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Feichtner A, Enzler F, Kugler V, Hoppe K, Mair S, Kremser L, Lindner H, Huber RG, Stelzl U, Stefan E, Torres-Quesada O. Phosphorylation of the compartmentalized PKA substrate TAF15 regulates RNA-protein interactions. Cell Mol Life Sci 2024; 81:162. [PMID: 38568213 PMCID: PMC10991009 DOI: 10.1007/s00018-024-05204-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 03/08/2024] [Accepted: 03/09/2024] [Indexed: 04/05/2024]
Abstract
Spatiotemporal-controlled second messengers alter molecular interactions of central signaling nodes for ensuring physiological signal transmission. One prototypical second messenger molecule which modulates kinase signal transmission is the cyclic-adenosine monophosphate (cAMP). The main proteinogenic cellular effectors of cAMP are compartmentalized protein kinase A (PKA) complexes. Their cell-type specific compositions precisely coordinate substrate phosphorylation and proper signal propagation which is indispensable for numerous cell-type specific functions. Here we present evidence that TAF15, which is implicated in the etiology of amyotrophic lateral sclerosis, represents a novel nuclear PKA substrate. In cross-linking and immunoprecipitation experiments (iCLIP) we showed that TAF15 phosphorylation alters the binding to target transcripts related to mRNA maturation, splicing and protein-binding related functions. TAF15 appears to be one of multiple PKA substrates that undergo RNA-binding dynamics upon phosphorylation. We observed that the activation of the cAMP-PKA signaling axis caused a change in the composition of a collection of RNA species that interact with TAF15. This observation appears to be a broader principle in the regulation of molecular interactions, as we identified a significant enrichment of RNA-binding proteins within endogenous PKA complexes. We assume that phosphorylation of RNA-binding domains adds another layer of regulation to binary protein-RNAs interactions with consequences to RNA features including binding specificities, localization, abundance and composition.
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Affiliation(s)
- Andreas Feichtner
- Tyrolean Cancer Research Institute (TKFI), Innrain 66, 6020, Innsbruck, Austria
- Institute of Molecular Biology and Center for Molecular Biosciences, University of Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
| | - Florian Enzler
- Daniel Swarovski Research Laboratory, Department of Visceral, Transplant and Thoracic Surgery, Medical University of Innsbruck, Innrain 66/66a, 6020, Innsbruck, Austria
| | - Valentina Kugler
- Tyrolean Cancer Research Institute (TKFI), Innrain 66, 6020, Innsbruck, Austria
- Institute of Molecular Biology and Center for Molecular Biosciences, University of Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
| | - Katharina Hoppe
- Institute of Developmental Immunology, Biocenter, Medical University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria
| | - Sophia Mair
- Department of Cardiac Surgery, Medical University of Innsbruck, Innrain 66/66a, 6020, Innsbruck, Austria
- Vascage, Center of Clinical Stroke Research, 6020, Innsbruck, Austria
| | - Leopold Kremser
- Division of Clinical Biochemistry, Biocenter, Medical University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria
| | - Herbert Lindner
- Division of Clinical Biochemistry, Biocenter, Medical University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria
| | - Roland G Huber
- Bioinformatics Institute, Agency for Science Technology and Research, Singapore, 138671, Singapore
| | - Ulrich Stelzl
- Institute of Pharmaceutical Sciences, University of Graz, Schubertstrasse 1, 8010, Graz, Austria
| | - Eduard Stefan
- Tyrolean Cancer Research Institute (TKFI), Innrain 66, 6020, Innsbruck, Austria.
- Institute of Molecular Biology and Center for Molecular Biosciences, University of Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria.
| | - Omar Torres-Quesada
- Tyrolean Cancer Research Institute (TKFI), Innrain 66, 6020, Innsbruck, Austria.
- Division of Medical Biochemistry, Biocenter, Medical University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria.
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Luna-Arias JP, Castro-Muñozledo F. Participation of the TBP-associated factors (TAFs) in cell differentiation. J Cell Physiol 2024; 239:e31167. [PMID: 38126142 DOI: 10.1002/jcp.31167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 11/04/2023] [Accepted: 11/27/2023] [Indexed: 12/23/2023]
Abstract
The understanding of the mechanisms that regulate gene expression to establish differentiation programs and determine cell lineages, is one of the major challenges in Developmental Biology. Besides the participation of tissue-specific transcription factors and epigenetic processes, the role of general transcription factors has been ignored. Only in recent years, there have been scarce studies that address this issue. Here, we review the studies on the biological activity of some TATA-box binding protein (TBP)-associated factors (TAFs) during the proliferation of stem/progenitor cells and their involvement in cell differentiation. Particularly, the accumulated evidence suggests that TAF4, TAF4b, TAF7L, TAF8, TAF9, and TAF10, among others, participate in nervous system development, adipogenesis, myogenesis, and epidermal differentiation; while TAF1, TAF7, TAF15 may be involved in the regulation of stem cell proliferative abilities and cell cycle progression. On the other hand, evidence suggests that TBP variants such as TBPL1 and TBPL2 might be regulating some developmental processes such as germ cell maturation and differentiation, myogenesis, or ventral specification during development. Our analysis shows that it is necessary to study in greater depth the biological function of these factors and its participation in the assembly of specific transcription complexes that contribute to the differential gene expression that gives rise to the great diversity of cell types existing in an organism. The understanding of TAFs' regulation might lead to the development of new therapies for patients which suffer from mutations, alterations, and dysregulation of these essential elements of the transcriptional machinery.
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Affiliation(s)
- Juan Pedro Luna-Arias
- Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del IPN, México City, Mexico
| | - Federico Castro-Muñozledo
- Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del IPN, México City, Mexico
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Du X, Xin R, Chen X, Wang G, Huang C, Zhou K, Zhang S. TAF15 regulates the BRD4/GREM1 axis and activates the gremlin-1-NF-κB pathway to promote OA progression. Regen Ther 2023; 24:227-236. [PMID: 37496731 PMCID: PMC10366938 DOI: 10.1016/j.reth.2023.06.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 06/18/2023] [Accepted: 06/29/2023] [Indexed: 07/28/2023] Open
Abstract
Background Anterior cruciate ligament (ACL) injury is recognized as a risk factor for osteoarthritis (OA) progression. Herein, the function of TAF15 in ACL injury-induced OA was investigated. Methods OA cell model and OA mouse model were established by interleukin-1 beta (IL-1β) stimulation and ACL transection administration, respectively. The pathological changes were analyzed by histopathology. The mRNA and protein expressions were assessed using qRT-PCR, Western blot and IHC. Chondrocyte viability and apoptosis were examined by CCK8 assay and TUNEL staining, respectively. The interactions between TAF15, BRD4 and GREM1 were analyzed by RIP or ChIP assay. Results TAF15 expression was markedly elevated in OA, and its knockdown suppressed IL-1β-induced chondrocyte apoptosis and ECM degradation in vivo and cartilage pathological changes in vitro. TAF15 promoted BRD4 mRNA stability, and TAF15 silencing's repression on chondrocyte apoptosis and ECM degradation induced by IL-1β was abrogated following BRD4 overexpression. BRD4 promoted GREM1 expression by directly binding with GREM1. In addition, the GREM1/NF-κB pathway functioned as the downstream pathway of BRD4 in promoting OA progression. Conclusion TAF15 upregulation facilitated chondrocyte apoptosis and ECM degradation during OA development by acting on the BRD4/GREM1/NF-κB axis, which provided a theoretical basis for the development of novel therapies for OA.
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Affiliation(s)
- Xiufan Du
- Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Department of Sports Medicine, Haikou, 570311, Hainan, PR China
| | - Ruomei Xin
- Danzhou People's Hospital, Nursing Department, Danzhou, 571700, Hainan, PR China
| | - Xiaoyan Chen
- Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Department of Stomatology, Haikou, 570311, Hainan, PR China
| | - Guangji Wang
- Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Department of Sports Medicine, Haikou, 570311, Hainan, PR China
| | - Chunhang Huang
- Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Department of Sports Medicine, Haikou, 570311, Hainan, PR China
| | - Kai Zhou
- Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Department of Sports Medicine, Haikou, 570311, Hainan, PR China
| | - Shunli Zhang
- The Second Affiliated Hospital of Hainan Medical University, Haikou, 570216, Hainan, PR China
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Eraso P, Mazón MJ, Jiménez V, Pizarro-García P, Cuevas EP, Majuelos-Melguizo J, Morillo-Bernal J, Cano A, Portillo F. New Functions of Intracellular LOXL2: Modulation of RNA-Binding Proteins. Molecules 2023; 28:molecules28114433. [PMID: 37298909 DOI: 10.3390/molecules28114433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/25/2023] [Accepted: 05/26/2023] [Indexed: 06/12/2023] Open
Abstract
Lysyl oxidase-like 2 (LOXL2) was initially described as an extracellular enzyme involved in extracellular matrix remodeling. Nevertheless, numerous recent reports have implicated intracellular LOXL2 in a wide variety of processes that impact on gene transcription, development, differentiation, proliferation, migration, cell adhesion, and angiogenesis, suggesting multiple different functions for this protein. In addition, increasing knowledge about LOXL2 points to a role in several types of human cancer. Moreover, LOXL2 is able to induce the epithelial-to-mesenchymal transition (EMT) process-the first step in the metastatic cascade. To uncover the underlying mechanisms of the great variety of functions of intracellular LOXL2, we carried out an analysis of LOXL2's nuclear interactome. This study reveals the interaction of LOXL2 with numerous RNA-binding proteins (RBPs) involved in several aspects of RNA metabolism. Gene expression profile analysis of cells silenced for LOXL2, combined with in silico identification of RBPs' targets, points to six RBPs as candidates to be substrates of LOXL2's action, and that deserve a more mechanistic analysis in the future. The results presented here allow us to hypothesize novel LOXL2 functions that might help to comprehend its multifaceted role in the tumorigenic process.
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Affiliation(s)
- Pilar Eraso
- Departamento de Bioquímica UAM, Instituto de Investigaciones Biomédicas Alberto Sols, CSIC-UAM, 28029 Madrid, Spain
| | - María J Mazón
- Departamento de Bioquímica UAM, Instituto de Investigaciones Biomédicas Alberto Sols, CSIC-UAM, 28029 Madrid, Spain
| | - Victoria Jiménez
- Departamento de Bioquímica UAM, Instituto de Investigaciones Biomédicas Alberto Sols, CSIC-UAM, 28029 Madrid, Spain
| | - Patricia Pizarro-García
- Departamento de Bioquímica UAM, Instituto de Investigaciones Biomédicas Alberto Sols, CSIC-UAM, 28029 Madrid, Spain
| | - Eva P Cuevas
- Departamento de Bioquímica UAM, Instituto de Investigaciones Biomédicas Alberto Sols, CSIC-UAM, 28029 Madrid, Spain
| | - Jara Majuelos-Melguizo
- Departamento de Bioquímica UAM, Instituto de Investigaciones Biomédicas Alberto Sols, CSIC-UAM, 28029 Madrid, Spain
| | - Jesús Morillo-Bernal
- Departamento de Bioquímica UAM, Instituto de Investigaciones Biomédicas Alberto Sols, CSIC-UAM, 28029 Madrid, Spain
| | - Amparo Cano
- Departamento de Bioquímica UAM, Instituto de Investigaciones Biomédicas Alberto Sols, CSIC-UAM, 28029 Madrid, Spain
- Instituto de Investigación Sanitaria del Hospital Universitario La Paz-IdiPAZ, 28029 Madrid, Spain
- Centro de Investigación Biomédica en Red, Área de Cáncer (CIBERONC), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Francisco Portillo
- Departamento de Bioquímica UAM, Instituto de Investigaciones Biomédicas Alberto Sols, CSIC-UAM, 28029 Madrid, Spain
- Instituto de Investigación Sanitaria del Hospital Universitario La Paz-IdiPAZ, 28029 Madrid, Spain
- Centro de Investigación Biomédica en Red, Área de Cáncer (CIBERONC), Instituto de Salud Carlos III, 28029 Madrid, Spain
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Zheng WH, Long ZQ, Zheng ZQ, Zhang LL, Liang YL, Li ZX, Lv JW, Kou J, Hong XH, He SW, Xu R, Zhou GQ, Liu N, Ma J, Sun Y, Lin L, Wei D. m6A-enriched lncRNA LINC00839 promotes tumor progression by enhancing TAF15-mediated transcription of amine oxidase AOC1 in nasopharyngeal carcinoma. J Biol Chem 2023:104873. [PMID: 37257820 PMCID: PMC10302167 DOI: 10.1016/j.jbc.2023.104873] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 05/15/2023] [Accepted: 05/16/2023] [Indexed: 06/02/2023] Open
Abstract
Dysregulation of long non-coding RNAs (lncRNAs) contributes to tumorigenesis by modulating specific cancer-related pathways, but the roles of m6A-enriched lncRNAs and underlying mechanisms remain elusive in nasopharyngeal carcinoma (NPC). Here, we reanalyzed the previous genome-wide analysis of lncRNA profiles in 18 pairs of NPC and normal tissues, as well as in 10 paired samples from NPC with or without posttreatment metastases. We discerned that an oncogenic m6A-enriched lncRNA, LINC00839, which was substantially upregulated in NPC and correlated with poor clinical prognosis, promoted NPC growth and metastasis both in vitro and in vivo. Mechanistically, by using RNA pulldown assay combined with mass spectrometry, we found that LINC00839 interacted directly with the transcription factor, TATA-box binding protein associated factor (TAF15). Besides, ChIP and dual-luciferase report assays demonstrated that LINC00839 coordinated the recruitment of TAF15 to the promoter region of amine oxidase copper-containing 1 (AOC1), which encodes a secreted glycoprotein playing vital roles in various cancers, thereby activating AOC1 transcription in trans. In this study, potential effects of AOC1 in NPC progression were first proposed. Moreover, ectopic expression of AOC1 partially rescued the inhibitory effect of downregulation of LINC00839 in NPC. Furthermore, we showed that silencing vir-like m6A methyltransferase-associated (VIRMA) and insulin-like growth factor 2 mRNA-binding proteins 1 (IGF2BP1) attenuated the expression level and RNA stability of LINC00839 in an m6A-dependent manner. Taken together, our study unveils a novel oncogenic VIRMA/IGF2BP1-LINC00839-TAF15-AOC1 axis, and highlights the significance and prognostic value of LINC00839 expression in NPC carcinogenesis.
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Affiliation(s)
- Wei-Hong Zheng
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou 510060, People's Republic of China; State Key Laboratory of Oncology in Southern China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center
| | - Zhi-Qing Long
- State Key Laboratory of Oncology in Southern China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center
| | - Zi-Qi Zheng
- State Key Laboratory of Oncology in Southern China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center
| | - Lu-Lu Zhang
- Department of Molecular Diagnostics, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou 510060, People's Republic of China
| | - Ye-Lin Liang
- State Key Laboratory of Oncology in Southern China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center
| | - Zhi-Xuan Li
- State Key Laboratory of Oncology in Southern China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center
| | - Jia-Wei Lv
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou 510060, People's Republic of China
| | - Jia Kou
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou 510060, People's Republic of China
| | - Xiao-Hong Hong
- State Key Laboratory of Oncology in Southern China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center
| | - Shi-Wei He
- State Key Laboratory of Oncology in Southern China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center
| | - Rui Xu
- State Key Laboratory of Oncology in Southern China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center
| | - Guan-Qun Zhou
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou 510060, People's Republic of China
| | - Na Liu
- State Key Laboratory of Oncology in Southern China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center
| | - Jun Ma
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou 510060, People's Republic of China; State Key Laboratory of Oncology in Southern China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center
| | - Ying Sun
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou 510060, People's Republic of China; State Key Laboratory of Oncology in Southern China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center
| | - Li Lin
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou 510060, People's Republic of China.
| | - Denghui Wei
- State Key Laboratory of Oncology in Southern China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center.
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Guo CM, Tang L, Li X, Huang LY. TATA-box-binding protein-associated factor 15 is a novel biomarker that promotes cell proliferation and migration in gastrointestinal stromal tumor. World J Gastroenterol 2023; 29:2932-2949. [PMID: 37274797 PMCID: PMC10237090 DOI: 10.3748/wjg.v29.i19.2932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 03/06/2023] [Accepted: 04/11/2023] [Indexed: 05/16/2023] Open
Abstract
BACKGROUND Gastrointestinal stromal tumor (GIST) is a common neoplasm with high rates of recurrence and metastasis, and its therapeutic efficacy is still not ideal. There is an unmet need to find new molecular therapeutic targets for GIST. TATA-box-binding protein-associated factor 15 (TAF15) contributes to the progress of various tumors, while the role and molecular mechanism of TAF15 in GIST progression are still unknown.
AIM To explore new molecular therapeutic targets for GIST and understand the biological role and underlying mechanisms of TAF15 in GIST progression.
METHODS Proteomic analysis was performed to explore the differentially expressed proteins in GIST. Western blotting and immunohistochemical analysis were used to verify the expression level of TAF15 in GIST tissues and cell lines. Cell counting kit-8, colony formation, wound-healing and transwell assay were executed to detect the ability of TAF15 on cell proliferation, migration and invasion. A xenograft mouse model was applied to explore the role of TAF15 in the progression of GIST. Western blotting was used to detect the phosphorylation level and total level of RAF1, MEK and ERK1/2.
RESULTS A total of 1669 proteins were identified as differentially expressed proteins with 762 upregulated and 907 downregulated in GIST. TAF15 was selected for the further study because of its important role in cell proliferation and migration. TAF15 was significantly over expressed in GIST tissues and cell lines. Overexpression of TAF15 was associated with larger tumor size and higher risk stage of GIST. TAF15 knockdown significantly inhibited the cell proliferation and migration of GIST in vitro and suppressed tumor growth in vivo. Moreover, the inhibition of TAF15 expression significantly decreased the phosphorylation level of RAF1, MEK and ERK1/2 in GIST cells and xenograft tissues, while the total RAF1, MEK and ERK1/2 had no significant change.
CONCLUSION TAF15 is over expressed in GIST tissues and cell lines. Overexpression of TAF15 was associated with a poor prognosis of GIST patients. TAF15 promotes cell proliferation and migration in GIST via the activation of the RAF1/MEK/ERK signaling pathway. Thus, TAF15 is expected to be a novel latent molecular biomarker or therapeutic target of GIST.
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Affiliation(s)
- Cheng-Ming Guo
- Department of Gastroenterology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai 264000, Shandong Province, China
| | - Li Tang
- Department of Gastroenterology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai 264000, Shandong Province, China
| | - Xu Li
- Department of Gastroenterology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai 264000, Shandong Province, China
| | - Liu-Ye Huang
- Department of Gastroenterology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai 264000, Shandong Province, China
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Tang L, Guo C, Li X, Zhang B, Huang L. TAF15 promotes cell proliferation, migration and invasion of gastric cancer via activation of the RAF1/MEK/ERK signalling pathway. Sci Rep 2023; 13:5846. [PMID: 37037864 PMCID: PMC10086039 DOI: 10.1038/s41598-023-31959-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 03/20/2023] [Indexed: 04/12/2023] Open
Abstract
TATA-box-binding protein-associated Factor 15 (TAF15), a member of the FUS/EWS/TAF15 (FET) family, contributes to the progression of various tumours. However, the role and molecular mechanism of TAF15 in gastric cancer (GC) progression are still unknown. In this study, we found that TAF15 was significantly upregulated in GC tumour tissues and cell lines. Overexpression of TAF15 was associated with a larger tumour size, high pathologic stage and high T stage of GC. TAF15 knockdown suppressed the proliferation, migration and invasion of GC cells in vitro and inhibited the tumour growth in vivo. Additionally, TAF15 knockdown led to the significant reductions in the phosphorylation levels of RAF1, MEK and ERK1/2, while total RAF1, MEK and ERK1/2 exhibited no significant change in GC cell lines. In summary, TAF15 is overexpressed in GC tumour tissues and cell lines, and promotes cell proliferation, migration and invasion in GC via the RAF1/MEK/ERK signaling pathway, which suggests that TAF15 might be a potential molecular diagnostic marker or therapeutic target for GC.
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Affiliation(s)
- Li Tang
- Department of Gastroenterology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, Shandong, People's Republic of China
| | - Chengming Guo
- Department of Gastroenterology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, Shandong, People's Republic of China
| | - Xu Li
- Department of Gastroenterology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, Shandong, People's Republic of China
| | - Bo Zhang
- Department of Gastroenterology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, Shandong, People's Republic of China
| | - Liuye Huang
- Department of Gastroenterology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, Shandong, People's Republic of China.
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SR Protein Kinase 1 Inhibition by TAF15. Cells 2022; 12:cells12010126. [PMID: 36611919 PMCID: PMC9818988 DOI: 10.3390/cells12010126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/21/2022] [Accepted: 12/24/2022] [Indexed: 12/29/2022] Open
Abstract
Although SRPKs were discovered nearly 30 years ago, our understanding of their mode of regulation is still limited. Regarded as constitutively active enzymes known to participate in diverse biological processes, their prominent mode of regulation mainly depends on their intracellular localization. Molecular chaperones associate with a large internal spacer sequence that separates the bipartite kinase catalytic core and modulates the kinases' partitioning between the cytoplasm and nucleus. Besides molecular chaperones that function as anchoring proteins, a few other proteins were shown to interact directly with SRPK1, the most-studied member of SRPKs, and alter its activity. In this study, we identified TAF15, which has been involved in transcription initiation, splicing, DNA repair, and RNA maturation, as a novel SRPK1-interacting protein. The C-terminal RGG domain of TAF15 was able to associate with SRPK1 and downregulate its activity. Furthermore, overexpression of this domain partially relocalized SRPK1 to the nucleus and resulted in hypophosphorylation of SR proteins, inhibition of splicing of a reporter minigene, and inhibition of Lamin B receptor phosphorylation. We further demonstrated that peptides comprising the RGG repeats of nucleolin, HNRPU, and HNRNPA2B1, were also able to inhibit SRPK1 activity, suggesting that negative regulation of SRPK1 activity might be a key biochemical property of RGG motif-containing proteins.
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He JY, Cheng M, Ye JL, Peng CH, Chen J, Luo B, Zhang XY, Fu Q. YY1-induced lncRNA XIST inhibits cartilage differentiation of BMSCs by binding with TAF15 to stabilizing FUT1 expression. Regen Ther 2022; 20:41-50. [PMID: 35402663 PMCID: PMC8968204 DOI: 10.1016/j.reth.2022.02.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/22/2022] [Accepted: 02/15/2022] [Indexed: 12/17/2022] Open
Abstract
Introduction The functional roles and mechanism of the XIST in osteoarthritis and the chondrogenic differentiation of BMSCs were clarified. Methods The expression levels of XIST, TAF15, FUT1 and YY1 were detected through quantitative RT-PCR. The protein expression of Sox9, ACAN, COL2A1 and FUT1 were detected by western blot and immunohistochemistry. The damage of cartilage tissue was detected by HE staining, and Safranin O-fast green. Alcian-Blue and Alizarin red S staining were performed to evaluate BMSCs chondrogenic differentiation. The relationship between XIST and TAF15, XIST and TAF15 were analyzed by RNA immunoprecipitation assay. Luciferase reporter assays and chromatin immunoprecipitation were performed to detect the interaction relationship between XIST and YY1. In addition, osteoarthritis mice were built to assess the function of XIST in vivo. Results The levels of XIST, TAF15 and FUT1 were upregulated in cartilage tissues from osteoarthritis patient. The level of XIST was decreased in BMSCs during chondrogenic differentiation. XIST overexpression inhibited the chondrogenic differentiation of BMSCs. Moreover, silencing of FUT1 reversed the effects of XIST overexpression on BMSCs chondrogenic differentiation. Mechanistically, in BMSCs, YY1 induced the expression of XIST in BMSCs, and XIST regulated FUT1 mRNA stability through targeting TAF15. Furthermore, silencing of XIST alleviated the symptoms of cartilage injury in OA mice. Conclusion Taken together, these results suggested that YY1 induced XIST was closely related to the chondrogenic differentiation of BMSCs and the progression of osteoarthritis by TAF15/FUT1 axis, and may be a new OA therapeutic target. XIST and TAF15 expression were upregulated in osteoarthritis. Overexpression of XIST suppressed the chondrogenic differentiation of BMSCs. XIST regulated BMSCs chondrogenic differentiation through enhancing FUT1 mRNA stability via TAF15. XIST silencing relieved cartilage damage in OA mice.
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Affiliation(s)
- Jian-Ying He
- Orthopedics Department, JiangXi Provinvcial People’s Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang, 330006, Jiangxi Province, PR China
| | - Min Cheng
- Orthopedics Department, People's Hospital of Poyang County, Shangrao, 333100, Jiangxi Province, PR China
| | - Jia-Lian Ye
- Orthopedics Department, People's Hospital of Poyang County, Shangrao, 333100, Jiangxi Province, PR China
| | - Chuan-Hua Peng
- Orthopedics Department, People's Hospital of Poyang County, Shangrao, 333100, Jiangxi Province, PR China
| | - Jian Chen
- Orthopedics Department, People's Hospital of Poyang County, Shangrao, 333100, Jiangxi Province, PR China
| | - Bin Luo
- Orthopedics Department, People's Hospital of Poyang County, Shangrao, 333100, Jiangxi Province, PR China
| | - Xian-Yu Zhang
- Orthopedics Department, Shangrao People's Hospital, Shangrao, 333400, Jiangxi Province, PR China
| | - Qiang Fu
- Department of Rheumatology, JiangXi Provinvcial People’s Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang, 330006, Jiangxi Province, PR China
- Corresponding author. Department of Rheumatology, JiangXi Provinvcial People’s Hospital, The First Affiliated Hospital of Nanchang Medical College, No. 92, Aiguo Road, Donghu District, Nanchang, 330006, Jiangxi Province, PR China.
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10
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In heart failure reactivation of RNA-binding proteins is associated with the expression of 1,523 fetal-specific isoforms. PLoS Comput Biol 2022; 18:e1009918. [PMID: 35226669 PMCID: PMC8912908 DOI: 10.1371/journal.pcbi.1009918] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 03/10/2022] [Accepted: 02/10/2022] [Indexed: 01/03/2023] Open
Abstract
Reactivation of fetal-specific genes and isoforms occurs during heart failure. However, the underlying molecular mechanisms and the extent to which the fetal program switch occurs remains unclear. Limitations hindering transcriptome-wide analyses of alternative splicing differences (i.e. isoform switching) in cardiovascular system (CVS) tissues between fetal, healthy adult and heart failure have included both cellular heterogeneity across bulk RNA-seq samples and limited availability of fetal tissue for research. To overcome these limitations, we have deconvoluted the cellular compositions of 996 RNA-seq samples representing heart failure, healthy adult (heart and arteria), and fetal-like (iPSC-derived cardiovascular progenitor cells) CVS tissues. Comparison of the expression profiles revealed that reactivation of fetal-specific RNA-binding proteins (RBPs), and the accompanied re-expression of 1,523 fetal-specific isoforms, contribute to the transcriptome differences between heart failure and healthy adult heart. Of note, isoforms for 20 different RBPs were among those that reverted in heart failure to the fetal-like expression pattern. We determined that, compared with adult-specific isoforms, fetal-specific isoforms encode proteins that tend to have more functions, are more likely to harbor RBP binding sites, have canonical sequences at their splice sites, and contain typical upstream polypyrimidine tracts. Our study suggests that compared with healthy adult, fetal cardiac tissue requires stricter transcriptional regulation, and that during heart failure reversion to this stricter transcriptional regulation occurs. Furthermore, we provide a resource of cardiac developmental stage-specific and heart failure-associated genes and isoforms, which are largely unexplored and can be exploited to investigate novel therapeutics for heart failure. Heart failure is a chronic condition in which the heart does not pump enough blood. It has been shown that in heart failure, the adult heart reverts to a fetal-like metabolic state and oxygen consumption. Additionally, genes and isoforms that are expressed in the heart only during fetal development (i.e. not in the healthy adult heart) are turned on in heart failure. However, the underlying molecular mechanisms and the extent to which the switch to a fetal gene program occurs remains unclear. In this study, we initially characterized the differences between the fetal and adult heart transcriptomes (entire set of expressed genes and isoforms). We found that RNA binding proteins (RBPs), a family of genes that regulate multiple aspects of a transcript’s maturation, including transcription, splicing and post-transcriptional modifications, play a central role in the differences between fetal and adult heart tissues. We observed that many RBPs that are only expressed in the heart during fetal development become reactivated in heart failure, resulting in the expression of 1,523 fetal-specific isoforms. These findings suggest that reactivation of fetal-specific RBPs in heart failure drives a transcriptome-wide switch to expression of fetal-specific isoforms; and hence that RBPs could potentially serve as novel therapeutic targets.
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11
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DeJong CS, Dichmann DS, Exner CRT, Xu Y, Harland RM. The atypical RNA-binding protein Taf15 regulates dorsoanterior neural development through diverse mechanisms in Xenopus tropicalis. Development 2021; 148:271175. [PMID: 34345915 DOI: 10.1242/dev.191619] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 06/08/2021] [Indexed: 11/20/2022]
Abstract
The FET family of atypical RNA-binding proteins includes Fused in sarcoma (FUS), Ewing's sarcoma (EWS) and the TATA-binding protein-associate factor 15 (TAF15). FET proteins are highly conserved, suggesting specialized requirements for each protein. Fus regulates splicing of transcripts required for mesoderm differentiation and cell adhesion in Xenopus, but the roles of Ews and Taf15 remain unknown. Here, we analyze the roles of maternally deposited and zygotically transcribed Taf15, which is essential for the correct development of dorsoanterior neural tissues. By measuring changes in exon usage and transcript abundance from Taf15-depleted embryos, we found that Taf15 may regulate dorsoanterior neural development through fgfr4 and ventx2.1. Taf15 uses distinct mechanisms to downregulate Fgfr4 expression, namely retention of a single intron within fgfr4 when maternal and zygotic Taf15 is depleted, and reduction in the total fgfr4 transcript when zygotic Taf15 alone is depleted. The two mechanisms of gene regulation (post-transcriptional versus transcriptional) suggest that Taf15-mediated gene regulation is target and co-factor dependent, contingent on the milieu of factors that are present at different stages of development.
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Affiliation(s)
- Caitlin S DeJong
- Molecular and Cell Biology Department, Genetics, Genomics and Development Division, University of California, Berkeley, CA 94720, USA
| | - Darwin S Dichmann
- Molecular and Cell Biology Department, Genetics, Genomics and Development Division, University of California, Berkeley, CA 94720, USA
| | - Cameron R T Exner
- Department of Psychiatry, Weill Institute for Neurosciences, Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA 94143, USA
| | - Yuxiao Xu
- Department of Psychiatry, Weill Institute for Neurosciences, Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA 94143, USA
| | - Richard M Harland
- Molecular and Cell Biology Department, Genetics, Genomics and Development Division, University of California, Berkeley, CA 94720, USA
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12
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Peng WX, He PX, Liu LJ, Zhu T, Zhong YQ, Xiang L, Peng K, Yang JJ, Xiang GD. LncRNA GAS5 activates the HIF1A/VEGF pathway by binding to TAF15 to promote wound healing in diabetic foot ulcers. J Transl Med 2021; 101:1071-1083. [PMID: 33875793 DOI: 10.1038/s41374-021-00598-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 03/01/2021] [Accepted: 03/05/2021] [Indexed: 12/14/2022] Open
Abstract
A diabetic foot ulcer (DFU) is one of the most devastating complications of diabetes. It has been reported that lncRNA GAS5 plays a vital role in wound healing in DFUs. However, the specific mechanism remains unclear. In this research, we aimed to investigate the role of GAS5 in wound healing in DFUs as well as the underlying mechanism. qPCR or western blotting was performed to measure the expression levels of GAS5, HIF1A, VEGF and TAF15. CCK-8 or EdU assays, flow cytometry, wound healing assays and tube formation assays were carried out to assess the proliferation, apoptosis, wound healing and in vitro angiogenesis of HUVECs, respectively. RNA pull-down and RIP assays were performed to verify the interaction between GAS5 and TAF15. ChIP and luciferase assays were conducted to verify the binding of TAF15 to the HIF1A promoter. In the DFU mouse model, H&E and Masson staining were used to determine epidermal and dermal thickness and collagen formation. GAS5 and HIF1A were downregulated in the skin tissues of DFU patients, and GAS5 overexpression promoted cell proliferation, wound healing and tubule formation in HG-treated HUVECs. In addition, GAS5 facilitated HIF1A expression by interacting with TAF15. Rescue assays demonstrated that the suppression of HIF1A/VEGF pathway activation partially reversed the functional roles of GAS5 in HUVECs. Furthermore, GAS5 accelerated wound healing by activating the HIF1A/VEGF pathway in mice with DFUs. GAS5 activates the HIF1A/VEGF pathway by binding to TAF15, resulting in accelerated wound healing in DFUs. Our findings may provide a theoretical basis for the clinical treatment of DFUs.
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Affiliation(s)
- Wei-Xia Peng
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong, PR China
- Department of Endocrine, Yiyang Central Hospital, Yiyang, Hunan, PR China
| | - Pei-Xiang He
- Department of Endocrine, Yiyang Central Hospital, Yiyang, Hunan, PR China
| | - Li-Jun Liu
- Department of Endocrine, Yiyang Central Hospital, Yiyang, Hunan, PR China
| | - Ting Zhu
- Department of Endocrine, Yiyang Central Hospital, Yiyang, Hunan, PR China
| | - Ya-Qin Zhong
- Department of Endocrine, Yiyang Central Hospital, Yiyang, Hunan, PR China
| | - Lin Xiang
- Department of Endocrine, Central Theater General Hospital of PLA, Wuhan, Hubei, PR China
| | - Ke Peng
- Department of Endocrine, Yiyang Central Hospital, Yiyang, Hunan, PR China
| | - Jing-Jin Yang
- Department of Endocrine, Huaihua First People's Hospital, Huaihua, Hunan, PR China
| | - Guang-Da Xiang
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong, PR China.
- Department of Endocrine, Central Theater General Hospital of PLA, Wuhan, Hubei, PR China.
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13
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Kinoshita C, Kubota N, Aoyama K. Interplay of RNA-Binding Proteins and microRNAs in Neurodegenerative Diseases. Int J Mol Sci 2021; 22:ijms22105292. [PMID: 34069857 PMCID: PMC8157344 DOI: 10.3390/ijms22105292] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/14/2021] [Accepted: 05/15/2021] [Indexed: 02/07/2023] Open
Abstract
The number of patients with neurodegenerative diseases (NDs) is increasing, along with the growing number of older adults. This escalation threatens to create a medical and social crisis. NDs include a large spectrum of heterogeneous and multifactorial pathologies, such as amyotrophic lateral sclerosis, frontotemporal dementia, Alzheimer’s disease, Parkinson’s disease, Huntington’s disease and multiple system atrophy, and the formation of inclusion bodies resulting from protein misfolding and aggregation is a hallmark of these disorders. The proteinaceous components of the pathological inclusions include several RNA-binding proteins (RBPs), which play important roles in splicing, stability, transcription and translation. In addition, RBPs were shown to play a critical role in regulating miRNA biogenesis and metabolism. The dysfunction of both RBPs and miRNAs is often observed in several NDs. Thus, the data about the interplay among RBPs and miRNAs and their cooperation in brain functions would be important to know for better understanding NDs and the development of effective therapeutics. In this review, we focused on the connection between miRNAs, RBPs and neurodegenerative diseases.
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Affiliation(s)
- Chisato Kinoshita
- Department of Pharmacology, Teikyo University School of Medicine, 2-11-1 Kaga, Itabashi, Tokyo 173-8605, Japan;
- Correspondence: (C.K.); (K.A.); Tel.: +81-3-3964-3794 (C.K.); +81-3-3964-3793 (K.A.)
| | - Noriko Kubota
- Department of Pharmacology, Teikyo University School of Medicine, 2-11-1 Kaga, Itabashi, Tokyo 173-8605, Japan;
- Teikyo University Support Center for Women Physicians and Researchers, 2-11-1 Kaga, Itabashi, Tokyo 173-8605, Japan
| | - Koji Aoyama
- Department of Pharmacology, Teikyo University School of Medicine, 2-11-1 Kaga, Itabashi, Tokyo 173-8605, Japan;
- Correspondence: (C.K.); (K.A.); Tel.: +81-3-3964-3794 (C.K.); +81-3-3964-3793 (K.A.)
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14
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Bock AS, Murthy AC, Tang WS, Jovic N, Shewmaker F, Mittal J, Fawzi NL. N-terminal acetylation modestly enhances phase separation and reduces aggregation of the low-complexity domain of RNA-binding protein fused in sarcoma. Protein Sci 2021; 30:1337-1349. [PMID: 33547841 DOI: 10.1002/pro.4029] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/19/2021] [Accepted: 01/22/2021] [Indexed: 12/22/2022]
Abstract
The RNA-binding protein fused in sarcoma (FUS) assembles via liquid-liquid phase separation (LLPS) into functional RNA granules and aggregates in amyotrophic lateral sclerosis associated neuronal inclusions. Several studies have demonstrated that posttranslational modification (PTM) can significantly alter FUS phase separation and aggregation, particularly charge-altering phosphorylation of the nearly uncharged N-terminal low complexity domain of FUS (FUS LC). However, the occurrence and impact of N-terminal acetylation on FUS phase separation remains unexplored, even though N-terminal acetylation is the most common PTM in mammals and changes the charge at the N-terminus. First, we find that FUS is predominantly acetylated in two human cell types and stress conditions. Next, we show that recombinant FUS LC can be acetylated when co-expressed with the NatA complex in Escherichia coli. Using NMR spectroscopy, we find that N-terminal acetylated FUS LC (FUS LC Nt-Ac) does not notably alter monomeric FUS LC structure or motions. Despite no difference in structure, Nt-Ac-FUS LC phase separates more avidly than unmodified FUS LC. More importantly, N-terminal acetylation of FUS LC reduces aggregation. Our findings highlight the importance of N-terminal acetylation of proteins that undergo physiological LLPS and pathological aggregation.
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Affiliation(s)
- Anna S Bock
- Graduate Program in Biotechnology, Brown University, Providence, Rhode Island, USA
| | - Anastasia C Murthy
- Graduate Program in Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island, USA
| | - Wai Shing Tang
- Graduate Program in Physics, Brown University, Providence, Rhode Island, USA
| | - Nina Jovic
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania, USA
| | - Frank Shewmaker
- Department of Biochemistry, Uniformed Services University, Bethesda, Maryland, USA
| | - Jeetain Mittal
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania, USA
| | - Nicolas L Fawzi
- The Robert J and Nancy D Carney Institute for Brain Science & Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, Rhode Island, USA
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15
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Bruschi M, Petretto A, Cama A, Pavanello M, Bartolucci M, Morana G, Ramenghi LA, Garré ML, Ghiggeri GM, Panfoli I, Candiano G. Potential biomarkers of childhood brain tumor identified by proteomics of cerebrospinal fluid from extraventricular drainage (EVD). Sci Rep 2021; 11:1818. [PMID: 33469081 PMCID: PMC7815722 DOI: 10.1038/s41598-020-80647-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 11/24/2020] [Indexed: 11/10/2022] Open
Abstract
Brain tumors are the most common solid tumors in childhood. There is the need for biomarkers of residual disease, therapy response and recurrence. Cerebrospinal fluid (CSF) is a source of brain tumor biomarkers. We analyzed the proteome of waste CSF from extraventricular drainage (EVD) from 29 children bearing different brain tumors and 17 controls needing EVD insertion for unrelated causes. 1598 and 1526 proteins were identified by liquid chromatography-coupled tandem mass spectrometry proteomics in CSF control and brain tumor patients, respectively, 263 and 191 proteins being exclusive of either condition. Bioinformatic analysis revealed promising protein biomarkers for the discrimination between control and tumor (TATA-binding protein-associated factor 15 and S100 protein B). Moreover, Thymosin beta-4 (TMSB4X) and CD109, and 14.3.3 and HSP90 alpha could discriminate among other brain tumors and low-grade gliomas plus glyoneuronal tumors/pilocytic astrocytoma, or embryonal tumors/medulloblastoma. Biomarkers were validated by ELISA assay. Our method was able to distinguish among brain tumor vs non-tumor/hemorrhagic conditions (controls) and to differentiate two large classes of brain tumors. Further prospective studies may assess whether the biomarkers proposed by our discovery approach can be identified in other bodily fluids, therefore less invasively, and are useful to guide therapy and predict recurrences.
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Affiliation(s)
- Maurizio Bruschi
- Laboratory of Molecular Nephrology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Andrea Petretto
- Core Facilities-Clinical Proteomics and Metabolomics, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Armando Cama
- Department of Neurosurgery, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Marco Pavanello
- Department of Neurosurgery, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Martina Bartolucci
- Core Facilities-Clinical Proteomics and Metabolomics, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Giovanni Morana
- Unit of Neuroradiology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | | | - Maria Luisa Garré
- Department of Neuroncology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Gian Marco Ghiggeri
- UO of Nephrology, Dialysis and Transplantation, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Isabella Panfoli
- Dipartimento di Farmacia (DIFAR), Università di Genova, V.le Benedetto XV, 3, 16132, Genoa, Italy.
| | - Giovanni Candiano
- Laboratory of Molecular Nephrology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
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16
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Zhang L, Sun P, Zhang Y, Xu Y, Sun Y. miR-182-5p inhibits the pathogenic Th17 response in experimental autoimmune uveitis mice via suppressing TAF15. Biochem Biophys Res Commun 2020; 529:784-792. [PMID: 32736708 DOI: 10.1016/j.bbrc.2020.06.073] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 06/15/2020] [Indexed: 11/27/2022]
Abstract
BACKGROUND CD4+ T helper 17 (Th17) cells play a contributory role in uveitis and other autoimmune disorders. However, less is understood about the contribution of microRNAs (miRNAs) in regulating the pathogenic Th17 response in uveitis. METHODS The in vivo experimental autoimmune uveitis (EAU) model was constructed in female C57BL/6 mice. Primary EAU mouse CD4+ T-cells and the murine T-cell line EL4 were used for in vitro experiments. miRNA mimic/inhibitor, lentiviral overexpression plasmids, and small interfering RNAs (siRNAs) were used to modulate miR-182-5p and TAF15 expression. CD4+ T-cells from healthy controls (HC, n = 15), active Behçet's disease with uveitis (BD, n = 15), or active sympathetic ophthalmia with uveitis (SO, n = 15) were analyzed for miR-182-5p, TAF15, and Th17 marker gene expression. RESULTS miR-182-5p was downregulated in EAU mouse-derived Th17 cells. miR-182-5p negatively regulated Th17 cell development in vitro. miR-182-5p mimic therapy in transplanted Th17 cells ameliorated EAU severity in vivo. Mechanistically, miR-182-5p directly inhibited the transcriptional initiator TATA-binding protein-associated factor 15 (TAF15, TAFII68). miR-182-5p's inhibition of TAF15 negatively regulated Th17 cell development by suppressing STAT3 phosphorylation. TAF15 and Th17 marker expression were positively correlated in CD4+ T-cells from BD and SO patients. CONCLUSION miR-182-5p mimic therapy inhibits the pathogenic Th17 response in EAU mice. miR-182-5p's inhibition of TAF15 negatively regulates Th17 cell development by suppressing STAT3 phosphorylation. As TAF15 shows a positive relationship with Th17 cell markers in uveitis patients, the miR-182-5p/TAF15 axis shows promise as a therapeutic target for uveitis.
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Affiliation(s)
| | - Peng Sun
- Refractive Surgery Center, Kunming Aier Eye Hospital, Kunming, China.
| | - Yu Zhang
- Department of Laboratory Medicine, First People's Hospital of Yunnan Province, Kunming, China; Medical College, Kunming University of Science and Technology, Kunming, China
| | - Ya Xu
- Department of Laboratory Medicine, First People's Hospital of Yunnan Province, Kunming, China
| | - Yi Sun
- Department of Laboratory Medicine, First People's Hospital of Yunnan Province, Kunming, China.
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17
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Singh AK, Kapoor V, Thotala D, Hallahan DE. TAF15 contributes to the radiation-inducible stress response in cancer. Oncotarget 2020; 11:2647-2659. [PMID: 32676166 PMCID: PMC7343639 DOI: 10.18632/oncotarget.27663] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 06/15/2020] [Indexed: 12/28/2022] Open
Abstract
Resistance to radiation therapy is a significant problem in the treatment of non-small cell lung cancer (NSCLC). There is an unmet need to discover new molecular targets for drug development in combination with standard of care cancer therapy. We found that TAF15 was radiation-inducible using phage-displayed peptide libraries. In this study, we report that overexpression of TAF15 is correlated with worsened survival in NSCLC patients. Radiation treatment led to surface induction of TAF15 in vitro and in vivo. We genetically silenced TAF15 which led to a significant reduction in proliferation of NSCLC cells. Cells depleted of TAF15 exhibited cell cycle arrest and enhanced apoptosis through activation and accumulation of p53. In combination with radiation, TAF15 knockdown led to a significant reduction in the surviving fraction of NSCLC cell lines. To determine the importance of TAF15 surface expression, we targeted TAF15 with an antibody. In combination with radiation, the anti-TAF15 antibody led to a reduction in the surviving fraction of cancer cells. These studies show that TAF15 is a radiation-inducible molecular target that is accessible to anti-cancer antibodies and enhances cell viability in response to radiation.
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Affiliation(s)
- Abhay Kumar Singh
- Department of Radiation Oncology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Vaishali Kapoor
- Department of Radiation Oncology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Dinesh Thotala
- Department of Radiation Oncology, Washington University in St. Louis, St. Louis, Missouri, USA.,Siteman Cancer Center, School of Medicine, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Dennis E Hallahan
- Department of Radiation Oncology, Washington University in St. Louis, St. Louis, Missouri, USA.,Siteman Cancer Center, School of Medicine, Washington University in St. Louis, St. Louis, Missouri, USA
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18
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Ruan X, Zheng J, Liu X, Liu Y, Liu L, Ma J, He Q, Yang C, Wang D, Cai H, Li Z, Liu J, Xue Y. lncRNA LINC00665 Stabilized by TAF15 Impeded the Malignant Biological Behaviors of Glioma Cells via STAU1-Mediated mRNA Degradation. MOLECULAR THERAPY-NUCLEIC ACIDS 2020; 20:823-840. [PMID: 32464546 PMCID: PMC7256440 DOI: 10.1016/j.omtn.2020.05.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 04/23/2020] [Accepted: 05/01/2020] [Indexed: 12/11/2022]
Abstract
Glioma is a brain cancer characterized by strong invasiveness with limited treatment options and poor prognosis. Recently, dysregulation of long non-coding RNAs (lncRNAs) has emerged as an important component in cellular processes and tumorigenesis. In this study, we demonstrated that TATA-box binding protein associated factor 15 (TAF15) and long intergenic non-protein coding RNA 665 (LINC00665) were both downregulated in glioma tissues and cells. TAF15 overexpression enhanced the stability of LINC00665, inhibiting malignant biological behaviors of glioma cells. Both metal regulatory transcription factor 1 (MTF1) and YY2 transcription factor (YY2) showed high expression levels in glioma tissues and cells, and their knockdown inhibited malignant progression. Mechanistically, overexpression of LINC00665 was confirmed to destabilize MTF1 and YY2 mRNA by interacting with STAU1, and knockdown of STAU1 could rescue the MTF1 and YY2 mRNA degradation caused by LINC00665 overexpression. G2 and S-phase expressed 1 (GTSE1) was identified as an oncogene in glioma, and knockdown of MTF1 or YY2 decreased the mRNA and protein expression levels of GTSE1 through direct binding to the GTSE1 promoter region. Our study highlights a key role of the TAF15/LINC00665/MTF1(YY2)/GTSE1 axis in modulating the malignant biological behaviors of glioma cells, suggesting novel mechanisms by which lncRNAs affect STAU1-mediated mRNA stability, which can inform new molecular therapies for glioma.
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Affiliation(s)
- Xuelei Ruan
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang 110122, China; Key Laboratory of Cell Biology, Ministry of Public Health of China, China Medical University, Shenyang 110122, China; Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang 110122, China
| | - Jian Zheng
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang 110004, China; Liaoning Clinical Medical Research Center in Nervous System Disease, Shenyang 110004, China; Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang 110004, China
| | - Xiaobai Liu
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang 110004, China; Liaoning Clinical Medical Research Center in Nervous System Disease, Shenyang 110004, China; Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang 110004, China
| | - Yunhui Liu
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang 110004, China; Liaoning Clinical Medical Research Center in Nervous System Disease, Shenyang 110004, China; Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang 110004, China
| | - Libo Liu
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang 110122, China; Key Laboratory of Cell Biology, Ministry of Public Health of China, China Medical University, Shenyang 110122, China; Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang 110122, China
| | - Jun Ma
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang 110122, China; Key Laboratory of Cell Biology, Ministry of Public Health of China, China Medical University, Shenyang 110122, China; Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang 110122, China
| | - Qianru He
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang 110122, China; Key Laboratory of Cell Biology, Ministry of Public Health of China, China Medical University, Shenyang 110122, China; Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang 110122, China
| | - Chunqing Yang
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang 110004, China; Liaoning Clinical Medical Research Center in Nervous System Disease, Shenyang 110004, China; Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang 110004, China
| | - Di Wang
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang 110004, China; Liaoning Clinical Medical Research Center in Nervous System Disease, Shenyang 110004, China; Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang 110004, China
| | - Heng Cai
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang 110004, China; Liaoning Clinical Medical Research Center in Nervous System Disease, Shenyang 110004, China; Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang 110004, China
| | - Zhen Li
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang 110004, China; Liaoning Clinical Medical Research Center in Nervous System Disease, Shenyang 110004, China; Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang 110004, China
| | - Jing Liu
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang 110004, China; Liaoning Clinical Medical Research Center in Nervous System Disease, Shenyang 110004, China; Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang 110004, China
| | - Yixue Xue
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang 110122, China; Key Laboratory of Cell Biology, Ministry of Public Health of China, China Medical University, Shenyang 110122, China; Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang 110122, China.
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19
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Loffreda A, Nizzardo M, Arosio A, Ruepp MD, Calogero RA, Volinia S, Galasso M, Bendotti C, Ferrarese C, Lunetta C, Rizzuti M, Ronchi AE, Mühlemann O, Tremolizzo L, Corti S, Barabino SML. miR-129-5p: A key factor and therapeutic target in amyotrophic lateral sclerosis. Prog Neurobiol 2020; 190:101803. [PMID: 32335272 DOI: 10.1016/j.pneurobio.2020.101803] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Revised: 04/02/2020] [Accepted: 04/09/2020] [Indexed: 12/30/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is a relentless and fatal neurological disease characterized by the selective degeneration of motor neurons. No effective therapy is available for this disease. Several lines of evidence indicate that alteration of RNA metabolism, including microRNA (miRNA) processing, is a relevant pathogenetic factor and a possible therapeutic target for ALS. Here, we showed that the abundance of components in the miRNA processing machinery is altered in a SOD1-linked cellular model, suggesting consequent dysregulation of miRNA biogenesis. Indeed, high-throughput sequencing of the small RNA fraction showed that among the altered miRNAs, miR-129-5p was increased in different models of SOD1-linked ALS and in peripheral blood cells of sporadic ALS patients. We demonstrated that miR-129-5p upregulation causes the downregulation of one of its targets: the RNA-binding protein ELAVL4/HuD. ELAVL4/HuD is predominantly expressed in neurons, where it controls several key neuronal mRNAs. Overexpression of pre-miR-129-1 inhibited neurite outgrowth and differentiation via HuD silencing in vitro, while its inhibition with an antagomir rescued the phenotype. Remarkably, we showed that administration of an antisense oligonucleotide (ASO) inhibitor of miR-129-5p to an ALS animal model, SOD1 (G93A) mice, result in a significant increase in survival and improved the neuromuscular phenotype in treated mice. These results identify miR-129-5p as a therapeutic target that is amenable to ASO modulation for the treatment of ALS patients.
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Affiliation(s)
- Alessia Loffreda
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Monica Nizzardo
- Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Neurology Unit, Milan, Italy
| | - Alessandro Arosio
- School of Medicine and Surgery and Milan Center for Neuroscience (NeuroMI), University of Milano-Bicocca, 20052 Monza, MB, Italy
| | - Marc-David Ruepp
- Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
| | - Raffaele A Calogero
- Department of Molecular Biotechnology and Health Sciences, University of Torino, 10126 Turin, Italy
| | - Stefano Volinia
- Department of Morphology, Surgery and Experimental Medicine, Università degli Studi, 44121 Ferrara, Italy
| | - Marco Galasso
- Department of Morphology, Surgery and Experimental Medicine, Università degli Studi, 44121 Ferrara, Italy
| | - Caterina Bendotti
- Department of Neuroscience, IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", 20156 Milan, Italy
| | - Carlo Ferrarese
- School of Medicine and Surgery and Milan Center for Neuroscience (NeuroMI), University of Milano-Bicocca, 20052 Monza, MB, Italy; Neurology Unit, San Gerardo Hospital, Monza, MB, Italy
| | - Christian Lunetta
- NEuroMuscular Omnicentre (NEMO), Fondazione Serena Onlus, 20162 Milan, Italy
| | - Mafalda Rizzuti
- Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Neurology Unit, Milan, Italy
| | - Antonella E Ronchi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Oliver Mühlemann
- Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
| | - Lucio Tremolizzo
- School of Medicine and Surgery and Milan Center for Neuroscience (NeuroMI), University of Milano-Bicocca, 20052 Monza, MB, Italy; Neurology Unit, San Gerardo Hospital, Monza, MB, Italy
| | - Stefania Corti
- Dino Ferrari Centre, Neuroscience Section, Department of Pathophysiology and Transplantation (DEPT), University of Milan, Italy; Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Neurology Unit, Milan, Italy
| | - Silvia M L Barabino
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
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20
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He B, Yang N, Man CH, Ng NK, Cher C, Leung H, Kan LL, Cheng BY, Lam SS, Wang ML, Zhang C, Kwok H, Cheng G, Sharma R, Ma AC, So CE, Kwong Y, Leung AY. Follistatin is a novel therapeutic target and biomarker in FLT3/ITD acute myeloid leukemia. EMBO Mol Med 2020; 12:e10895. [PMID: 32134197 PMCID: PMC7136967 DOI: 10.15252/emmm.201910895] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 02/07/2020] [Accepted: 02/14/2020] [Indexed: 12/12/2022] Open
Abstract
Internal tandem duplication of Fms-like tyrosine kinase 3 (FLT3/ITD) occurs in about 30% of acute myeloid leukemia (AML) and is associated with poor response to conventional treatment and adverse outcome. Here, we reported that human FLT3/ITD expression led to axis duplication and dorsalization in about 50% of zebrafish embryos. The morphologic phenotype was accompanied by ectopic expression of a morphogen follistatin (fst) during early embryonic development. Increase in fst expression also occurred in adult FLT3/ITD-transgenic zebrafish, Flt3/ITD knock-in mice, and human FLT3/ITD AML cells. Overexpression of human FST317 and FST344 isoforms enhanced clonogenicity and leukemia engraftment in xenotransplantation model via RET, IL2RA, and CCL5 upregulation. Specific targeting of FST by shRNA, CRISPR/Cas9, or antisense oligo inhibited leukemic growth in vitro and in vivo. Importantly, serum FST positively correlated with leukemia engraftment in FLT3/ITD AML patient-derived xenograft mice and leukemia blast percentage in primary AML patients. In FLT3/ITD AML patients treated with FLT3 inhibitor quizartinib, serum FST levels correlated with clinical response. These observations supported FST as a novel therapeutic target and biomarker in FLT3/ITD AML.
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Affiliation(s)
- Bai‐Liang He
- Division of HematologyDepartment of MedicineLi Ka Shing Faculty of MedicineThe University of Hong KongHong Kong SARChina
- Guangdong Provincial Key Laboratory of Biomedical ImagingThe Fifth Affiliated HospitalSun Yat‐sen UniversityZhuhaiGuangdong ProvinceChina
| | - Ning Yang
- Division of HematologyDepartment of MedicineLi Ka Shing Faculty of MedicineThe University of Hong KongHong Kong SARChina
| | - Cheuk Him Man
- Division of HematologyDepartment of MedicineLi Ka Shing Faculty of MedicineThe University of Hong KongHong Kong SARChina
| | - Nelson Ka‐Lam Ng
- Division of HematologyDepartment of MedicineLi Ka Shing Faculty of MedicineThe University of Hong KongHong Kong SARChina
| | - Chae‐Yin Cher
- Division of HematologyDepartment of MedicineLi Ka Shing Faculty of MedicineThe University of Hong KongHong Kong SARChina
| | - Ho‐Ching Leung
- Division of HematologyDepartment of MedicineLi Ka Shing Faculty of MedicineThe University of Hong KongHong Kong SARChina
| | - Leo Lai‐Hok Kan
- Division of HematologyDepartment of MedicineLi Ka Shing Faculty of MedicineThe University of Hong KongHong Kong SARChina
| | - Bowie Yik‐Ling Cheng
- Division of HematologyDepartment of MedicineLi Ka Shing Faculty of MedicineThe University of Hong KongHong Kong SARChina
| | - Stephen Sze‐Yuen Lam
- Division of HematologyDepartment of MedicineLi Ka Shing Faculty of MedicineThe University of Hong KongHong Kong SARChina
| | - Michelle Lu‐Lu Wang
- Division of HematologyDepartment of MedicineLi Ka Shing Faculty of MedicineThe University of Hong KongHong Kong SARChina
| | - Chun‐Xiao Zhang
- Division of HematologyDepartment of MedicineLi Ka Shing Faculty of MedicineThe University of Hong KongHong Kong SARChina
| | - Hin Kwok
- Centre for Genomic SciencesThe University of Hong KongHong Kong SARChina
| | - Grace Cheng
- Centre for Genomic SciencesThe University of Hong KongHong Kong SARChina
| | - Rakesh Sharma
- Centre for Genomic SciencesThe University of Hong KongHong Kong SARChina
| | - Alvin Chun‐Hang Ma
- Department of Health Technology and InformaticsThe Hong Kong Polytechnic UniversityHong Kong SARChina
| | - Chi‐Wai Eric So
- Leukemia and Stem Cell Biology GroupDivision of Cancer StudiesDepartment of Hematological MedicineKing's College LondonLondonUK
| | - Yok‐Lam Kwong
- Division of HematologyDepartment of MedicineLi Ka Shing Faculty of MedicineThe University of Hong KongHong Kong SARChina
| | - Anskar Yu‐Hung Leung
- Division of HematologyDepartment of MedicineLi Ka Shing Faculty of MedicineThe University of Hong KongHong Kong SARChina
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21
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Masuda A, Kawachi T, Takeda JI, Ohkawara B, Ito M, Ohno K. tRIP-seq reveals repression of premature polyadenylation by co-transcriptional FUS-U1 snRNP assembly. EMBO Rep 2020; 21:e49890. [PMID: 32189459 DOI: 10.15252/embr.201949890] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 02/19/2020] [Accepted: 02/23/2020] [Indexed: 12/27/2022] Open
Abstract
RNA processing occurs co-transcriptionally through the dynamic recruitment of RNA processing factors to RNA polymerase II (RNAPII). However, transcriptome-wide identification of protein-RNA interactions specifically assembled on transcribing RNAPII is challenging. Here, we develop the targeted RNA immunoprecipitation sequencing (tRIP-seq) method that detects protein-RNA interaction sites in thousands of cells. The high sensitivity of tRIP-seq enables identification of protein-RNA interactions at functional subcellular levels. Application of tRIP-seq to the FUS-RNA complex in the RNAPII machinery reveals that FUS binds upstream of alternative polyadenylation (APA) sites of nascent RNA bound to RNAPII, which retards RNAPII and suppresses the recognition of the polyadenylation signal by CPSF. Further tRIP-seq analyses demonstrate that the repression of APA is achieved by a complex composed of FUS and U1 snRNP on RNAPII, but not by either one alone. Moreover, our analysis reveals that FUS mutations in familial amyotrophic lateral sclerosis (ALS) that impair the FUS-U1 snRNP interaction aberrantly activate the APA sites. tRIP-seq provides new insights into the regulatory mechanism of co-transcriptional RNA processing by RNA processing factors.
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Affiliation(s)
- Akio Masuda
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Toshihiko Kawachi
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Jun-Ichi Takeda
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Bisei Ohkawara
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Mikako Ito
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kinji Ohno
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan
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22
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TRPM2-AS promotes cancer cell proliferation through control of TAF15. Int J Biochem Cell Biol 2019; 120:105683. [PMID: 31887411 DOI: 10.1016/j.biocel.2019.105683] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 12/23/2019] [Accepted: 12/26/2019] [Indexed: 12/19/2022]
Abstract
BACKGROUND Colorectal cancer (CRC) ranks the third among all common malignancy worldwide. Long noncoding RNAs (lncRNAs) have been demonstrated as implicated in CRC, but the roles of many lncRNAs in CRC remain unclear. Exploration of lncRNA TRMP2-AS and its nearby gene in CRC progress was the focus of current study. METHODS The expression of TRPM2-AS and its nearby mRNA TRPM2 was measured by using RT-qPCR. The protein levels of TRPM2 and TAF15 were determined using western blot. Cell proliferation was detected by using CCK-8, colony formation and EdU assays. The interaction between TAF15 and TRPM2-AS or TRPM2 was evaluated by RNA pull-down and RIP assays. The TRPM2 mRNA stability was probed using the transcriptional inhibitor Actinomycin D. RESULTS TRPM2-AS was significantly upregulated in CRC cells. Knock-down of TRPM2-AS inhibited CRC cell proliferation. Mechanically, TRPM2-AS directly interacted with RNA-binding protein (RBP) TAF15 and thus maintained the mRNA stability of TRPM2. TRPM2 was a prerequisite for TRPM2-AS to exert its promoting function in CRC cell proliferation. CONCLUSION This research demonstrated that TRPM2-AS facilitated proliferation of CRC cells by enhancing TAF15-mediated mRNA stability of TRPM2, unmasking the role of TRPM2-AS in CRC.
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23
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Gennaro VJ, Wedegaertner H, McMahon SB. Interaction between the BAG1S isoform and HSP70 mediates the stability of anti-apoptotic proteins and the survival of osteosarcoma cells expressing oncogenic MYC. BMC Cancer 2019; 19:258. [PMID: 30902071 PMCID: PMC6429775 DOI: 10.1186/s12885-019-5454-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 03/12/2019] [Indexed: 02/07/2023] Open
Abstract
Background The oncoprotein MYC has the dual capacity to drive cell cycle progression or induce apoptosis, depending on the cellular context. BAG1 was previously identified as a transcriptional target of MYC that functions as a critical determinant of this cell fate decision. The BAG1 protein is expressed as multiple isoforms, each having an array of distinct biochemical functions; however, the specific effector function of BAG1 that directs MYC-dependent cell survival has not been defined. Methods In our studies the human osteosarcoma line U2OS expressing a conditional MYC-ER allele was used to induce oncogenic levels of MYC. We interrogated MYC-driven survival processes by modifying BAG1 protein expression. The function of the separate BAG1 isoforms was investigated by depleting cells of endogenous BAG1 and reintroducing the distinct isoforms. Flow cytometry and immunoblot assays were performed to analyze the effect of specific BAG1 isoforms on MYC-dependent apoptosis. These experiments were repeated to determine the role of the HSP70 chaperone complex in BAG1 survival processes. Finally, a proteomic approach was used to identify a set of specific pro-survival proteins controlled by the HSP70/BAG1 complex. Results Loss of BAG1 resulted in robust MYC-induced apoptosis. Expression of the larger isoforms of BAG1, BAG1L and BAG1M, were insufficient to rescue survival in cells with oncogenic levels of MYC. Alternatively, reintroduction of BAG1S significantly reduced the level of apoptosis. Manipulation of the BAG1S interaction with HSP70 revealed that BAG1S provides its pro-survival function by serving as a cofactor for the HSP70 chaperone complex. Via a proteomic approach we identified and classified a set of pro-survival proteins controlled by this HSP70/BAG1 chaperone complex that contribute to the BAG1 anti-apoptotic phenotype. Conclusions The small isoform of BAG1, BAG1S, in cooperation with the HSP70 chaperone complex, selectively mediates cell survival in MYC overexpressing tumor cells. We identified a set of specific pro-survival clients controlled by the HSP70/BAG1S chaperone complex. These clients define new nodes that could be therapeutically targeted to disrupt the survival of tumor cells driven by MYC activation. With MYC overexpression occurring in most human cancers, this introduces new strategies for cancer treatment. Electronic supplementary material The online version of this article (10.1186/s12885-019-5454-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Victoria J Gennaro
- Department of Biochemistry and Molecular Biology Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Helen Wedegaertner
- Department of Biochemistry and Molecular Biology Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Steven B McMahon
- Department of Biochemistry and Molecular Biology Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA.
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24
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S-adenosyl-methionine (SAM) alters the transcriptome and methylome and specifically blocks growth and invasiveness of liver cancer cells. Oncotarget 2017; 8:111866-111881. [PMID: 29340097 PMCID: PMC5762365 DOI: 10.18632/oncotarget.22942] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 07/29/2017] [Indexed: 12/17/2022] Open
Abstract
S-adenosyl methionine (SAM) is a ubiquitous methyl donor that was reported to have chemo- protective activity against liver cancer, however the molecular footprint of SAM is unknown. We show here that SAM selectively inhibits growth, transformation and invasiveness of hepatocellular carcinoma cell lines but not normal primary liver cells. Analysis of the transcriptome of SAM treated and untreated liver cancer cell lines HepG2 and SKhep1 and primary liver cells reveals pathways involved in cancer and metastasis that are upregulated in cancer cells and are downregulated by SAM. Analysis of the methylome using bisulfite mapping of captured promoters and enhancers reveals that SAM hyper-methylates and downregulates genes in pathways of growth and metastasis that are upregulated in liver cancer cells. Depletion of two SAM downregulated genes STMN1 and TAF15 reduces cellular transformation and invasiveness, providing evidence that SAM targets are genes important for cancer growth and invasiveness. Taken together these data provide a molecular rationale for SAM as an anticancer agent.
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25
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Hawley ZCE, Campos-Melo D, Droppelmann CA, Strong MJ. MotomiRs: miRNAs in Motor Neuron Function and Disease. Front Mol Neurosci 2017; 10:127. [PMID: 28522960 PMCID: PMC5415563 DOI: 10.3389/fnmol.2017.00127] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Accepted: 04/18/2017] [Indexed: 12/12/2022] Open
Abstract
MiRNAs are key regulators of the mammalian transcriptome that have been increasingly linked to degenerative diseases of the motor neurons. Although many of the miRNAs currently incriminated as participants in the pathogenesis of these diseases are also important to the normal development and function of motor neurons, at present there is no knowledge of the complete miRNA profile of motor neurons. In this review, we examine the current understanding with respect to miRNAs that are specifically required for motor neuron development, function and viability, and provide evidence that these should be considered as a functional network of miRNAs which we have collectively termed MotomiRs. We will also summarize those MotomiRs currently known to be associated with both amyotrophic lateral sclerosis (ALS) and spinal muscular atrophy (SMA), and discuss their potential use as biomarkers.
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Affiliation(s)
- Zachary C E Hawley
- Molecular Medicine Group, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western UniversityLondon, ON, Canada
| | - Danae Campos-Melo
- Molecular Medicine Group, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western UniversityLondon, ON, Canada
| | - Cristian A Droppelmann
- Molecular Medicine Group, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western UniversityLondon, ON, Canada
| | - Michael J Strong
- Molecular Medicine Group, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western UniversityLondon, ON, Canada.,Department of Pathology, Schulich School of Medicine and Dentistry, Western UniversityLondon, ON, Canada.,Department of Clinical Neurological Sciences, Schulich School of Medicine and Dentistry, Western UniversityLondon, ON, Canada
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26
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Kaplan A, Akalin Ciftci G, Kutlu HM. The apoptotic and genomic studies on A549 cell line induced by silver nitrate. Tumour Biol 2017; 39:1010428317695033. [PMID: 28381165 DOI: 10.1177/1010428317695033] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Lung cancer is the leading cause of male cancer deaths worldwide. Metal-based anticancer drugs have evolved significantly during the past decades. Recently, silver ions have been investigated for their anticancer effects. We aimed to study the time-course cytotoxic effects of silver nitrate on A549 adenocarcinomic human alveolar basal epithelial cells to provide insights into the molecular-level understanding of growth suppression mechanism involved in apoptosis. The influences of silver nitrate were studied via MTT assay, flow cytometry, immunocytochemical, confocal and transmission electron microscopy, and microarray assays. Silver nitrate showed inhibitory effects against A549 cells in a dose- and time-dependent manner for 24, 48, and 72 h and induced apoptosis. The early and late apoptotic cells and depolarized mitochondrial membrane potential were determined by the half-maximal inhibitory concentration (IC50) value of silver nitrate treated for 72 h. But cysteinyl aspartate proteinase-3 was not activated for 72 h. Furthermore, IC50 value of silver nitrate also induced apoptosis according to immunocytochemical assays for 72 h. The downregulated CCNY, HNRNPL, ASF1B, PIAS4, HNRNPH1, EIF2C2, TAF15, FOXC1, LEP, and PCB2 genes administered with silver nitrate IC50 were identified as apoptosis-leading genes. Silver nitrate may be a suitable therapeutic agent against lung cancer.
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Affiliation(s)
- Ayse Kaplan
- 1 Faculty of Science, Department of Biology, Anadolu University, Eskişehir, Turkey
| | - Gulsen Akalin Ciftci
- 2 Faculty of Pharmacy, Department of Biochemistry, Anadolu University, Eskişehir, Turkey
| | - Hatice Mehtap Kutlu
- 1 Faculty of Science, Department of Biology, Anadolu University, Eskişehir, Turkey
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27
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Chau BL, Ng KP, Li KKC, Lee KA. RGG boxes within the TET/FET family of RNA-binding proteins are functionally distinct. Transcription 2016; 7:141-51. [PMID: 27159574 PMCID: PMC4984686 DOI: 10.1080/21541264.2016.1183071] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 04/20/2016] [Accepted: 04/21/2016] [Indexed: 01/08/2023] Open
Abstract
The multi-functional TET (TAF15/EWS/TLS) or FET (FUS/EWS/TLS) protein family of higher organisms harbor a transcriptional-activation domain (EAD) and an RNA-binding domain (RBD). The transcriptional activation function is, however, only revealed in oncogenic TET-fusion proteins because in native TET proteins it is auto-repressed by RGG-boxes within the TET RBD. Auto-repression is suggested to involve direct cation-pi interactions between multiple Arg residues within RGG boxes and EAD aromatics. Via analysis of TET transcriptional activity in different organisms, we report herein that repression is not autonomous but instead requires additional trans-acting factors. This finding is not supportive of a proposed model whereby repression occurs via a simple intramolecular EAD/RGG-box interaction. We also show that RGG-boxes present within reiterated YGGDRGG repeats that are unique to TAF15, are defective for repression due to the conserved Asp residue. Thus, RGG boxes within TET proteins can be functionally distinguished. While our results show that YGGDRGG repeats are not involved in TAF15 auto-repression, their remarkable number and conservation strongly suggest that they may confer specialized properties to TAF15 and thus contribute to functional differentiation within the TET/FET protein family.
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Affiliation(s)
- Bess Ling Chau
- Division of Life Science, The Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong S.A.R., China
| | - King Pan Ng
- Division of Life Science, The Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong S.A.R., China
| | - Kim K C Li
- Division of Life Science, The Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong S.A.R., China
| | - Kevin A.W. Lee
- Division of Life Science, The Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong S.A.R., China
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28
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Preusse M, Marr C, Saunders S, Maticzka D, Lickert H, Backofen R, Theis F. SimiRa: A tool to identify coregulation between microRNAs and RNA-binding proteins. RNA Biol 2016; 12:998-1009. [PMID: 26383775 PMCID: PMC4615630 DOI: 10.1080/15476286.2015.1068496] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
microRNAs and microRNA-independent RNA-binding proteins are 2 classes of post-transcriptional regulators that have been shown to cooperate in gene-expression regulation. We compared the genome-wide target sets of microRNAs and RBPs identified by recent CLIP-Seq technologies, finding that RBPs have distinct target sets and favor gene interaction network hubs. To identify microRNAs and RBPs with a similar functional context, we developed simiRa, a tool that compares enriched functional categories such as pathways and GO terms. We applied simiRa to the known functional cooperation between Pumilio family proteins and miR-221/222 in the regulation of tumor supressor gene p27 and show that the cooperation is reflected by similar enriched categories but not by target genes. SimiRa also predicts possible cooperation of microRNAs and RBPs beyond direct interaction on the target mRNA for the nuclear RBP TAF15. To further facilitate research into cooperation of microRNAs and RBPs, we made simiRa available as a web tool that displays the functional neighborhood and similarity of microRNAs and RBPs: http://vsicb-simira.helmholtz-muenchen.de.
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Affiliation(s)
- Martin Preusse
- a Helmholtz Zentrum München - German Research Center for Environmental Health; Institute of Computational Biology ; Neuherberg , Germany.,b Helmholtz Zentrum München - German Research Center for Environmental Health; Institute of Diabetes and Regeneration Research ; Neuherberg , Germany
| | - Carsten Marr
- a Helmholtz Zentrum München - German Research Center for Environmental Health; Institute of Computational Biology ; Neuherberg , Germany
| | - Sita Saunders
- c Bioinformatics; Department of Computer Science; University of Freiburg ; Freiburg , Germany
| | - Daniel Maticzka
- c Bioinformatics; Department of Computer Science; University of Freiburg ; Freiburg , Germany
| | - Heiko Lickert
- b Helmholtz Zentrum München - German Research Center for Environmental Health; Institute of Diabetes and Regeneration Research ; Neuherberg , Germany.,d Medical Faculty; Technische Universität München ; Munich , Germany
| | - Rolf Backofen
- c Bioinformatics; Department of Computer Science; University of Freiburg ; Freiburg , Germany.,e BIOSS Center for Biological Signaling Studies; Cluster of Excellence; University of Freiburg ; Freiburg , Germany
| | - Fabian Theis
- b Helmholtz Zentrum München - German Research Center for Environmental Health; Institute of Diabetes and Regeneration Research ; Neuherberg , Germany.,f Technische Universität München; Center for Mathematics; Chair of Mathematical Modeling of Biological Systems ; Garching , Germany
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29
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Kume K, Ikeda M, Miura S, Ito K, Sato KA, Ohmori Y, Endo F, Katagiri H, Ishida K, Ito C, Iwaya T, Nishizuka SS. α-Amanitin Restrains Cancer Relapse from Drug-Tolerant Cell Subpopulations via TAF15. Sci Rep 2016; 6:25895. [PMID: 27181033 PMCID: PMC4867652 DOI: 10.1038/srep25895] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 04/25/2016] [Indexed: 12/30/2022] Open
Abstract
Cancer relapse occurs with substantial frequency even after treatment with curative intent. Here we studied drug-tolerant colonies (DTCs), which are subpopulations of cancer cells that survive in the presence of drugs. Proteomic characterization of DTCs identified stemness- and epithelial-dominant subpopulations, but functional screening suggested that DTC formation was regulated at the transcriptional level independent from protein expression patterns. We consistently found that α-amanitin, an RNA polymerase II (RNAPII) inhibitor, effectively inhibited DTCs by suppressing TAF15 expression, which binds to RNA to modulate transcription and RNA processing. Sequential administration of α-amanitin and cisplatin extended overall survival in a cancer-relapse mouse model, namely peritonitis carcinomatosa. Therefore, post-treatment cancer relapse may occur through non-distinct subpopulations and may be effectively prevented by α-amanitin to disrupt transcriptional machinery, including TAF15.
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Affiliation(s)
- Kohei Kume
- Molecular Therapeutics Laboratory, Department of Surgery, Iwate Medical University School of Medicine, Morioka, Iwate 020-8505, Japan.,MIAST (Medical Innovation by Advanced Science and Technology) project, Iwate Medical University School of Medicine, Morioka, Iwate 020-8505, Japan.,Institute of Biomedical Science, Iwate Medical University, Yahaba, Iwate 028-3694, Japan
| | - Miyuki Ikeda
- Molecular Therapeutics Laboratory, Department of Surgery, Iwate Medical University School of Medicine, Morioka, Iwate 020-8505, Japan
| | - Sawako Miura
- Molecular Therapeutics Laboratory, Department of Surgery, Iwate Medical University School of Medicine, Morioka, Iwate 020-8505, Japan
| | - Kohei Ito
- Molecular Therapeutics Laboratory, Department of Surgery, Iwate Medical University School of Medicine, Morioka, Iwate 020-8505, Japan
| | - Kei A Sato
- Molecular Therapeutics Laboratory, Department of Surgery, Iwate Medical University School of Medicine, Morioka, Iwate 020-8505, Japan
| | - Yukimi Ohmori
- Molecular Therapeutics Laboratory, Department of Surgery, Iwate Medical University School of Medicine, Morioka, Iwate 020-8505, Japan.,MIAST (Medical Innovation by Advanced Science and Technology) project, Iwate Medical University School of Medicine, Morioka, Iwate 020-8505, Japan
| | - Fumitaka Endo
- Molecular Therapeutics Laboratory, Department of Surgery, Iwate Medical University School of Medicine, Morioka, Iwate 020-8505, Japan
| | - Hirokatsu Katagiri
- Molecular Therapeutics Laboratory, Department of Surgery, Iwate Medical University School of Medicine, Morioka, Iwate 020-8505, Japan
| | - Kaoru Ishida
- Molecular Therapeutics Laboratory, Department of Surgery, Iwate Medical University School of Medicine, Morioka, Iwate 020-8505, Japan
| | - Chie Ito
- Molecular Therapeutics Laboratory, Department of Surgery, Iwate Medical University School of Medicine, Morioka, Iwate 020-8505, Japan
| | - Takeshi Iwaya
- Molecular Therapeutics Laboratory, Department of Surgery, Iwate Medical University School of Medicine, Morioka, Iwate 020-8505, Japan
| | - Satoshi S Nishizuka
- Molecular Therapeutics Laboratory, Department of Surgery, Iwate Medical University School of Medicine, Morioka, Iwate 020-8505, Japan.,MIAST (Medical Innovation by Advanced Science and Technology) project, Iwate Medical University School of Medicine, Morioka, Iwate 020-8505, Japan.,Institute of Biomedical Science, Iwate Medical University, Yahaba, Iwate 028-3694, Japan
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Kashyap M, Ganguly AK, Bhavesh NS. Structural delineation of stem-loop RNA binding by human TAF15 protein. Sci Rep 2015; 5:17298. [PMID: 26612539 PMCID: PMC4661536 DOI: 10.1038/srep17298] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 10/28/2015] [Indexed: 11/09/2022] Open
Abstract
Human TATA binding protein associated factor 2 N (TAF15) and Fused in sarcoma (FUS) are nucleic acid binding proteins belonging to the conserved FET family of proteins. They are involved in diverse processes such as pre-mRNA splicing, mRNA transport, and DNA binding. The absence of information regarding the structural mechanism employed by the FET family in recognizing and discriminating their cognate and non-cognate RNA targets has hampered the attainment of consensus on modes of protein-RNA binding for this family. Our study provides a molecular basis of this RNA recognition using a combination of solution-state NMR spectroscopy, calorimetry, docking and molecular dynamics simulation. Analysis of TAF15-RRM solution structure and its binding with stem-loop RNA has yielded conclusive evidence of a non-canonical mode of RNA recognition. Rather than classical stacking interactions that occur across nitrogen bases and aromatic amino acids on ribonucleoprotein sites, moderate-affinity hydrogen bonding network between the nitrogen bases in the stem-loop RNA and a concave face on the RRM surface primarily mediate TAF15-RRM RNA interaction. We have compared the binding affinities across a set of single-stranded RNA oligonucleotides to conclusively establish that RNA binding is dependent upon structural elements in the RNA rather than sequence.
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Affiliation(s)
- Maruthi Kashyap
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, 110 067, New Delhi, India
| | - Akshay Kumar Ganguly
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, 110 067, New Delhi, India
| | - Neel Sarovar Bhavesh
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, 110 067, New Delhi, India
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31
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RNA-Binding Proteins in the Regulation of miRNA Activity: A Focus on Neuronal Functions. Biomolecules 2015; 5:2363-87. [PMID: 26437437 PMCID: PMC4693239 DOI: 10.3390/biom5042363] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 09/16/2015] [Accepted: 09/23/2015] [Indexed: 02/07/2023] Open
Abstract
Posttranscriptional modifications of messenger RNAs (mRNAs) are key processes in the fine-tuning of cellular homeostasis. Two major actors in this scenario are RNA binding proteins (RBPs) and microRNAs (miRNAs) that together play important roles in the biogenesis, turnover, translation and localization of mRNAs. This review will highlight recent advances in the understanding of the role of RBPs in the regulation of the maturation and the function of miRNAs. The interplay between miRNAs and RBPs is discussed specifically in the context of neuronal development and function.
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32
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Clinically acceptable colchicine concentrations have potential for the palliative treatment of human cholangiocarcinoma. Kaohsiung J Med Sci 2015; 31:229-34. [PMID: 25910557 DOI: 10.1016/j.kjms.2015.01.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 01/15/2015] [Accepted: 01/19/2015] [Indexed: 01/16/2023] Open
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Duggimpudi S, Larsson E, Nabhani S, Borkhardt A, Hoell JI. The cell cycle regulator CCDC6 is a key target of RNA-binding protein EWS. PLoS One 2015; 10:e0119066. [PMID: 25751255 PMCID: PMC4353705 DOI: 10.1371/journal.pone.0119066] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 01/27/2015] [Indexed: 12/27/2022] Open
Abstract
Genetic translocation of EWSR1 to ETS transcription factor coding region is considered as primary cause for Ewing sarcoma. Previous studies focused on the biology of chimeric transcription factors formed due to this translocation. However, the physiological consequences of heterozygous EWSR1 loss in these tumors have largely remained elusive. Previously, we have identified various mRNAs bound to EWS using PAR-CLIP. In this study, we demonstrate CCDC6, a known cell cycle regulator protein, as a novel target regulated by EWS. siRNA mediated down regulation of EWS caused an elevated apoptosis in cells in a CCDC6-dependant manner. This effect was rescued upon re-expression of CCDC6. This study provides evidence for a novel functional link through which wild-type EWS operates in a target-dependant manner in Ewing sarcoma.
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Affiliation(s)
- Sujitha Duggimpudi
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Center for Child and Adolescent Health, Heinrich Heine University, Medical Faculty, Duesseldorf, Germany
| | - Erik Larsson
- Department of Medical Biochemistry and Cell biology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Sweden
| | - Schafiq Nabhani
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Center for Child and Adolescent Health, Heinrich Heine University, Medical Faculty, Duesseldorf, Germany
| | - Arndt Borkhardt
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Center for Child and Adolescent Health, Heinrich Heine University, Medical Faculty, Duesseldorf, Germany
| | - Jessica I Hoell
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Center for Child and Adolescent Health, Heinrich Heine University, Medical Faculty, Duesseldorf, Germany
- * E-mail:
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Abstract
Members of the FET protein family, consisting of FUS, EWSR1, and TAF15, bind to RNA and contribute to the control of transcription, RNA processing, and the cytoplasmic fates of messenger RNAs in metazoa. FET proteins can also bind DNA, which may be important in transcription and DNA damage responses. FET proteins are of medical interest because chromosomal rearrangements of their genes promote various sarcomas and because point mutations in FUS or TAF15 can cause neurodegenerative diseases such as amyotrophic lateral sclerosis and frontotemporal lobar dementia. Recent results suggest that both the normal and pathological effects of FET proteins are modulated by low-complexity or prion-like domains, which can form higher-order assemblies with novel interaction properties. Herein, we review FET proteins with an emphasis on how the biochemical properties of FET proteins may relate to their biological functions and to pathogenesis.
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Affiliation(s)
- Jacob C Schwartz
- Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, and BioFrontiers Institute, University of Colorado, Boulder, Colorado 80309; , ,
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35
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Chen TC, Sung ML, Kuo HC, Chien SJ, Yen CK, Chen CN. Differential regulation of human aortic smooth muscle cell proliferation by monocyte-derived macrophages from diabetic patients. PLoS One 2014; 9:e113752. [PMID: 25409512 PMCID: PMC4237499 DOI: 10.1371/journal.pone.0113752] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 10/28/2014] [Indexed: 11/18/2022] Open
Abstract
Macrophage accumulation in the arterial wall and smooth muscle cell (SMC) proliferation are features of type 2 diabetes mellitus (DM) and its vascular complications. However, the effects of diabetic monocyte-derived macrophages on vascular SMC proliferation are not clearly understood. In the present study, we investigated the pro-proliferative effect of macrophages isolated from DM patients on vascular SMCs. Macrophage-conditioned media (MCM) were prepared from macrophages isolated from DM patients. DM-MCM treatment induced HASMC proliferation, decreased p21(Cip1) and p27(Kip1) expressions, and increased microRNA (miR)-17-5p and miR-221 expressions. Inhibition of either miR-17-5p or miR-221 inhibited DM-MCM-induced cell proliferation. Inhibition of miR-17-5p abolished DM-MCM-induced p21(Cip1) down-regulation; and inhibition of miR-221 attenuated the DM-MCM-induced p27(Kip1) down-regulation. Furthermore, blocking assays demonstrated that PDGF-CC in DM-MCM is the major mediators of cell proliferation in SMCs. In conclusion, our present data support the hypothesis that SMC proliferation stimulated by macrophages may play critical roles in vascular complications in DM patients and suggest a new mechanism by which arterial disease is accelerated in diabetes.
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MESH Headings
- Adult
- Aorta/cytology
- Becaplermin
- Cell Proliferation/drug effects
- Cells, Cultured
- Culture Media, Conditioned/pharmacology
- Cyclin-Dependent Kinase Inhibitor p21/metabolism
- Cyclin-Dependent Kinase Inhibitor p27/metabolism
- Diabetes Mellitus, Type 2/metabolism
- Diabetes Mellitus, Type 2/pathology
- Down-Regulation/drug effects
- Enzyme-Linked Immunosorbent Assay
- Humans
- Lymphokines/analysis
- Macrophages/cytology
- Macrophages/immunology
- Macrophages/metabolism
- MicroRNAs/metabolism
- Middle Aged
- Monocytes/cytology
- Monocytes/immunology
- Monocytes/metabolism
- Muscle, Smooth, Vascular/cytology
- Muscle, Smooth, Vascular/drug effects
- Muscle, Smooth, Vascular/metabolism
- Osteopontin/genetics
- Osteopontin/metabolism
- Platelet-Derived Growth Factor/analysis
- Proto-Oncogene Proteins c-sis/analysis
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Affiliation(s)
- Te-Chuan Chen
- Division of Nephrology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Mao-Ling Sung
- Department of Cardiology, St. Martin De Porres Hospital, Chiayi, Taiwan
| | - Hsing-Chun Kuo
- Institute of Nursing and Department of Nursing, Chang Gung University of Science and Technology, Chronic Diseases and Health Promotion Research Center, CGUST, Taoyuan, Taiwan
- Research Center for Industry of Human Ecology, Chang Gung University of Science and Technology, Taoyuan, Taiwan
| | - Shao-Ju Chien
- Division of Pediatric Cardiology, Department of Pediatrics, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Chia-Kuang Yen
- Department of Cardiology, St. Martin De Porres Hospital, Chiayi, Taiwan
| | - Cheng-Nan Chen
- Department of Biochemical Science and Technology, National Chiayi University, Chiayi, Taiwan
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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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Droppelmann CA, Campos-Melo D, Ishtiaq M, Volkening K, Strong MJ. RNA metabolism in ALS: When normal processes become pathological. Amyotroph Lateral Scler Frontotemporal Degener 2014; 15:321-36. [DOI: 10.3109/21678421.2014.881377] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Koestler DC, Chalise P, Cicek MS, Cunningham JM, Armasu S, Larson MC, Chien J, Block M, Kalli KR, Sellers TA, Fridley BL, Goode EL. Integrative genomic analysis identifies epigenetic marks that mediate genetic risk for epithelial ovarian cancer. BMC Med Genomics 2014; 7:8. [PMID: 24479488 PMCID: PMC3916313 DOI: 10.1186/1755-8794-7-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Accepted: 01/22/2014] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Both genetic and epigenetic factors influence the development and progression of epithelial ovarian cancer (EOC). However, there is an incomplete understanding of the interrelationship between these factors and the extent to which they interact to impact disease risk. In the present study, we aimed to gain insight into this relationship by identifying DNA methylation marks that are candidate mediators of ovarian cancer genetic risk. METHODS We used 214 cases and 214 age-matched controls from the Mayo Clinic Ovarian Cancer Study. Pretreatment, blood-derived DNA was profiled for genome-wide methylation (Illumina Infinium HumanMethylation27 BeadArray) and single nucleotide polymorphisms (SNPs, Illumina Infinium HD Human610-Quad BeadArray). The Causal Inference Test (CIT) was implemented to distinguish CpG sites that mediate genetic risk, from those that are consequential or independently acted on by genotype. RESULTS Controlling for the estimated distribution of immune cells and other key covariates, our initial epigenome-wide association analysis revealed 1,993 significantly differentially methylated CpGs that between cases and controls (FDR, q < 0.05). The relationship between methylation and case-control status for these 1,993 CpGs was found to be highly consistent with the results of previously published, independent study that consisted of peripheral blood DNA methylation signatures in 131 pretreatment cases and 274 controls. Implementation of the CIT test revealed 17 CpG/SNP pairs, comprising 13 unique CpGs and 17 unique SNPs, which represent potential methylation-mediated relationships between genotype and EOC risk. Of these 13 CpGs, several are associated with immune related genes and genes that have been previously shown to exhibit altered expression in the context of cancer. CONCLUSIONS These findings provide additional insight into EOC etiology and may serve as novel biomarkers for EOC susceptibility.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Brooke L Fridley
- Department of Biostatistics, University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City, KS 66160, USA.
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Abstract
MicroRNAs (miRs) have emerged recently as important regulators of gene expression in the cell. Frequently dysregulated in cancer, miRs have shed new light on molecular mechanisms of oncogenesis, and have generated substantial interest as biomarkers, and novel therapeutic agents and targets. Recently, a number of studies have examined miR biology in Ewing sarcoma. Findings indicate that alterations in miR expression in Ewing Sarcoma are widespread, involve both EWS/Ets oncogenic fusion-dependent and independent mechanisms, and contribute to malignant phenotypes. miRs with prognostic potential have been identified, and several preclinical studies suggest that miR manipulation could be therapeutically useful in this aggressive disease. These and future studies of miR biology stand to expand our understanding of Ewing sarcoma pathogenesis, and may identify new biomarkers and treatment options.
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Affiliation(s)
- Layne Dylla
- Medical Scientist Training Program, University of Colorado DenverDenver, CO, USA
- Cancer Biology Graduate Program, University of Colorado DenverDenver, CO, USA
- Anschutz Medical Campus, University of Colorado DenverDenver, CO, USA
| | - Colin Moore
- Anschutz Medical Campus, University of Colorado DenverDenver, CO, USA
- Center for Cancer and Blood Disorders, University of Colorado DenverAurora, CO, USA
- Departments of Pediatrics, University of Colorado DenverDenver, CO, USA
- Children’s Hospital ColoradoAurora, CO, USA
| | - Paul Jedlicka
- Medical Scientist Training Program, University of Colorado DenverDenver, CO, USA
- Cancer Biology Graduate Program, University of Colorado DenverDenver, CO, USA
- Anschutz Medical Campus, University of Colorado DenverDenver, CO, USA
- Children’s Hospital ColoradoAurora, CO, USA
- Department of Pathology, University of Colorado DenverDenver, CO, USA
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40
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Martin FL. Epigenetic influences in the aetiology of cancers arising from breast and prostate: a hypothesised transgenerational evolution in chromatin accessibility. ISRN ONCOLOGY 2013; 2013:624794. [PMID: 23431470 PMCID: PMC3574745 DOI: 10.1155/2013/624794] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2012] [Accepted: 12/26/2012] [Indexed: 01/12/2023]
Abstract
Epidemiological studies have consistently supported the notion that environmental and/or dietary factors play a central role in the aetiology of cancers of the breast and prostate. However, for more than five decades investigators have failed to identify a single cause-and-effect factor, which could be implicated; identification of a causative entity would allow the implementation of an intervention strategy in at-risk populations. This suggests a more complex pathoaetiology for these cancer sites, compared to others. When one examines the increases or decreases in incidence of specific cancers amongst migrant populations, it is notable that disease arising in colon or stomach requires one or at most two generations to exhibit a change in incidence to match that of high-incidence regions, whereas for breast or prostate cancer, at least three generations are required. This generational threshold could suggest a requirement for nonmutation-driven epigenetic alterations in the F0/F1 generations (parental/offspring adopting a more westernized lifestyle), which then predisposes the inherited genome of subsequent generations to mutagenic/genotoxic alterations leading to the development of sporadic cancer in these target sites. As such, individual susceptibility to carcinogen insult would not be based per se on polymorphisms in activating/detoxifying/repair enzymes, but on elevated accessibility of crucial target genes (e.g., oncogenes, tumour suppressor genes) or hotspots therein to mutation events. This could be termed a genomic susceptibility organizational structure (SOS). Several exposures including alcohol and heavy metals are epigens (i.e., modifiers of the epigenome), whereas others are mutagenic/genotoxic, for example, heterocyclic aromatic amines; humans are continuously and variously exposed to mixtures of these agents. Within such a transgenerational multistage model of cancer development, determining the interaction between epigenetic modification to generate a genomic SOS and genotoxic insult will facilitate a new level of understanding in the aetiology of cancer.
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Affiliation(s)
- Francis L. Martin
- Centre for Biophotonics, Lancaster Environment Centre, Lancaster University, Bailrigg, Lancaster LA1 4YQ, UK
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