1
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Li H, Sun X, Lv Y, Wei G, Ni T, Qin W, Jin H, Jia Q. Downregulation of Splicing Factor PTBP1 Curtails FBXO5 Expression to Promote Cellular Senescence in Lung Adenocarcinoma. Curr Issues Mol Biol 2024; 46:7730-7744. [PMID: 39057099 PMCID: PMC11276454 DOI: 10.3390/cimb46070458] [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: 06/03/2024] [Revised: 07/08/2024] [Accepted: 07/16/2024] [Indexed: 07/28/2024] Open
Abstract
Polypyrimidine tract-binding protein 1 (PTBP1) plays an essential role in splicing and post-transcriptional regulation. Moreover, PTBP1 has been implicated as a causal factor in tumorigenesis. However, the involvement of PTBP1 in cellular senescence, a key biological process in aging and cancer suppression, remains to be clarified. Here, it is shown that PTBP1 is associated with the facilitation of tumor growth and the prognosis in lung adenocarcinoma (LUAD). PTBP1 exhibited significantly increased expression in various cancer types including LUAD and showed consistently decreased expression in multiple cellular senescence models. Suppression of PTBP1 induced cellular senescence in LUAD cells. In terms of molecular mechanisms, the silencing of PTBP1 enhanced the skipping of exon 3 in F-box protein 5 (FBXO5), resulting in the generation of a less stable RNA splice variant, FBXO5-S, which subsequently reduces the overall FBXO5 expression. Additionally, downregulation of FBXO5 was found to induce senescence in LUAD. Collectively, these findings illustrate that PTBP1 possesses an oncogenic function in LUAD through inhibiting senescence, and that targeting aberrant splicing mediated by PTBP1 has therapeutic potential in cancer treatment.
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Affiliation(s)
- Haoyu Li
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200032, China; (H.L.); (X.S.); (Y.L.); (W.Q.); (H.J.)
| | - Xiaoxiao Sun
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200032, China; (H.L.); (X.S.); (Y.L.); (W.Q.); (H.J.)
| | - Yuanyuan Lv
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200032, China; (H.L.); (X.S.); (Y.L.); (W.Q.); (H.J.)
| | - Gang Wei
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, School of Life Sciences, Fudan University, Shanghai 200438, China; (G.W.); (T.N.)
| | - Ting Ni
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, School of Life Sciences, Fudan University, Shanghai 200438, China; (G.W.); (T.N.)
| | - Wenxin Qin
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200032, China; (H.L.); (X.S.); (Y.L.); (W.Q.); (H.J.)
| | - Haojie Jin
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200032, China; (H.L.); (X.S.); (Y.L.); (W.Q.); (H.J.)
| | - Qi Jia
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200032, China; (H.L.); (X.S.); (Y.L.); (W.Q.); (H.J.)
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2
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Chu Z, Zhu M, Luo Y, Hu Y, Feng X, Wang H, Sunagawa M, Liu Y. PTBP1 plays an important role in the development of gastric cancer. Cancer Cell Int 2023; 23:195. [PMID: 37670313 PMCID: PMC10478210 DOI: 10.1186/s12935-023-03043-0] [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: 03/23/2023] [Accepted: 08/25/2023] [Indexed: 09/07/2023] Open
Abstract
BACKGROUND Polypyrimidine tract binding protein 1 (PTBP1) has been found to play an important role in the occurrence and development of various tumors. At present, the role of PTBP1 in gastric cancer (GC) is still unknown and worthy of further investigation. METHODS We used bioinformatics to analyze the expression of PTBP1 in patients with GC. Cell proliferation related experiments were used to detect cell proliferation after PTBP1 knockdown. Skeleton staining, scanning electron microscopy and transmission electron microscopy were used to observe the changes of actin skeleton. Proliferation and actin skeleton remodeling signaling pathways were detected by Western Blots. The relationship between PTBP1 and proliferation of gastric cancer cells was further detected by subcutaneous tumor transplantation. Finally, tissue microarray data from clinical samples were used to further explore the expression of PTBP1 in patients with gastric cancer and its correlation with prognosis. RESULTS Through bioinformatics studies, we found that PTBP1 was highly expressed in GC patients and correlated with poor prognosis. Cell proliferation and cycle analysis showed that PTBP1 down-regulation could significantly inhibit cell proliferation. The results of cell proliferation detection related experiments showed that PTBP1 down-regulation could inhibit the division and proliferation of GC cells. Furthermore, changes in the morphology of the actin skeleton of cells showed that PTBP1 down-regulation inhibited actin skeletal remodeling in GC cells. Western Blots showed that PTBP1 could regulate proliferation and actin skeleton remodeling signaling pathways. In addition, we constructed PTBP1 Cas9-KO mouse model and performed xenograft assays to further confirm that down-regulation of PTBP1 could inhibit the proliferation of GC cells. Finally, tissue microarray was used to further verify the close correlation between PTBP1 and poor prognosis in patients with GC. CONCLUSIONS Our study demonstrates for the first time that PTBP1 may affect the proliferation of GC cells by regulating actin skeleton remodeling. In addition, PTBP1 is closely related to actin skeleton remodeling and proliferation signaling pathways. We suppose that PTBP1 might be a potential target for the treatment of GC.
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Affiliation(s)
- Zewen Chu
- The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, China
- The Key Laboratory of Syndrome Differentiation and Treatment of Gastric Cancer of the State Administration of Traditional Chinese Medicine, Yangzhou, China
| | - Miao Zhu
- The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, China
- The Key Laboratory of Syndrome Differentiation and Treatment of Gastric Cancer of the State Administration of Traditional Chinese Medicine, Yangzhou, China
| | - Yuanyuan Luo
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, China
- The Key Laboratory of Syndrome Differentiation and Treatment of Gastric Cancer of the State Administration of Traditional Chinese Medicine, Yangzhou, China
| | - Yaqi Hu
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, China
- The Key Laboratory of Syndrome Differentiation and Treatment of Gastric Cancer of the State Administration of Traditional Chinese Medicine, Yangzhou, China
| | - Xinyi Feng
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, China
- The Key Laboratory of Syndrome Differentiation and Treatment of Gastric Cancer of the State Administration of Traditional Chinese Medicine, Yangzhou, China
| | - Haibo Wang
- The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China.
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, China.
- The Key Laboratory of Syndrome Differentiation and Treatment of Gastric Cancer of the State Administration of Traditional Chinese Medicine, Yangzhou, China.
| | - Masataka Sunagawa
- Department of physiology, School of Medicine, Showa University, Tokyo, Japan.
| | - Yanqing Liu
- The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China.
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, China.
- The Key Laboratory of Syndrome Differentiation and Treatment of Gastric Cancer of the State Administration of Traditional Chinese Medicine, Yangzhou, China.
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3
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He Z, Ni Q, Li X, Zhao M, Mo Q, Duo Y. PTBP1 promotes hepatocellular carcinoma progression by regulating the skipping of exon 9 in NUMB pre-mRNA. Heliyon 2023; 9:e17387. [PMID: 37408905 PMCID: PMC10318449 DOI: 10.1016/j.heliyon.2023.e17387] [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: 01/18/2023] [Revised: 06/15/2023] [Accepted: 06/15/2023] [Indexed: 07/07/2023] Open
Abstract
Aberrant alternative splicing is one of the important causes of cancer. Polypyrimidine tract binding protein 1 (PTBP1) has been found to be involved in splicing regulation in a variety of tumors. Here, we observed significant up-regulation of PTBP1 in primary hepatocellular carcinoma (HCC) tissues. High levels of PTBP1 expression were associated with poor prognosis and increased metastatic potential in HCC. In vitro studies demonstrated that elevated PTBP1 promoted both migration and invasion by HCC cells. In contrast, knockdown of PTBP1 significantly inhibited the migration and invasion of HCC cells in vitro. Further, up-regulation of PTBP1 markedly accumulated the expression of oncogenic isoform of NUMB, NUMB-PRRL. We observed two isoforms of NUMB, NUMB-PRRL and NUMB-PRRS exhibit opposite function in HCC cells, which partially explain PTBP1 plays the tumor promoting roles in a NUMB splicing-dependent manner. In summary, our study indicates that PTBP1 may serve as an oncogene in HCC patients by regulating the alternative splicing of NUMB exon 9 and could potentially serve as a prognostic indicator.
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Role of a small GTPase Cdc42 in aging and age-related diseases. Biogerontology 2023; 24:27-46. [PMID: 36598630 DOI: 10.1007/s10522-022-10008-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 12/13/2022] [Indexed: 01/05/2023]
Abstract
A small GTPase, Cdc42 is evolutionarily one of the most ancient members of the Rho family, which is ubiquitously expressed and involved in a wide range of fundamental cellular functions. The crucial role of Cdc42 includes regulation of the actin cytoskeleton, cell polarity, morphology and migration, endocytosis and exocytosis, cell cycle, and proliferation in many different cell types. Many studies have provided compelling yet contradicting evidence that Cdc42 dysregulation plays an important role in cellular and tissue aging. Furthermore, Cdc42 is a critical factor in the development and progression of aging-related pathologies, such as neurodegenerative and cardiovascular disorders, diabetes type 2, and aging-related disorders of the joints and bones, and the inhibition of the Cdc42 demonstrates potentially significant therapeutic and anti-aging effects in animal models of aging and disease. However, regulation of Cdc42 expression and activity is very complex and depends on many factors, such as the origin and complexity of the tissues, hormonal status, etc. Therefore, this review is focused on current advances in understanding the underlying cellular and molecular mechanisms associated with Cdc42 activity and regulation of senescence in different cell types since they may provide a foundation for novel therapeutic strategies and targeted drugs to reverse the aging process and treat aging-associated disorders.
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5
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Wirth A, Ponimaskin E. Lipidation of small GTPase Cdc42 as regulator of its physiological and pathophysiological functions. Front Physiol 2023; 13:1088840. [PMID: 36699687 PMCID: PMC9868626 DOI: 10.3389/fphys.2022.1088840] [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: 11/03/2022] [Accepted: 12/26/2022] [Indexed: 01/11/2023] Open
Abstract
The protein cell division cycle 42 (Cdc42) is a small GTPase of the Rho family regulating a plethora of physiological functions in a tissue, cell and subcellular-specific manner via participating in multiple signaling pathways. Since the corresponding signaling hubs are mainly organized along the cellular membranes, cytosolic proteins like Cdc42 need to be properly targeted and held at the membrane. Here, lipid modifications come into play: Cdc42 can be associated with membranes by different lipid anchors including prenylation (Cdc42-prenyl) and palmitoylation (Cdc42-palm). While Cdc42-prenyl is ubiquitously expressed, Cdc42-palm splicing variant in mainly expressed in the brain. Mechanisms underlying Cdc42 lipidation as well as its regulation are the main topic of this review. Furthermore, we will discuss the functional importance of Cdc42 lipid modifications with the focus on the role of different lipids in regulating defined Cdc42 functions. Finally, we will provide an overview of the possible implementation of Cdc42 lipidation in pathological conditions and different diseases.
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6
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Rehn M, Wenzel A, Frank AK, Schuster MB, Pundhir S, Jørgensen N, Vitting-Seerup K, Ge Y, Jendholm J, Michaut M, Schoof EM, Jensen TL, Rapin N, Sapio RT, Andersen KL, Lund AH, Solimena M, Holzenberger M, Pestov DG, Porse BT. PTBP1 promotes hematopoietic stem cell maintenance and red blood cell development by ensuring sufficient availability of ribosomal constituents. Cell Rep 2022; 39:110793. [PMID: 35545054 DOI: 10.1016/j.celrep.2022.110793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 03/14/2022] [Accepted: 04/15/2022] [Indexed: 11/18/2022] Open
Abstract
Ribosomopathies constitute a range of disorders associated with defective protein synthesis mainly affecting hematopoietic stem cells (HSCs) and erythroid development. Here, we demonstrate that deletion of poly-pyrimidine-tract-binding protein 1 (PTBP1) in the hematopoietic compartment leads to the development of a ribosomopathy-like condition. Specifically, loss of PTBP1 is associated with decreases in HSC self-renewal, erythroid differentiation, and protein synthesis. Consistent with its function as a splicing regulator, PTBP1 deficiency results in splicing defects in hundreds of genes, and we demonstrate that the up-regulation of a specific isoform of CDC42 partly mimics the protein-synthesis defect associated with loss of PTBP1. Furthermore, PTBP1 deficiency is associated with a marked defect in ribosome biogenesis and a selective reduction in the translation of mRNAs encoding ribosomal proteins. Collectively, this work identifies PTBP1 as a key integrator of ribosomal functions and highlights the broad functional repertoire of RNA-binding proteins.
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Affiliation(s)
- Matilda Rehn
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; Biotech Research and Innovation Center (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark; Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Anne Wenzel
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; Biotech Research and Innovation Center (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark; Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Anne-Katrine Frank
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; Biotech Research and Innovation Center (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark; Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Mikkel Bruhn Schuster
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; Biotech Research and Innovation Center (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark; Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Sachin Pundhir
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; Biotech Research and Innovation Center (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark; Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Nanna Jørgensen
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; Biotech Research and Innovation Center (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark; Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | | | - Ying Ge
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; Biotech Research and Innovation Center (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark; Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Johan Jendholm
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; Biotech Research and Innovation Center (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark; Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Magali Michaut
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; Biotech Research and Innovation Center (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark; Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Erwin M Schoof
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; Biotech Research and Innovation Center (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark; Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; DTU Bioengineering, Danish Technical University, 2800 Kgs. Lyngby, Denmark
| | - Tanja Lyholm Jensen
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; Biotech Research and Innovation Center (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark; Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Nicolas Rapin
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; Biotech Research and Innovation Center (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark; Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Russell T Sapio
- Department of Cell Biology and Neuroscience, Rowan University School of Osteopathic Medicine, Stratford, NJ 08084, USA
| | | | - Anders H Lund
- Biotech Research and Innovation Center (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark
| | - Michele Solimena
- Molecular Diabetology, University Hospital and Faculty of Medicine, Technische Universität Dresden, Dresden, Germany; Paul Langerhans Institute Dresden of the Helmholtz Center Munich at University Hospital and Faculty of Medicine, Technische Universität Dresden, Dresden, Germany; Max Planck Institute for Molecular Cell Biology and Genetics, Dresden, Germany; German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Martin Holzenberger
- Sorbonne University, INSERM, Research Center Saint-Antoine, CRSA, 75012 Paris, France
| | - Dimitri G Pestov
- Department of Cell Biology and Neuroscience, Rowan University School of Osteopathic Medicine, Stratford, NJ 08084, USA
| | - Bo Torben Porse
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; Biotech Research and Innovation Center (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark; Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark.
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7
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Dai S, Wang C, Zhang C, Feng L, Zhang W, Zhou X, He Y, Xia X, Chen B, Song W. PTB: Not just a polypyrimidine tract-binding protein. J Cell Physiol 2022; 237:2357-2373. [PMID: 35288937 DOI: 10.1002/jcp.30716] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 02/19/2022] [Accepted: 02/22/2022] [Indexed: 01/21/2023]
Abstract
Polypyrimidine tract-binding protein (PTB), as a member of the heterogeneous nuclear ribonucleoprotein family, functions by rapidly shuttling between the nucleus and the cytoplasm. PTB is involved in the alternative splicing of pre-messenger RNA (mRNA) and almost all steps of mRNA metabolism. PTB regulation is organ-specific; brain- or muscle-specific microRNAs and long noncoding RNAs partially contribute to regulating PTB, thereby modulating many physiological and pathological processes, such as embryonic development, cell development, spermatogenesis, and neuron growth and differentiation. Previous studies have shown that PTB knockout can inhibit tumorigenesis and development. The knockout of PTB in glial cells can be reprogrammed into functional neurons, which shows great promise in the field of nerve regeneration but is controversial.
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Affiliation(s)
- Shirui Dai
- National Clinical Research Center for Geriatric Diseases, Xiangya Hospital of Central South University, Changsha, Hunan, P. R. China.,Eye Center of Xiangya Hospital, Central South University, Changsha, Hunan, P. R. China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, P. R. China.,Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, P. R. China.,Hunan Clinical Research Center of Ophthalmic Disease, Changsha, Hunan, P. R. China
| | - Chao Wang
- National Clinical Research Center for Geriatric Diseases, Xiangya Hospital of Central South University, Changsha, Hunan, P. R. China.,Eye Center of Xiangya Hospital, Central South University, Changsha, Hunan, P. R. China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, P. R. China
| | - Cheng Zhang
- National Clinical Research Center for Geriatric Diseases, Xiangya Hospital of Central South University, Changsha, Hunan, P. R. China.,Eye Center of Xiangya Hospital, Central South University, Changsha, Hunan, P. R. China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, P. R. China
| | - Lemeng Feng
- National Clinical Research Center for Geriatric Diseases, Xiangya Hospital of Central South University, Changsha, Hunan, P. R. China.,Eye Center of Xiangya Hospital, Central South University, Changsha, Hunan, P. R. China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, P. R. China
| | - Wulong Zhang
- National Clinical Research Center for Geriatric Diseases, Xiangya Hospital of Central South University, Changsha, Hunan, P. R. China.,Eye Center of Xiangya Hospital, Central South University, Changsha, Hunan, P. R. China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, P. R. China
| | - Xuezhi Zhou
- National Clinical Research Center for Geriatric Diseases, Xiangya Hospital of Central South University, Changsha, Hunan, P. R. China.,Eye Center of Xiangya Hospital, Central South University, Changsha, Hunan, P. R. China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, P. R. China
| | - Ye He
- National Clinical Research Center for Geriatric Diseases, Xiangya Hospital of Central South University, Changsha, Hunan, P. R. China.,Eye Center of Xiangya Hospital, Central South University, Changsha, Hunan, P. R. China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, P. R. China
| | - Xiaobo Xia
- National Clinical Research Center for Geriatric Diseases, Xiangya Hospital of Central South University, Changsha, Hunan, P. R. China.,Eye Center of Xiangya Hospital, Central South University, Changsha, Hunan, P. R. China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, P. R. China
| | - Baihua Chen
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, P. R. China.,Hunan Clinical Research Center of Ophthalmic Disease, Changsha, Hunan, P. R. China
| | - Weitao Song
- National Clinical Research Center for Geriatric Diseases, Xiangya Hospital of Central South University, Changsha, Hunan, P. R. China.,Eye Center of Xiangya Hospital, Central South University, Changsha, Hunan, P. R. China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, P. R. China
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8
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Targeting Cancer by Using Nanoparticles to Modulate RHO GTPase Signaling. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1357:115-127. [DOI: 10.1007/978-3-030-88071-2_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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9
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Identification of survival-related alternative splicing signatures in acute myeloid leukemia. Biosci Rep 2021; 41:229155. [PMID: 34212178 PMCID: PMC8292762 DOI: 10.1042/bsr20204037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 06/11/2021] [Accepted: 06/30/2021] [Indexed: 01/25/2023] Open
Abstract
Aberrant RNA alternative splicing (AS) variants play critical roles in tumorigenesis and prognosis in human cancers. Here, we conducted a comprehensive profiling of aberrant AS events in acute myeloid leukemia (AML). RNA AS profile, including seven AS types, and the percent spliced in (PSI) value for each patient were generated by SpliceSeq using RNA-seq data from TCGA. Univariate followed by multivariate Cox regression analysis were used to identify survival-related AS events and develop the AS signatures. A nomogram was developed, and its predictive efficacy was assessed. About 27,892 AS events and 3,178 events were associated with overall survival (OS) after strict filtering. Parent genes of survival-associated AS events were mainly enriched in leukemia-associated processes including chromatin modification, autophagy, and T-cell receptor signaling pathway. The 10 AS signature based on seven types of AS events showed better efficacy in predicting OS of patients than those built on a single AS event type. The area under curve (AUC) value of the 10 AS signature for 3-year OS was 0.91. Gene set enrichment analysis (GSEA) confirmed that these survival-related AS events contribute to AML progression. Moreover, the nomogram showed good predictive performance for patient's prognosis. Finally, the correlation network of AS variants with splicing factor genes found potential important regulatory genes in AML. The present study presented a systematic analysis of survival-related AS events and developed AS signatures for predicting the patient’s survival. Further studies are needed to validate the signatures in independent AML cohorts and might provide a promising perspective for developing therapeutic targets.
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10
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Magalhaes YT, Farias JO, Silva LE, Forti FL. GTPases, genome, actin: A hidden story in DNA damage response and repair mechanisms. DNA Repair (Amst) 2021; 100:103070. [PMID: 33618126 DOI: 10.1016/j.dnarep.2021.103070] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 02/01/2021] [Accepted: 02/04/2021] [Indexed: 12/18/2022]
Abstract
The classical small Rho GTPase (Rho, Rac, and Cdc42) protein family is mainly responsible for regulating cell motility and polarity, membrane trafficking, cell cycle control, and gene transcription. Cumulative recent evidence supports important roles for these proteins in the maintenance of genomic stability. Indeed, DNA damage response (DDR) and repair mechanisms are some of the prime biological processes that underlie several disease phenotypes, including genetic disorders, cancer, senescence, and premature aging. Many reports guided by different experimental approaches and molecular hypotheses have demonstrated that, to some extent, direct modulation of Rho GTPase activity, their downstream effectors, or actin cytoskeleton regulation contribute to these cellular events. Although much attention has been paid to this family in the context of canonical actin cytoskeleton remodeling, here we provide a contextualized review of the interplay between Rho GTPase signaling pathways and the DDR and DNA repair signaling components. Interesting questions yet to be addressed relate to the spatiotemporal dynamics of this collective response and whether it correlates with different subcellular pools of Rho GTPases. We highlight the direct and indirect targets, some of which still lack experimental validation data, likely associated with Rho GTPase activation that provides compelling evidence for further investigation in DNA damage-associated events and with potential therapeutic applications in translational medicine.
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Affiliation(s)
- Yuli T Magalhaes
- Laboratory of Biomolecular Systems Signaling, Department of Biochemistry, Institute of Chemistry, University of São Paulo, SP, Brazil
| | - Jessica O Farias
- Laboratory of Biomolecular Systems Signaling, Department of Biochemistry, Institute of Chemistry, University of São Paulo, SP, Brazil
| | - Luiz E Silva
- Laboratory of Biomolecular Systems Signaling, Department of Biochemistry, Institute of Chemistry, University of São Paulo, SP, Brazil
| | - Fabio L Forti
- Laboratory of Biomolecular Systems Signaling, Department of Biochemistry, Institute of Chemistry, University of São Paulo, SP, Brazil.
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11
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Wu HY, Li QQ, Liang L, Qiu LL, Wei HW, Huang BY, Gang- C, He RQ, Huang ZG, Hou W, Hu QP, Pan SL. Prognostic alternative splicing signature in cervical squamous cell carcinoma. IET Syst Biol 2020; 14:314-322. [PMID: 33399095 PMCID: PMC8687194 DOI: 10.1049/iet-syb.2019.0095] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Revised: 04/18/2020] [Accepted: 04/30/2020] [Indexed: 01/01/2023] Open
Abstract
Basing on alternative splicing events (ASEs) databases, the authors herein aim to explore potential prognostic biomarkers for cervical squamous cell carcinoma (CESC). mRNA expression profiles and relevant clinical data of 223 patients with CESC were obtained from The Cancer Genome Atlas (TCGA). Correlated genes, ASEs and percent-splice-in (PSI) were downloaded from SpliceSeq, respectively. The PSI values of survival-associated alternative splicing events (SASEs) were used to construct the basis of a prognostic index (PI). A protein-protein interaction (PPI) network of genes related to SASEs was generated by STRING and analysed with Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). Consequently, 41,776 ASEs were discovered in 19,724 genes, 2596 of which linked with 3669 SASEs. The PPI network of SASEs related genes revealed that TP53 and UBA52 were core genes. The low-risk group had a longer survival period than high-risk counterparts, both groups being defined according to PI constructed upon the top 20 splicing events or PI on the overall splicing events. The AUC value of ROC reached up to 0.88, demonstrating the prognostic potential of PI in CESC. These findings suggested that ASEs involve in the pathogenesis of CESC and may serve as promising prognostic biomarkers for this female malignancy.
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Affiliation(s)
- Hua-Yu Wu
- Department of Cell Biology and Genetics, School of Pre-clinical Medicine, Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Qi-Qi Li
- Department of Pathophysiology, School of Pre-clinical Medicine, Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Liang Liang
- Department of Gastrointestinal Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, People's Republic of China
| | - Lan-Lan Qiu
- Department of Pathophysiology, School of Pre-clinical Medicine, Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Hong-Wei Wei
- Department of Obstetrics and Gynecology, Women and Children Hospital of Guangxi Zhuang Autonomous Region, Nanning 530003, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Bing-Ying Huang
- Department of Nephrology, Second Affiliated Hospital of Guangxi Medical University, Nanning, 530007, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Chen Gang-
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Rong-Quan He
- Department of Medical Oncology, First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Zhi-Guang Huang
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Wei Hou
- Department of Pediatrics, Guangxi Key Laboratory of Thalassemia Research, Nanning 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Qi-Ping Hu
- Department of Cell Biology and Genetics, School of Pre-clinical Medicine, Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Shang-Ling Pan
- Department of Pathophysiology, School of Pre-clinical Medicine, Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, People's Republic of China.
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12
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Zhao Z, Li GZ, Liu YQ, Huang RY, Wang KY, Jiang HY, Li RP, Chai RC, Zhang CB, Wu F. Characterization and prognostic significance of alternative splicing events in lower-grade diffuse gliomas. J Cell Mol Med 2020; 24:13171-13180. [PMID: 33006444 PMCID: PMC7701518 DOI: 10.1111/jcmm.15924] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/03/2020] [Accepted: 09/10/2020] [Indexed: 01/17/2023] Open
Abstract
Alternative splicing (AS) is assumed to play important roles in the progression and prognosis of cancer. Currently, the comprehensive analysis and clinical relevance of AS in lower-grade diffuse gliomas have not been systematically addressed. Here, we gathered alternative splicing data of lower-grade diffuse gliomas from SpliceSeq. Based on the Percent Spliced In (PSI) values of 515 lower-grade diffuse glioma patients from the Cancer Genome Atlas (TCGA), we performed subtype-differential AS analysis and consensus clustering to determine robust clusters of patients. A total of 48 050 AS events in 10 787 genes in lower-grade diffuse gliomas were profiled. Subtype-differential splicing analysis and functional annotation revealed that spliced genes were significantly enriched in numerous cancer-related biological phenotypes and signalling pathways. Consensus clustering using AS events identified three robust clusters of patients with distinguished pathological and prognostic features. Moreover, each cluster was also associated with distinct genomic alterations. Finally, we developed and validated an AS-related signature with Cox proportional hazards model. The signature, significantly associated with clinical and molecular features, could serve as an independent prognostic factor for lower-grade diffuse gliomas. Thus, our results indicated that AS events could discriminate molecular subtypes and have prognostic impact in lower-grade diffuse gliomas.
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Affiliation(s)
- Zheng Zhao
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Guan-Zhang Li
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yu-Qing Liu
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Ruo-Yu Huang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Kuan-Yu Wang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Hao-Yu Jiang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Ren-Peng Li
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Rui-Chao Chai
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Chuan-Bao Zhang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Fan Wu
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
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13
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Zhu W, Zhou BL, Rong LJ, Ye L, Xu HJ, Zhou Y, Yan XJ, Liu WD, Zhu B, Wang L, Jiang XJ, Ren CP. Roles of PTBP1 in alternative splicing, glycolysis, and oncogensis. J Zhejiang Univ Sci B 2020; 21:122-136. [PMID: 32115910 DOI: 10.1631/jzus.b1900422] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Polypyrimidine tract-binding protein 1 (PTBP1) plays an essential role in splicing and is expressed in almost all cell types in humans, unlike the other proteins of the PTBP family. PTBP1 mediates several cellular processes in certain types of cells, including the growth and differentiation of neuronal cells and activation of immune cells. Its function is regulated by various molecules, including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and RNA-binding proteins. PTBP1 plays roles in various diseases, particularly in some cancers, including colorectal cancer, renal cell cancer, breast cancer, and glioma. In cancers, it acts mainly as a regulator of glycolysis, apoptosis, proliferation, tumorigenesis, invasion, and migration. The role of PTBP1 in cancer has become a popular research topic in recent years, and this research has contributed greatly to the formulation of a useful therapeutic strategy for cancer. In this review, we summarize recent findings related to PTBP1 and discuss how it regulates the development of cancer cells.
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Affiliation(s)
- Wei Zhu
- NHC Key Laboratory of Carcinogenesis (Central South University) and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Bo-Lun Zhou
- NHC Key Laboratory of Carcinogenesis (Central South University) and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Li-Juan Rong
- NHC Key Laboratory of Carcinogenesis (Central South University) and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Li Ye
- NHC Key Laboratory of Carcinogenesis (Central South University) and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Hong-Juan Xu
- NHC Key Laboratory of Carcinogenesis (Central South University) and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Yao Zhou
- NHC Key Laboratory of Carcinogenesis (Central South University) and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Xue-Jun Yan
- NHC Key Laboratory of Carcinogenesis (Central South University) and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Wei-Dong Liu
- NHC Key Laboratory of Carcinogenesis (Central South University) and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Bin Zhu
- NHC Key Laboratory of Carcinogenesis (Central South University) and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Lei Wang
- NHC Key Laboratory of Carcinogenesis (Central South University) and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Xing-Jun Jiang
- NHC Key Laboratory of Carcinogenesis (Central South University) and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Cai-Ping Ren
- NHC Key Laboratory of Carcinogenesis (Central South University) and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, China
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14
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Wu F, Chen Q, Liu C, Duan X, Hu J, Liu J, Cao H, Li W, Li H. Profiles of prognostic alternative splicing signature in hepatocellular carcinoma. Cancer Med 2020; 9:2171-2180. [PMID: 31975560 PMCID: PMC7064038 DOI: 10.1002/cam4.2875] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 12/16/2019] [Accepted: 01/10/2020] [Indexed: 12/13/2022] Open
Abstract
Previous studies have demonstrated the role of abnormal alternative splicing (AS) in tumor progression. This study examines the prognostic index (PI) of alternative splices (ASs) in patients with hepatocellular carcinoma (HCC). The clinical features and splicing events of patients with HCC were downloaded from The Cancer Genome Atlas (TCGA). Differentially expressed AS (DEAS) were compared between HCC and adjacent normal samples. Univariate Cox regression analysis was used to determine changes in DEAS associated with overall survival (OS). A PI was generated from OS‐associated DEASs using Kaplan‐Meier curves, receiver operating characteristic (ROC) curves, multivariate Cox regression, and cluster analysis. Then, the correlation between DEASs and splicing factors was assessed, followed by functional and pathway enrichment analysis. We identified 34 163 ASs of 8985 genes in HCC, and 153 OS‐ASs were identified using univariate Cox regression analysis. Low‐ and high‐PI groups were determined based on the median “PI‐ALL” value according to significantly different survival (P = 2.2e − 16). The ROC curve of all PI (PI‐ALL) had an area under the curve (AUC) of 0.993 for survival status in patients with HCC. A potential regulatory network associated with prognosis of patients with HCC was established. Enrichment analysis also resulted in the identification of several pathways potentially associated with carcinogenesis and progression of HCC. Four clusters were identified that were associated with clinical features and prognosis. Our study generated comprehensive profiles of ASs in HCC. The interaction network and functional connections were used to elucidate the underlying mechanisms of AS in HCC.
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Affiliation(s)
- Fangming Wu
- Department of Comprehensive Intervention, Henan Provincial People's Hospital, Zhengzhou, China.,Department of Comprehensive Intervention, Zhengzhou University People's Hospital, Zhengzhou, China
| | - Qifeng Chen
- Department of Medical Imaging and Interventional Radiology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Chaojun Liu
- Biotherapy Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiaoran Duan
- Biotherapy Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jinlong Hu
- Department of Oncology, Henan Provincial People's Hospital, Zhengzhou, China
| | - Jian Liu
- Department of Comprehensive Intervention, Henan Provincial People's Hospital, Zhengzhou, China.,Department of Comprehensive Intervention, Zhengzhou University People's Hospital, Zhengzhou, China
| | - Huicun Cao
- Department of Comprehensive Intervention, Henan Provincial People's Hospital, Zhengzhou, China.,Department of Comprehensive Intervention, Zhengzhou University People's Hospital, Zhengzhou, China
| | - Wang Li
- Department of Medical Imaging and Interventional Radiology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Hui Li
- Department of Comprehensive Intervention, Henan Provincial People's Hospital, Zhengzhou, China.,Department of Comprehensive Intervention, Zhengzhou University People's Hospital, Zhengzhou, China
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15
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Chen T, Zheng W, Chen J, Lin S, Zou Z, Li X, Tan Z. Systematic analysis of survival-associated alternative splicing signatures in clear cell renal cell carcinoma. J Cell Biochem 2019; 121:4074-4084. [PMID: 31886566 DOI: 10.1002/jcb.29590] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 12/09/2019] [Indexed: 12/29/2022]
Abstract
Alternative splicing (AS) constitutes a major reason for messenger RNA (mRNA) and protein diversity. Increasing studies have shown a link to splicing dysfunction associated with malignant neoplasia. Systematic analysis of AS events in kidney cancer remains poorly reported. Therefore, we generated AS profiles in 533 kidney renal clear cell carcinoma (KIRC) patients in The Cancer Genome Atlas (TCGA) database using RNA-seq data. Then, prognostic models were developed in a primary cohort (N = 351) and validated in a validation cohort (N = 182). In addition, splicing networks were built by integrating bioinformatics analyses. A total of 11 268 and 8083 AS variants were significantly associated with patient overall survival time in the primary and validation KIRC cohorts, respectively, including STAT1, DAZAP1, IDS, NUDT7, and KLHDC4. The AS events in the primary KIRC cohorts served as candidate AS events to screen the independent risk factors associated with survival in the primary cohort and to develop prognostic models. The area under the curve of the receiver-operator characteristic curve for prognostic prediction in the primary and validation KIRC cohorts was 0.84 and 0.82 at 2500 days of overall survival, respectively. In addition, splicing correlation networks revealed key splicing factors (SFs) in KIRC, such as HNRNPH1, HNRNPU, KHDBS1, KHDBS3, SRSF9, RBMX, SFQ, SRP54, HNRNPA0, and SRSF6. In this study, we analyzed the AS landscape in the TCGA KIRC cohort and detected predictors (prognostic) based on AS variants with high performance for risk stratification of the KIRC cohort and revealed key SFs in splicing networks, which could act as underlying mechanisms.
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Affiliation(s)
- Tao Chen
- Department of Anesthesiology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Wenzhong Zheng
- Department of Anesthesiology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
- Department of Urology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jianbo Chen
- Department of Surgery, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Shouren Lin
- Department of Reproductive Medicine, Peking University Shenzhen Hospital, Shenzhen, China
| | - Zihao Zou
- Department of Urology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Xianxin Li
- Department of Surgery, Shenzhen Sun Yat-Sen Cardiovascular Hospital, Shenzhen, China
| | - Zhengling Tan
- Department of Anesthesiology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
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16
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Chen QF, Li W, Wu P, Shen L, Huang ZL. Alternative splicing events are prognostic in hepatocellular carcinoma. Aging (Albany NY) 2019; 11:4720-4735. [PMID: 31301224 PMCID: PMC6660027 DOI: 10.18632/aging.102085] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 07/01/2019] [Indexed: 02/06/2023]
Abstract
Alternative splicing events (ASEs) play a role in cancer development and progression. We investigated whether ASEs are prognostic for overall survival (OS) in hepatocellular carcinoma (HCC). RNA sequencing data was obtained for 343 patients included in The Cancer Genome Atlas. Matched splicing event data for these patients was then obtained from the TCGASpliceSeq database, which includes data for seven types of ASEs. Univariate and multivariate Cox regression analysis demonstrated that 3,814 OS-associated splicing events (OS-SEs) were correlated with OS. Prognostic indices were developed based on the most significant OS-SEs. The prognostic index based on all seven types of ASEs (PI-ALL) demonstrated superior efficacy in predicting OS of HCC patients at 2,000 days compared to those based on single ASE types. Patients were stratified into two risk groups (high and low) based on the median prognostic index. Kaplan-Meier survival analysis demonstrated that PI-ALL had the greatest capacity to distinguish between patients with favorable vs. poor outcomes. Finally, univariate Cox regression analysis demonstrated that the expression of 23 splicing factors was correlated with OS-SEs in the HCC cohort. Our data indicate that a prognostic index based on ASEs is prognostic for OS in HCC.
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Affiliation(s)
- Qi-Feng Chen
- Department of Medical Imaging and Interventional Radiology, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong 510060, P.R. China
- State Key Laboratory of Oncology in South China, Guangzhou, Guangdong 510060, P.R. China
- Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong 510060, P.R. China
| | - Wang Li
- Department of Medical Imaging and Interventional Radiology, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong 510060, P.R. China
| | - Peihong Wu
- Department of Medical Imaging and Interventional Radiology, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong 510060, P.R. China
| | - Lujun Shen
- Department of Medical Imaging and Interventional Radiology, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong 510060, P.R. China
- State Key Laboratory of Oncology in South China, Guangzhou, Guangdong 510060, P.R. China
- Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong 510060, P.R. China
| | - Zi-Lin Huang
- Department of Medical Imaging and Interventional Radiology, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong 510060, P.R. China
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17
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Li S, Shen L, Huang L, Lei S, Cai X, Breitzig M, Zhang B, Yang A, Ji W, Huang M, Zheng Q, Sun H, Wang F. PTBP1 enhances exon11a skipping in Mena pre-mRNA to promote migration and invasion in lung carcinoma cells. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:858-869. [PMID: 31075540 DOI: 10.1016/j.bbagrm.2019.04.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 04/16/2019] [Accepted: 04/18/2019] [Indexed: 12/13/2022]
Abstract
Alternative splicing (AS) events occur in the majority of human genes. AS in a single gene can give rise to different functions among multiple isoforms. Human ortholog of mammalian enabled (Mena) is a conserved regulator of actin dynamics that plays an important role in metastasis. Mena has been shown to have multiple splice variants in human tumor cells due to AS. However, the mechanism mediated Mena AS has not been elucidated. Here we showed that polypyrimidine tract-binding protein 1 (PTBP1) could modulate Mena AS. First, PTBP1 levels were elevated in metastatic lung cancer cells as well as during epithelial-mesenchymal transition (EMT) process. Then, knockdown of PTBP1 using shRNA inhibited migration and invasion of lung carcinoma cells and decreased the Mena exon11a skipping, whereas overexpression of PTBP1 had the opposite effects. The results of RNA pull-down assays and mutation analyses demonstrated that PTBP1 functionally targeted and physically interacted with polypyrimidine sequences on both upstream intron11 (TTTTCCCCTT) and downstream intron11a (TTTTTTTTTCTTT). In addition, the results of migration and invasion assays as well as detection of filopodia revealed that the effect of PTBP1 was reversed by knockdown of Mena but not Mena11a+. Overexpressed MenaΔ11a also rescued the PTBP1-induced migration and invasion. Taken together, our study provides a novel mechanism that PTBP1 modulates Mena exon11a skipping, and indicates that PTBP1 depends on the level of Mena11a- to promote lung cancer cells migration and invasion. The regulation of Mena AS may be a potential prognostic marker and a promising target for treatment of lung carcinoma.
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Affiliation(s)
- Shuaiguang Li
- Institute of Genomic Medicine, College of Pharmacy, Jinan University, Guangzhou 510632, China; Guangdong Provincial Key Laboratory of Pharmacodynamics Constituents of TCM and New Drugs Research, Jinan University, Guangzhou 510632, China; International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), College of pharmacy, Jinan University, Guangzhou 510632, China
| | - Lianghua Shen
- Institute of Genomic Medicine, College of Pharmacy, Jinan University, Guangzhou 510632, China; Guangdong Provincial Key Laboratory of Pharmacodynamics Constituents of TCM and New Drugs Research, Jinan University, Guangzhou 510632, China; International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), College of pharmacy, Jinan University, Guangzhou 510632, China
| | - Luyuan Huang
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Sijia Lei
- Institute of Genomic Medicine, College of Pharmacy, Jinan University, Guangzhou 510632, China; Guangdong Provincial Key Laboratory of Pharmacodynamics Constituents of TCM and New Drugs Research, Jinan University, Guangzhou 510632, China; International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), College of pharmacy, Jinan University, Guangzhou 510632, China
| | - Xingdong Cai
- Department of Respiratory, The First Affiliated Hospital of Jinan University, Guangzhou 510630, China
| | - Mason Breitzig
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, 12901 Bruce B Downs Blvd, MDC 19, Tampa, FL 33612, USA
| | - Bin Zhang
- Institute of Genomic Medicine, College of Pharmacy, Jinan University, Guangzhou 510632, China; Guangdong Provincial Key Laboratory of Pharmacodynamics Constituents of TCM and New Drugs Research, Jinan University, Guangzhou 510632, China; International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), College of pharmacy, Jinan University, Guangzhou 510632, China
| | - Annan Yang
- Institute of Genomic Medicine, College of Pharmacy, Jinan University, Guangzhou 510632, China; Guangdong Provincial Key Laboratory of Pharmacodynamics Constituents of TCM and New Drugs Research, Jinan University, Guangzhou 510632, China; International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), College of pharmacy, Jinan University, Guangzhou 510632, China
| | - Wenzuo Ji
- Institute of Genomic Medicine, College of Pharmacy, Jinan University, Guangzhou 510632, China; Guangdong Provincial Key Laboratory of Pharmacodynamics Constituents of TCM and New Drugs Research, Jinan University, Guangzhou 510632, China; International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), College of pharmacy, Jinan University, Guangzhou 510632, China
| | - Meiyan Huang
- Institute of Genomic Medicine, College of Pharmacy, Jinan University, Guangzhou 510632, China; Guangdong Provincial Key Laboratory of Pharmacodynamics Constituents of TCM and New Drugs Research, Jinan University, Guangzhou 510632, China; International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), College of pharmacy, Jinan University, Guangzhou 510632, China
| | - Qing Zheng
- Institute of Genomic Medicine, College of Pharmacy, Jinan University, Guangzhou 510632, China; Guangdong Provincial Key Laboratory of Pharmacodynamics Constituents of TCM and New Drugs Research, Jinan University, Guangzhou 510632, China; International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), College of pharmacy, Jinan University, Guangzhou 510632, China
| | - Hanxiao Sun
- Institute of Genomic Medicine, College of Pharmacy, Jinan University, Guangzhou 510632, China; Guangdong Provincial Key Laboratory of Pharmacodynamics Constituents of TCM and New Drugs Research, Jinan University, Guangzhou 510632, China; International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), College of pharmacy, Jinan University, Guangzhou 510632, China
| | - Feng Wang
- Institute of Genomic Medicine, College of Pharmacy, Jinan University, Guangzhou 510632, China; Guangdong Provincial Key Laboratory of Pharmacodynamics Constituents of TCM and New Drugs Research, Jinan University, Guangzhou 510632, China; International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), College of pharmacy, Jinan University, Guangzhou 510632, China.
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18
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Liu J, Wang L, Zhang Y, Li S, Sun F, Wang G, Yang T, Wei D, Guo L, Xiao H. Induction of entosis in prostate cancer cells by nintedanib and its therapeutic implications. Oncol Lett 2019; 17:3151-3162. [PMID: 30867745 PMCID: PMC6396220 DOI: 10.3892/ol.2019.9951] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 12/17/2018] [Indexed: 02/07/2023] Open
Abstract
Entosis is a homogeneous cell-in-cell phenomenon and a non-apoptotic cell death process. Tyrosine kinase inhibitors have been used in the treatment of prostate cancer and have already demonstrated efficacy in a clinical setting. The present study investigated the role of entosis in prostate cancer treated with the tyrosine kinase inhibitor nintedanib. Prostate cancer cells were treated with nintedanib in vitro and entosis was observed. Mice xenografts were created to evaluate whether nintedanib is able to induce entosis in vivo. The reverse transcription-quantitative polymerase chain reaction, western blotting and immunofluorescence were performed to investigate whether the entosis pathway is induced by nintedanib. It was also investigated whether entosis can contribute to cell survival and progression under nintedanib stress, and nintedanib was revealed to enhance prostate cancer cell entosis. Nintedanib-induced entosis in prostate cancer cells occurred through phosphoinositide 3-kinase/cell division cycle 42 (CDC42) inhibition, followed by the upregulation of epithelial (E-)cadherin and components of the Rho kinase (ROCK) signaling pathway. In addition, nintedanib-resistant cells exhibiting entosis had a higher invasive ability. In addition, in vivo treatment of mice xenografts with nintedanib also increased the expression of E-cadherin and components of the ROCK signaling pathway. Nintedanib can promote entosis during prostate cancer treatment by modulating the CDC42 pathway. Furthermore, prostate cancer cells acquired nintedanib resistance and survived by activating entosis.
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Affiliation(s)
- Junjiang Liu
- Department of Urology, Hebei General Hospital, Shijiazhuang, Hebei 050051, P.R. China
| | - Lei Wang
- Department of Urology, The First Hospital of Hebei Medical University, Shijiazhuang, Hebei 050051, P.R. China
| | - Yunxia Zhang
- Department of Obstetrics and Gynecology, Hebei General Hospital, Shijiazhuang, Hebei 050051, P.R. China
| | - Shoubin Li
- Department of Urology, Hebei General Hospital, Shijiazhuang, Hebei 050051, P.R. China
| | - Fuzhen Sun
- Department of Urology, Hebei General Hospital, Shijiazhuang, Hebei 050051, P.R. China
| | - Gang Wang
- Department of Urology, Hebei General Hospital, Shijiazhuang, Hebei 050051, P.R. China
| | - Tao Yang
- Department of Urology, Hebei General Hospital, Shijiazhuang, Hebei 050051, P.R. China
| | - Dong Wei
- Department of Urology, Hebei General Hospital, Shijiazhuang, Hebei 050051, P.R. China
| | - Liuxiong Guo
- Department of Urology, Hebei General Hospital, Shijiazhuang, Hebei 050051, P.R. China
| | - Helong Xiao
- Department of Urology, Hebei General Hospital, Shijiazhuang, Hebei 050051, P.R. China
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19
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Bustelo XR. RHO GTPases in cancer: known facts, open questions, and therapeutic challenges. Biochem Soc Trans 2018; 46:741-760. [PMID: 29871878 PMCID: PMC7615761 DOI: 10.1042/bst20170531] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 04/17/2018] [Accepted: 05/03/2018] [Indexed: 02/06/2023]
Abstract
RHO GTPases have been traditionally associated with protumorigenic functions. While this paradigm is still valid in many cases, recent data have unexpectedly revealed that RHO proteins can also play tumor suppressor roles. RHO signaling elements can also promote both pro- and antitumorigenic effects using GTPase-independent mechanisms, thus giving an extra layer of complexity to the role of these proteins in cancer. Consistent with these variegated roles, both gain- and loss-of-function mutations in RHO pathway genes have been found in cancer patients. Collectively, these observations challenge long-held functional archetypes for RHO proteins in both normal and cancer cells. In this review, I will summarize these data and discuss new questions arising from them such as the functional and clinical relevance of the mutations found in patients, the mechanistic orchestration of those antagonistic functions in tumors, and the pros and cons that these results represent for the development of RHO-based anticancer drugs.
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Affiliation(s)
- Xosé R Bustelo
- Centro de Investigación del Cáncer, Instituto de Biología Molecular y Celular del Cáncer, and Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, 37007 Salamanca, Spain
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20
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Wang X, Li Y, Fan Y, Yu X, Mao X, Jin F. PTBP1 promotes the growth of breast cancer cells through the PTEN/Akt pathway and autophagy. J Cell Physiol 2018; 233:8930-8939. [PMID: 29856478 PMCID: PMC6175200 DOI: 10.1002/jcp.26823] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Accepted: 04/30/2018] [Indexed: 12/22/2022]
Abstract
Invasion and migration is the hallmark of malignant tumors as well as the major cause for breast cancer death. The polypyrimidine tract binding, PTB, protein serves as an important model for understanding how RNA binding proteins affect proliferation and invasion and how changes in the expression of these proteins can control complex programs of tumorigenesis. We have investigated some roles of polypyrimidine tract binding protein 1 (PTBP1) in human breast cancer. We found that PTBP1 was upregulated in breast cancer tissues compared with normal tissues and the same result was confirmed in breast cancer cell lines. Knockdown of PTBP1 substantially inhibited tumor cell growth, migration, and invasion. These results suggest that PTBP1 is associated with breast tumorigenesis and appears to be required for tumor cell growth and maintenance of metastasis. We further analyzed the relationship between PTBP1 and clinicopathological parameters and found that PTBP1 was correlated with her‐2 expression, lymph node metastasis, and pathological stage. This will be a novel target for her‐2(+) breast cancer. PTBP1 exerts these effects, in part, by regulating the phosphatase and tensin homolog‐phosphatidylinositol‐4,5‐bisphosphate 3‐kinase/protein kinase B (PTEN‐PI3K/Akt) pathway and autophagy, and consequently alters cell growth and contributes to the invasion and metastasis.
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Affiliation(s)
- Xu Wang
- Department of Breast Surgery, The First Affiliated Hospital of China Medical University, Shenyang City, Liaoning, China
| | - Yang Li
- Department of Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health, and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang, China
| | - Yan Fan
- Department of Pediatrics, The First Affiliated Hospital of China Medical University, Shenyang City, Liaoning, China
| | - Xinmiao Yu
- Department of Breast Surgery, The First Affiliated Hospital of China Medical University, Shenyang City, Liaoning, China
| | - Xiaoyun Mao
- Department of Breast Surgery, The First Affiliated Hospital of China Medical University, Shenyang City, Liaoning, China
| | - Feng Jin
- Department of Breast Surgery, The First Affiliated Hospital of China Medical University, Shenyang City, Liaoning, China
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21
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Blue RE, Curry EG, Engels NM, Lee EY, Giudice J. How alternative splicing affects membrane-trafficking dynamics. J Cell Sci 2018; 131:jcs216465. [PMID: 29769303 PMCID: PMC6031328 DOI: 10.1242/jcs.216465] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The cell biology field has outstanding working knowledge of the fundamentals of membrane-trafficking pathways, which are of critical importance in health and disease. Current challenges include understanding how trafficking pathways are fine-tuned for specialized tissue functions in vivo and during development. In parallel, the ENCODE project and numerous genetic studies have revealed that alternative splicing regulates gene expression in tissues and throughout development at a post-transcriptional level. This Review summarizes recent discoveries demonstrating that alternative splicing affects tissue specialization and membrane-trafficking proteins during development, and examines how this regulation is altered in human disease. We first discuss how alternative splicing of clathrin, SNAREs and BAR-domain proteins influences endocytosis, secretion and membrane dynamics, respectively. We then focus on the role of RNA-binding proteins in the regulation of splicing of membrane-trafficking proteins in health and disease. Overall, our aim is to comprehensively summarize how trafficking is molecularly influenced by alternative splicing and identify future directions centered on its physiological relevance.
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Affiliation(s)
- R Eric Blue
- Department of Cell Biology & Physiology, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ennessa G Curry
- Department of Cell Biology & Physiology, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Nichlas M Engels
- Department of Cell Biology & Physiology, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Eunice Y Lee
- Department of Cell Biology & Physiology, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jimena Giudice
- Department of Cell Biology & Physiology, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- McAllister Heart Institute, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Curriculum in Genetics and Molecular Biology (GMB), The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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22
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Zhu J, Chen Z, Yong L. Systematic profiling of alternative splicing signature reveals prognostic predictor for ovarian cancer. Gynecol Oncol 2017; 148:368-374. [PMID: 29191436 DOI: 10.1016/j.ygyno.2017.11.028] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 11/13/2017] [Accepted: 11/23/2017] [Indexed: 02/03/2023]
Abstract
OBJECTIVE The majority of genes are alternatively spliced and growing evidence suggests that alternative splicing is modified in cancer and is associated with cancer progression. Systematic analysis of alternative splicing signature in ovarian cancer is lacking and greatly needed. METHODS We profiled genome-wide alternative splicing events in 408 ovarian serous cystadenocarcinoma (OV) patients in TCGA. Seven types of alternative splicing events were curated and prognostic analyses were performed with predictive models and splicing network built for OV patients. RESULTS Among 48,049 mRNA splicing events in 10,582 genes, we detected 2,611 alternative splicing events in 2,036 genes which were significant associated with overall survival of OV patients. Exon skip events were the most powerful prognostic factors among the seven types. The area under the curve of the receiver-operator characteristic curve for prognostic predictor, which was built with top significant alternative splicing events, was 0.937 at 2,000 days of overall survival, indicating powerful efficiency in distinguishing patient outcome. Interestingly, splicing correlation network suggested obvious trends in the role of splicing factors in OV. CONCLUSIONS In summary, we built powerful prognostic predictors for OV patients and uncovered interesting splicing networks which could be underlying mechanisms.
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Affiliation(s)
- Junyong Zhu
- School of Medicine, Wuhan University, Wuhan, China.
| | - Zuhua Chen
- Department of Gastrointestinal Oncology, Peking University Cancer Hospital and Institute, Beijing, China
| | - Lei Yong
- Department of Orthopedics, Peking University Third Hospital, Beijing, China
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23
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Jiang J, Chen X, Liu H, Shao J, Xie R, Gu P, Duan C. Polypyrimidine Tract-Binding Protein 1 promotes proliferation, migration and invasion in clear-cell renal cell carcinoma by regulating alternative splicing of PKM. Am J Cancer Res 2017; 7:245-259. [PMID: 28337374 PMCID: PMC5336499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 01/16/2017] [Indexed: 06/06/2023] Open
Abstract
Polypyrimidine Tract-Binding Protein 1 (PTBP1) is an essential RNA-binding protein that regulates diverse biological events through regulating alternative splice of mRNA. PTBP1 induces cancer-promoting splice variants and is related to tumorigenesis in several cancers. However, both the expression patterns and biological mechanisms of PTBP1 in clear-cell renal cell carcinoma (ccRCC) are unclear. We investigated PTBP1 expression in 533 ccRCC patients from TCGA and 30 ccRCC patients by immunohistochemistry, and found that PTBP1 expression levels were significantly increased in ccRCC tissues and that high PTBP1 expression was closely correlated with advanced tumor stage, AJCC stage and poor prognosis. Cell biological assays with siRNA-mediated knockdown and lentivirus vector-mediated over-expression demonstrated that PTBP1 promoted proliferation, migration and invasion in ccRCC cells in vitro. Furthermore, PTBP1 increased the transformation from pyruvate kinase muscle 1 (PKM1) to PKM2. Knockdown of PKM2 mainly abolished PTBP1-induced proliferation, migration and invasion in ccRCC cells in vitro. In conclusion, our study indicates that PTBP1 plays a tumorigenic role in ccRCC by mediating PKM2 alternative splicing and it may be a potential prognostic marker and a promising target for treatment of ccRCC.
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Affiliation(s)
- Junyi Jiang
- Department of Laboratory Medicine, Sun Yat-sen Memorial Hospital, Sun Yat-sen UniversityGuangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen UniversityGuangzhou, China
| | - Xu Chen
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen UniversityGuangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen UniversityGuangzhou, China
| | - Hao Liu
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen UniversityGuangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen UniversityGuangzhou, China
| | - Jing Shao
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen UniversityGuangzhou, China
- Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen UniversityGuangzhou, China
| | - Ruihui Xie
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen UniversityGuangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen UniversityGuangzhou, China
| | - Peng Gu
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen UniversityGuangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen UniversityGuangzhou, China
| | - Chaohui Duan
- Department of Laboratory Medicine, Sun Yat-sen Memorial Hospital, Sun Yat-sen UniversityGuangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen UniversityGuangzhou, China
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