interactions in situ using modified-MTRIPs and proximity ligation. Nucleic Acids Res 2012; 41:e12. [PMID: 22952158 PMCID: PMC3592441 DOI: 10.1093/nar/gks837] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The stabilization, translation and degradation of RNA are regulated by interactions between trans-acting factors, such as microRNA and RNA-binding proteins (RBP). In order to investigate the relationships between these events and their significance, a method that detects the localization of these interactions within a single cell, as well as their variability across a cell population, is needed. To visualize and quantify RNA–protein interactions in situ, we developed a proximity ligation assay (PLA) that combined peptide-modified, multiply-labelled tetravalent RNA imaging probes (MTRIPs), targeted to sequences near RBP binding sites, with proximity ligation and rolling circle amplification (RCA). Using this method, we detected and quantified, with single-interaction sensitivity, the localization and frequency of interactions of the human respiratory syncytial virus (hRSV) nucleocapsid protein (N) with viral genomic RNA (gRNA). We also described the effects of actinomycin D (actD) on the interactions of HuR with β-actin mRNA and with poly(A)+ mRNA at both native and increased HuR expression levels.
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Affiliation(s)
- Jeenah Jung
- Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 313 Ferst Drive, UA Whitaker Bldg, Atlanta, GA 30332, USA
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