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Yaghoubi Naei V, Monkman J, Sadeghirad H, Mehdi A, Blick T, Mullally W, O'Byrne K, Warkiani ME, Kulasinghe A. Spatial proteomic profiling of tumor and stromal compartments in non-small-cell lung cancer identifies signatures associated with overall survival. Clin Transl Immunology 2024; 13:e1522. [PMID: 39026528 PMCID: PMC11257771 DOI: 10.1002/cti2.1522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 07/04/2024] [Accepted: 07/05/2024] [Indexed: 07/20/2024] Open
Abstract
Objectives Non-small-cell lung carcinoma (NSCLC) is the most prevalent and lethal form of lung cancer. The need for biomarker-informed stratification of targeted therapies has underpinned the need to uncover the underlying properties of the tumor microenvironment (TME) through high-plex quantitative assays. Methods In this study, we profiled resected NSCLC tissues from 102 patients by targeted spatial proteomics of 78 proteins across tumor, immune activation, immune cell typing, immune-oncology, drug targets, cell death and PI3K/AKT modules to identify the tumor and stromal signatures associated with overall survival (OS). Results Survival analysis revealed that stromal CD56 (HR = 0.384, P = 0.06) and tumoral TIM3 (HR = 0.703, P = 0.05) were associated with better survival in univariate Cox models. In contrast, after adjusting for stage, BCLXL (HR = 2.093, P = 0.02) and cleaved caspase 9 (HR = 1.575, P = 0.1) negatively influenced survival. Delta testing indicated the protective effect of TIM-3 (HR = 0.614, P = 0.04) on OS. In multivariate analysis, CD56 (HR = 0.172, P = 0.001) was associated with better survival in the stroma, while B7.H3 (HR = 1.72, P = 0.008) was linked to poorer survival in the tumor. Conclusions Deciphering the TME using high-plex spatially resolved methods is giving us new insights into compartmentalised tumor and stromal protein signatures associated with clinical endpoints in NSCLC.
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Affiliation(s)
- Vahid Yaghoubi Naei
- School of Biomedical EngineeringUniversity of Technology SydneySydneyNSWAustralia
- Frazer Institute, Faculty of MedicineThe University of QueenslandBrisbaneQLDAustralia
| | - James Monkman
- Frazer Institute, Faculty of MedicineThe University of QueenslandBrisbaneQLDAustralia
| | - Habib Sadeghirad
- Frazer Institute, Faculty of MedicineThe University of QueenslandBrisbaneQLDAustralia
| | - Ahmed Mehdi
- Queensland Cyber Infrastructure Foundation (QCIF) LtdThe University of QueenslandBrisbaneQLDAustralia
| | - Tony Blick
- Frazer Institute, Faculty of MedicineThe University of QueenslandBrisbaneQLDAustralia
| | | | - Ken O'Byrne
- The Princess Alexandra HospitalBrisbaneQLDAustralia
| | | | - Arutha Kulasinghe
- Frazer Institute, Faculty of MedicineThe University of QueenslandBrisbaneQLDAustralia
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Xie X, Macknight HP, Lu AL, Chalfant CE. RNA splicing variants of the novel long non-coding RNA, CyKILR, possess divergent biological functions in non-small cell lung cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.08.602494. [PMID: 39026815 PMCID: PMC11257467 DOI: 10.1101/2024.07.08.602494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
The CDKN2A gene, responsible for encoding the tumor suppressors p16(INK4A) and p14(ARF), is frequently inactivated in non-small cell lung cancer (NSCLC). In this study, an uncharacterized long non-coding RNA (lncRNA) (ENSG00000267053) on chromosome 19p13.12 was found to be overexpressed in NSCLC cells with an active CDKN2A gene. This lncRNA, named Cy clin-Dependent K inase I nhibitor 2A-regulated l nc R NA (CyKILR), also correlated with the STK11 gene-coded tumor suppressor Liver kinase B1 (LKB1). CyKILR displayed two splice variants, CyKILRa (with exon 3) and CyKILRb (without exon 3), which are synergistically regulated by CDKN2A and STK11 as knockdown of both tumor suppressor genes led to a significant loss of exon 3 inclusion in mature CyKILR RNA. CyKILRa localized to the nucleus, and its downregulation using antisense RNA oligonucleotides enhanced cellular proliferation, migration, clonogenic survival, and tumor incidence. In contrast, CyKILRb localized to the cytoplasm, and downregulation of CyKILRb using siRNA reduced cell proliferation, migration, clonogenic survival, and tumor incidence. Transcriptomics analyses revealed enhancement of apoptotic pathways with concomitant suppression of key cell cycle pathways by CyKILRa demonstrating its tumor-suppressive role, while CyKILRb inhibited tumor suppressor microRNAs, indicating an oncogenic nature. These findings elucidate the intricate roles of lncRNAs in cell signaling and tumorigenesis.
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Wang J, Chen S, Sawant H, Chen Y, Bihl JC. The miR-210 Primed Endothelial Progenitor Cell Exosomes Alleviate Acute Ischemic Brain Injury. Curr Stem Cell Res Ther 2024; 19:1164-1174. [PMID: 37957914 PMCID: PMC11082070 DOI: 10.2174/011574888x266357230923113642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/14/2023] [Accepted: 08/24/2023] [Indexed: 11/15/2023]
Abstract
BACKGROUND Stem cell-released exosomes (EXs) have shown beneficial effects on regenerative diseases. Our previous study has revealed that EXs of endothelial progenitor cells (EPC-EXs) can elicit favorable effects on endothelial function. EXs may vary greatly in size, composition, and cargo uptake rate depending on the origins and stimulus; notably, EXs are promising vehicles for delivering microRNAs (miRs). Since miR-210 is known to protect cerebral endothelial cell mitochondria by reducing oxidative stress, here we study the effects of miR-210-loaded EPC-EXs (miR210-EPC-EXs) on ischemic brain damage in acute ischemic stroke (IS). METHODS The miR210-EPC-EXs were generated from EPCs transfected with miR-210 mimic. Middle cerebral artery occlusion (MCAO) surgery was performed to induce acute IS in C57BL/6 mice. EPC-EXs or miR210-EPC-EXs were administrated via tail vein injection 2 hrs after IS. To explore the potential mechanisms, inhibitors of the vascular endothelial growth factor receptor 2 (VEGFR2)/PI3 kinase (PI3K) or tyrosine receptor kinase B (TrkB)/PI3k pathways were used. The brain tissue was collected after treatments for infarct size, cell apoptosis, oxidative stress, and protein expression (VEGFR2, TrkB) analyses on day two. The neurological deficit score (NDS) was evaluated before collecting the samples. RESULTS 1) As compared to EPC-EXs, miR210-EPC-EXs profoundly reduced the infarct volume and improved the NDS on day two post-IS. 2) Fewer apoptosis cells were detected in the peri-infarct brain of mice treated with miR210-EPC-EXs than in EPC-EXs-treated mice. Meanwhile, the oxidative stress was profoundly reduced by miR210-EPC-EXs. 3) The ratios of p-PI3k/PI3k, p- VEGFR2/VEGFR2, and p-TrkB/TrkB in the ipsilateral brain were raised by miR210-EPC-EXs treatment. These effects could be significantly blocked or partially inhibited by PI3k, VEGFR2, or TrkB pathway inhibitors. CONCLUSION These findings suggest that miR210-EPC-EXs protect the brain from acute ischemia- induced cell apoptosis and oxidative stress partially through the VEGFR2/PI3k and TrkB/PI3k signal pathways.
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Affiliation(s)
- Jinju Wang
- Department of Biomedical Sciences, Joan C Edwards School of Medicine, Marshall University, Huntington, WV25755, USA
| | - Shuzhen Chen
- Department of Biomedical Sciences, Joan C Edwards School of Medicine, Marshall University, Huntington, WV25755, USA
| | - Harshal Sawant
- Department of Biomedical Sciences, Joan C Edwards School of Medicine, Marshall University, Huntington, WV25755, USA
| | - Yanfang Chen
- Department of Pharmacology and Toxicology, Boonshoft School of Medicine, Wright State University, Dayton, OH45435, USA
| | - Ji Chen Bihl
- Department of Biomedical Sciences, Joan C Edwards School of Medicine, Marshall University, Huntington, WV25755, USA
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Recent insights into the role of Akt in CD4 T-cell activation and differentiation: alternative splicing and beyond. IMMUNOMETABOLISM (COBHAM (SURREY, ENGLAND)) 2023; 5:e00015. [PMID: 36710922 PMCID: PMC9869951 DOI: 10.1097/in9.0000000000000015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 11/03/2022] [Indexed: 01/31/2023]
Abstract
The activation and differentiation of CD4+ T cells is a complex process that is controlled by many factors. A critical component of the signaling pathway triggered following T-cell receptor (TCR) engagement is the serine threonine kinase Akt. Akt is involved in the control of many cellular processes including proliferation, metabolism, and differentiation of specific TH-cell subsets. Recent work has shown that, depending on the nature or strength of the TCR activation, Akt may activate different sets of substrates which then lead to differential cellular outcomes. Akt plays an important role in controlling the strength of the TCR signal and several recent studies have identified novel mechanisms including control of the expression of negative regulators of TCR signaling, and the influence on regulatory T cells (Treg) and TH17 differentiation. Many of these functions are mediated via control of the FoxO family of transcription factors, that play an important role in metabolism and Th cell differentiation. A theme that is emerging is that Akt does not function in the same way in all T-cell types. We highlight differences between CD4 and CD8 T cells as well as between Treg, TH17, and TFH cells. While Akt activity has been implicated in the control of alternative splicing in tumor cells, recent studies are emerging that indicate that similar functions may exist in CD4 T cells. In this mini review, we highlight some of the recent advances in these areas of Akt function that demonstrate the varied role that Akt plays in the function of CD4 T cells.
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Wan L, Deng M, Zhang H. SR Splicing Factors Promote Cancer via Multiple Regulatory Mechanisms. Genes (Basel) 2022; 13:1659. [PMID: 36140826 PMCID: PMC9498594 DOI: 10.3390/genes13091659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/09/2022] [Accepted: 09/14/2022] [Indexed: 11/17/2022] Open
Abstract
Substantial emerging evidence supports that dysregulated RNA metabolism is associated with tumor initiation and development. Serine/Arginine-Rich proteins (SR) are a number of ultraconserved and structurally related proteins that contain a characteristic RS domain rich in arginine and serine residues. SR proteins perform a critical role in spliceosome assembling and conformational transformation, contributing to precise alternative RNA splicing. Moreover, SR proteins have been reported to participate in multiple other RNA-processing-related mechanisms than RNA splicing, such as genome stability, RNA export, and translation. The dysregulation of SR proteins has been reported to contribute to tumorigenesis through multiple mechanisms. Here we reviewed the different biological roles of SR proteins and strategies for functional rectification of SR proteins that may serve as potential therapeutic approaches for cancer.
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Affiliation(s)
- Ledong Wan
- Department of Pathology, Research Unit of Intelligence Classification of Tumor Pathology and Precision Therapy of Chinese Academy of Medical Sciences (2019RU042), Zhejiang University School of Medicine, Hangzhou 310058, China
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Min Deng
- Department of Pathology, First Peoples Hospital Fuyang, Hangzhou 311400, China
| | - Honghe Zhang
- Department of Pathology, Research Unit of Intelligence Classification of Tumor Pathology and Precision Therapy of Chinese Academy of Medical Sciences (2019RU042), Zhejiang University School of Medicine, Hangzhou 310058, China
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Vu NT, Kim M, Stephenson DJ, MacKnight HP, Chalfant CE. Ceramide Kinase Inhibition Drives Ferroptosis and Sensitivity to Cisplatin in Mutant KRAS Lung Cancer by Dysregulating VDAC-Mediated Mitochondria Function. Mol Cancer Res 2022; 20:1429-1442. [PMID: 35560154 PMCID: PMC9444881 DOI: 10.1158/1541-7786.mcr-22-0085] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 04/15/2022] [Accepted: 05/11/2022] [Indexed: 11/16/2022]
Abstract
Ceramide kinase (CERK) is the mammalian lipid kinase from which the bioactive sphingolipid, ceramide-1-phosphate (C1P), is derived. CERK has been implicated in several promalignant phenotypes with little known as to mechanistic underpinnings. In this study, the mechanism of how CERK inhibition decreases cell survival in mutant (Mut) KRAS non-small cell lung cancer (NSCLC), a major lung cancer subtype, was revealed. Specifically, NSCLC cells possessing a KRAS mutation were more responsive to inhibition, downregulation, and genetic ablation of CERK compared with those with wild-type (WT) KRAS regarding a reduction in cell survival. Inhibition of CERK induced ferroptosis in Mut KRAS NSCLC cells, which required elevating VDAC-regulated mitochondria membrane potential (MMP) and the generation of cellular reactive oxygen species (ROS). Importantly, through modulation of VDAC, CERK inhibition synergized with the first-line NSCLC treatment, cisplatin, in reducing cell survival and in vivo tumor growth. Further mechanistic studies indicated that CERK inhibition affected MMP and cell survival by limiting AKT activation and translocation to mitochondria, and thus, blocking VDAC phosphorylation and tubulin recruitment. IMPLICATIONS Our findings depict how CERK inhibition may serve as a new key point in combination therapeutic strategy for NSCLC, specifically precision therapeutics targeting NSCLC possessing a KRAS mutation.
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Affiliation(s)
- Ngoc T. Vu
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL 33620, USA,Institute of Biotechnology and Food Technology, Industrial University of Ho Chi Minh City, Vietnam
| | - Minjung Kim
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL 33620, USA
| | - Daniel J. Stephenson
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL 33620, USA,Department of Medicine, Division of Hematology & Oncology, University of Virginia, Charlottesville, VA, 22903
| | - H. Patrick MacKnight
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL 33620, USA,Department of Medicine, Division of Hematology & Oncology, University of Virginia, Charlottesville, VA, 22903
| | - Charles E. Chalfant
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL 33620, USA,Department of Medicine, Division of Hematology & Oncology, University of Virginia, Charlottesville, VA, 22903,Department of Cell Biology, University of Virginia, Charlottesville, VA, 22903,Program in Cancer Biology, University of Virginia Cancer Center, Charlottesville, VA, 22903,Research Service, Richmond Veterans Administration Medical Center, Richmond VA, 23298,To whom correspondence should be addressed: Charles E. Chalfant, Professor, Department of Medicine, Division of Hematology & Oncology, P.O. Box 801398, University of Virginia, Charlottesville, VA, 22903, or
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7
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Kim M, Vu NT, Wang X, Bulut GB, Wang MH, Uram-Tuculescu C, Pillappa R, Kim S, Chalfant CE. Caspase-9b drives cellular transformation, lung inflammation, and lung tumorigenesis. Mol Cancer Res 2022; 20:1284-1294. [PMID: 35412615 DOI: 10.1158/1541-7786.mcr-21-0905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 02/28/2022] [Accepted: 04/08/2022] [Indexed: 11/16/2022]
Abstract
Caspase 9 undergoes alternative splicing to produce two opposing isoforms: pro-apoptotic Caspase-9a (C9a) and pro-survival Caspase-9b (C9b). Previously, our laboratory reported that C9b is expressed in majority of non-small cell lung cancer tumors and directly activates the NF-κB pathway. In this study, the role of C9b in activation of the NF-κB pathway in vivo, lung inflammation and immune responses, and lung tumorigenesis were examined. Specifically, a transgenic mouse model expressing human C9b in the lung pneumocytes developed inflammatory lung lesions, which correlated with enhanced activation of the NF-κB pathway and increased influx of immunosuppressive MDSCs in contrast to wild-type mice. C9b mice presented with facial dermatitis, a thickened and disorganized dermis, enhanced collagen depth, and increased serum levels of IL-6. C9b mice also developed spontaneous lung tumors, and C9b cooperated with oncogenic KRAS in lung tumorigenesis. C9b expression also cooperated with oncogenic KRAS and p53 downregulation to drive the full cell transformation of human bronchial epithelial cells (e.g., tumor formation). Implications: Our findings show that C9b can directly activate NF-κB pathway in vivo to modulate lung inflammation, immune cell influx, and peripheral immune responses, which demonstrates that C9b is key factor in driving cell transformation and lung tumorigenesis.
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Affiliation(s)
- Minjung Kim
- University of South Florida, Tampa, FL, United States
| | - Ngoc T Vu
- University of South Florida, United States
| | - Xue Wang
- University of South Florida, Tampa, Virginia, United States
| | - Gamze B Bulut
- Virginia Commonwealth University-School of Medicine, Richmond, Virginia, United States
| | - Min-Hsuan Wang
- H. Lee Moffitt Cancer Center & Research, Tampa, Florida, United States
| | | | - Raghavendra Pillappa
- Virginia Commonwealth University-School of Medicine, Richmond, Virginia, United States
| | | | - Charles E Chalfant
- University of Virginia School of Medicine, Charlottesville, Virginia, United States
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8
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Maus KD, Stephenson DJ, Ali AN, MacKnight HP, Huang HJ, Serrats J, Kim M, Diegelmann RF, Chalfant CE. Ceramide kinase regulates acute wound healing by suppressing 5-oxo-ETE biosynthesis and signaling via its receptor OXER1. J Lipid Res 2022; 63:100187. [PMID: 35219746 PMCID: PMC8980959 DOI: 10.1016/j.jlr.2022.100187] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 02/18/2022] [Accepted: 02/21/2022] [Indexed: 01/10/2023] Open
Abstract
The sphingolipid, ceramide-1-phosphate (C1P), has been shown to promote the inflammatory phase and inhibit the proliferation and remodeling stages of wound repair via direct interaction with group IVA cytosolic phospholipase A2, a regulator of eicosanoid biosynthesis that fine-tunes the behaviors of various cell types during wound healing. However, the anabolic enzyme responsible for the production of C1P that suppresses wound healing as well as bioactive eicosanoids and target receptors that drive enhanced wound remodeling have not been characterized. Herein, we determined that decreasing C1P activity via inhibitors or genetic ablation of the anabolic enzyme ceramide kinase (CERK) significantly enhanced wound healing phenotypes. Importantly, postwounding inhibition of CERK enhanced the closure rate of acute wounds, improved the quality of healing, and increased fibroblast migration via a "class switch" in the eicosanoid profile. This switch reduced pro-inflammatory prostaglandins (e.g., prostaglandin E2) and increased levels of 5-hydroxyeicosatetraenoic acid and the downstream metabolite 5-oxo-eicosatetraenoic acid (5-oxo-ETE). Moreover, dermal fibroblasts from mice with genetically ablated CERK showed enhanced wound healing markers, while blockage of the murine 5-oxo-ETE receptor (oxoeicosanoid receptor 1) inhibited the enhanced migration phenotype of these cell models. Together, these studies reinforce the vital roles eicosanoids play in the wound healing process and demonstrate a novel role for CERK-derived C1P as a negative regulator of 5-oxo-ETE biosynthesis and the activation of oxoeicosanoid receptor 1 in wound healing. These findings provide foundational preclinical results for the use of CERK inhibitors to shift the balance from inflammation to resolution and increase the wound healing rate.
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Affiliation(s)
- Kenneth D Maus
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL, USA
| | - Daniel J Stephenson
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL, USA
| | - Anika N Ali
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL, USA
| | - Henry Patrick MacKnight
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL, USA
| | - Huey-Jing Huang
- Neuroscience Drug Discovery Unit, Takeda California, San Diego, CA, USA
| | - Jordi Serrats
- Neuroscience Drug Discovery Unit, Takeda California, San Diego, CA, USA
| | - Minjung Kim
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL, USA
| | - Robert F Diegelmann
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University-School of Medicine, Richmond, VA, USA
| | - Charles E Chalfant
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL, USA; Cancer Biology and Evolution Program, The Moffitt Cancer Center, Tampa, FL, USA; Research Service, James A. Haley Veterans Hospital, Tampa, FL, USA; Division of Hematology & Oncology, Department of Medicine, University of Virginia, Charlottesville, VA, USA; Department of Cell Biology, University of Virginia, Charlottesville, VA, USA; Program in Cancer Biology, University of Virginia Cancer Center, Charlottesville, VA, USA; Research Service, Hunter Holmes McGuire Veterans Administration Medical Center, Richmond, VA, USA.
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9
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Ye H, He Y, Zheng C, Wang F, Yang M, Lin J, Xu R, Zhang D. Type 2 Diabetes Complicated With Heart Failure: Research on Therapeutic Mechanism and Potential Drug Development Based on Insulin Signaling Pathway. Front Pharmacol 2022; 13:816588. [PMID: 35308248 PMCID: PMC8927800 DOI: 10.3389/fphar.2022.816588] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 01/31/2022] [Indexed: 01/16/2023] Open
Abstract
Type 2 diabetes mellitus (T2DM) and heart failure (HF) are diseases characterized by high morbidity and mortality. They often occur simultaneously and increase the risk of each other. T2DM complicated with HF, as one of the most dangerous disease combinations in modern medicine, is more common in middle-aged and elderly people, making the treatment more difficult. At present, the combination of blood glucose control and anti-heart failure is a common therapy for patients with T2DM complicated with HF, but their effect is not ideal, and many hypoglycemic drugs have the risk of heart failure. Abnormal insulin signaling pathway, as a common pathogenic mechanism in T2DM and HF, could lead to pathological features such as insulin resistance (IR), myocardial energy metabolism disorders, and vascular endothelial disorders. The therapy based on the insulin signaling pathway may become a specific therapeutic target for T2DM patients with HF. Here, we reviewed the mechanisms and potential drugs of insulin signaling pathway in the treatment of T2DM complicated with HF, with a view to opening up a new perspective for the treatment of T2DM patients with HF and the research and development of new drugs.
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Affiliation(s)
- Hui Ye
- State Key Laboratory of Southwestern Chinese Medicine Resources, Pharmacy School, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yanan He
- State Key Laboratory of Southwestern Chinese Medicine Resources, Pharmacy School, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Chuan Zheng
- TCM Regulating Metabolic Diseases Key Laboratory of Sichuan Province, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Fang Wang
- State Key Laboratory of Innovation Medicine and High Efficiency and Energy Saving Pharmaceutical Equipment, Jiangxi University of Traditional Chinese Medicine, Nanchang, China
| | - Ming Yang
- State Key Laboratory of Innovation Medicine and High Efficiency and Energy Saving Pharmaceutical Equipment, Jiangxi University of Traditional Chinese Medicine, Nanchang, China
| | - Junzhi Lin
- TCM Regulating Metabolic Diseases Key Laboratory of Sichuan Province, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Runchun Xu
- State Key Laboratory of Southwestern Chinese Medicine Resources, Pharmacy School, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Dingkun Zhang
- State Key Laboratory of Southwestern Chinese Medicine Resources, Pharmacy School, Chengdu University of Traditional Chinese Medicine, Chengdu, China
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10
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Xiao D, Kim HJ, Pang I, Yang P. Functional analysis of the stable phosphoproteome reveals cancer vulnerabilities. Bioinformatics 2022; 38:1956-1963. [PMID: 35015814 PMCID: PMC9113330 DOI: 10.1093/bioinformatics/btac015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 12/21/2021] [Accepted: 01/06/2022] [Indexed: 11/29/2022] Open
Abstract
Motivation The advance of mass spectrometry-based technologies enabled the profiling of the phosphoproteomes of a multitude of cell and tissue types. However, current research primarily focused on investigating the phosphorylation dynamics in specific cell types and experimental conditions, whereas the phosphorylation events that are common across cell/tissue types and stable regardless of experimental conditions are, so far, mostly ignored. Results Here, we developed a statistical framework to identify the stable phosphoproteome across 53 human phosphoproteomics datasets, covering 40 cell/tissue types and 194 conditions/treatments. We demonstrate that the stably phosphorylated sites (SPSs) identified from our statistical framework are evolutionarily conserved, functionally important and enriched in a range of core signaling and gene pathways. Particularly, we show that SPSs are highly enriched in the RNA splicing pathway, an essential cellular process in mammalian cells, and frequently disrupted by cancer mutations, suggesting a link between the dysregulation of RNA splicing and cancer development through mutations on SPSs. Availability and implementation The source code for data analysis in this study is available from Github repository https://github.com/PYangLab/SPSs under the open-source license of GPL-3. The data used in this study are publicly available (see Section 2.8). Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Di Xiao
- Computational Systems Biology Group
| | - Hani Jieun Kim
- Computational Systems Biology Group.,Charles Perkins Centre, School of Mathematics and Statistics, The University of Sydney, Sydney, NSW, Australia
| | - Ignatius Pang
- Bioinformatics Group, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia
| | - Pengyi Yang
- Computational Systems Biology Group.,Charles Perkins Centre, School of Mathematics and Statistics, The University of Sydney, Sydney, NSW, Australia
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11
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Blake D, Radens CM, Ferretti MB, Gazzara MR, Lynch KW. Alternative splicing of apoptosis genes promotes human T cell survival. eLife 2022; 11:80953. [PMID: 36264057 PMCID: PMC9625086 DOI: 10.7554/elife.80953] [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: 06/10/2022] [Accepted: 10/19/2022] [Indexed: 11/13/2022] Open
Abstract
Alternative splicing occurs in the vast majority of human genes, giving rise to distinct mRNA and protein isoforms. We, and others, have previously identified hundreds of genes that change their isoform expression upon T cell activation via alternative splicing; however, how these changes link activation input with functional output remains largely unknown. Here, we investigate how costimulation of T cells through the CD28 receptor impacts alternative splicing in T cells activated through the T cell receptor (TCR, CD3) and find that while CD28 signaling alone has minimal impact on splicing, it enhances the extent of change for up to 20% of TCR-induced alternative splicing events. Interestingly, a set of CD28-enhanced splicing events occur within genes encoding key components of the apoptotic signaling pathway; namely caspase-9, Bax, and Bim. Using both CRISPR-edited cells and antisense oligos to force expression of specific isoforms, we show for all three of these genes that the isoform induced by CD3/CD28 costimulation promotes resistance to apoptosis, and that changes in all three genes together function combinatorially to further promote cell viability. Finally, we show that the JNK signaling pathway, induced downstream of CD3/CD28 costimulation, is required for each of these splicing events, further highlighting their co-regulation. Together, these findings demonstrate that alternative splicing is a key mechanism by which costimulation of CD28 promotes viability of activated T cells.
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Affiliation(s)
- Davia Blake
- Immunology Graduate Group, University of PennsylvaniaPhiladelphiaUnited States,Department of Biochemistry and Biophysics, University of PennsylvaniaPhiladelphiaUnited States
| | - Caleb M Radens
- Department of Biochemistry and Biophysics, University of PennsylvaniaPhiladelphiaUnited States
| | - Max B Ferretti
- Department of Biochemistry and Biophysics, University of PennsylvaniaPhiladelphiaUnited States
| | - Matthew R Gazzara
- Department of Biochemistry and Biophysics, University of PennsylvaniaPhiladelphiaUnited States,Department of Genetics, University of PennsylvaniaPhildelphiaUnited States
| | - Kristen W Lynch
- Immunology Graduate Group, University of PennsylvaniaPhiladelphiaUnited States,Department of Biochemistry and Biophysics, University of PennsylvaniaPhiladelphiaUnited States
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12
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Ruta V, Pagliarini V, Sette C. Coordination of RNA Processing Regulation by Signal Transduction Pathways. Biomolecules 2021; 11:biom11101475. [PMID: 34680108 PMCID: PMC8533259 DOI: 10.3390/biom11101475] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/01/2021] [Accepted: 10/05/2021] [Indexed: 02/06/2023] Open
Abstract
Signal transduction pathways transmit the information received from external and internal cues and generate a response that allows the cell to adapt to changes in the surrounding environment. Signaling pathways trigger rapid responses by changing the activity or localization of existing molecules, as well as long-term responses that require the activation of gene expression programs. All steps involved in the regulation of gene expression, from transcription to processing and utilization of new transcripts, are modulated by multiple signal transduction pathways. This review provides a broad overview of the post-translational regulation of factors involved in RNA processing events by signal transduction pathways, with particular focus on the regulation of pre-mRNA splicing, cleavage and polyadenylation. The effects of several post-translational modifications (i.e., sumoylation, ubiquitination, methylation, acetylation and phosphorylation) on the expression, subcellular localization, stability and affinity for RNA and protein partners of many RNA-binding proteins are highlighted. Moreover, examples of how some of the most common signal transduction pathways can modulate biological processes through changes in RNA processing regulation are illustrated. Lastly, we discuss challenges and opportunities of therapeutic approaches that correct RNA processing defects and target signaling molecules.
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Affiliation(s)
- Veronica Ruta
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168 Rome, Italy; (V.R.); (V.P.)
- Organoids Facility, IRCCS Fondazione Policlinico Universitario Agostino Gemelli, 00168 Rome, Italy
| | - Vittoria Pagliarini
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168 Rome, Italy; (V.R.); (V.P.)
- Organoids Facility, IRCCS Fondazione Policlinico Universitario Agostino Gemelli, 00168 Rome, Italy
| | - Claudio Sette
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168 Rome, Italy; (V.R.); (V.P.)
- Laboratory of Neuroembryology, IRCCS Fondazione Santa Lucia, 00143 Rome, Italy
- Correspondence:
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Ramanayake-Mudiyanselage V, Embogama DM, Pflum MKH. Kinase-Catalyzed Biotinylation to Map Cell Signaling Pathways: Application to Epidermal Growth Factor Signaling. J Proteome Res 2021; 20:4852-4861. [PMID: 34491762 DOI: 10.1021/acs.jproteome.1c00562] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cell signaling involves a network of protein-protein interactions and post-translational modifications that govern cellular responses to environmental cues. To understand and ultimately modulate these signaling pathways to confront disease, the complex web of proteins that becomes phosphorylated after extracellular stimulation has been studied using mass spectrometry-based proteomics methods. To complement prior work and fully characterize all phosphorylated proteins after the stimulation of cell signaling, we developed K-BMAPS (kinase-catalyzed biotinylation to map signaling), which utilizes ATP-biotin as a kinase cosubstrate to biotin label substrates. As a first application of the K-BMAPS method, the well-characterized epidermal growth factor receptor (EGFR) kinase signaling pathway was monitored by treating epidermal growth factor (EGF)-stimulated HeLa lysates with ATP-biotin, followed by streptavidin enrichment and quantitative mass spectrometry analysis. On the basis of the dynamic phosphoproteins identified, a pathway map was developed considering functional categories and known interactors of EGFR. Remarkably, 94% of the K-BMAPS hit proteins were included in the EGFR pathway map. With many proteins involved in transcription, translation, cell adhesion, and GTPase signaling, K-BMAPS identified phosphoproteins were associated with late and continuous signaling events. In summary, the K-BMAPS method is a powerful tool to map the dynamic phosphorylation governing cell signaling pathways.
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Affiliation(s)
| | - D Maheeka Embogama
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, United States
| | - Mary Kay H Pflum
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, United States
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14
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Mollaei M, Hassan ZM, Khorshidi F, Langroudi L. Chemotherapeutic drugs: Cell death- and resistance-related signaling pathways. Are they really as smart as the tumor cells? Transl Oncol 2021; 14:101056. [PMID: 33684837 PMCID: PMC7938256 DOI: 10.1016/j.tranon.2021.101056] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 02/05/2021] [Accepted: 02/22/2021] [Indexed: 02/07/2023] Open
Abstract
Chemotherapeutic drugs kill cancer cells or control their progression all over the patient's body, while radiation- and surgery-based treatments perform in a particular site. Based on their mechanisms of action, they are classified into different groups, including alkylating substrates, antimetabolite agents, anti-tumor antibiotics, inhibitors of topoisomerase I and II, mitotic inhibitors, and finally, corticosteroids. Although chemotherapeutic drugs have brought about more life expectancy, two major and severe complications during chemotherapy are chemoresistance and tumor relapse. Therefore, we aimed to review the underlying intracellular signaling pathways involved in cell death and resistance in different chemotherapeutic drug families to clarify the shortcomings in the conventional single chemotherapy applications. Moreover, we have summarized the current combination chemotherapy applications, including numerous combined-, and encapsulated-combined-chemotherapeutic drugs. We further discussed the possibilities and applications of precision medicine, machine learning, next-generation sequencing (NGS), and whole-exome sequencing (WES) in promoting cancer immunotherapies. Finally, some of the recent clinical trials concerning the application of immunotherapies and combination chemotherapies were included as well, in order to provide a practical perspective toward the future of therapies in cancer cases.
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Affiliation(s)
- Mojtaba Mollaei
- Department of Immunology, School of Medicine, Tarbiat Modares University, Tehran, Iran.
| | | | - Fatemeh Khorshidi
- Department of Immunology, School of Medicine, Tarbiat Modares University, Tehran, Iran; Department of Immunology, Pasteur Institute of Iran, Tehran, Iran
| | - Ladan Langroudi
- Department of Immunology, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
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15
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Vasudeva K, Dutta A, Munshi A. Role of lncRNAs in the Development of Ischemic Stroke and Their Therapeutic Potential. Mol Neurobiol 2021; 58:3712-3728. [PMID: 33818737 DOI: 10.1007/s12035-021-02359-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 03/11/2021] [Indexed: 12/20/2022]
Abstract
Stroke is a major cause of premature mortality and disability around the world. Therefore, identification of cellular and molecular processes implicated in the pathogenesis and progression of ischemic stroke has become a priority. Long non-coding RNAs (lncRNAs) are emerging as significant players in the pathophysiology of cerebral ischemia. They are involved in different signalling pathways of cellular processes like cell apoptosis, autophagy, angiogenesis, inflammation, and cell death, impacting the progression of cerebral damage. Exploring the functions of these lncRNAs and their mechanism of action may help in the development of promising treatment strategies. In this review, the current knowledge of lncRNAs in ischemic stroke, focusing on the mechanism by which they cause cellular apoptosis, inflammation, and microglial activation, has been summarized. Very few lncRNAs have been functionally annotated. Therefore, the therapies based on lncRNAs still face many hurdles since the potential targets are likely to increase with the identification of new ones. Majority of experiments involving the identification and function of lncRNAs have been carried out in animal models, and the role of lncRNAs in human stroke presents a challenge. However, mitigating these issues through more rational experimental design might lead to the development of lncRNA-based stroke therapies to treat ischemic stroke.
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Affiliation(s)
- Kanika Vasudeva
- Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, 151001, India
| | - Anyeasha Dutta
- Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, 151001, India
| | - Anjana Munshi
- Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, 151001, India.
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16
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Zhang Y, Qian J, Gu C, Yang Y. Alternative splicing and cancer: a systematic review. Signal Transduct Target Ther 2021; 6:78. [PMID: 33623018 PMCID: PMC7902610 DOI: 10.1038/s41392-021-00486-7] [Citation(s) in RCA: 163] [Impact Index Per Article: 54.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 09/24/2020] [Accepted: 09/28/2020] [Indexed: 01/31/2023] Open
Abstract
The abnormal regulation of alternative splicing is usually accompanied by the occurrence and development of tumors, which would produce multiple different isoforms and diversify protein expression. The aim of the present study was to conduct a systematic review in order to describe the regulatory mechanisms of alternative splicing, as well as its functions in tumor cells, from proliferation and apoptosis to invasion and metastasis, and from angiogenesis to metabolism. The abnormal splicing events contributed to tumor progression as oncogenic drivers and/or bystander factors. The alterations in splicing factors detected in tumors and other mis-splicing events (i.e., long non-coding and circular RNAs) in tumorigenesis were also included. The findings of recent therapeutic approaches targeting splicing catalysis and splicing regulatory proteins to modulate pathogenically spliced events (including tumor-specific neo-antigens for cancer immunotherapy) were introduced. The emerging RNA-based strategies for the treatment of cancer with abnormally alternative splicing isoforms were also discussed. However, further studies are still required to address the association between alternative splicing and cancer in more detail.
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Affiliation(s)
- Yuanjiao Zhang
- The Third Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Jinjun Qian
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Chunyan Gu
- The Third Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China.
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China.
| | - Ye Yang
- The Third Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China.
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China.
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17
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Bessa C, Matos P, Jordan P, Gonçalves V. Alternative Splicing: Expanding the Landscape of Cancer Biomarkers and Therapeutics. Int J Mol Sci 2020; 21:ijms21239032. [PMID: 33261131 PMCID: PMC7729450 DOI: 10.3390/ijms21239032] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 11/24/2020] [Accepted: 11/25/2020] [Indexed: 02/07/2023] Open
Abstract
Alternative splicing (AS) is a critical post-transcriptional regulatory mechanism used by more than 95% of transcribed human genes and responsible for structural transcript variation and proteome diversity. In the past decade, genome-wide transcriptome sequencing has revealed that AS is tightly regulated in a tissue- and developmental stage-specific manner, and also frequently dysregulated in multiple human cancer types. It is currently recognized that splicing defects, including genetic alterations in the spliced gene, altered expression of both core components or regulators of the precursor messenger RNA (pre-mRNA) splicing machinery, or both, are major drivers of tumorigenesis. Hence, in this review we provide an overview of our current understanding of splicing alterations in cancer, and emphasize the need to further explore the cancer-specific splicing programs in order to obtain new insights in oncology. Furthermore, we also discuss the recent advances in the identification of dysregulated splicing signatures on a genome-wide scale and their potential use as biomarkers. Finally, we highlight the therapeutic opportunities arising from dysregulated splicing and summarize the current approaches to therapeutically target AS in cancer.
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Affiliation(s)
- Cláudia Bessa
- Department of Human Genetics, National Health Institute Dr. Ricardo Jorge, 1649-016 Lisbon, Portugal; (C.B.); (P.M.)
- BioISI—Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal
| | - Paulo Matos
- Department of Human Genetics, National Health Institute Dr. Ricardo Jorge, 1649-016 Lisbon, Portugal; (C.B.); (P.M.)
- BioISI—Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal
| | - Peter Jordan
- Department of Human Genetics, National Health Institute Dr. Ricardo Jorge, 1649-016 Lisbon, Portugal; (C.B.); (P.M.)
- BioISI—Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal
- Correspondence: (P.J.); (V.G.); Tel.: +351-217-519-380 (P.J.)
| | - Vânia Gonçalves
- Department of Human Genetics, National Health Institute Dr. Ricardo Jorge, 1649-016 Lisbon, Portugal; (C.B.); (P.M.)
- BioISI—Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal
- Correspondence: (P.J.); (V.G.); Tel.: +351-217-519-380 (P.J.)
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18
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Lin W, Ji J, Zhu Y, Li M, Zhao J, Xue F, Yuan Z. PMINR: Pointwise Mutual Information-Based Network Regression - With Application to Studies of Lung Cancer and Alzheimer's Disease. Front Genet 2020; 11:556259. [PMID: 33193633 PMCID: PMC7594515 DOI: 10.3389/fgene.2020.556259] [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: 04/27/2020] [Accepted: 08/12/2020] [Indexed: 11/13/2022] Open
Abstract
Complex diseases are believed to be the consequence of intracellular network(s) involving a range of factors. An improved understanding of a disease-predisposing biological network could lead to better identification of genes and pathways that confer disease risk and therefore inform drug development. The group difference in biological networks, as is often characterized by graphs of nodes and edges, is attributable to effects of these nodes and edges. Here we introduced pointwise mutual information (PMI) as a measure of the connection between a pair of nodes with either a linear relationship or nonlinear dependence. We then proposed a PMI-based network regression (PMINR) model to differentiate patterns of network changes (in node or edge) linking a disease outcome. Through simulation studies with various sample sizes and inter-node correlation structures, we showed that PMINR can accurately identify these changes with higher power than current methods and be robust to the network topology. Finally, we illustrated, with publicly available data on lung cancer and gene methylation data on aging and Alzheimer’s disease, an evaluation of the practical performance of PMINR. We concluded that PMI is able to capture the generic inter-node correlation pattern in biological networks, and PMINR is a powerful and efficient approach for biological network analysis.
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Affiliation(s)
- Weiqiang Lin
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Jiadong Ji
- Department of Data Science, School of Statistics, Shandong University of Finance and Economics, Jinan, China
| | - Yuchen Zhu
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Mingzhuo Li
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Jinghua Zhao
- Cardiovasucular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Fuzhong Xue
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Zhongshang Yuan
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
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Purdue MP, Song L, Scélo G, Houlston RS, Wu X, Sakoda LC, Thai K, Graff RE, Rothman N, Brennan P, Chanock SJ, Yu K. Pathway Analysis of Renal Cell Carcinoma Genome-Wide Association Studies Identifies Novel Associations. Cancer Epidemiol Biomarkers Prev 2020; 29:2065-2069. [PMID: 32732251 PMCID: PMC9438507 DOI: 10.1158/1055-9965.epi-20-0472] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 05/23/2020] [Accepted: 07/23/2020] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Much of the heritable risk of renal cell carcinoma (RCC) associated with common genetic variation is unexplained. New analytic approaches have been developed to increase the discovery of risk variants in genome-wide association studies (GWAS), including multi-locus testing through pathway analysis. METHODS We conducted a pathway analysis using GWAS summary data from six previous scans (10,784 cases and 20,406 controls) and evaluated 3,678 pathways and gene sets drawn from the Molecular Signatures Database. To replicate findings, we analyzed GWAS summary data from the UK Biobank (903 cases and 451,361 controls) and the Genetic Epidemiology Research on Adult Health and Aging cohort (317 cases and 50,511 controls). RESULTS We identified 14 pathways/gene sets associated with RCC in both the discovery (P < 1.36 × 10-5, the Bonferroni correction threshold) and replication (P < 0.05) sets, 10 of which include components of the PI3K/AKT pathway. In tests across 2,035 genes in these pathways, associations (Bonferroni corrected P < 2.46 × 10-5 in discovery and replication sets combined) were observed for CASP9, TIPIN, and CDKN2C. The strongest SNP signal was for rs12124078 (P Discovery = 2.6 × 10-5; P Replication = 1.5 × 10-4; P Combined = 6.9 × 10-8), a CASP9 expression quantitative trait locus. CONCLUSIONS Our pathway analysis implicates genetic variation within the PI3K/AKT pathway as a source of RCC heritability and identifies several promising novel susceptibility genes, including CASP9, which warrant further investigation. IMPACT Our findings illustrate the value of pathway analysis as a complementary approach to analyzing GWAS data.
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Affiliation(s)
- Mark P Purdue
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland.
| | - Lei Song
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland
| | - Ghislaine Scélo
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, London, United Kingdom
| | - Xifeng Wu
- Department of Big Data in Health Science, Zhejiang University School of Public Health, Hangzhou, Zhejiang, China
| | - Lori C Sakoda
- Division of Research, Kaiser Permanente Northern California, Oakland, California
| | - Khanh Thai
- Division of Research, Kaiser Permanente Northern California, Oakland, California
| | - Rebecca E Graff
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland
| | - Paul Brennan
- International Agency for Research on Cancer, Lyon, France
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland
| | - Kai Yu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland
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20
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Babu N, Pinto SM, Biswas M, Subbannayya T, Rajappa M, Mohan SV, Advani J, Rajagopalan P, Sathe G, Syed N, Radhakrishna VD, Muthusamy O, Navani S, Kumar RV, Gopisetty G, Rajkumar T, Radhakrishnan P, Thiyagarajan S, Pandey A, Gowda H, Majumder P, Chatterjee A. Phosphoproteomic analysis identifies CLK1 as a novel therapeutic target in gastric cancer. Gastric Cancer 2020; 23:796-810. [PMID: 32333232 DOI: 10.1007/s10120-020-01062-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 03/12/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND Phosphorylation is an important regulatory mechanism of protein activity in cells. Studies in various cancers have reported perturbations in kinases resulting in aberrant phosphorylation of oncoproteins and tumor suppressor proteins. METHODS In this study, we carried out quantitative phosphoproteomic analysis of gastric cancer tissues and corresponding xenograft samples. Using these data, we employed bioinformatics analysis to identify aberrant signaling pathways. We further performed molecular inhibition and silencing of the upstream regulatory kinase in gastric cancer cell lines and validated its effect on cellular phenotype. Through an ex vivo technology utilizing patient tumor and blood sample, we sought to understand the therapeutic potential of the kinase by recreating the tumor microenvironment. RESULTS Using mass spectrometry-based high-throughput analysis, we identified 1,344 phosphosites and 848 phosphoproteins, including differential phosphorylation of 177 proteins (fold change cut-off ≥ 1.5). Our data showed that a subset of differentially phosphorylated proteins belonged to splicing machinery. Pathway analysis highlighted Cdc2-like kinase (CLK1) as upstream kinase. Inhibition of CLK1 using TG003 and CLK1 siRNA resulted in a decreased cell viability, proliferation, invasion and migration as well as modulation in the phosphorylation of SRSF2. Ex vivo experiments which utilizes patient's own tumor and blood to recreate the tumor microenvironment validated the use of CLK1 as a potential target for gastric cancer treatment. CONCLUSIONS Our data indicates that CLK1 plays a crucial role in the regulation of splicing process in gastric cancer and that CLK1 can act as a novel therapeutic target in gastric cancer.
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Affiliation(s)
- Niraj Babu
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India.,Manipal Academy of Higher Education, Manipal, 576104, India
| | - Sneha M Pinto
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India.,Center for Systems Biology and Molecular Medicine, Yenepoya (Deemed To Be University), Mangalore, 575018, India
| | | | - Tejaswini Subbannayya
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India.,Mitra Biotech, Bangalore, 560100, India
| | | | - Sonali V Mohan
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India.,Manipal Academy of Higher Education, Manipal, 576104, India
| | - Jayshree Advani
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India
| | - Pavithra Rajagopalan
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India
| | - Gajanan Sathe
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India
| | - Nazia Syed
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India
| | | | | | | | - Rekha V Kumar
- Department of Pathology, Kidwai Memorial Institute of Oncology, Bangalore, 560029, India
| | - Gopal Gopisetty
- Department of Molecular Oncology, Cancer Institute (WIA), Chennai, 600020, India
| | - Thangarajan Rajkumar
- Department of Molecular Oncology, Cancer Institute (WIA), Chennai, 600020, India
| | | | | | - Akhilesh Pandey
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India.,Manipal Academy of Higher Education, Manipal, 576104, India.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA.,Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA.,Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Hosur Road, Bangalore, 560029, India
| | - Harsha Gowda
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India.,Manipal Academy of Higher Education, Manipal, 576104, India.,Cancer Precision Medicine, QIMR Berghofer, Royal Brisbane Hospital, Brisbane, QLD, 4029, Australia
| | | | - Aditi Chatterjee
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India. .,Manipal Academy of Higher Education, Manipal, 576104, India. .,Mitra Biotech, Bangalore, 560100, India.
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21
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Dlamini Z, Shoba B, Hull R. Splicing machinery genomics events in acute myeloid leukaemia (AML): in search for therapeutic targets, diagnostic and prognostic biomarkers. Am J Cancer Res 2020; 10:2690-2704. [PMID: 33042611 PMCID: PMC7539770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 07/05/2020] [Indexed: 06/11/2023] Open
Abstract
Acute myeloid leukemia (AML) is the most common form of acute leukaemia and has the highest mortality rate. Screening for mutations in patients with AML has shown that in many cases genes carrying mutations are involved in the alternate splicing of mRNA. These include members of the Serine Arginine (SR) family of splicing factors, as well as components of the spliceosome. Mutations in associated genes also affect the function of members of the heterogeneous nuclear ribonucleoproteins (hnRNPs). These mutations in splicing factors can lead to changes in the expression of different isoforms whose splicing is controlled by these splicing factors. These different isoforms may have completely different functions, for example, members of the BCl-2 family are alternately spliced to give rise to pro and anti-apoptotic members. Mutations in the splicing factors that control the splicing of these mRNAs can lead to changes in the expression level of these isoforms. In this review we will examine the mechanics of the regulation of the various splice isoforms and how this drives the development of tumors. This information is pertinent for drug discovery, and the splicing factors with the most promise for pharmacological control will be discussed.
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Affiliation(s)
- Zodwa Dlamini
- SAMRC/UP Precision Prevention and Novel Drug Targets for HIV-Associated Cancers Extramural Unit, Pan African Cancer Research Institute, University of Pretoria, Faculty of Health SciencesHatfield 0028, South Africa
| | - Bonginkosi Shoba
- Department of Medical Oncology, University of Pretoria, Faculty of Health SciencesHatfield 0028, South Africa
| | - Rodney Hull
- SAMRC/UP Precision Prevention and Novel Drug Targets for HIV-Associated Cancers Extramural Unit, Pan African Cancer Research Institute, University of Pretoria, Faculty of Health SciencesHatfield 0028, South Africa
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22
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Cerasuolo A, Buonaguro L, Buonaguro FM, Tornesello ML. The Role of RNA Splicing Factors in Cancer: Regulation of Viral and Human Gene Expression in Human Papillomavirus-Related Cervical Cancer. Front Cell Dev Biol 2020; 8:474. [PMID: 32596243 PMCID: PMC7303290 DOI: 10.3389/fcell.2020.00474] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 05/20/2020] [Indexed: 12/12/2022] Open
Abstract
The spliceosomal complex components, together with the heterogeneous nuclear ribonucleoproteins (hnRNPs) and serine/arginine-rich (SR) proteins, regulate the process of constitutive and alternative splicing, the latter leading to the production of mRNA isoforms coding multiple proteins from a single pre-mRNA molecule. The expression of splicing factors is frequently deregulated in different cancer types causing the generation of oncogenic proteins involved in cancer hallmarks. Cervical cancer is caused by persistent infection with oncogenic human papillomaviruses (HPVs) and constitutive expression of viral oncogenes. The aberrant activity of hnRNPs and SR proteins in cervical neoplasia has been shown to trigger the production of oncoproteins through the processing of pre-mRNA transcripts either derived from human genes or HPV genomes. Indeed, hnRNP and SR splicing factors have been shown to regulate the production of viral oncoprotein isoforms necessary for the completion of viral life cycle and for cell transformation. Target-therapy strategies against hnRNPs and SR proteins, causing simultaneous reduction of oncogenic factors and inhibition of HPV replication, are under development. In this review, we describe the current knowledge of the functional link between RNA splicing factors and deregulated cellular as well as viral RNA maturation in cervical cancer and the opportunity of new therapeutic strategies.
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Affiliation(s)
| | | | | | - Maria Lina Tornesello
- Molecular Biology and Viral Oncology Unit, Istituto Nazionale Tumouri IRCCS–Fondazione G. Pascale, Naples, Italy
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Botto AEC, Muñoz JC, Giono LE, Nieto-Moreno N, Cuenca C, Kornblihtt AR, Muñoz MJ. Reciprocal regulation between alternative splicing and the DNA damage response. Genet Mol Biol 2020; 43:e20190111. [PMID: 32236390 PMCID: PMC7197977 DOI: 10.1590/1678-4685-gmb-2019-0111] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 12/16/2019] [Indexed: 12/16/2022] Open
Abstract
Splicing, the process that catalyzes intron removal and flanking exon ligation, can occur in different ways (alternative splicing) in immature RNAs transcribed from a single gene. In order to adapt to a particular context, cells modulate not only the quantity but also the quality (alternative isoforms) of their transcriptome. Since 95% of the human coding genome is subjected to alternative splicing regulation, it is expected that many cellular pathways are modulated by alternative splicing, as is the case for the DNA damage response. Moreover, recent evidence demonstrates that upon a genotoxic insult, classical DNA damage response kinases such as ATM, ATR and DNA-PK orchestrate the gene expression response therefore modulating alternative splicing which, in a reciprocal way, shapes the response to a damaging agent.
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Affiliation(s)
- Adrian E Cambindo Botto
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Fisiologia, Biologia Molecular y Celular, Instituto de Fisiologia, Biologia Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Buenos Aires, Argentina
| | - Juan C Muñoz
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Fisiologia, Biologia Molecular y Celular, Instituto de Fisiologia, Biologia Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Buenos Aires, Argentina
| | - Luciana E Giono
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Fisiologia, Biologia Molecular y Celular, Instituto de Fisiologia, Biologia Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Buenos Aires, Argentina
| | - Nicolás Nieto-Moreno
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Fisiologia, Biologia Molecular y Celular, Instituto de Fisiologia, Biologia Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Buenos Aires, Argentina
| | - Carmen Cuenca
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Fisiologia, Biologia Molecular y Celular, Instituto de Fisiologia, Biologia Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Buenos Aires, Argentina
| | - Alberto R Kornblihtt
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Fisiologia, Biologia Molecular y Celular, Instituto de Fisiologia, Biologia Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Buenos Aires, Argentina
| | - Manuel J Muñoz
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Fisiologia, Biologia Molecular y Celular, Instituto de Fisiologia, Biologia Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Buenos Aires, Argentina.,Fondazione Istituto FIRC di Oncologia Molecolare (IFOM), Milan, Italy.,Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Biodiversidad y Biología Experimental, Buenos Aires, Argentina
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Tang M, Dai W, Wu H, Xu X, Jiang B, Wei Y, Qian H, Han L. Transcriptome analysis of tongue cancer based on high‑throughput sequencing. Oncol Rep 2020; 43:2004-2016. [PMID: 32236620 PMCID: PMC7160550 DOI: 10.3892/or.2020.7560] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 02/28/2020] [Indexed: 12/14/2022] Open
Abstract
Tongue cancer is one of the most common types of cancer, but its molecular etiology and pathogenesis remain unclear. The aim of the present study was to elucidate the pathogenesis of tongue cancer and investigate novel potential diagnostic and therapeutic targets. Four matched pairs of tongue cancer and paracancerous tissues were collected for RNA sequencing (RNA-Seq), and the differentially expressed genes were analyzed. The RNA-Seq data of tongue cancer tissues were further analyzed using bioinformatics and reverse transcription-quantitative PCR analysis. The sequenced reads were quantified and qualified in accordance with the analysis demands. The transcriptomes of the tongue cancer tissues and paired paracancerous tissues were analyzed, and 1,700 upregulated and 2,249 downregulated genes were identified. Gene Ontology analysis uncovered a significant enrichment in the terms associated with extracellular matrix (ECM) organization, cell adhesion and collagen catabolic processes. Kyoto Encyclopedia of Genes and Genomes analysis demonstrated that these differentially expressed genes were mainly enriched in the focal adhesion pathway, ECM-receptor interaction pathway, phosphoinositide 3-kinase (PI3K)-Akt pathway, and cell adhesion molecules. Comprehensive analyses of the gene tree and pathway network revealed that the majority of cell cycle genes were upregulated, while the majority of the genes associated with intracellular response, cell adhesion and cell differentiation were downregulated. The ECM-receptor interaction, focal adhesion kinase (FAK) and PI3K-Akt pathways were closely associated with one another and held key positions in differential signaling pathways. The ECM-receptor, FAK and PI3K-Akt signaling pathways were found to synergistically promote tongue cancer occurrence and progression, and may serve as potential diagnostic and therapeutic targets for this type of cancer.
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Affiliation(s)
- Mingming Tang
- Department of Head and Neck Surgery, Nantong Tumor Hospital, Nantong, Jiangsu 226361, P.R. China
| | - Wencheng Dai
- Department of Head and Neck Surgery, Nantong Tumor Hospital, Nantong, Jiangsu 226361, P.R. China
| | - Hao Wu
- Department of Otorhinolaryngology Head and Neck Surgery, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Xinjiang Xu
- Department of Head and Neck Surgery, Nantong Tumor Hospital, Nantong, Jiangsu 226361, P.R. China
| | - Bin Jiang
- Department of Head and Neck Surgery, Nantong Tumor Hospital, Nantong, Jiangsu 226361, P.R. China
| | - Yingze Wei
- Department of Clinical Pathology, Nantong Tumor Hospital, Nantong, Jiangsu 226361, P.R. China
| | - Hongyan Qian
- Key Laboratory of Cancer Research Center Nantong, Nantong Tumor Hospital, Nantong, Jiangsu 226361, P.R. China
| | - Liang Han
- Department of Head and Neck Surgery, Nantong Tumor Hospital, Nantong, Jiangsu 226361, P.R. China
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Abstract
Alternative splicing of precursor mRNA is a key mediator of gene expression regulation leading to greater diversity of the proteome in complex organisms. Systematic sequencing of the human genome and transcriptome has led to our understanding of how alternative splicing of critical genes leads to multiple pathological conditions such as cancer. For many years, proteases were known only for their roles as proteolytic enzymes, acting to regulate/process proteins associated with diverse cellular functions. However, the differential expression and altered function of various protease isoforms, such as (i) anti-apoptotic activities, (ii) mediating intercellular adhesion, and (iii) modifying the extracellular matrix, are evidence of their specific contribution towards shaping the tumor microenvironment. Revealing the alternative splicing of protease genes and characterization of their protein products/isoforms with distinct and opposing functions creates a platform to understand how protease isoforms contribute to specific cancer hallmarks. Here, in this review, we address cancer-specific isoforms produced by the alternative splicing of proteases and their distinctive roles in the tumor microenvironment.
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Affiliation(s)
- Chamikara Liyanage
- School of Biomedical Sciences, Faculty of Health, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia
- Australian Prostate Cancer Research Centre-Queensland (APCRC-Q), Translational Research Institute, Queensland University of Technology, Brisbane, Australia
| | - Achala Fernando
- School of Biomedical Sciences, Faculty of Health, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia
- Australian Prostate Cancer Research Centre-Queensland (APCRC-Q), Translational Research Institute, Queensland University of Technology, Brisbane, Australia
| | - Jyotsna Batra
- School of Biomedical Sciences, Faculty of Health, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia.
- Australian Prostate Cancer Research Centre-Queensland (APCRC-Q), Translational Research Institute, Queensland University of Technology, Brisbane, Australia.
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Silva AL, Faria M, Matos P. Inflammatory Microenvironment Modulation of Alternative Splicing in Cancer: A Way to Adapt. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1219:243-258. [PMID: 32130703 DOI: 10.1007/978-3-030-34025-4_13] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The relationship between inflammation and cancer has been long recognized by the medical and scientific community. In the last decades, it has returned to the forefront of clinical oncology since a wealth of knowledge has been gathered about the cells, cytokines and physiological processes that are central to both inflammation and cancer. It is now robustly established that chronic inflammation can induce certain cancers but also that solid tumors, in turn, can initiate and perpetuate local inflammatory processes that foster tumor growth and dissemination. Inflammation is the hallmark of the innate immune response to tissue damage or infection, but also mediates the activation, expansion and recruitment to the tissues of cells and antibodies of the adaptive immune system. The functional integration of both components of the immune response is crucial to identify and subdue tumor development, progression and dissemination. When this tight control goes awry, altered cells can avoid the immune surveillance and even subvert the innate immunity to promote their full oncogenic transformation. In this chapter, we make a general overview of the most recent data linking the inflammatory process to cancer. We start with the overall inflammatory cues and processes that influence the relationship between tumor and the microenvironment that surrounds it and follow the ever-increasing complexity of processes that end up producing subtle changes in the splicing of certain genes to ascertain survival advantage to cancer cells.
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Affiliation(s)
- Ana Luísa Silva
- Serviço de Endocrinologia, Diabetes e Metabolismo do CHLN-Hospital Santa Maria, Lisbon, Portugal
- ISAMB-Instituto de Saúde Ambiental, Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal
| | - Márcia Faria
- Serviço de Endocrinologia, Diabetes e Metabolismo do CHLN-Hospital Santa Maria, Lisbon, Portugal
- Faculdade de Ciências, BioISI-Biosystems and Integrative Sciences Institute, Universidade de Lisboa, Lisbon, Portugal
| | - Paulo Matos
- Faculdade de Ciências, BioISI-Biosystems and Integrative Sciences Institute, Universidade de Lisboa, Lisbon, Portugal
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal
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Yang H, Zhang R, Jia C, Chen M, Yin W, Wei L, Jiao H. Neuronal protective effect of Songling Xuemaikang capsules alone and in combination with carbamazepine on epilepsy in kainic acid-kindled rats. PHARMACEUTICAL BIOLOGY 2019; 57:22-28. [PMID: 30724642 PMCID: PMC6366425 DOI: 10.1080/13880209.2018.1563619] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 10/19/2018] [Accepted: 12/12/2018] [Indexed: 06/09/2023]
Abstract
CONTEXT Epilepsy is a common life-threatening neurological disorder that is often drug-resistant and associated with cognitive impairment. The traditional Chinese patent medicine Songling Xuemaikang capsules (SXC) is clinically used for epilepsy therapy and alleviation of cognitive impairment. OBJECTIVE This study investigates the neuronal protective effect of SXC combined with carbamazepine (CBZ) on epilepsy and cognitive impairment in kainic acid-kindled SD rats. MATERIALS AND METHODS Kainic acid-kindled rats were established by injection of 0.45 μg kainic acid and randomly divided into 5 groups (n = 14): saline (sham-operated), control, CBZ, SXC and CBZ + SXC combined group. Rats in the treatment groups received CBZ (50 mg/kg/d), SXC (600 mg/kg/d) or combined CBZ (50 mg/kg/d) + SXC (600 mg/kg/d) via intragastric injection for 60 days. Epileptic behaviours, cognitive impairment, neuronal apoptosis and expression of p-Akt, Akt and caspase-9 were measured, and the alleviation of cognitive damage and neuronal apoptosis was analyzed. RESULTS The combined administration of SXC and CBZ significantly decreased the frequency of seizures (1.2 ± 0.3) and the number of episodes (1.3 ± 0.5) above stage III (p < 0.05). Neuronal apoptosis was improved (p < 0.01), and cognitive damage was ameliorated (p < 0.05).The level of p-Akt was enhanced (p < 0.01) whereas the expression of caspase-9 was evidently inhibited (p < 0.01) in the combined group. CONCLUSIONS The present findings confirm that the combined use of SXC with CBZ can effectively control epileptic seizures, alleviate damage to hippocampal neurons and protect against cognitive impairment. The mechanism of action might be related to the upregulation of p-Akt and inhibition of caspase-9 expression.
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Affiliation(s)
- Haiyan Yang
- Department of Pharmacy, Lanzhou University Second Hospital, Lanzhou, China
| | - Rui Zhang
- College of Pharmacy, Lanzhou University, Lanzhou, China
| | - Chen Jia
- Department of Pharmacy, Lanzhou University Second Hospital, Lanzhou, China
| | - Mengyu Chen
- College of Pharmacy, Lanzhou University, Lanzhou, China
| | - Wen Yin
- Department of Pharmacy, Lanzhou University Second Hospital, Lanzhou, China
| | - Liming Wei
- Department of Pharmacy, Lanzhou University Second Hospital, Lanzhou, China
| | - Haisheng Jiao
- Department of Pharmacy, Lanzhou University Second Hospital, Lanzhou, China
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28
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DeLigio JT, Stevens SC, Nazario-Muñoz GS, MacKnight HP, Doe KK, Chalfant CE, Park MA. Serine/Arginine-Rich Splicing Factor 3 Modulates the Alternative Splicing of Cytoplasmic Polyadenylation Element Binding Protein 2. Mol Cancer Res 2019; 17:1920-1930. [PMID: 31138601 PMCID: PMC6726571 DOI: 10.1158/1541-7786.mcr-18-1291] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 04/17/2019] [Accepted: 05/21/2019] [Indexed: 02/06/2023]
Abstract
Triple negative breast cancer (TNBC) has an unusually low 5-year survival rate linked to higher metastatic rates. Our laboratory recently delineated a role for the alternative RNA splicing (AS) of cytoplasmic polyadenylation element binding protein 2 (CPEB2), via inclusion/exclusion of exon 4, in the metastasis of TNBC. In these studies, the mechanism governing the inclusion/exclusion of exon 4 was examined. Specifically, the RNA trans-factor, SRSF3, was found to be explicitly associated with CPEB2 exon 4. A SRSF3 consensus sequence was identified in exon 4, and mutation of this sequence abolished the association of SRSF3. The expression of SRSF3 was upregulated in TNBC cells upon the acquisition of anoikis resistance correlating with a reduction in the CPEB2A/B ratio. Importantly, downregulation of SRSF3 in these cells by siRNA induced the exclusion of exon 4 in cells increasing the ratio of CPEB2A (exon 4 excluded) to CPEB2B (exon 4 included). Downregulation of SRSF3 also reversed the CPEB2A/B ratio of a wild-type CPEB2 exon 4 minigene and endogenous CPEB2 pre-mRNA, but not a mutant CPEB2 minigene with the SRSF3 RNA cis-element ablated. SRSF3 downregulation ablated the anoikis resistance of TNBC cells, which was "rescued" by ectopic expression of CPEB2B. Finally, analysis of The Cancer Genome Atlas database showed a positive relationship between SRSF3 expression and lower CPEB2A/B ratios in aggressive breast cancers. IMPLICATIONS: These findings demonstrate that SRSF3 modulates CPEB2 AS to induce the expression of the CPEB2B isoform that drives TNBC phenotypes correlating with aggressive human breast cancer. VISUAL OVERVIEW: http://mcr.aacrjournals.org/content/molcanres/17/9/1920/F1.large.jpg.
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Affiliation(s)
- James T DeLigio
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University (VCU), Richmond Virginia
| | - Shaun C Stevens
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, Florida
| | - Gina S Nazario-Muñoz
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, Florida
| | - H Patrick MacKnight
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University (VCU), Richmond Virginia
| | - Keli K Doe
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University (VCU), Richmond Virginia
| | - Charles E Chalfant
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University (VCU), Richmond Virginia.
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, Florida
- VCU Massey Cancer Center, Cancer Cell Signaling Program, VCU, Richmond Virginia
- Research Service, Hunter Holmes McGuire Veterans Administration Medical Center, Richmond, Virginia
- VCU Institute of Molecular Medicine, Richmond, Virginia
- VCU Johnson Center for Critical Care and Pulmonary Research, Richmond, Virginia
- Research Service, James A. Haley Veterans Hospital, Tampa, Florida
- The Moffitt Cancer Center, Tampa, Florida
| | - Margaret A Park
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University (VCU), Richmond Virginia.
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, Florida
- VCU Massey Cancer Center, Cancer Cell Signaling Program, VCU, Richmond Virginia
- VCU Johnson Center for Critical Care and Pulmonary Research, Richmond, Virginia
- Research Service, James A. Haley Veterans Hospital, Tampa, Florida
- The Moffitt Cancer Center, Tampa, Florida
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Lee C, Chang W, Chang Y, Yang J, Chang C, Hsu K, Chen Y, Liu T, Chen Y, Lin S, Wu Y, Chang J. Alternative splicing in human cancer cells is modulated by the amiloride derivative 3,5-diamino-6-chloro-N-(N-(2,6-dichlorobenzoyl)carbamimidoyl)pyrazine-2-carboxide. Mol Oncol 2019; 13:1744-1762. [PMID: 31152681 PMCID: PMC6670021 DOI: 10.1002/1878-0261.12524] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 04/30/2019] [Accepted: 05/30/2019] [Indexed: 12/11/2022] Open
Abstract
Alternative splicing (AS) is a process that enables the generation of multiple protein isoforms with different biological properties from a single mRNA. Cancer cells often use the maneuverability conferred by AS to produce proteins that contribute to growth and survival. In our previous studies, we identified that amiloride modulates AS in cancer cells. However, the effective concentration of amiloride required to modulate AS is too high for use in cancer treatment. In this study, we used computational algorithms to screen potential amiloride derivatives for their ability to regulate AS in cancer cells. We found that 3,5-diamino-6-chloro-N-(N-(2,6-dichlorobenzoyl)carbamimidoyl)pyrazine-2-carboxamide (BS008) can regulate AS of apoptotic gene transcripts, including HIPK3, SMAC, and BCL-X, at a lower concentration than amiloride. This splicing regulation involved various splicing factors, and it was accompanied by a change in the phosphorylation state of serine/arginine-rich proteins (SR proteins). RNA sequencing was performed to reveal that AS of many other apoptotic gene transcripts, such as AATF, ATM, AIFM1, NFKB1, and API5, was also modulated by BS008. In vivo experiments further indicated that treatment of tumor-bearing mice with BS008 resulted in a marked decrease in tumor size. BS008 also had inhibitory effects in vitro, either alone or in a synergistic combination with the cytotoxic chemotherapeutic agents sorafenib and nilotinib. BS008 enabled sorafenib dose reduction without compromising antitumor activity. These findings suggest that BS008 may possess therapeutic potential for cancer treatment.
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Affiliation(s)
- Chien‐Chin Lee
- Epigenome Research CenterChina Medical University HospitalTaichungTaiwan
| | - Wen‐Hsin Chang
- Epigenome Research CenterChina Medical University HospitalTaichungTaiwan
- Department of Primary Care MedicineTaipei Medical University HospitalTaiwan
| | - Ya‐Sian Chang
- Epigenome Research CenterChina Medical University HospitalTaichungTaiwan
- Department of Laboratory MedicineChina Medical University HospitalTaichungTaiwan
- Center for Precision MedicineChina Medical University HospitalTaichungTaiwan
| | - Jinn‐Moon Yang
- TIGP‐BioinformaticsInstitute of Information ScienceAcademia SinicaTaipeiTaiwan
- Institute of Bioinformatics and Systems BiologyNational Chiao Tung UniversityHsinchuTaiwan
- Department of Biological Science and TechnologyNational Chiao Tung UniversityHsinchuTaiwan
| | - Chih‐Shiang Chang
- Graduate Institute of Pharmaceutical ChemistryChina Medical UniversityTaichungTaiwan
| | - Kai‐Cheng Hsu
- Graduate Institute of Cancer Molecular Biology and Drug DiscoveryCollege of Medical Science and TechnologyTaipei Medical UniversityTaiwan
| | - Yun‐Ti Chen
- Institute of Bioinformatics and Systems BiologyNational Chiao Tung UniversityHsinchuTaiwan
| | - Ting‐Yuan Liu
- Department of Laboratory MedicineChina Medical University HospitalTaichungTaiwan
| | - Yu‐Chia Chen
- Department of Laboratory MedicineChina Medical University HospitalTaichungTaiwan
| | - Shyr‐Yi Lin
- Department of Primary Care MedicineTaipei Medical University HospitalTaiwan
- Department of General MedicineSchool of MedicineCollege of MedicineTaipei Medical UniversityTaiwan
- TMU Research Center of Cancer Translational MedicineTaipei Medical UniversityTaiwan
| | - Yang‐Chang Wu
- Graduate Institute of Natural ProductsKaohsiung Medical UniversityTaiwan
- Research Center for Natural Products and Drug DevelopmentKaohsiung Medical UniversityTaiwan
- Department of Medical ResearchKaohsiung Medical University HospitalTaiwan
- Chinese Medicine Research and Development CenterChina Medical University HospitalTaichungTaiwan
| | - Jan‐Gowth Chang
- Epigenome Research CenterChina Medical University HospitalTaichungTaiwan
- Department of Primary Care MedicineTaipei Medical University HospitalTaiwan
- Department of Laboratory MedicineChina Medical University HospitalTaichungTaiwan
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30
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Zhang Z, Zheng X, Li J, Duan J, Cui L, Yang L, Zhang L, Zhang Q, Wang X. Overexpression of UBR5 promotes tumor growth in gallbladder cancer via PTEN/PI3K/Akt signal pathway. J Cell Biochem 2019; 120:11517-11524. [PMID: 30775814 DOI: 10.1002/jcb.28431] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 12/29/2018] [Accepted: 01/09/2019] [Indexed: 01/24/2023]
Abstract
As a key regulator of the ubiquitin-proteasome system, ubiquitin protein ligase E3 component N-recognin 5 (UBR5) plays an important role in various cancers. In this study, our results showed for the first time that UBR5 was overexpressed in gallbladder cancer (GBC) tumor tissues. UBR5 overexpression was significantly associated with tumor size, histological and tumor differentiation. UBR5 overexpression was also associated with poor prognosis in patients with GBC. The knockdown of UBR5 remarkably inhibited the cell proliferation and colony formation of GBC-Shandong (SD) cells in vitro and in vivo. UBR5 potentially increases the level of protein kinase B phosphorylation via the degradation of phosphatase and tensin homolog, which contributes to tumor growth in GBC. UBR5 may be an important biomarker for predicting the prognosis of patients with GBC.
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Affiliation(s)
- Zhen Zhang
- Department of Gastrointestinal Surgery, Peking University People's Hospital, Beijing, China.,Tianjin Key Laboratory of Acute Abdomen Disease Associated Organ Injury and ITCWM Repair, Institute of Acute Abdominal Diseases, Tianjin Nankai Hospital, Tianjin, China
| | - Xin Zheng
- Graduate School of Tianjin Medical University, Tianjin, China.,Tianjin Key Laboratory of Acute Abdomen Disease Associated Organ Injury and ITCWM Repair, Institute of Acute Abdominal Diseases, Tianjin Nankai Hospital, Tianjin, China
| | - Jiaxin Li
- Graduate School of Tianjin Medical University, Tianjin, China.,Tianjin Key Laboratory of Acute Abdomen Disease Associated Organ Injury and ITCWM Repair, Institute of Acute Abdominal Diseases, Tianjin Nankai Hospital, Tianjin, China
| | - Jutao Duan
- Department of Minimal Invasive Surgery, Tianjin Nankai Hospital, Tianjin, China
| | - Lihua Cui
- Tianjin Key Laboratory of Acute Abdomen Disease Associated Organ Injury and ITCWM Repair, Institute of Acute Abdominal Diseases, Tianjin Nankai Hospital, Tianjin, China
| | - Lei Yang
- Tianjin Key Laboratory of Acute Abdomen Disease Associated Organ Injury and ITCWM Repair, Institute of Acute Abdominal Diseases, Tianjin Nankai Hospital, Tianjin, China
| | - Lanqiu Zhang
- Tianjin Key Laboratory of Acute Abdomen Disease Associated Organ Injury and ITCWM Repair, Institute of Acute Abdominal Diseases, Tianjin Nankai Hospital, Tianjin, China
| | - Qi Zhang
- Tianjin Key Laboratory of Acute Abdomen Disease Associated Organ Injury and ITCWM Repair, Institute of Acute Abdominal Diseases, Tianjin Nankai Hospital, Tianjin, China
| | - Ximo Wang
- Tianjin Key Laboratory of Acute Abdomen Disease Associated Organ Injury and ITCWM Repair, Institute of Acute Abdominal Diseases, Tianjin Nankai Hospital, Tianjin, China
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31
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Gao T, Zhao P, Yu X, Cao S, Zhang B, Dai M. Use of Saikosaponin D and JNK inhibitor SP600125, alone or in combination, inhibits malignant properties of human osteosarcoma U2 cells. Am J Transl Res 2019; 11:2070-2080. [PMID: 31105818 PMCID: PMC6511790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 03/13/2019] [Indexed: 06/09/2023]
Abstract
Saikosaponin D (Ssd) is a major active ingredient derived from the traditional Chinese medicinal herb Bupleurum falcatum, and SP600125 is a specific inhibitor of JNK that competes with adenosine triphosphate. In this study, we co-analyzed cell proliferation, apoptosis, migration, and invasion in U-2OS osteosarcoma cells treated with Ssd and SP600125 alone or in combination. Cell death and signaling were analyzed using western blotting and flow cytometry. We observed dramatic inhibition of cellular proliferation, invasion, and migration in cells treated with Ssd alone or in combination with SP600125. Ssd, alone or in combination with SP600125, enhanced Cytochrome C release, increased the Bax/Bcl-2 ratio, and activated caspase-3, -8 and -9, indicating that cellular apoptosis was induced via both the mitochondrial and death receptor pathways. The effect of SP600125 alone on U2 cells was not significant. Additional evaluation of Mcl-1, Akt, p-Akt, ERK, and p-ERK supported an anti-tumor effect of Ssd, which was enhanced in combination with SP600125. This study provides a theoretical basis for the treatment of osteosarcoma with Ssd alone or in combination with SP600125.
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Affiliation(s)
- Tian Gao
- Department of Orthopedics, Artificial Joints Engineering and Technology Research Center of Jiangxi Province, The First Affiliated Hospital of Nanchang UniversityNanchang 330006, P. R. China
| | - Ping Zhao
- Medical School of Nanchang UniversityNanchang 330006, P. R. China
| | - Xiaolong Yu
- Department of Orthopedics, Artificial Joints Engineering and Technology Research Center of Jiangxi Province, The First Affiliated Hospital of Nanchang UniversityNanchang 330006, P. R. China
| | - Suixia Cao
- Medical School of Nanchang UniversityNanchang 330006, P. R. China
| | - Bin Zhang
- Department of Orthopedics, Artificial Joints Engineering and Technology Research Center of Jiangxi Province, The First Affiliated Hospital of Nanchang UniversityNanchang 330006, P. R. China
| | - Min Dai
- Department of Orthopedics, Artificial Joints Engineering and Technology Research Center of Jiangxi Province, The First Affiliated Hospital of Nanchang UniversityNanchang 330006, P. R. China
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32
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Wang F, Cheng Y, Zhang C, Chang G, Geng X. A novel antisense oligonucleotide anchored on the intronic splicing enhancer of hTERT pre-mRNA inhibits telomerase activity and induces apoptosis in glioma cells. J Neurooncol 2019; 143:57-68. [PMID: 30887243 DOI: 10.1007/s11060-019-03150-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Accepted: 03/11/2019] [Indexed: 12/15/2022]
Abstract
INTRODUCTION Alternative splicing of hTERT pre-mRNA is an important step in the regulation of telomerase activity, but the regulation mechanisms and functions remain unclear. METHODS RT-PCR analysis was used to detect hTERT splicing in glioma cell lines and brain tissues. TRAP assay was used to detect the telomerase activity. Then, we designed and synthesized 2'-O-methyl-RNA phosphorothioate AONs and transfected them into glioma cells to detect the changes in telomerase activity. MTT assay, plate colony formation assay, western blotting and Annexin V/PI assay were used to detect cell proliferation and apoptosis. At last, bioinformatics analyses were used to predict the expression and function of splicing protein SRSF2 in gliomas. RESULTS hTERT splicing occurs both in glioma cell lines and glioma patients' tissues. The telomerase activity was related to the expression level of the full-length hTERT, rather than the total hTERT transcript level. AON-Ex726 was complementary to the sequence of the intronic splicing enhancer (ISE) in intron six, and significantly altered the splicing pattern of hTERT pre-mRNA, reducing the expression level of the full-length hTERT mRNA and increasing the expression level of the -β hTERT mRNA. After transfection with AON-Ex726, the level of apoptosis was increased, while telomerase activity and cell proliferation were significantly decreased. By bioinformatic predictions, we found the AON-Ex726 anchoring sequence in ISE overlaps the binding site of SRSF2 protein, which is up-regulated during the development of gliomas. CONCLUSIONS Our findings provided new targets and important clues for the gene therapy of gliomas by regulating the alternative splicing pattern of hTERT pre-mRNA.
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Affiliation(s)
- Fei Wang
- Department of Neurology, General Hospital, Tianjin Medical University, Tianjin, 300052, China
| | - Yajing Cheng
- Department of Neurology, General Hospital, Tianjin Medical University, Tianjin, 300052, China
| | - Chi Zhang
- Department of Neurology, General Hospital, Tianjin Medical University, Tianjin, 300052, China
| | - Guangming Chang
- Department of Clinical Laboratory, General Hospital, Tianjin Medical University, Tianjin, 300052, China
| | - Xin Geng
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Tianjin Medical University, 22nd Qixiangtai Road, Tianjin, 300070, China.
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Jing L, Li H, Zhang T, Lu J, Zhong L. MicroRNA‑4530 suppresses cell proliferation and induces apoptosis by targeting RASA1 in human umbilical vein endothelial cells. Mol Med Rep 2019; 19:3393-3402. [PMID: 30864691 PMCID: PMC6472120 DOI: 10.3892/mmr.2019.10000] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 08/02/2018] [Indexed: 02/07/2023] Open
Abstract
MicroRNAs (miRNAs/miRs) are a class of endogenous and non-coding RNAs that are present in eukaryotes. In previous studies, miRNAs have been revealed to have an important role in cell growth and apoptosis. In the present study, the function of a novel and rarely studied miRNA, miR-4530, was investigated in human umbilical vein endothelial cells (HUVECs). The expression level of miR-4530 in HUVECs was investigated using reverse transcription-quantitative polymerase chain reaction following transfection with miR-4530 precursor plasmids, anti-miR-4530 plasmids and empty vector plasmids. Following this, it was revealed that overexpression of miR-4530 can suppress cell proliferation and enhance cell apoptosis. TargetScan analysis suggested that Ras p21 protein activator 1 (RASA1) is a target gene of miR-4530. The results of a dual-luciferase reporter assay also suggested that miR-4530 targets RASA1. Furthermore, the results of dual-luciferase reporter assay suggested that miR-4530 enhanced luciferase activity of the wild-type reporter, but not the mutant RASA1 reporter activity, thus suggesting that miR-4530 enhances the expression of RASA1. In addition, western blot analysis demonstrated that the protein expression level of RASA1 was enhanced following upregulation of miR-4530. The exact mechanism underlying this process has not yet been determined and requires further investigation. In addition, a RASA1 overexpression plasmid vector was transfected into HUVECs. The results suggest that overexpression of RASA1 suppresses cell growth and promotes apoptosis, which was in agreement with the results regarding the overexpression of miR-4530. To investigate how miRNA-4530 affects cellular function, numerous proteins associated with the extracellular signal-regulated kinase (ERK)/mitogen-activated protein kinase (MAPK) and phosphoinositide 3-kinase (PI3K)/AKT serine/threonine kinase pathways were investigated via western blot analysis. The results suggested that miRNA-4530 suppresses cell proliferation and enhances apoptosis by targeting RASA1 via the ERK/MAPK and PI3K/AKT signaling pathways.
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Affiliation(s)
- Li Jing
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, P.R. China
| | - Hong Li
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, P.R. China
| | - Tao Zhang
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, P.R. China
| | - Jianxin Lu
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, P.R. China
| | - Lianjin Zhong
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, P.R. China
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Patel M, Sachidanandan M, Adnan M. Serine arginine protein kinase 1 (SRPK1): a moonlighting protein with theranostic ability in cancer prevention. Mol Biol Rep 2018; 46:1487-1497. [PMID: 30535769 DOI: 10.1007/s11033-018-4545-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 11/30/2018] [Indexed: 12/15/2022]
Abstract
Serine/arginine protein kinase 1 (SRPK1); a versatile functional moonlighting protein involved in varied cellular activities comprised of cell cycle progression, innate immune response, chromatin reorganization, negative and positive regulation of viral genome replication, protein amino acid phosphorylation, regulation of numerous mRNA-processing pathways, germ cell development as well as inflammation due to acquaintances with many transcription factors and signaling pathways. Several diseases including cancer have been associated with dysregulation of SRPK1. The function of SRPK1 in cancer is contradictory and inexplicable because it acts as both tumor suppressor and promoter based on the type of cell and locale. Over expression of SRPK1 including its role has been recently narrated and associated with several cancers, which includes, lung, glioma, prostate and breast via dysregulated signals from the Akt/eIF4E/HIF-1/VEGF, Erk or MAPK, PI3K/AKT/mTOR, TGF-β, and Wnt/β-catenin signaling pathways. Therefore, SRPK1 has occurred as a promising and possible curative target in cancer. In recent years, few natural and synthetic SRPK1 inhibitors have been discovered. This review emphasizes and highlights the complicated connections between SRPK1 and oncogenic signaling circuits together with the possibility of aiming SRPK1 in the treatment of cancer.
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Affiliation(s)
- Mitesh Patel
- Department of Biosciences, Bapalal Vaidya Botanical Research Centre, Veer Narmad South Gujarat University, Surat, Gujarat, India
| | - Manojkumar Sachidanandan
- Department of Oral Radiology, College of Dentistry, University of Hail, P O Box 2440, Hail, Saudi Arabia
| | - Mohd Adnan
- Department of Biology, Faculty of Science, University of Hail, P O Box 2440, Hail, Saudi Arabia.
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Xu L, Zhang H, Mei M, Du C, Huang X, Li J, Wang Y, Bao S, Zheng H. Phosphorylation of serine/arginine-rich splicing factor 1 at tyrosine 19 promotes cell proliferation in pediatric acute lymphoblastic leukemia. Cancer Sci 2018; 109:3805-3815. [PMID: 30320932 PMCID: PMC6272096 DOI: 10.1111/cas.13834] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 09/21/2018] [Accepted: 10/04/2018] [Indexed: 12/21/2022] Open
Abstract
Serine/arginine‐rich splicing factor 1 (SRSF1) has been linked to various human cancers including pediatric acute lymphoblastic leukemia (ALL). Our previous study has shown that SRSF1 potentially contributes to leukemogenesis; however, its underlying mechanism remains unclear. In this study, leukemic cells were isolated from pediatric ALL bone marrow samples, followed by immunoprecipitation assays and mass spectrometry analysis specific to SRSF1. Subcellular localization of the SRSF1 protein and its mutants were analyzed by immunofluorescence staining. Cell growth, colony formation, cell apoptosis, and the cell cycle were investigated using stable leukemic cell lines generated with lentivirus‐mediated overexpressed WT or mutant plasmids. Cytotoxicity of the Tie2 kinase inhibitor was also evaluated. Our results showed the phosphorylation of SRSF1 at tyrosine 19 (Tyr‐19) was identified in newly diagnosed ALL samples, but not in complete remission or normal control samples. Compared to the SRSF1 WT cells, the missense mutants of the Tyr‐19 phosphorylation affected the subcellular localization of SRSF1. In addition, the Tyr‐19 phosphorylation of SRSF1 also led to increased cell proliferation and enhanced colony‐forming properties by promoting the cell cycle. Remarkably, we further identified the kinase Tie2 as a potential therapeutic target in leukemia cells. In conclusion, we identify for the first time that the phosphorylation state of SRSF1 is linked to different phases in pediatric ALL. The Tyr‐19 phosphorylation of SRSF1 disrupts its subcellular localization and promotes proliferation in leukemia cells by driving cell‐cycle progression. Inhibitors targeting Tie2 kinase that could catalyze Tyr‐19 phosphorylation of SRSF1 offer a promising therapeutic target for treatment of pediatric ALL.
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Affiliation(s)
- Liting Xu
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Key Discipline of Pediatrics, Ministry of Education, Key Laboratory of Major Diseases in Children, Ministry of Education, Hematology Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Han Zhang
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Key Discipline of Pediatrics, Ministry of Education, Key Laboratory of Major Diseases in Children, Ministry of Education, Hematology Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Mei Mei
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Chaohao Du
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Xiahe Huang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Jing Li
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Key Discipline of Pediatrics, Ministry of Education, Key Laboratory of Major Diseases in Children, Ministry of Education, Hematology Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Yingchun Wang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Shilai Bao
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Huyong Zheng
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Key Discipline of Pediatrics, Ministry of Education, Key Laboratory of Major Diseases in Children, Ministry of Education, Hematology Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
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36
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Caruso JA, Carruthers NJ, Thibodeau B, Geddes TJ, Dombkowski AA, Stemmer PM. Global Signaling Profiling in a Human Model of Tumorigenic Progression Indicates a Role for Alternative RNA Splicing in Cellular Reprogramming. Int J Mol Sci 2018; 19:ijms19102847. [PMID: 30241319 PMCID: PMC6213538 DOI: 10.3390/ijms19102847] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 09/13/2018] [Accepted: 09/15/2018] [Indexed: 12/13/2022] Open
Abstract
Intracellular signaling is controlled to a large extent by the phosphorylation status of proteins. To determine how human breast cells can be reprogrammed during tumorigenic progression, we profiled cell lines in the MCF10A lineage by phosphoproteomic analyses. A large cluster of proteins involved in RNA splicing were hypophosphorylated as cells progressed to a hyperplastic state, and then hyperphosphorylated after progression to a fully metastatic phenotype. A comprehensive transcriptomic approach was used to determine whether alterations in splicing factor phosphorylation status would be reflected in changes in mRNA splicing. Results indicated that the degree of mRNA splicing trended with the degree of tumorigenicity of the 4 cell lines tested. That is, highly metastatic cell cultures had the greatest number of genes with splice variants, and these genes had greater fluctuations in expression intensities. Genes with high splicing indices were mapped against gene ontology terms to determine whether they have known roles in cancer. This group showed highly significant associations for angiogenesis, cytokine-mediated signaling, cell migration, programmed cell death and epithelial cell differentiation. In summary, data from global profiling of a human model of breast cancer development suggest that therapeutics should be developed which target signaling pathways that regulate RNA splicing.
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Affiliation(s)
- Joseph A Caruso
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI 48201, USA.
| | - Nicholas J Carruthers
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI 48201, USA.
| | - Bryan Thibodeau
- Beaumont BioBank and Molecular Core Laboratory, Royal Oak, MI 48073, USA.
| | - Timothy J Geddes
- Beaumont BioBank and Molecular Core Laboratory, Royal Oak, MI 48073, USA.
| | - Alan A Dombkowski
- Department of Pediatrics, Wayne State University, Detroit, MI 48201, USA.
| | - Paul M Stemmer
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI 48201, USA.
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37
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El Marabti E, Younis I. The Cancer Spliceome: Reprograming of Alternative Splicing in Cancer. Front Mol Biosci 2018; 5:80. [PMID: 30246013 PMCID: PMC6137424 DOI: 10.3389/fmolb.2018.00080] [Citation(s) in RCA: 152] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 08/09/2018] [Indexed: 12/15/2022] Open
Abstract
Alternative splicing allows for the expression of multiple RNA and protein isoforms from one gene, making it a major contributor to transcriptome and proteome diversification in eukaryotes. Advances in next generation sequencing technologies and genome-wide analyses have recently underscored the fact that the vast majority of multi-exon genes under normal physiology engage in alternative splicing in tissue-specific and developmental-specific manner. On the other hand, cancer cells exhibit remarkable transcriptome alterations partly by adopting cancer-specific splicing isoforms. These isoforms and their encoded proteins are not insignificant byproducts of the abnormal physiology of cancer cells, but either drivers of cancer progression or small but significant contributors to specific cancer hallmarks. Thus, it is paramount that the pathways that regulate alternative splicing in cancer, including the splicing factors that bind to pre-mRNAs and modulate spliceosome recruitment. In this review, we present a few distinct cases of alternative splicing in cancer, with an emphasis on their regulation as well as their contribution to cancer cell phenotype. Several categories of splicing aberrations are highlighted, including alterations in cancer-related genes that directly affect their pre-mRNA splicing, mutations in genes encoding splicing factors or core spliceosomal subunits, and the seemingly mutation-free disruptions in the balance of the expression of RNA-binding proteins, including components of both the major (U2-dependent) and minor (U12-dependent) spliceosomes. Given that the latter two classes cause global alterations in splicing that affect a wide range of genes, it remains a challenge to identify the ones that contribute to cancer progression. These challenges necessitate a systematic approach to decipher these aberrations and their impact on cancer. Ultimately, a sufficient understanding of splicing deregulation in cancer is predicted to pave the way for novel and innovative RNA-based therapies.
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Affiliation(s)
- Ettaib El Marabti
- Biological Sciences Program, Carnegie Mellon University in Qatar, Doha, Qatar
| | - Ihab Younis
- Biological Sciences Program, Carnegie Mellon University in Qatar, Doha, Qatar
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38
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Liu X, Klein PS. Glycogen synthase kinase-3 and alternative splicing. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 9:e1501. [PMID: 30118183 DOI: 10.1002/wrna.1501] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 07/03/2018] [Accepted: 07/09/2018] [Indexed: 12/16/2022]
Abstract
Glycogen synthase kinase-3 (GSK-3) is a highly conserved negative regulator of receptor tyrosine kinase, cytokine, and Wnt signaling pathways. Stimulation of these pathways inhibits GSK-3 to modulate diverse downstream effectors that include transcription factors, nutrient sensors, glycogen synthesis, mitochondrial function, circadian rhythm, and cell fate. GSK-3 also regulates alternative splicing in response to T-cell receptor activation, and recent phosphoproteomic studies have revealed that multiple splicing factors and regulators of RNA biosynthesis are phosphorylated in a GSK-3-dependent manner. Furthermore, inhibition of GSK-3 alters the splicing of hundreds of mRNAs, indicating a broad role for GSK-3 in the regulation of RNA processing. GSK-3-regulated phosphoproteins include SF3B1, SRSF2, PSF, RBM8A, nucleophosmin 1 (NPM1), and PHF6, many of which are mutated in leukemia and myelodysplasia. As GSK-3 is inhibited by pathways that are pathologically activated in leukemia and loss of Gsk3 in hematopoietic cells causes a severe myelodysplastic neoplasm in mice, these findings strongly implicate GSK-3 as a critical regulator of mRNA processing in normal and malignant hematopoiesis. This article is categorized under: RNA Processing > Splicing Mechanisms RNA Processing > Splicing Regulation/Alternative Splicing RNA in Disease and Development > RNA in Disease RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Xiaolei Liu
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Peter S Klein
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
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39
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Signaling Pathways Driving Aberrant Splicing in Cancer Cells. Genes (Basel) 2017; 9:genes9010009. [PMID: 29286307 PMCID: PMC5793162 DOI: 10.3390/genes9010009] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 12/07/2017] [Accepted: 12/18/2017] [Indexed: 12/17/2022] Open
Abstract
Aberrant profiles of pre-mRNA splicing are frequently observed in cancer. At the molecular level, an altered profile results from a complex interplay between chromatin modifications, the transcriptional elongation rate of RNA polymerase, and effective binding of the spliceosome to the generated transcripts. Key players in this interplay are regulatory splicing factors (SFs) that bind to gene-specific splice-regulatory sequence elements. Although mutations in genes of some SFs were described, a major driver of aberrant splicing profiles is oncogenic signal transduction pathways. Signaling can affect either the transcriptional expression levels of SFs or the post-translational modification of SF proteins, and both modulate the ratio of nuclear versus cytoplasmic SFs in a given cell. Here, we will review currently known mechanisms by which cancer cell signaling, including the mitogen-activated protein kinases (MAPK), phosphatidylinositol 3 (PI3)-kinase pathway (PI3K) and wingless (Wnt) pathways but also signals from the tumor microenvironment, modulate the activity or subcellular localization of the Ser/Arg rich (SR) proteins and heterogeneous nuclear ribonucleoproteins (hnRNPs) families of SFs.
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40
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Kajitani N, Glahder J, Wu C, Yu H, Nilsson K, Schwartz S. hnRNP L controls HPV16 RNA polyadenylation and splicing in an Akt kinase-dependent manner. Nucleic Acids Res 2017; 45:9654-9678. [PMID: 28934469 PMCID: PMC5766200 DOI: 10.1093/nar/gkx606] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 07/04/2017] [Indexed: 11/14/2022] Open
Abstract
Inhibition of the Akt kinase activates HPV16 late gene expression by reducing HPV16 early polyadenylation and by activating HPV16 late L1 mRNA splicing. We identified ‘hot spots’ for RNA binding proteins at the early polyA signal and at splice sites on HPV16 late mRNAs. We observed that hnRNP L was associated with sequences at all HPV16 late splice sites and at the early polyA signal. Akt kinase inhibition resulted in hnRNP L dephosphorylation and reduced association of hnRNP L with HPV16 mRNAs. This was accompanied by an increased binding of U2AF65 and Sam68 to HPV16 mRNAs. Furthermore, siRNA knock-down of hnRNP L or Akt induced HPV16 gene expression. Treatment of HPV16 immortalized keratinocytes with Akt kinase inhibitor reduced hnRNP L binding to HPV16 mRNAs and induced HPV16 L1 mRNA production. Finally, deletion of the hnRNP L binding sites in HPV16 subgenomic expression plasmids resulted in activation of HPV16 late gene expression. In conclusion, the Akt kinase inhibits HPV16 late gene expression at the level of RNA processing by controlling the RNA-binding protein hnRNP L. We speculate that Akt kinase activity upholds an intracellular milieu that favours HPV16 early gene expression and suppresses HPV16 late gene expression.
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Affiliation(s)
- Naoko Kajitani
- Department of Laboratory Medicine, Lund University, BMC-B13, 223 62 Lund, Sweden
| | - Jacob Glahder
- Department of Laboratory Medicine, Lund University, BMC-B13, 223 62 Lund, Sweden
| | - Chengjun Wu
- Department of Laboratory Medicine, Lund University, BMC-B13, 223 62 Lund, Sweden
| | - Haoran Yu
- Department of Laboratory Medicine, Lund University, BMC-B13, 223 62 Lund, Sweden
| | - Kersti Nilsson
- Department of Laboratory Medicine, Lund University, BMC-B13, 223 62 Lund, Sweden
| | - Stefan Schwartz
- Department of Laboratory Medicine, Lund University, BMC-B13, 223 62 Lund, Sweden
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41
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Li P, Zhou L, Zhao T, Liu X, Zhang P, Liu Y, Zheng X, Li Q. Caspase-9: structure, mechanisms and clinical application. Oncotarget 2017; 8:23996-24008. [PMID: 28177918 PMCID: PMC5410359 DOI: 10.18632/oncotarget.15098] [Citation(s) in RCA: 173] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 01/22/2017] [Indexed: 12/27/2022] Open
Abstract
As the most intensively studied initiator caspase, caspase-9 is a key player in the intrinsic or mitochondrial pathway which is involved in various stimuli, including chemotherapies, stress agents and radiation. Caspase-9 is activated on the apoptosome complex to remain catalytic status and is thought of involving homo-dimerization monomeric zymogens. Failing to activate caspase-9 has profound physiological and pathophysiological outcomes, leading to degenerative and developmental disorders even cancer. To govern the apoptotic commitment process appropriately, plenty of proteins and small molecules involved in regulating caspase-9. Therefore, this review is to summarize recent pertinent literature on the comprehensive description of the molecular events implicated in caspase-9 activation and inhibition, as well as the clinical trials in progress to give deep insight into caspase-9 for suppressing cancer. We hope that our concerns will be helpful for further clinical studies addressing the roles of caspase-9 and its regulators demanded to identify more effective solutions to overcome intrinsic apoptosis-related diseases especially cancer.
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Affiliation(s)
- Ping Li
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, People's Republic of China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, People's Republic of China.,Key Laboratory of Basic Research on Heavy Ion Radiation Application in Medicine, Gansu Province, Lanzhou, People's Republic of China
| | - Libin Zhou
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, People's Republic of China
| | - Ting Zhao
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, People's Republic of China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, People's Republic of China.,Key Laboratory of Basic Research on Heavy Ion Radiation Application in Medicine, Gansu Province, Lanzhou, People's Republic of China
| | - Xiongxiong Liu
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, People's Republic of China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, People's Republic of China.,Key Laboratory of Basic Research on Heavy Ion Radiation Application in Medicine, Gansu Province, Lanzhou, People's Republic of China
| | - Pengcheng Zhang
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, People's Republic of China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, People's Republic of China.,Key Laboratory of Basic Research on Heavy Ion Radiation Application in Medicine, Gansu Province, Lanzhou, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Yan Liu
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, People's Republic of China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, People's Republic of China.,Key Laboratory of Basic Research on Heavy Ion Radiation Application in Medicine, Gansu Province, Lanzhou, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Xiaogang Zheng
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, People's Republic of China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, People's Republic of China.,Key Laboratory of Basic Research on Heavy Ion Radiation Application in Medicine, Gansu Province, Lanzhou, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Qiang Li
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, People's Republic of China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, People's Republic of China.,Key Laboratory of Basic Research on Heavy Ion Radiation Application in Medicine, Gansu Province, Lanzhou, People's Republic of China
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42
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Lambert CA, Garbacki N, Colige AC. Chemotherapy induces alternative transcription and splicing: Facts and hopes for cancer treatment. Int J Biochem Cell Biol 2017; 91:84-97. [DOI: 10.1016/j.biocel.2017.04.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 04/04/2017] [Accepted: 04/15/2017] [Indexed: 01/14/2023]
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43
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Lee CC, Chang WH, Chang YS, Liu TY, Chen YC, Wu YC, Chang JG. 4β-Hydroxywithanolide E Modulates Alternative Splicing of Apoptotic Genes in Human Hepatocellular Carcinoma Huh-7 Cells. Sci Rep 2017; 7:7290. [PMID: 28779122 PMCID: PMC5544667 DOI: 10.1038/s41598-017-07472-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 06/27/2017] [Indexed: 01/31/2023] Open
Abstract
Alternative splicing is a mechanism for increasing protein diversity from a limited number of genes. Studies have demonstrated that aberrant regulation in the alternative splicing of apoptotic gene transcripts may contribute to the development of cancer. In this study, we isolated 4β-Hydroxywithanolide E (4bHWE) from the traditional herb Physalis peruviana and investigated its biological effect in cancer cells. The results demonstrated that 4bHWE modulates the alternative splicing of various apoptotic genes, including HIPK3, SMAC/DIABLO, and SURVIVIN. We also discovered that the levels of SRSF1 phospho-isoform were decreased and the levels of H3K36me3 were increased in 4bHWE treatment. Knockdown experiments revealed that the splicing site selection of SMAC/DIABLO could be mediated by changes in the level of H3K36me3 in 4bHWE-treated cells. Furthermore, we extended our study to apoptosis-associated molecules, and detected increased levels of poly ADP-ribose polymerase cleavage and the active form of CASPASE-3 in 4bHWE-induced apoptosis. In vivo experiments indicated that the treatment of tumor-bearing mice with 4bHWE resulted in a marked decrease in tumor size. This study is the first to demonstrate that 4bHWE affects alternative splicing by modulating splicing factors and histone modifications, and provides a novel view of the antitumor mechanism of 4bHWE.
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Affiliation(s)
- Chien-Chin Lee
- Epigenome Research Center, China Medical University Hospital, Taichung, Taiwan
| | - Wen-Hsin Chang
- Department of Primary Care Medicine, Taipei Medical University Hospital, Taipei, Taiwan
| | - Ya-Sian Chang
- Epigenome Research Center, China Medical University Hospital, Taichung, Taiwan.,Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan.,Center for Precision Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Ting-Yuan Liu
- Center for Precision Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Yu-Chia Chen
- Center for Precision Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Yang-Chang Wu
- Graduate Institute of Natural Products, Kaohsiung Medical University, Kaohsiung, Taiwan. .,Research Center for Natural Products and Drug Development, Kaohsiung Medical University, Kaohsiung, Taiwan. .,Chinese Medicine Research and Development Center, China Medical University Hospital, Taichung, Taiwan.
| | - Jan-Gowth Chang
- Epigenome Research Center, China Medical University Hospital, Taichung, Taiwan. .,Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan. .,Center for Precision Medicine, China Medical University Hospital, Taichung, Taiwan. .,Department of Bioinformatics and Medical Engineering, Asia University, Taichung, Taiwan.
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44
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Insulin regulates titin pre-mRNA splicing through the PI3K-Akt-mTOR kinase axis in a RBM20-dependent manner. Biochim Biophys Acta Mol Basis Dis 2017; 1863:2363-2371. [PMID: 28676430 DOI: 10.1016/j.bbadis.2017.06.023] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 06/25/2017] [Accepted: 06/29/2017] [Indexed: 12/13/2022]
Abstract
Titin, a giant sarcomeric protein, is largely responsible for the diastolic properties of the heart. It has two major isoforms, N2B and N2BA due to pre-mRNA splicing regulated mainly by a splicing factor RNA binding motif 20 (RBM20). Mis-splicing of titin pre-mRNA in response to external stimuli may lead to altered ratio of N2B to N2BA, and thus, impaired cardiac contractile function. However, little is known about titin alternative splicing in response to external stimuli. Here, we reported the detailed mechanisms of titin alternative splicing in response to insulin. Insulin treatment in cultured neonatal rat cardiomyocytes (NRCMs) activated the PI3K-Akt-mTOR kinase axis, leading to increased N2B expression in the presence of RBM20, but not in NRCMs in the absence of RBM20. By inhibiting this kinase axis with inhibitors, decreased N2B isoform was observed in NRCMs and also in diabetic rat model treated with streptozotocin, but not in NRCMs and diabetic rats in the absence of RBM20. In addition to the alteration of titin isoform ratios in response to insulin, we found that RBM20 expression was increased in NRCMs with insulin treatment, suggesting that RBM20 levels were also regulated by insulin-induced kinase axis. Further, knockdown of p70S6K1 with siRNA reduced both RBM20 and N2B levels, while knockdown of 4E-BP1 elevated expression levels of RBM20 and N2B. These findings reveal a major signal transduction pathway for insulin-induced titin alternative splicing, and place RBM20 in a central position in the pathway, which is consistent with the reputed role of RBM20 in titin alternative splicing. Findings from this study shed light on gene therapeutic strategies at the molecular level by correction of pre-mRNA mis-splicing.
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Bates DO, Morris JC, Oltean S, Donaldson LF. Pharmacology of Modulators of Alternative Splicing. Pharmacol Rev 2017; 69:63-79. [PMID: 28034912 PMCID: PMC5226212 DOI: 10.1124/pr.115.011239] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
More than 95% of genes in the human genome are alternatively spliced to form multiple transcripts, often encoding proteins with differing or opposing function. The control of alternative splicing is now being elucidated, and with this comes the opportunity to develop modulators of alternative splicing that can control cellular function. A number of approaches have been taken to develop compounds that can experimentally, and sometimes clinically, affect splicing control, resulting in potential novel therapeutics. Here we develop the concepts that targeting alternative splicing can result in relatively specific pathway inhibitors/activators that result in dampening down of physiologic or pathologic processes, from changes in muscle physiology to altering angiogenesis or pain. The targets and pharmacology of some of the current inhibitors/activators of alternative splicing are demonstrated and future directions discussed.
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Affiliation(s)
- David O Bates
- Cancer Biology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom (D.O.B.); School of Chemistry, UNSW Australia, Sydney, Australia (J.C.M.); School of Physiology, Pharmacology and Neurosciences, School of Clinical Sciences/Bristol Renal, University of Bristol, Bristol, United Kingdom (S.O.); and School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom (L.F.D.)
| | - Jonathan C Morris
- Cancer Biology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom (D.O.B.); School of Chemistry, UNSW Australia, Sydney, Australia (J.C.M.); School of Physiology, Pharmacology and Neurosciences, School of Clinical Sciences/Bristol Renal, University of Bristol, Bristol, United Kingdom (S.O.); and School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom (L.F.D.)
| | - Sebastian Oltean
- Cancer Biology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom (D.O.B.); School of Chemistry, UNSW Australia, Sydney, Australia (J.C.M.); School of Physiology, Pharmacology and Neurosciences, School of Clinical Sciences/Bristol Renal, University of Bristol, Bristol, United Kingdom (S.O.); and School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom (L.F.D.)
| | - Lucy F Donaldson
- Cancer Biology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom (D.O.B.); School of Chemistry, UNSW Australia, Sydney, Australia (J.C.M.); School of Physiology, Pharmacology and Neurosciences, School of Clinical Sciences/Bristol Renal, University of Bristol, Bristol, United Kingdom (S.O.); and School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom (L.F.D.)
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46
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Czubaty A, Piekiełko-Witkowska A. Protein kinases that phosphorylate splicing factors: Roles in cancer development, progression and possible therapeutic options. Int J Biochem Cell Biol 2017; 91:102-115. [PMID: 28552434 DOI: 10.1016/j.biocel.2017.05.024] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 05/16/2017] [Accepted: 05/18/2017] [Indexed: 11/30/2022]
Abstract
Disturbed alternative splicing is a common feature of human tumors. Splicing factors that control alternative splicing are phosphorylated by multiple kinases, including these that specifically add phosphoryl groups to serine-arginine rich proteins (e.g. SR-protein kinases, cdc2-like kinases, topoisomerase 1), and protein kinases that govern key cellular signaling pathways (i.e. AKT). Phosphorylation of splicing factors regulates their subcellular localization and interactions with target transcripts and protein partners, and thus significantly contributes the final result of splicing reactions. In this review we aim to summarize the current knowledge on the role of splicing kinases in cancer. Published studies and recently released data of The Cancer Genome Atlas demonstrate that expressions and activities of splicing kinases are commonly disturbed in cancers. Aberrant functioning of splicing kinases results in changed alternative splicing of tumor suppressors (e.g. p53) and regulators of cell signaling (e.g. MAPKs), apoptosis (e.g. MCL), and angiogenesis (VEGF). Splicing kinases act in complicated regulatory networks in which they mutually affect each other's activity to provide tight control of cellular signaling. Dysregulation of these regulatory networks contributes to oncogenic transformation, uncontrolled proliferation, enhanced migration and invasion. Furthermore, the activities of splicing kinases significantly contribute to cellular responses to genotoxic stress. In conclusion, published data provide strong evidence that splicing kinases emerge as important regulators of key processes governing malignant transformation, progression, and response to therapeutic treatments, suggesting their potential as clinically relevant targets.
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Affiliation(s)
- Alicja Czubaty
- Department of Molecular Biology, Faculty of Biology, University of Warsaw, ul. Miecznikowa 1, 02-096 Warsaw, Poland
| | - Agnieszka Piekiełko-Witkowska
- Department of Biochemistry and Molecular Biology, Centre of Postgraduate Medical Education, ul. Marymoncka 99/103, 01-813 Warsaw, Poland.
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47
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Kędzierska H, Piekiełko-Witkowska A. Splicing factors of SR and hnRNP families as regulators of apoptosis in cancer. Cancer Lett 2017; 396:53-65. [PMID: 28315432 DOI: 10.1016/j.canlet.2017.03.013] [Citation(s) in RCA: 149] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 03/08/2017] [Accepted: 03/08/2017] [Indexed: 12/19/2022]
Abstract
SR and hnRNP proteins were initially discovered as regulators of alternative splicing: the process of controlled removal of introns and selective joining of exons through which multiple transcripts and, subsequently, proteins can be expressed from a single gene. Alternative splicing affects genes involved in all crucial cellular processes, including apoptosis. During cancerogenesis impaired apoptotic control facilitates survival of cells bearing molecular aberrations, contributing to their unrestricted proliferation and chemoresistance. Apparently, SR and hnRNP proteins regulate all levels of expression of apoptotic genes, including transcription initiation and elongation, alternative splicing, mRNA stability, translation, and protein degradation. The frequently disturbed expressions of SR/hnRNP proteins in cancers lead to impaired functioning of target apoptotic genes, including regulators of the extrinsic (Fas, caspase-8, caspase-2, c-FLIP) and the intrinsic pathway (Apaf-1, caspase-9, ICAD), genes encoding Bcl-2 proteins, IAPs, and p53 tumor suppressor. Prototypical members of SR/hnRNP families, SRSF1 and hnRNP A1, promote synthesis of anti-apoptotic splice variants of Bcl-x and Mcl-1, which results in attenuation of programmed cell death in breast cancer and chronic myeloid leukemia. SR/hnRNP proteins significantly affect responses to chemotherapy, acting as mediators or modulators of drug-induced apoptosis. Aberrant expression of SRSF1 and hnRNP K can interfere with tumor responses to chemotherapy in pancreatic and liver cancers. Currently, a number of splicing factor inhibitors is being tested in pre-clinical and clinical trials. In this review we discuss recent findings on the role of SR and hnRNP proteins in apoptotic control in cancer cells as well as their significance in anticancer treatments.
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Affiliation(s)
- Hanna Kędzierska
- Department of Biochemistry and Molecular Biology, Centre of Postgraduate Medical Education, ul. Marymoncka 99/103, 01-813 Warsaw, Poland
| | - Agnieszka Piekiełko-Witkowska
- Department of Biochemistry and Molecular Biology, Centre of Postgraduate Medical Education, ul. Marymoncka 99/103, 01-813 Warsaw, Poland.
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48
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MiR-222 promotes drug-resistance of breast cancer cells to adriamycin via modulation of PTEN/Akt/FOXO1 pathway. Gene 2017; 596:110-118. [DOI: 10.1016/j.gene.2016.10.016] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 10/07/2016] [Accepted: 10/12/2016] [Indexed: 12/25/2022]
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de Necochea-Campion R, Shouse GP, Zhou Q, Mirshahidi S, Chen CS. Aberrant splicing and drug resistance in AML. J Hematol Oncol 2016; 9:85. [PMID: 27613060 PMCID: PMC5018179 DOI: 10.1186/s13045-016-0315-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 09/02/2016] [Indexed: 02/08/2023] Open
Abstract
The advent of next-generation sequencing technologies has unveiled a new window into the heterogeneity of acute myeloid leukemia (AML). In particular, recurrent mutations in spliceosome machinery and genome-wide aberrant splicing events have been recognized as a prominent component of this disease. This review will focus on how these factors influence drug resistance through altered splicing of tumor suppressor and oncogenes and dysregulation of the apoptotic signaling network. A better understanding of these factors in disease progression is necessary to design appropriate therapeutic strategies recognizing specific alternatively spliced or mutated oncogenic targets.
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Affiliation(s)
- Rosalia de Necochea-Campion
- Biospecimen Laboratory, Loma Linda University Cancer Center, Loma Linda University School of Medicine, Loma Linda, CA, 92354, USA
| | - Geoffrey P Shouse
- Division of Hematology/Oncology, Loma Linda University School of Medicine, 11175 Campus Street, Chan Shun Pavilion 11015, Loma Linda, CA, 92354, USA
| | - Qi Zhou
- Biospecimen Laboratory, Loma Linda University Cancer Center, Loma Linda University School of Medicine, Loma Linda, CA, 92354, USA
| | - Saied Mirshahidi
- Biospecimen Laboratory, Loma Linda University Cancer Center, Loma Linda University School of Medicine, Loma Linda, CA, 92354, USA
| | - Chien-Shing Chen
- Biospecimen Laboratory, Loma Linda University Cancer Center, Loma Linda University School of Medicine, Loma Linda, CA, 92354, USA. .,Division of Hematology/Oncology, Loma Linda University School of Medicine, 11175 Campus Street, Chan Shun Pavilion 11015, Loma Linda, CA, 92354, USA.
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50
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Shapiro BA, Vu NT, Shultz MD, Shultz JC, Mietla JA, Gouda MM, Yacoub A, Dent P, Fisher PB, Park MA, Chalfant CE. Melanoma Differentiation-associated Gene 7/IL-24 Exerts Cytotoxic Effects by Altering the Alternative Splicing of Bcl-x Pre-mRNA via the SRC/PKCδ Signaling Axis. J Biol Chem 2016; 291:21669-21681. [PMID: 27519412 DOI: 10.1074/jbc.m116.737569] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 08/02/2016] [Indexed: 11/06/2022] Open
Abstract
Melanoma differentiation-associated gene 7 (MDA-7/IL-24) exhibits cytotoxic effects on tumor cells while sparing untransformed cells, and Bcl-x(L) is reported to efficiently block the induction of cell death by MDA-7/IL-24. The expression of Bcl-x(L) is regulated at the level of RNA splicing via alternative 5' splice site selection within exon 2 to produce either the pro-apoptotic Bcl-x(s) or the anti-apoptotic Bcl-x(L). Our laboratory previously reported that Bcl-x RNA splicing is dysregulated in a large percentage of human non-small cell lung cancer (NSCLC) tumors. Therefore, we investigated whether the alternative RNA splicing of Bcl-x pre-mRNA was modulated by MDA-7/IL-24, which would suggest that specific NSCLC tumors are valid targets for this cytokine therapy. Adenovirus-delivered MDA-7/IL-24 (Ad.mda-7) reduced the viability of NSCLC cells of varying oncogenotypes, which was preceded by a decrease in the ratio of Bcl-x(L)/Bcl-x(s) mRNA and Bcl-x(L) protein expression. Importantly, both the expression of Bcl-x(L) and the loss of cell viability were "rescued" in Ad.mda-7-treated cells incubated with Bcl-x(s) siRNA. In addition, NSCLC cells ectopically expressing Bcl-x(s) exhibited significantly reduced Bcl-x(L) expression, which was again restored by Bcl-x(s) siRNA, suggesting the existence of a novel mechanism by which Bcl-x(s) mRNA restrains the expression of Bcl-x(L). In additional mechanistic studies, inhibition of SRC and PKCδ completely ablated the ability of MDA-7/IL-24 to reduce the Bcl-x(L)/(s) mRNA ratio and cell viability. These findings show that Bcl-x(s) expression is an important mediator of MDA-7/IL-24-induced cytotoxicity requiring the SRC/PKCδ signaling axis in NSCLC cells.
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Affiliation(s)
- Brian A Shapiro
- From the Hunter Holmes McGuire Veterans Administration Medical Center, Richmond, Virginia 23249.,the Department of Biochemistry and Molecular Biology, Virginia Commonwealth University-School of Medicine, Richmond, Virginia 23298-0614
| | - Ngoc T Vu
- the Department of Biochemistry and Molecular Biology, Virginia Commonwealth University-School of Medicine, Richmond, Virginia 23298-0614
| | - Michael D Shultz
- From the Hunter Holmes McGuire Veterans Administration Medical Center, Richmond, Virginia 23249
| | - Jacqueline C Shultz
- the Department of Biochemistry and Molecular Biology, Virginia Commonwealth University-School of Medicine, Richmond, Virginia 23298-0614
| | - Jennifer A Mietla
- the Department of Biochemistry and Molecular Biology, Virginia Commonwealth University-School of Medicine, Richmond, Virginia 23298-0614
| | - Mazen M Gouda
- the Department of Biochemistry and Molecular Biology, Virginia Commonwealth University-School of Medicine, Richmond, Virginia 23298-0614
| | - Adly Yacoub
- the Department of Neurosurgery, Virginia Commonwealth University-School of Medicine, Richmond, Virginia 23298-0614
| | - Paul Dent
- the Department of Biochemistry and Molecular Biology, Virginia Commonwealth University-School of Medicine, Richmond, Virginia 23298-0614.,the Virginia Commonwealth University Institute of Molecular Medicine, Richmond, Virginia 23298.,the Virginia Commonwealth University Massey Cancer Center, Richmond, Virginia 23298, and
| | - Paul B Fisher
- the Virginia Commonwealth University Institute of Molecular Medicine, Richmond, Virginia 23298, .,the Virginia Commonwealth University Massey Cancer Center, Richmond, Virginia 23298, and.,the Department of Human and Molecular Genetics, Virginia Commonwealth University-School of Medicine, Richmond, Virginia 23298
| | - Margaret A Park
- the Department of Biochemistry and Molecular Biology, Virginia Commonwealth University-School of Medicine, Richmond, Virginia 23298-0614, .,the Virginia Commonwealth University Massey Cancer Center, Richmond, Virginia 23298, and
| | - Charles E Chalfant
- From the Hunter Holmes McGuire Veterans Administration Medical Center, Richmond, Virginia 23249, .,the Department of Biochemistry and Molecular Biology, Virginia Commonwealth University-School of Medicine, Richmond, Virginia 23298-0614.,the Virginia Commonwealth University Institute of Molecular Medicine, Richmond, Virginia 23298.,the Virginia Commonwealth University Massey Cancer Center, Richmond, Virginia 23298, and.,the Virginia Commonwealth University Johnson Center for Critical Care and Pulmonary Research, Richmond, Virginia 23298
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