1
|
Rihan M, Sharma SS. Compound 3K attenuates isoproterenol-induced cardiac hypertrophy by inhibiting pyruvate kinase M2 (PKM2) pathway. Life Sci 2024; 351:122837. [PMID: 38879156 DOI: 10.1016/j.lfs.2024.122837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Revised: 05/31/2024] [Accepted: 06/11/2024] [Indexed: 06/21/2024]
Abstract
AIM Chronic sympathetic stimulation has been identified as a primary factor in the pathogenesis of cardiac hypertrophy (CH). However, there is no appropriate treatment available for the management of CH. Recently, it has been revealed that pyruvate kinase M2 (PKM2) plays a significant role in cardiac remodeling, fibrosis, and hypertrophy. However, the therapeutic potential of selective PKM2 inhibitor has not yet been explored in cardiac hypertrophy. Thus, in the current study, we have studied the cardioprotective potential of Compound 3K, a selective PKM2 inhibitor in isoproterenol-induced CH model. METHODS To induce cardiac hypertrophy, male Wistar rats were subcutaneously administered isoproterenol (ISO, 5 mg/kg/day) for 14 days. Compound 3K at dosages of 2 and 4 mg/kg orally was administered to ISO-treated rats for 14 days to explore its effects on various parameters like ECG, ventricular functions, hypertrophic markers, histology, inflammation, and protein expression were performed. RESULTS Fourteen days administration of ISO resulted in the induction of CH, which was evidenced by alterations in ECG, ventricular dysfunctions, increase in hypertrophy markers, and fibrosis. The immunoblotting of hypertrophy heart revealed the significant rise in PKM2 and reduction in PKM1 protein expression. Treatment with Compound 3K led to downregulation of PKM2 and upregulation of PKM1 protein expression. Compound 3K showed cardioprotective effects by improving ECG, cardiac functions, hypertrophy markers, inflammation, and fibrosis. Further, it also reduced cardiac expression of PKM2-associated splicing protein, HIF-1α, and caspase-3. CONCLUSION Our findings suggest that Compound 3K has a potential cardioprotective effect via PKM2 inhibition in isoproterenol-induced CH.
Collapse
Affiliation(s)
- Mohd Rihan
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), S.A.S Nagar (Mohali) 160062, Punjab, India
| | - Shyam Sunder Sharma
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), S.A.S Nagar (Mohali) 160062, Punjab, India.
| |
Collapse
|
2
|
Ye Z, Zhong Y, Zhang Z. Pan-cancer multi-omics analysis of PTBP1 reveals it as an inflammatory, progressive and prognostic marker in glioma. Sci Rep 2024; 14:14584. [PMID: 38918441 PMCID: PMC11199703 DOI: 10.1038/s41598-024-64979-5] [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: 12/27/2023] [Accepted: 06/14/2024] [Indexed: 06/27/2024] Open
Abstract
PTBP1 is an oncogene that regulates the splicing of precursor mRNA. However, the relationship between PTBP1 expression and gene methylation, cancer prognosis, and tumor microenvironment remains unclear. The expression profiles of PTBP1 across various cancers were derived from the TCGA, as well as the GTEx and CGGA databases. The CGGA mRNA_325, CGGA mRNA_301, and CGGA mRNA_693 datasets were utilized as validation cohorts. Immune cell infiltration scores were approximated using the TIMER 2.0 tool. Functional enrichment analysis for groups with high and low PTBP1 expression was conducted using Gene Set Enrichment Analysis (GSEA). Methylation data were predominantly sourced from the SMART and Mexpress databases. Linked-omics analysis was employed to perform functional enrichment analysis of genes related to PTBP1 methylation, as well as to conduct protein functional enrichment analysis. Single-cell transcriptome analysis and spatial transcriptome analysis were carried out using Seurat version 4.10. Compared to normal tissues, PTBP1 is significantly overexpressed and hypomethylated in various cancers. It is implicated in prognosis, immune cell infiltration, immune checkpoint expression, genomic variation, tumor neoantigen load, and tumor mutational burden across a spectrum of cancers, with particularly notable effects in low-grade gliomas. In the context of gliomas, PTBP1 expression correlates with WHO grade and IDH1 mutation status. PTBP1 expression and methylation play an important role in a variety of cancers. PTBP1 can be used as a marker of inflammation, progression and prognosis in gliomas.
Collapse
Affiliation(s)
- Zheng Ye
- Institute of Computational Science and Technology, Guangzhou University, Guangzhou, 510006, Guangdong, China
- Zhongda Hospital, Southeast University, Nanjing, China
| | - Yan Zhong
- People's Hospital of Dongxihu District, Wuhan, China
| | - Zhiyuan Zhang
- Department of Neurosurgery, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China.
| |
Collapse
|
3
|
Shi Y, Pan Z, Feng Y, Zhou Q, Wang Q, Wang H, Dong G, Xia W, Jiang F. tRF-29-79 regulates lung adenocarcinoma progression through mediating glutamine transporter SLC1A5. Carcinogenesis 2024; 45:409-423. [PMID: 38366384 DOI: 10.1093/carcin/bgae010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 01/17/2024] [Accepted: 02/14/2024] [Indexed: 02/18/2024] Open
Abstract
In recent decades, considerable evidence has emerged indicating the involvement of tRNA-derived fragments (tRFs) in cancer progression through various mechanisms. However, the biological effects and mechanisms of tRFs in lung adenocarcinoma (LUAD) remain unclear. In this study, we screen out tRF-29-79, a 5'-tRF derived from tRNAGlyGCC, through profiling the tRF expressions in three pairs of LUAD tissues. We show that tRF-29-79 is downregulated in LUAD and downregulation of tRF-29-79 is associated with poorer prognosis. In vivo and in vitro assay reveal that tRF-29-79 inhibits proliferation, migration and invasion of LUAD cells. Mechanistically, we discovered that tRF-29-79 interacts with the RNA-binding protein PTBP1 and facilitates the transportation of PTBP1 from nucleus to cytoplasm, which regulates alternative splicing in the 3' untranslated region (UTR) of SLC1A5 pre-mRNA. Given that SLC1A5 is a core transporter of glutamine, we proved that tRF-29-79 mediate glutamine metabolism of LUAD through affecting the stability of SLC1A5 mRNA, thus exerts its anticancer function. In summary, our findings uncover the novel mechanism that tRF-29-79 participates in glutamine metabolism through interacting with PTBP1 and regulating alternative splicing in the 3' UTR of SLC1A5 pre-mRNA.
Collapse
Affiliation(s)
- Yuanjian Shi
- Department of Thoracic Surgery, Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, 42 Baiziting Road, Xuanwu District, Nanjing 210009, China
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, 42 Baiziting Road, Xuanwu District, Nanjing 210009, China
- The Fourth Clinical College of Nanjing Medical University, Nanjing, China
| | - Zehao Pan
- Department of Thoracic Surgery, Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, 42 Baiziting Road, Xuanwu District, Nanjing 210009, China
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, 42 Baiziting Road, Xuanwu District, Nanjing 210009, China
- The Fourth Clinical College of Nanjing Medical University, Nanjing, China
| | - Yipeng Feng
- Department of Thoracic Surgery, Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, 42 Baiziting Road, Xuanwu District, Nanjing 210009, China
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, 42 Baiziting Road, Xuanwu District, Nanjing 210009, China
- The Fourth Clinical College of Nanjing Medical University, Nanjing, China
| | - Qinyao Zhou
- The First Clinical College of Nanjing Medical University, Nanjing, China
| | - Qinglin Wang
- Department of Thoracic Surgery, Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, 42 Baiziting Road, Xuanwu District, Nanjing 210009, China
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, 42 Baiziting Road, Xuanwu District, Nanjing 210009, China
- The Fourth Clinical College of Nanjing Medical University, Nanjing, China
| | - Hui Wang
- Department of Thoracic Surgery, Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, 42 Baiziting Road, Xuanwu District, Nanjing 210009, China
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, 42 Baiziting Road, Xuanwu District, Nanjing 210009, China
- The Fourth Clinical College of Nanjing Medical University, Nanjing, China
| | - Gaochao Dong
- Department of Thoracic Surgery, Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, 42 Baiziting Road, Xuanwu District, Nanjing 210009, China
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, 42 Baiziting Road, Xuanwu District, Nanjing 210009, China
| | - Wenjie Xia
- Department of Thoracic Surgery, Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, 42 Baiziting Road, Xuanwu District, Nanjing 210009, China
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, 42 Baiziting Road, Xuanwu District, Nanjing 210009, China
- The Fourth Clinical College of Nanjing Medical University, Nanjing, China
| | - Feng Jiang
- Department of Thoracic Surgery, Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, 42 Baiziting Road, Xuanwu District, Nanjing 210009, China
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, 42 Baiziting Road, Xuanwu District, Nanjing 210009, China
- The Fourth Clinical College of Nanjing Medical University, Nanjing, China
| |
Collapse
|
4
|
Li Y, Zhang S, Li Y, Liu J, Li Q, Zang W, Pan Y. The Regulatory Network of hnRNPs Underlying Regulating PKM Alternative Splicing in Tumor Progression. Biomolecules 2024; 14:566. [PMID: 38785973 PMCID: PMC11117501 DOI: 10.3390/biom14050566] [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: 03/30/2024] [Revised: 04/26/2024] [Accepted: 05/07/2024] [Indexed: 05/25/2024] Open
Abstract
One of the hallmarks of cancer is metabolic reprogramming in tumor cells, and aerobic glycolysis is the primary mechanism by which glucose is quickly transformed into lactate. As one of the primary rate-limiting enzymes, pyruvate kinase (PK) M is engaged in the last phase of aerobic glycolysis. Alternative splicing is a crucial mechanism for protein diversity, and it promotes PKM precursor mRNA splicing to produce PKM2 dominance, resulting in low PKM1 expression. Specific splicing isoforms are produced in various tissues or illness situations, and the post-translational modifications are linked to numerous disorders, including cancers. hnRNPs are one of the main components of the splicing factor families. However, there have been no comprehensive studies on hnRNPs regulating PKM alternative splicing. Therefore, this review focuses on the regulatory network of hnRNPs on PKM pre-mRNA alternative splicing in tumors and clinical drug research. We elucidate the role of alternative splicing in tumor progression, prognosis, and the potential mechanism of abnormal RNA splicing. We also summarize the drug targets retarding tumorous splicing events, which may be critical to improving the specificity and effectiveness of current therapeutic interventions.
Collapse
Affiliation(s)
- Yuchao Li
- Liaoning Provincial Key Laboratory of Oral Diseases, School and Hospital of Stomatology, China Medical University, Shenyang 110002, China; (Y.L.); (S.Z.); (J.L.); (Q.L.); (W.Z.)
| | - Shuwei Zhang
- Liaoning Provincial Key Laboratory of Oral Diseases, School and Hospital of Stomatology, China Medical University, Shenyang 110002, China; (Y.L.); (S.Z.); (J.L.); (Q.L.); (W.Z.)
| | - Yuexian Li
- Department of Radiation Oncology Gastrointestinal and Urinary and Musculoskeletal Cancer, Liaoning Cancer Hospital & Institute, Cancer Hospital of China Medical University, Shenyang 110042, China;
| | - Junchao Liu
- Liaoning Provincial Key Laboratory of Oral Diseases, School and Hospital of Stomatology, China Medical University, Shenyang 110002, China; (Y.L.); (S.Z.); (J.L.); (Q.L.); (W.Z.)
| | - Qian Li
- Liaoning Provincial Key Laboratory of Oral Diseases, School and Hospital of Stomatology, China Medical University, Shenyang 110002, China; (Y.L.); (S.Z.); (J.L.); (Q.L.); (W.Z.)
| | - Wenli Zang
- Liaoning Provincial Key Laboratory of Oral Diseases, School and Hospital of Stomatology, China Medical University, Shenyang 110002, China; (Y.L.); (S.Z.); (J.L.); (Q.L.); (W.Z.)
| | - Yaping Pan
- Liaoning Provincial Key Laboratory of Oral Diseases, School and Hospital of Stomatology, China Medical University, Shenyang 110002, China; (Y.L.); (S.Z.); (J.L.); (Q.L.); (W.Z.)
| |
Collapse
|
5
|
Gao S, Wang Y, Xu Y, Liu L, Liu S. USP46 enhances tamoxifen resistance in breast cancer cells by stabilizing PTBP1 to facilitate glycolysis. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167011. [PMID: 38176460 DOI: 10.1016/j.bbadis.2023.167011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 12/10/2023] [Accepted: 12/27/2023] [Indexed: 01/06/2024]
Abstract
Tamoxifen (TAM) is the primary drug for treating estrogen receptor alpha-positive (ER+) breast cancer (BC). However, resistance to TAM can develop in some patients, limiting its therapeutic efficacy. The ubiquitin-specific protease (USP) family has been associated with the development, progression, and drug resistance of various cancers. To explore the role of USPs in TAM resistance in BC, we used qRT-PCR to compare USP expression between TAM-sensitive (MCF-7 and T47D) and TAM-resistant cells (MCF-7R and T47DR). We then modulated USP46 expression and examined its impact on cell proliferation, drug resistance (via CCK-8 and EdU experiments), glycolysis levels (using a glycolysis detection assay), protein interactions (confirmed by co-IP), and protein changes (analyzed through Western blotting). Our findings revealed that USP46 was significantly overexpressed in TAM-resistant BC cells, leading to the inhibition of the ubiquitin degradation of polypyrimidine tract-binding protein 1 (PTBP1). Overexpression of PTBP1 increased the PKM2/PKM1 ratio, promoted glycolysis, and intensified TAM resistance in BC cells. Knockdown of USP46 induced downregulation of PTBP1 protein by promoting its K48-linked ubiquitination, resulting in a decreased PKM2/PKM1 ratio, reduced glycolysis, and heightened TAM sensitivity in BC cells. In conclusion, this study highlights the critical role of the USP46/PTBP1/PKM2 axis in TAM resistance in BC. Targeted therapy against USP46 may represent a promising strategy to improve the prognosis of TAM-resistant patients.
Collapse
Affiliation(s)
- Shun Gao
- Department of Breast and Thyroid Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Yuan Wang
- Department of Breast and Thyroid Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Yingkun Xu
- Department of Breast and Thyroid Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Li Liu
- Department of Breast and Thyroid Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Shengchun Liu
- Department of Breast and Thyroid Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China.
| |
Collapse
|
6
|
Li Q, Zhang W, Qiao XY, Liu C, Dao JJ, Qiao CM, Cui C, Shen YQ, Zhao WJ. Reducing polypyrimidine tract‑binding protein 1 fails to promote neuronal transdifferentiation on HT22 and mouse astrocyte cells under physiological conditions. Exp Ther Med 2024; 27:72. [PMID: 38234625 PMCID: PMC10792410 DOI: 10.3892/etm.2023.12360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 11/27/2023] [Indexed: 01/19/2024] Open
Abstract
In contrast to prior findings that have illustrated the conversion of non-neuronal cells into functional neurons through the specific targeting of polypyrimidine tract-binding protein 1 (PTBP1), accumulated evidence suggests the impracticality of inducing neuronal transdifferentiation through suppressing PTBP1 expression in pathological circumstances. Therefore, the present study explored the effect of knocking down PTBP1 under physiological conditions on the transdifferentiation of mouse hippocampal neuron HT22 cells and mouse astrocyte (MA) cells. A total of 20 µM negative control small interfering (si)RNA and siRNA targeting PTBP1 were transfected into HT22 and MA cells using Lipo8000™ for 3 and 5 days, respectively. The expression of early neuronal marker βIII-Tubulin and mature neuronal markers NeuN and microtubule-associated protein 2 (MAP2) were detected using western blotting. In addition, βIII-tubulin, NeuN and MAP2 were labeled with immunofluorescence staining to evaluate neuronal cell differentiation in response to PTBP1 downregulation. Under physiological conditions, no significant changes in the expression of βIII-Tubulin, NeuN and MAP2 were found after 3 and 5 days of knockdown of PTBP1 protein in both HT22 and MA cells. In addition, the immunofluorescence staining results showed no apparent transdifferentiation in maker levels and morphology. The results suggested that the knockdown of PTBP1 failed to induce neuronal differentiation under physiological conditions.
Collapse
Affiliation(s)
- Qian Li
- Department of Cell Biology, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu 214122, P.R. China
| | - Wei Zhang
- Department of Cell Biology, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu 214122, P.R. China
- Department of Pathogen Biology, Guizhou Nursing Vocational College, Guiyang, Guizhou 550081, P.R. China
| | - Xin-Yu Qiao
- Department of Cell Biology, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu 214122, P.R. China
| | - Chong Liu
- Department of Cell Biology, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu 214122, P.R. China
| | - Ji-Ji Dao
- Department of Cell Biology, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu 214122, P.R. China
| | - Chen-Meng Qiao
- Department of Neurodegeneration and Neuroinjury, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu 214122, P.R. China
| | - Chun Cui
- Department of Neurodegeneration and Neuroinjury, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu 214122, P.R. China
| | - Yan-Qin Shen
- Department of Neurodegeneration and Neuroinjury, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu 214122, P.R. China
| | - Wei-Jiang Zhao
- Department of Cell Biology, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu 214122, P.R. China
| |
Collapse
|
7
|
Cao Y, Li J, Zhang G, Fang H, Du Y, Liang Y. KLF15 transcriptionally activates LINC00689 to inhibit colorectal cancer development. Commun Biol 2024; 7:130. [PMID: 38273088 PMCID: PMC10810960 DOI: 10.1038/s42003-023-05757-3] [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: 04/21/2023] [Accepted: 12/29/2023] [Indexed: 01/27/2024] Open
Abstract
Colorectal cancer is a grievous health concern, we have proved long non-coding RNA LINC00689 is considered as a potential diagnosis biomarker for colorectal cancer, and it is necessary to further investigate its upstream and downstream mechanisms. Here, we show that KLF15, a transcription factor, exhibits the reduced expression in colorectal cancer. KLF15 suppresses the proliferative and metastatic capacities of colorectal cancer cells both in vitro and in vivo by transcriptionally activating LINC00689. Subsequently, LINC00689 recruits PTBP1 protein to enhance the stability of LATS2 mRNA in the cytoplasm. This stabilization causes the suppression of the YAP1/β-catenin pathway and its target downstream genes. Our findings highlight a regulatory network involving KLF15, LINC00689, PTBP1, LATS2, and the YAP1/β-catenin pathway in colorectal cancer, shedding light on potential therapeutic targets for colorectal cancer therapy.
Collapse
Affiliation(s)
- Yan Cao
- Department of Nuclear Medicine, Xiangya Third Hospital, Central South University, Changsha, 410013, Hunan Province, PR China
| | - Jian Li
- Department of Nuclear Medicine, Xiangya Third Hospital, Central South University, Changsha, 410013, Hunan Province, PR China
| | - Gang Zhang
- Department 2 of Gastrointestinal Surgery, Haikou Hospital Affiliated to Xiangya Medical College of Central South University, Haikou People's Hospital, Haikou, 570208, Hainan Province, PR China
| | - Hao Fang
- Department of Nuclear Medicine, Xiangya Third Hospital, Central South University, Changsha, 410013, Hunan Province, PR China
| | - Yongliang Du
- Department of Nuclear Medicine, Xiangya Third Hospital, Central South University, Changsha, 410013, Hunan Province, PR China
| | - Yan Liang
- Department of Nuclear Medicine, Xiangya Third Hospital, Central South University, Changsha, 410013, Hunan Province, PR China.
| |
Collapse
|
8
|
Yu Q, Wu T, Xu W, Wei J, Zhao A, Wang M, Li M, Chi G. PTBP1 as a potential regulator of disease. Mol Cell Biochem 2023:10.1007/s11010-023-04905-x. [PMID: 38129625 DOI: 10.1007/s11010-023-04905-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 11/16/2023] [Indexed: 12/23/2023]
Abstract
Polypyrimidine tract-binding protein 1 (PTBP1) is a member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family, which plays a key role in alternative splicing of precursor mRNA and RNA metabolism. PTBP1 is universally expressed in various tissues and binds to multiple downstream transcripts to interfere with physiological and pathological processes such as the tumor growth, body metabolism, cardiovascular homeostasis, and central nervous system damage, showing great prospects in many fields. The function of PTBP1 involves the regulation and interaction of various upstream molecules, including circular RNAs (circRNAs), microRNAs (miRNAs) and long non-coding RNAs (lncRNAs). These regulatory systems are inseparable from the development and treatment of diseases. Here, we review the latest knowledge regarding the structure and molecular functions of PTBP1 and summarize its functions and mechanisms of PTBP1 in various diseases, including controversial studies. Furthermore, we recommend future studies on PTBP1 and discuss the prospects of targeting PTBP1 in new clinical therapeutic approaches.
Collapse
Affiliation(s)
- Qi Yu
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, 130021, Jilin, People's Republic of China
| | - Tongtong Wu
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, 130021, Jilin, People's Republic of China
| | - Wenhong Xu
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, 130021, Jilin, People's Republic of China
| | - Junyuan Wei
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, 130021, Jilin, People's Republic of China
| | - Anqi Zhao
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, 130021, Jilin, People's Republic of China
| | - Miaomiao Wang
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, 130021, Jilin, People's Republic of China
| | - Meiying Li
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, 130021, Jilin, People's Republic of China.
| | - Guangfan Chi
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, 130021, Jilin, People's Republic of China.
| |
Collapse
|
9
|
Pirmoradi S, Hosseiniyan Khatibi SM, Zununi Vahed S, Homaei Rad H, Khamaneh AM, Akbarpour Z, Seyedrezazadeh E, Teshnehlab M, Chapman KR, Ansarin K. Unraveling the link between PTBP1 and severe asthma through machine learning and association rule mining method. Sci Rep 2023; 13:15399. [PMID: 37717070 PMCID: PMC10505163 DOI: 10.1038/s41598-023-42581-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 09/12/2023] [Indexed: 09/18/2023] Open
Abstract
Severe asthma is a chronic inflammatory airway disease with great therapeutic challenges. Understanding the genetic and molecular mechanisms of severe asthma may help identify therapeutic strategies for this complex condition. RNA expression data were analyzed using a combination of artificial intelligence methods to identify novel genes related to severe asthma. Through the ANOVA feature selection approach, 100 candidate genes were selected among 54,715 mRNAs in blood samples of patients with severe asthmatic and healthy groups. A deep learning model was used to validate the significance of the candidate genes. The accuracy, F1-score, AUC-ROC, and precision of the 100 genes were 83%, 0.86, 0.89, and 0.9, respectively. To discover hidden associations among selected genes, association rule mining was applied. The top 20 genes including the PTBP1, RAB11FIP3, APH1A, and MYD88 were recognized as the most frequent items among severe asthma association rules. The PTBP1 was found to be the most frequent gene associated with severe asthma among those 20 genes. PTBP1 was the gene most frequently associated with severe asthma among candidate genes. Identification of master genes involved in the initiation and development of asthma can offer novel targets for its diagnosis, prognosis, and targeted-signaling therapy.
Collapse
Affiliation(s)
- Saeed Pirmoradi
- Clinical Research Development Unit of Tabriz Valiasr Hospital, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Seyed Mahdi Hosseiniyan Khatibi
- Kidney Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Rahat Breath and Sleep Research Center, Tabriz University of Medical Science, Tabriz, Iran
| | | | - Hamed Homaei Rad
- Rahat Breath and Sleep Research Center, Tabriz University of Medical Science, Tabriz, Iran
| | - Amir Mahdi Khamaneh
- Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Zahra Akbarpour
- Rahat Breath and Sleep Research Center, Tabriz University of Medical Science, Tabriz, Iran
| | - Ensiyeh Seyedrezazadeh
- Tuberculosis and Lung Disease Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Teshnehlab
- Department of Electric and Computer Engineering, K.N. Toosi University of Technology, Tehran, Iran
| | - Kenneth R Chapman
- Division of Respiratory Medicine, Department of Medicine, University of Toronto, Toronto, ON, Canada.
| | - Khalil Ansarin
- Rahat Breath and Sleep Research Center, Tabriz University of Medical Science, Tabriz, Iran.
| |
Collapse
|
10
|
He Z, Ni Q, Li X, Zhao M, Mo Q, Duo Y. PTBP1 promotes hepatocellular carcinoma progression by regulating the skipping of exon 9 in NUMB pre-mRNA. Heliyon 2023; 9:e17387. [PMID: 37408905 PMCID: PMC10318449 DOI: 10.1016/j.heliyon.2023.e17387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 06/15/2023] [Accepted: 06/15/2023] [Indexed: 07/07/2023] Open
Abstract
Aberrant alternative splicing is one of the important causes of cancer. Polypyrimidine tract binding protein 1 (PTBP1) has been found to be involved in splicing regulation in a variety of tumors. Here, we observed significant up-regulation of PTBP1 in primary hepatocellular carcinoma (HCC) tissues. High levels of PTBP1 expression were associated with poor prognosis and increased metastatic potential in HCC. In vitro studies demonstrated that elevated PTBP1 promoted both migration and invasion by HCC cells. In contrast, knockdown of PTBP1 significantly inhibited the migration and invasion of HCC cells in vitro. Further, up-regulation of PTBP1 markedly accumulated the expression of oncogenic isoform of NUMB, NUMB-PRRL. We observed two isoforms of NUMB, NUMB-PRRL and NUMB-PRRS exhibit opposite function in HCC cells, which partially explain PTBP1 plays the tumor promoting roles in a NUMB splicing-dependent manner. In summary, our study indicates that PTBP1 may serve as an oncogene in HCC patients by regulating the alternative splicing of NUMB exon 9 and could potentially serve as a prognostic indicator.
Collapse
|
11
|
Tsujimura N, Ogino T, Hiraki M, Kai T, Yamamoto H, Hirose H, Yokoyama Y, Sekido Y, Hata T, Miyoshi N, Takahashi H, Uemura M, Mizushima T, Doki Y, Eguchi H, Yamamoto H. Super Carbonate Apatite-miR-497a-5p Complex Is a Promising Therapeutic Option against Inflammatory Bowel Disease. Pharmaceuticals (Basel) 2023; 16:618. [PMID: 37111375 PMCID: PMC10146939 DOI: 10.3390/ph16040618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/10/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
The incidence of inflammatory bowel disease (IBD) is increasing worldwide. It is reported that TGF-β/Smad signal pathway is inactivated in patients with Crohn's disease by overexpression of Smad 7. With expectation of multiple molecular targeting by microRNAs (miRNAs), we currently attempted to identify certain miRNAs that activate TGF-β/Smad signal pathway and aimed to prove in vivo therapeutic efficacy in mouse model. Through Smad binding element (SBE) reporter assays, we focused on miR-497a-5p. This miRNA is common between mouse and human species and enhanced the activity of TGF-β/Smad signal pathway, decreased Smad 7 and/or increased phosphorylated Smad 3 expression in non-tumor cell line HEK293, colorectal cancer cell line HCT116 and mouse macrophage J774a.1 cells. MiR-497a-5p also suppressed the production of inflammatory cytokines TNF-α, IL-12p40, a subunit of IL-23, and IL-6 when J774a.1 cells were stimulated by lipopolysaccharides (LPS). In a long-term therapeutic model for mouse dextran sodium sulfate (DSS)-induced colitis, systemic delivery of miR-497a-5p load on super carbonate apatite (sCA) nanoparticle as a vehicle restored epithelial structure of the colonic mucosa and suppressed bowel inflammation compared with negative control miRNA treatment. Our data suggest that sCA-miR-497a-5p may potentially have a therapeutic ability against IBD although further investigation is essential.
Collapse
Affiliation(s)
- Naoto Tsujimura
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Yamadaoka 2-2, Suita City 565-0871, Japan (T.O.); (Y.S.); (T.H.); (N.M.); (H.T.); (M.U.); (Y.D.); (H.E.)
| | - Takayuki Ogino
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Yamadaoka 2-2, Suita City 565-0871, Japan (T.O.); (Y.S.); (T.H.); (N.M.); (H.T.); (M.U.); (Y.D.); (H.E.)
| | - Masayuki Hiraki
- Department of Gastroenterological Surgery, Kansai Rosai Hospital, 3-1-69 Inabaso, Amagasaki 660-8511, Japan
| | - Taisei Kai
- Department of Molecular Pathology, Division of Health Sciences, Graduate School of Medicine, Osaka University, Yamadaoka 1-7, Suita City 565-0871, Japan (Y.Y.)
| | - Hiroyuki Yamamoto
- Department of Molecular Pathology, Division of Health Sciences, Graduate School of Medicine, Osaka University, Yamadaoka 1-7, Suita City 565-0871, Japan (Y.Y.)
| | - Haruka Hirose
- Division of Systems Biology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Yuhki Yokoyama
- Department of Molecular Pathology, Division of Health Sciences, Graduate School of Medicine, Osaka University, Yamadaoka 1-7, Suita City 565-0871, Japan (Y.Y.)
| | - Yuki Sekido
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Yamadaoka 2-2, Suita City 565-0871, Japan (T.O.); (Y.S.); (T.H.); (N.M.); (H.T.); (M.U.); (Y.D.); (H.E.)
| | - Tsuyoshi Hata
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Yamadaoka 2-2, Suita City 565-0871, Japan (T.O.); (Y.S.); (T.H.); (N.M.); (H.T.); (M.U.); (Y.D.); (H.E.)
| | - Norikatsu Miyoshi
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Yamadaoka 2-2, Suita City 565-0871, Japan (T.O.); (Y.S.); (T.H.); (N.M.); (H.T.); (M.U.); (Y.D.); (H.E.)
| | - Hidekazu Takahashi
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Yamadaoka 2-2, Suita City 565-0871, Japan (T.O.); (Y.S.); (T.H.); (N.M.); (H.T.); (M.U.); (Y.D.); (H.E.)
| | - Mamoru Uemura
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Yamadaoka 2-2, Suita City 565-0871, Japan (T.O.); (Y.S.); (T.H.); (N.M.); (H.T.); (M.U.); (Y.D.); (H.E.)
| | - Tsunekazu Mizushima
- Department of Gastroenterological Surgery, Osaka Police Hospital, Osaka 543-0035, Japan;
| | - Yuichiro Doki
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Yamadaoka 2-2, Suita City 565-0871, Japan (T.O.); (Y.S.); (T.H.); (N.M.); (H.T.); (M.U.); (Y.D.); (H.E.)
| | - Hidetoshi Eguchi
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Yamadaoka 2-2, Suita City 565-0871, Japan (T.O.); (Y.S.); (T.H.); (N.M.); (H.T.); (M.U.); (Y.D.); (H.E.)
| | - Hirofumi Yamamoto
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Yamadaoka 2-2, Suita City 565-0871, Japan (T.O.); (Y.S.); (T.H.); (N.M.); (H.T.); (M.U.); (Y.D.); (H.E.)
- Department of Molecular Pathology, Division of Health Sciences, Graduate School of Medicine, Osaka University, Yamadaoka 1-7, Suita City 565-0871, Japan (Y.Y.)
| |
Collapse
|
12
|
Yang Y, Qin H, Ding M, Ji C, Chen W, Diao W, Yin H, Chen M, Gan W, Guo H. Small ankyrin 1 (sANK1) promotes docetaxel resistance in castration-resistant prostate cancer cells by enhancing oxidative phosphorylation. FEBS Open Bio 2022; 13:257-269. [PMID: 36508323 PMCID: PMC9900087 DOI: 10.1002/2211-5463.13535] [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: 07/08/2022] [Revised: 11/09/2022] [Accepted: 12/11/2022] [Indexed: 12/14/2022] Open
Abstract
Docetaxel (DTX) plays an important role in treating advanced prostate cancer (PCa). However, nearly all patients receiving DTX therapy ultimately progress to DTX resistance. How to address DTX resistance in PCa remains a key challenge for all urologists. Small ankyrin 1 (sAnk1) is an integral membrane protein in the endoplasmic reticulum. In the present study, we identified that sAnk1 is upregulated in PCa tissues and is positively associated with DTX therapy resistance in PCa. Further investigation demonstrated that overexpression of sAnk1 can significantly increase the DTX-resistant ability of PCa cells in vitro and in vivo. In addition, overexpression of sAnk1 could enhance oxidative phosphorylation (OXPHOS) levels in PCa cells, which was consistent with the higher OXPHOS levels observed in DTX-resistant PCa cells as compared to DTX-sensitive PCa cells. sAnk1 was also found to interact with polypyrimidine-tract-binding protein (PTBP1), an alternative splicing factor, and suppressed PTBP1-mediated alternative splicing of the pyruvate kinase gene (PKM). Thus, overexpression of sAnk1 decreased the ratio of PKM2/PKM1, enhanced the OXPHOS level, and ultimately promoted the resistance of PCa cells to DTX. In summary, our data suggest that sAnk1 enhances DTX resistance in PCa cells.
Collapse
Affiliation(s)
- Yang Yang
- Department of Urology, Drum Tower Hospital, Medical School of Nanjing University, Institute of UrologyNanjing UniversityChina
| | - Haixiang Qin
- Department of Urology, Drum Tower Hospital, Medical School of Nanjing University, Institute of UrologyNanjing UniversityChina
| | - Meng Ding
- Department of Urology, Drum Tower Hospital, Medical School of Nanjing University, Institute of UrologyNanjing UniversityChina
| | - Changwei Ji
- Department of Urology, Drum Tower Hospital, Medical School of Nanjing University, Institute of UrologyNanjing UniversityChina
| | - Wei Chen
- Department of Urology, Drum Tower Hospital, Medical School of Nanjing University, Institute of UrologyNanjing UniversityChina
| | - Wenli Diao
- Department of Urology, Drum Tower Hospital, Medical School of Nanjing University, Institute of UrologyNanjing UniversityChina
| | - Haoli Yin
- Department of Urology, Drum Tower Hospital, Medical School of Nanjing University, Institute of UrologyNanjing UniversityChina
| | - Mengxia Chen
- Department of Urology, Drum Tower Hospital, Medical School of Nanjing University, Institute of UrologyNanjing UniversityChina
| | - Weidong Gan
- Department of Urology, Drum Tower Hospital, Medical School of Nanjing University, Institute of UrologyNanjing UniversityChina
| | - Hongqian Guo
- Department of Urology, Drum Tower Hospital, Medical School of Nanjing University, Institute of UrologyNanjing UniversityChina
| |
Collapse
|
13
|
Pan YJ, Liu BW, Pei DS. The Role of Alternative Splicing in Cancer: Regulatory Mechanism, Therapeutic Strategy, and Bioinformatics Application. DNA Cell Biol 2022; 41:790-809. [PMID: 35947859 DOI: 10.1089/dna.2022.0322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
[Formula: see text] Alternative splicing (AS) can generate distinct transcripts and subsequent isoforms that play differential functions from the same pre-mRNA. Recently, increasing numbers of studies have emerged, unmasking the association between AS and cancer. In this review, we arranged AS events that are closely related to cancer progression and presented promising treatments based on AS for cancer therapy. Obtaining proliferative capacity, acquiring invasive properties, gaining angiogenic features, shifting metabolic ability, and getting immune escape inclination are all splicing events involved in biological processes. Spliceosome-targeted and antisense oligonucleotide technologies are two novel strategies that are hopeful in tumor therapy. In addition, bioinformatics applications based on AS were summarized for better prediction and elucidation of regulatory routines mingled in. Together, we aimed to provide a better understanding of complicated AS events associated with cancer biology and reveal AS a promising target of cancer treatment in the future.
Collapse
Affiliation(s)
- Yao-Jie Pan
- Department of Pathology, Laboratory of Clinical and Experimental Pathology, Xuzhou Medical University, Xuzhou, China
| | - Bo-Wen Liu
- Department of General Surgery, Xuzhou Medical University, Xuzhou, China
| | - Dong-Sheng Pei
- Department of Pathology, Laboratory of Clinical and Experimental Pathology, Xuzhou Medical University, Xuzhou, China
| |
Collapse
|
14
|
PTBP1 as a Promising Predictor of Poor Prognosis by Regulating Cell Proliferation, Immunosuppression, and Drug Sensitivity in SARC. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:5687238. [PMID: 35651729 PMCID: PMC9151003 DOI: 10.1155/2022/5687238] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 04/28/2022] [Indexed: 11/17/2022]
Abstract
Background. Sarcomas (SARC) have been found as rare and heterogeneous malignancies with poor prognosis. PTBP1, belonging to the hnRNPs family, plays an essential role in some biological functions (e.g., pre-mRNA splicing, cell growth, and nervous system development). However, the role of PTBP1 in SARC remains unclear. In this study, the aim was to investigate the potential role of PTBP1 with a focus on SARC. Methods. The expression, prognostic value, possible biological pathways of PTBP1, and its relationship with immune infiltration and drug sensitivity were comprehensively analyzed based on multiple databases. PTBP1 was further validated in osteosarcoma as the most prominent bone SARC. The expression of PTBP1 was investigated through IHC. The prognostic value of PTBP1 was verified in TARGET-OS databases. CRISPR/Cas9-mediated PTBP1 knockout HOS human osteosarcoma cell lines were used to assess the effect of PTBP1 on cell proliferation, migration, metastasis and cell cycle by CCK-8, Transwell migration, invasion, and FACS experiment. Result. PTBP1 was highly expressed and significantly correlated with poor prognosis in several cancers, especially in SARC, which was validated in the clinical cohort and osteosarcoma cell lines. The genetic alteration of PTBP1 was found most frequently in SARC. Besides, PTBP1 played a role in oncogenesis and immunity through cell cycle, TGFB, autophagy, and WNT pathways at a pan-cancer level. Knockout of PTBP1 was observed to negatively affect proliferation, migration, metastasis, and cell cycle of osteosarcoma in vitro. Furthermore, PTBP1 was significantly correlated with tumor immune infiltration, DNA methylation, TMB, and MSI in a wide variety of cancers. Moreover, the potential of the expression level of PTBP1 in predicting drug sensitivity was assessed. Conclusions. PTBP1 is highly expressed and correlated with prognosis and plays a vital pathogenic role in oncogenesis and immune infiltration of various cancers, especially for SARC, which suggests that it may be a promising prognostic marker and therapeutic target in the future.
Collapse
|
15
|
Dai S, Wang C, Zhang C, Feng L, Zhang W, Zhou X, He Y, Xia X, Chen B, Song W. PTB: Not just a polypyrimidine tract-binding protein. J Cell Physiol 2022; 237:2357-2373. [PMID: 35288937 DOI: 10.1002/jcp.30716] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 02/19/2022] [Accepted: 02/22/2022] [Indexed: 01/21/2023]
Abstract
Polypyrimidine tract-binding protein (PTB), as a member of the heterogeneous nuclear ribonucleoprotein family, functions by rapidly shuttling between the nucleus and the cytoplasm. PTB is involved in the alternative splicing of pre-messenger RNA (mRNA) and almost all steps of mRNA metabolism. PTB regulation is organ-specific; brain- or muscle-specific microRNAs and long noncoding RNAs partially contribute to regulating PTB, thereby modulating many physiological and pathological processes, such as embryonic development, cell development, spermatogenesis, and neuron growth and differentiation. Previous studies have shown that PTB knockout can inhibit tumorigenesis and development. The knockout of PTB in glial cells can be reprogrammed into functional neurons, which shows great promise in the field of nerve regeneration but is controversial.
Collapse
Affiliation(s)
- Shirui Dai
- National Clinical Research Center for Geriatric Diseases, Xiangya Hospital of Central South University, Changsha, Hunan, P. R. China.,Eye Center of Xiangya Hospital, Central South University, Changsha, Hunan, P. R. China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, P. R. China.,Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, P. R. China.,Hunan Clinical Research Center of Ophthalmic Disease, Changsha, Hunan, P. R. China
| | - Chao Wang
- National Clinical Research Center for Geriatric Diseases, Xiangya Hospital of Central South University, Changsha, Hunan, P. R. China.,Eye Center of Xiangya Hospital, Central South University, Changsha, Hunan, P. R. China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, P. R. China
| | - Cheng Zhang
- National Clinical Research Center for Geriatric Diseases, Xiangya Hospital of Central South University, Changsha, Hunan, P. R. China.,Eye Center of Xiangya Hospital, Central South University, Changsha, Hunan, P. R. China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, P. R. China
| | - Lemeng Feng
- National Clinical Research Center for Geriatric Diseases, Xiangya Hospital of Central South University, Changsha, Hunan, P. R. China.,Eye Center of Xiangya Hospital, Central South University, Changsha, Hunan, P. R. China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, P. R. China
| | - Wulong Zhang
- National Clinical Research Center for Geriatric Diseases, Xiangya Hospital of Central South University, Changsha, Hunan, P. R. China.,Eye Center of Xiangya Hospital, Central South University, Changsha, Hunan, P. R. China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, P. R. China
| | - Xuezhi Zhou
- National Clinical Research Center for Geriatric Diseases, Xiangya Hospital of Central South University, Changsha, Hunan, P. R. China.,Eye Center of Xiangya Hospital, Central South University, Changsha, Hunan, P. R. China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, P. R. China
| | - Ye He
- National Clinical Research Center for Geriatric Diseases, Xiangya Hospital of Central South University, Changsha, Hunan, P. R. China.,Eye Center of Xiangya Hospital, Central South University, Changsha, Hunan, P. R. China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, P. R. China
| | - Xiaobo Xia
- National Clinical Research Center for Geriatric Diseases, Xiangya Hospital of Central South University, Changsha, Hunan, P. R. China.,Eye Center of Xiangya Hospital, Central South University, Changsha, Hunan, P. R. China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, P. R. China
| | - Baihua Chen
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, P. R. China.,Hunan Clinical Research Center of Ophthalmic Disease, Changsha, Hunan, P. R. China
| | - Weitao Song
- National Clinical Research Center for Geriatric Diseases, Xiangya Hospital of Central South University, Changsha, Hunan, P. R. China.,Eye Center of Xiangya Hospital, Central South University, Changsha, Hunan, P. R. China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, P. R. China
| |
Collapse
|
16
|
Shi L, Han X, Liu C, Li X, Lu S, Jiang Q, Yao J. Long Non-Coding RNA PNKY Modulates the Development of Choroidal Neovascularization. Front Cell Dev Biol 2022; 10:836031. [PMID: 35265621 PMCID: PMC8899849 DOI: 10.3389/fcell.2022.836031] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 01/18/2022] [Indexed: 11/18/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) have been widely implicated in human diseases. Our aim was to explore the regulatory role of changes in the expression levels of PNKY and its linked signaling networks in mediating stress-induced choroidal neovascularization. PNKY expression levels were reduced in mice by laser and exposure of endothelial cell to hypoxic stress. PNKY silencing exacerbated the formation of CNV in a laser-induced CNV model and an ex vivo model, while overexpression inhibited CNV development. Silencing or overexpression of PNKY altered the viability, proliferation, migration, and tube-forming capacity of endothelial cells in vitro. Mechanistically, through the lncRNA–RNA binding protein–miRNA interaction analysis involving loss of function and gain-of-function experiments, we found that lncRNA PNKY inhibited the binding of miR124 to PTBP1 and maintained the homeostasis of choroidal vascular function by promoting Bcl-2 like protein 11 (BIM), and its dysfunction led to exacerbation of CNV lesion. Therefore, this study suggests that the lncPNKY/PTBP1–miR-124 axis is involved in regulating the development of CNV, providing a potential therapeutic target for the treatment of CNV.
Collapse
Affiliation(s)
- Lianjun Shi
- The Affiliated Eye Hospital, Nanjing Medical University, Nanjing, China.,The Fourth School of Clinical Medicine, Nanjing Medical University, Nanjing, China
| | - Xue Han
- The Affiliated Eye Hospital, Nanjing Medical University, Nanjing, China.,The Fourth School of Clinical Medicine, Nanjing Medical University, Nanjing, China
| | - Chang Liu
- Eye Institute, Eye and ENT Hospital, Shanghai Medical College, Fudan University, Shanghai, China.,NHC Key Laboratory of Myopia Fudan University, Key Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Fudan University, Shanghai, China
| | - Xiumiao Li
- The Affiliated Eye Hospital, Nanjing Medical University, Nanjing, China.,The Fourth School of Clinical Medicine, Nanjing Medical University, Nanjing, China
| | - Shuting Lu
- The Affiliated Eye Hospital, Nanjing Medical University, Nanjing, China.,The Fourth School of Clinical Medicine, Nanjing Medical University, Nanjing, China
| | - Qin Jiang
- The Affiliated Eye Hospital, Nanjing Medical University, Nanjing, China.,The Fourth School of Clinical Medicine, Nanjing Medical University, Nanjing, China
| | - Jin Yao
- The Affiliated Eye Hospital, Nanjing Medical University, Nanjing, China.,The Fourth School of Clinical Medicine, Nanjing Medical University, Nanjing, China
| |
Collapse
|
17
|
Wang Y, Li Z, Xu S, Li W, Chen M, Jiang M, Fan X. LncRNA FIRRE functions as a tumor promoter by interaction with PTBP1 to stabilize BECN1 mRNA and facilitate autophagy. Cell Death Dis 2022. [PMID: 35110535 DOI: 10.1038/s41419-022-04509-1.] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Long non-coding RNAs (lncRNAs) play critical functions in various cancers. Firre intergenic repeating RNA element (FIRRE), a lncRNA located in the nucleus, was overexpressed in colorectal cancer (CRC). However, the detailed mechanism of FIRRE in CRC remains elusive. Results of RNA sequence and qPCR illustrated overexpression of FIRRE in CRC cell lines and tissues. The aberrant expression of FIRRE was correlated with the migration, invasion, and proliferation in cell lines. In accordance, it was also associated with lymphatic metastasis and distant metastasis in patients with CRC. FIRRE was identified to physically interact with Polypyrimidine tract-binding protein (PTBP1) by RNA pull-down and RNA immunoprecipitation (RIP). Overexpression of FIRRE induced the translocation of PTBP1 from nucleus to cytoplasm, which was displayed by immunofluorescence and western blot. In turn, delocalization of FIRRE from nucleus to cytoplasm is observed after the loss of PTBP1. The RNA-protein complex in the cytoplasm directly bound to BECN1 mRNA, and the binding site was at the 3' end of the mRNA. Cells with FIRRE and PTBP1 depletion alone or in combination were treated by Actinomycin D (ACD). Results of qPCR showed FIRRE stabilized BECN1 mRNA in a PTBP1-medieated manner. In addition, FIRRE contributed to autophagy activity. These findings indicate FIRRE acts as an oncogenic factor in CRC, which induces tumor development through stabilizing BECN1 mRNA and facilitating autophagy in a PTBP1-mediated manner.
Collapse
Affiliation(s)
- Yajie Wang
- Department of Gastroenterology, Jinshan Hospital, Fudan University, 1508 Longhang Road, Shanghai, 201508, China
| | - Zhengyang Li
- Department of Gastroenterology, Jinshan Hospital, Fudan University, 1508 Longhang Road, Shanghai, 201508, China
| | - Shizan Xu
- Department of Gastroenterology, Jinshan Hospital, Fudan University, 1508 Longhang Road, Shanghai, 201508, China
| | - Wenjun Li
- Department of Anaesthesiology, Shanghai Public Health Clinical Center, Fudan University, 2901 Caolang Road, Shanghai, 201503, China
| | - Mengyun Chen
- General Practice of Huamu Community Health Service Center, 90 Yulan Road, Shanghai, 201204, China
| | - Miao Jiang
- Department of Gastroenterology, Jinshan Hospital, Fudan University, 1508 Longhang Road, Shanghai, 201508, China.
| | - Xiaoming Fan
- Department of Gastroenterology, Jinshan Hospital, Fudan University, 1508 Longhang Road, Shanghai, 201508, China.
| |
Collapse
|
18
|
Wang Y, Li Z, Xu S, Li W, Chen M, Jiang M, Fan X. LncRNA FIRRE functions as a tumor promoter by interaction with PTBP1 to stabilize BECN1 mRNA and facilitate autophagy. Cell Death Dis 2022; 13:98. [PMID: 35110535 PMCID: PMC8811066 DOI: 10.1038/s41419-022-04509-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 12/02/2021] [Accepted: 12/30/2021] [Indexed: 12/16/2022]
Abstract
Long non-coding RNAs (lncRNAs) play critical functions in various cancers. Firre intergenic repeating RNA element (FIRRE), a lncRNA located in the nucleus, was overexpressed in colorectal cancer (CRC). However, the detailed mechanism of FIRRE in CRC remains elusive. Results of RNA sequence and qPCR illustrated overexpression of FIRRE in CRC cell lines and tissues. The aberrant expression of FIRRE was correlated with the migration, invasion, and proliferation in cell lines. In accordance, it was also associated with lymphatic metastasis and distant metastasis in patients with CRC. FIRRE was identified to physically interact with Polypyrimidine tract-binding protein (PTBP1) by RNA pull-down and RNA immunoprecipitation (RIP). Overexpression of FIRRE induced the translocation of PTBP1 from nucleus to cytoplasm, which was displayed by immunofluorescence and western blot. In turn, delocalization of FIRRE from nucleus to cytoplasm is observed after the loss of PTBP1. The RNA-protein complex in the cytoplasm directly bound to BECN1 mRNA, and the binding site was at the 3' end of the mRNA. Cells with FIRRE and PTBP1 depletion alone or in combination were treated by Actinomycin D (ACD). Results of qPCR showed FIRRE stabilized BECN1 mRNA in a PTBP1-medieated manner. In addition, FIRRE contributed to autophagy activity. These findings indicate FIRRE acts as an oncogenic factor in CRC, which induces tumor development through stabilizing BECN1 mRNA and facilitating autophagy in a PTBP1-mediated manner.
Collapse
Affiliation(s)
- Yajie Wang
- Department of Gastroenterology, Jinshan Hospital, Fudan University, 1508 Longhang Road, Shanghai, 201508, China
| | - Zhengyang Li
- Department of Gastroenterology, Jinshan Hospital, Fudan University, 1508 Longhang Road, Shanghai, 201508, China
| | - Shizan Xu
- Department of Gastroenterology, Jinshan Hospital, Fudan University, 1508 Longhang Road, Shanghai, 201508, China
| | - Wenjun Li
- Department of Anaesthesiology, Shanghai Public Health Clinical Center, Fudan University, 2901 Caolang Road, Shanghai, 201503, China
| | - Mengyun Chen
- General Practice of Huamu Community Health Service Center, 90 Yulan Road, Shanghai, 201204, China
| | - Miao Jiang
- Department of Gastroenterology, Jinshan Hospital, Fudan University, 1508 Longhang Road, Shanghai, 201508, China.
| | - Xiaoming Fan
- Department of Gastroenterology, Jinshan Hospital, Fudan University, 1508 Longhang Road, Shanghai, 201508, China.
| |
Collapse
|
19
|
Zheng X, Zhu J, Liu J, Wang H, Qin Y, Jiang P, Xiao L, Gong T, Li Y, Peng X, Xu X, Cheng L, Huang L, Chen Q, Zhou X, Margolskee RF. Sweet taste perception in mice is blunted by PTBP1-regulated skipping of Tas1r2 exon 4. Chem Senses 2022; 47:6884719. [PMID: 36484118 DOI: 10.1093/chemse/bjac034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Taste perception, initiated by activation of taste receptors in taste bud cells, is crucial for regulating nutrient intake. Genetic polymorphisms in taste receptor genes cannot fully explain the wide individual variations of taste sensitivity. Alternative splicing (AS) is a ubiquitous posttranscriptional mode of gene regulation that enriches the functional diversity of proteins. Here, we report the identification of a novel splicing variant of sweet taste receptor gene Tas1r2 (Tas1r2_∆e4) in mouse taste buds and the mechanism by which it diminishes sweet taste responses in vitro and in vivo. Skipping of Tas1r2 exon 4 in Tas1r2_∆e4 led to loss of amino acids in the extracellular Venus flytrap domain, and the truncated isoform reduced the response of sweet taste receptors (STRs) to all sweet compounds tested by generating nonfunctional T1R2/T1R3 STR heterodimers. The splicing factor PTBP1 (polypyrimidine tract-binding protein 1) promoted Tas1r2_∆e4 generation through binding to a polypyrimidine-rich splicing silencer in Tas1r2 exon 4, thus decreasing STR function and sweet taste perception in mice. Taken together, these data reveal the existence of a regulated AS event in Tas1r2 expression and its effect on sweet taste perception, providing a novel mechanism for modulating taste sensitivity at the posttranscriptional level.
Collapse
Affiliation(s)
- Xin Zheng
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, P. R. China
| | - Jianhui Zhu
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou 310006, P. R. China
| | - Jiaxin Liu
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, P. R. China
| | - Hong Wang
- Monell Chemical Senses Center, Philadelphia, PA 19104, USA
| | - Yumei Qin
- School of Food Science and Bioengineering, Zhejiang Gongshang University, Hangzhou 310006, P. R. China
| | - Peihua Jiang
- Monell Chemical Senses Center, Philadelphia, PA 19104, USA
| | - Li Xiao
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, P. R. China
| | - Tao Gong
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, P. R. China
| | - Yuqing Li
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, P. R. China
| | - Xian Peng
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, P. R. China
| | - Xin Xu
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, P. R. China
| | - Lei Cheng
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, P. R. China
| | - Liquan Huang
- College of Life Sciences, Zhejiang University, Hangzhou 310058, P. R. China
| | - Qianming Chen
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou 310006, P. R. China
| | - Xuedong Zhou
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, P. R. China
| | | |
Collapse
|
20
|
Tang Y, Chen Y, Zhang Z, Tang B, Zhou Z, Chen H. Nanoparticle-Based RNAi Therapeutics Targeting Cancer Stem Cells: Update and Prospective. Pharmaceutics 2021; 13:pharmaceutics13122116. [PMID: 34959397 PMCID: PMC8708448 DOI: 10.3390/pharmaceutics13122116] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 11/19/2021] [Accepted: 12/02/2021] [Indexed: 02/05/2023] Open
Abstract
Cancer stem cells (CSCs) are characterized by intrinsic self-renewal and tumorigenic properties, and play important roles in tumor initiation, progression, and resistance to diverse forms of anticancer therapy. Accordingly, targeting signaling pathways that are critical for CSC maintenance and biofunctions, including the Wnt, Notch, Hippo, and Hedgehog signaling cascades, remains a promising therapeutic strategy in multiple cancer types. Furthermore, advances in various cancer omics approaches have largely increased our knowledge of the molecular basis of CSCs, and provided numerous novel targets for anticancer therapy. However, the majority of recently identified targets remain ‘undruggable’ through small-molecule agents, whereas the implications of exogenous RNA interference (RNAi, including siRNA and miRNA) may make it possible to translate our knowledge into therapeutics in a timely manner. With the recent advances of nanomedicine, in vivo delivery of RNAi using elaborate nanoparticles can potently overcome the intrinsic limitations of RNAi alone, as it is rapidly degraded and has unpredictable off-target side effects. Herein, we present an update on the development of RNAi-delivering nanoplatforms in CSC-targeted anticancer therapy and discuss their potential implications in clinical trials.
Collapse
Affiliation(s)
- Yongquan Tang
- Department of Pediatric Surgery, West China Hospital, Sichuan University, Chengdu 610041, China;
- Department of Gastrointestinal Surgery, West China Hospital, Sichuan University, Chengdu 610041, China
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China; (Y.C.); (Z.Z.)
| | - Yan Chen
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China; (Y.C.); (Z.Z.)
| | - Zhe Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China; (Y.C.); (Z.Z.)
| | - Bo Tang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu 610041, China;
| | - Zongguang Zhou
- Department of Gastrointestinal Surgery, West China Hospital, Sichuan University, Chengdu 610041, China
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China; (Y.C.); (Z.Z.)
- Correspondence: (Z.Z.); (H.C.)
| | - Haining Chen
- Department of Gastrointestinal Surgery, West China Hospital, Sichuan University, Chengdu 610041, China
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China; (Y.C.); (Z.Z.)
- Correspondence: (Z.Z.); (H.C.)
| |
Collapse
|
21
|
Wu X, Yokoyama Y, Takahashi H, Kouda S, Yamamoto H, Wang J, Morimoto Y, Minami K, Hata T, Shamma A, Inoue A, Ohtsuka M, Shibata S, Kobayashi S, Akai S, Yamamoto H. Improved In Vivo Delivery of Small RNA Based on the Calcium Phosphate Method. J Pers Med 2021; 11:jpm11111160. [PMID: 34834512 PMCID: PMC8623677 DOI: 10.3390/jpm11111160] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 10/31/2021] [Accepted: 11/03/2021] [Indexed: 01/06/2023] Open
Abstract
In the past few years, we have demonstrated the efficacy of a nanoparticle system, super carbonate apatite (sCA), for the in vivo delivery of siRNA/miRNA. Intravenous injection of sCA loaded with small RNAs results in safe, high tumor delivery in mouse models. To further improve the efficiency of tumor delivery and avoid liver toxicity, we successfully developed an inorganic nanoparticle device (iNaD) via high-frequency ultrasonic pulverization combined with PEG blending during the production of sCA. Compared to sCA loaded with 24 μg of miRNA, systemic administration of iNaD loaded with 0.75 μg of miRNA demonstrated similar delivery efficiency to mouse tumors with little accumulation in the liver. In the mouse therapeutic model, iNaD loaded with 3 μg of the tumor suppressor small RNA MIRTX resulted in an improved anti-tumor effect compared to sCA loaded with 24 μg. Our findings on the bio-distribution and therapeutic effect of iNaD provide new perspectives for future nanomedicine engineering.
Collapse
Affiliation(s)
- Xin Wu
- Department of Molecular Pathology, Division of Health Sciences, Graduate School of Medicine, Osaka University, Yamadaoka 1-7, Suita, Osaka 565-0871, Japan; (X.W.); (Y.Y.); (S.K.); (H.Y.); (J.W.); (A.S.); (S.S.)
| | - Yuhki Yokoyama
- Department of Molecular Pathology, Division of Health Sciences, Graduate School of Medicine, Osaka University, Yamadaoka 1-7, Suita, Osaka 565-0871, Japan; (X.W.); (Y.Y.); (S.K.); (H.Y.); (J.W.); (A.S.); (S.S.)
| | - Hidekazu Takahashi
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Yamadaoka 2-2, Suita, Osaka 565-0871, Japan; (H.T.); (Y.M.); (T.H.); (A.I.); (M.O.); (S.K.)
| | - Shihori Kouda
- Department of Molecular Pathology, Division of Health Sciences, Graduate School of Medicine, Osaka University, Yamadaoka 1-7, Suita, Osaka 565-0871, Japan; (X.W.); (Y.Y.); (S.K.); (H.Y.); (J.W.); (A.S.); (S.S.)
| | - Hiroyuki Yamamoto
- Department of Molecular Pathology, Division of Health Sciences, Graduate School of Medicine, Osaka University, Yamadaoka 1-7, Suita, Osaka 565-0871, Japan; (X.W.); (Y.Y.); (S.K.); (H.Y.); (J.W.); (A.S.); (S.S.)
| | - Jiaqi Wang
- Department of Molecular Pathology, Division of Health Sciences, Graduate School of Medicine, Osaka University, Yamadaoka 1-7, Suita, Osaka 565-0871, Japan; (X.W.); (Y.Y.); (S.K.); (H.Y.); (J.W.); (A.S.); (S.S.)
| | - Yoshihiro Morimoto
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Yamadaoka 2-2, Suita, Osaka 565-0871, Japan; (H.T.); (Y.M.); (T.H.); (A.I.); (M.O.); (S.K.)
| | - Kazumasa Minami
- Department of Radiation Oncology, Graduate School of Medicine, Osaka University, Yamadaoka 2-2, Suita, Osaka 565-0871, Japan;
| | - Tsuyoshi Hata
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Yamadaoka 2-2, Suita, Osaka 565-0871, Japan; (H.T.); (Y.M.); (T.H.); (A.I.); (M.O.); (S.K.)
| | - Awad Shamma
- Department of Molecular Pathology, Division of Health Sciences, Graduate School of Medicine, Osaka University, Yamadaoka 1-7, Suita, Osaka 565-0871, Japan; (X.W.); (Y.Y.); (S.K.); (H.Y.); (J.W.); (A.S.); (S.S.)
| | - Akira Inoue
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Yamadaoka 2-2, Suita, Osaka 565-0871, Japan; (H.T.); (Y.M.); (T.H.); (A.I.); (M.O.); (S.K.)
| | - Masahisa Ohtsuka
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Yamadaoka 2-2, Suita, Osaka 565-0871, Japan; (H.T.); (Y.M.); (T.H.); (A.I.); (M.O.); (S.K.)
| | - Satoshi Shibata
- Department of Molecular Pathology, Division of Health Sciences, Graduate School of Medicine, Osaka University, Yamadaoka 1-7, Suita, Osaka 565-0871, Japan; (X.W.); (Y.Y.); (S.K.); (H.Y.); (J.W.); (A.S.); (S.S.)
| | - Shogo Kobayashi
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Yamadaoka 2-2, Suita, Osaka 565-0871, Japan; (H.T.); (Y.M.); (T.H.); (A.I.); (M.O.); (S.K.)
| | - Shuji Akai
- Graduate School of Pharmaceutical Sciences, Osaka University, Yamadaoka 1-6, Suita, Osaka 565-0871, Japan;
| | - Hirofumi Yamamoto
- Department of Molecular Pathology, Division of Health Sciences, Graduate School of Medicine, Osaka University, Yamadaoka 1-7, Suita, Osaka 565-0871, Japan; (X.W.); (Y.Y.); (S.K.); (H.Y.); (J.W.); (A.S.); (S.S.)
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Yamadaoka 2-2, Suita, Osaka 565-0871, Japan; (H.T.); (Y.M.); (T.H.); (A.I.); (M.O.); (S.K.)
- Correspondence: ; Tel.: +81-6-6879-2591; Fax: +81-6-6879-2591
| |
Collapse
|
22
|
Schorr AL, Mangone M. miRNA-Based Regulation of Alternative RNA Splicing in Metazoans. Int J Mol Sci 2021; 22:ijms222111618. [PMID: 34769047 PMCID: PMC8584187 DOI: 10.3390/ijms222111618] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 10/21/2021] [Accepted: 10/22/2021] [Indexed: 12/15/2022] Open
Abstract
Alternative RNA splicing is an important regulatory process used by genes to increase their diversity. This process is mainly executed by specific classes of RNA binding proteins that act in a dosage-dependent manner to include or exclude selected exons in the final transcripts. While these processes are tightly regulated in cells and tissues, little is known on how the dosage of these factors is achieved and maintained. Several recent studies have suggested that alternative RNA splicing may be in part modulated by microRNAs (miRNAs), which are short, non-coding RNAs (~22 nt in length) that inhibit translation of specific mRNA transcripts. As evidenced in tissues and in diseases, such as cancer and neurological disorders, the dysregulation of miRNA pathways disrupts downstream alternative RNA splicing events by altering the dosage of splicing factors involved in RNA splicing. This attractive model suggests that miRNAs can not only influence the dosage of gene expression at the post-transcriptional level but also indirectly interfere in pre-mRNA splicing at the co-transcriptional level. The purpose of this review is to compile and analyze recent studies on miRNAs modulating alternative RNA splicing factors, and how these events contribute to transcript rearrangements in tissue development and disease.
Collapse
Affiliation(s)
- Anna L. Schorr
- Molecular and Cellular Biology Graduate Program, School of Life Sciences, 427 East Tyler Mall, Tempe, AZ 85287, USA;
| | - Marco Mangone
- Virginia G. Piper Center for Personalized Diagnostics, The Biodesign Institute at Arizona State University, 1001 S McAllister Ave., Tempe, AZ 85287, USA
- Correspondence: ; Tel.: +1-480-965-7957
| |
Collapse
|
23
|
Kim JH, Jeong K, Li J, Murphy JM, Vukadin L, Stone JK, Richard A, Tran J, Gillespie GY, Flemington EK, Sobol RW, Lim STS, Ahn EYE. SON drives oncogenic RNA splicing in glioblastoma by regulating PTBP1/PTBP2 switching and RBFOX2 activity. Nat Commun 2021; 12:5551. [PMID: 34548489 PMCID: PMC8455679 DOI: 10.1038/s41467-021-25892-x] [Citation(s) in RCA: 18] [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: 04/15/2019] [Accepted: 09/01/2021] [Indexed: 12/15/2022] Open
Abstract
While dysregulation of RNA splicing has been recognized as an emerging target for cancer therapy, the functional significance of RNA splicing and individual splicing factors in brain tumors is poorly understood. Here, we identify SON as a master regulator that activates PTBP1-mediated oncogenic splicing while suppressing RBFOX2-mediated non-oncogenic neuronal splicing in glioblastoma multiforme (GBM). SON is overexpressed in GBM patients and SON knockdown causes failure in intron removal from the PTBP1 transcript, resulting in PTBP1 downregulation and inhibition of its downstream oncogenic splicing. Furthermore, SON forms a complex with hnRNP A2B1 and antagonizes RBFOX2, which leads to skipping of RBFOX2-targeted cassette exons, including the PTBP2 neuronal exon. SON knockdown inhibits proliferation and clonogenicity of GBM cells in vitro and significantly suppresses tumor growth in orthotopic xenografts in vivo. Collectively, our study reveals that SON-mediated RNA splicing is a GBM vulnerability, implicating SON as a potential therapeutic target in brain tumors.
Collapse
Affiliation(s)
- Jung-Hyun Kim
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, USA
- Department of Biochemistry and Molecular Biology, College of Medicine, University of South Alabama, Mobile, AL, USA
| | - Kyuho Jeong
- Department of Biochemistry and Molecular Biology, College of Medicine, University of South Alabama, Mobile, AL, USA
| | - Jianfeng Li
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, USA
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL, USA
| | - James M Murphy
- Department of Biochemistry and Molecular Biology, College of Medicine, University of South Alabama, Mobile, AL, USA
| | - Lana Vukadin
- Department of Pathology, Division of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Joshua K Stone
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, USA
| | - Alexander Richard
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, USA
| | - Johnny Tran
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, USA
| | - G Yancey Gillespie
- Department of Neurosurgery, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Erik K Flemington
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, LA, USA
| | - Robert W Sobol
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, USA.
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL, USA.
| | - Ssang-Teak Steve Lim
- Department of Biochemistry and Molecular Biology, College of Medicine, University of South Alabama, Mobile, AL, USA.
| | - Eun-Young Erin Ahn
- Department of Pathology, Division of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL, USA.
- O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA.
| |
Collapse
|
24
|
Wang Z, Zhou S, Zhao J, Nie S, Sun J, Gao X, Lenahan C, Lin Z, Huang Y, Chen G. Tobacco Smoking Increases Methylation of Polypyrimidine Tract Binding Protein 1 Promoter in Intracranial Aneurysms. Front Aging Neurosci 2021; 13:688179. [PMID: 34295240 PMCID: PMC8292010 DOI: 10.3389/fnagi.2021.688179] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 06/14/2021] [Indexed: 11/20/2022] Open
Abstract
DNA methylation at the gene promoter region is reportedly involved in the development of intracranial aneurysm (IA). This study aims to investigate the methylation levels of polypyrimidine tract-binding protein 1 (PTBP1) in IA, as well as its potential to predict IA. Forty-eight patients with IA and 48 age- and sex-matched healthy controls were recruited into this study. Methylation levels of CpG sites were determined via bisulfite pyrosequencing. The PTBP1 levels in the blood were determined using a real-time quantitative reverse transcription-polymerase chain reaction test. Significant differences were found between IAs and controls in CpG1 (p = 0.001), CpG2 (p < 0.001), CpG3 (p = 0.037), CpG4 (p = 0.003), CpG5 (p = 0.006), CpG6 (p = 0.02), and mean methylation (p < 0.001). The mRNA level of PTBP1 in the blood was much lower in IAs compared with controls (p = 0.002), and the PTBP1 expression was significantly associated with DNA methylation promoter levels in individuals (r = −0.73, p < 0.0001). In addition, stratification analysis comparing smokers and non-smokers revealed that tobacco smokers had significantly higher levels of DNA methylation in PTBP1 than non-smokers (p = 0.002). However, no statistical difference in PTBP1 methylation was found between ruptured and unruptured IA groups (p > 0.05). The ROC analyses of curves revealed that PTBP1 methylation may be a predictor of IA regardless of sex (both sexes, area under curve (AUC) = 0.78, p < 0.0001; male, AUC = 0.76, p = 0.002; female, AUC = 0.79, p < 0.0001). These findings suggest that long-term tobacco smoke exposure led to DNA methylation in the promoter region of the PTBP1 gene, which further decreased PTBP1 gene expression and participated in the pathogenesis of IA. The methylation of PTBP1 may be a potential predictive marker for the occurrence of IA.
Collapse
Affiliation(s)
- Zhepei Wang
- Department of Neurosurgery, Ningbo Hospital, Zhejiang University School of Medicine, Ningbo, China.,Department of Neurosurgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Shengjun Zhou
- Department of Neurosurgery, Ningbo Hospital, Zhejiang University School of Medicine, Ningbo, China.,Department of Neurosurgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jikuang Zhao
- Department of Neurosurgery, Ningbo Hospital, Zhejiang University School of Medicine, Ningbo, China.,Department of Neurosurgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Sheng Nie
- Department of Neurosurgery, Ningbo Hospital, Zhejiang University School of Medicine, Ningbo, China
| | - Jie Sun
- Department of Neurosurgery, Ningbo Hospital, Zhejiang University School of Medicine, Ningbo, China
| | - Xiang Gao
- Department of Neurosurgery, Ningbo Hospital, Zhejiang University School of Medicine, Ningbo, China
| | - Cameron Lenahan
- Burrell College of Osteopathic Medicine, Las Cruces, NM, United States
| | - Zhiqin Lin
- Department of Neurosurgery, Ningbo Hospital, Zhejiang University School of Medicine, Ningbo, China
| | - Yi Huang
- Department of Neurosurgery, Ningbo Hospital, Zhejiang University School of Medicine, Ningbo, China.,Department of Neurosurgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Gao Chen
- Department of Neurosurgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| |
Collapse
|
25
|
Polypyrimidine tract-binding protein 1 regulates the Sertoli cell blood-testis barrier by promoting the expression of tight junction proteins. Exp Ther Med 2021; 22:847. [PMID: 34149893 DOI: 10.3892/etm.2021.10279] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 04/20/2021] [Indexed: 11/05/2022] Open
Abstract
Sertoli cells (SCs) are an important component of spermatogenic tubules. The blood-testis barrier (BTB) is composed of SCs and is necessary for the development and maturity of spermatogenic cells. When the tight connection between SCs is destroyed, the BTB loses its integrity, leading to impaired spermatogenesis. Polypyrimidine tract-binding protein 1 (PTBP1) is a key protein involved in precursor mRNA splicing and selective splicing events, which directly affects tumor cell proliferation and influences the formation of the blood-tumor barrier by regulating the expression levels of tight junction-associated proteins. The present study revealed that the expression of PTBP1 was downregulated following a decrease in spermatogenic activity at the phase of senescence. TM4 cells were transfected with lentivirus-short hairpinRNA-PTBP1 to evaluate the effect of silencing PTBP1 on the expression levels of tight junction proteins and the integrity of tight junctions between adjacent SCs. Western blot analysis indicated that the expression levels of Zonula occludens 1, occludin and claudin-5 decreased significantly due to silencing of PTBP1 in SCs. Through detecting trans-epithelial electrical resistance, it was revealed that silencing of PTBP1 broke the integrity of tight junctions between adjacent SCs. The results suggested that PTBP1 maintained the integrity of the BTB by promoting the expression levels of tight junction-associated proteins and revealed the possible mechanism of PTBP1 in regulating spermatogenesis.
Collapse
|
26
|
Chen J, Wu Y, Luo X, Jin D, Zhou W, Ju Z, Wang D, Meng Q, Wang H, Fu X, Xu J, Song Z. Circular RNA circRHOBTB3 represses metastasis by regulating the HuR-mediated mRNA stability of PTBP1 in colorectal cancer. Am J Cancer Res 2021; 11:7507-7526. [PMID: 34158864 PMCID: PMC8210600 DOI: 10.7150/thno.59546] [Citation(s) in RCA: 93] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 05/21/2021] [Indexed: 01/17/2023] Open
Abstract
Background: Tumor metastasis of colorectal cancer (CRC) is the main cause of death in most patients and the major difficulty in comprehensive CRC treatment. Circular RNAs (circRNAs) affect many biological functions in solid tumors. However, their mechanisms in CRC metastasis remain unclear. Methods: RNA sequencing (RNA-seq) and quantitative real-time PCR were performed to screen differentially expressed circRNAs between CRC tissues and adjacent normal tissues. CCK-8, cell migration and wound healing assays were performed to determine the functions of circRHOBTB3 in cell proliferation and metastasis. RNA pulldown and RNA immunoprecipitation assays were performed to verify the interaction between circRHOBTB3 and the HuR (ELAVL1) protein. Further RNA-seq and rescue experiments were applied to search for the downstream target. We also conducted a mouse xenograft model to elucidate the effect of circRHOBTB3 on cancer metastasis in vivo. Results: We identified circRHOBTB3 which is markedly downregulated in CRC tissues and cell lines. Furthermore, lower circRHOBTB3 levels were significantly associated with advanced clinical stages and greater risk of metastases. Overexpression of circRHOBTB3 suppresses tumor metastasis in CRC cells. Mechanistically, circRHOBTB3 binds to HuR, which is a ubiquitously expressed and functional RNA-binding protein (RBP) in CRC development, and promotes β-Trcp1-mediated ubiquitination of HuR. Normally, HuR binds to the 3'UTR of target mRNAs to facilitate their stabilization, whereas the interaction between circRHOBTB3 and HuR degrades HuR to reduce the expression level of the downstream target PTBP1. Furthermore, overexpressed circRHOBTB3 suppresses lung metastases in vivo, and this effect can be partly reversed by PTBP1 overexpression. In addition, the transcription of circRHOBTB3 can be improved by both FUS and ADARB2 in CRC cells. Conclusions: Our findings indicate that circRHOBTB3 exerts suppressive effects on CRC aggressiveness through the HuR/PTBP1 axis.
Collapse
|
27
|
Epigenetic Mechanisms Are Involved in the Oncogenic Properties of ZNF518B in Colorectal Cancer. Cancers (Basel) 2021; 13:cancers13061433. [PMID: 33801071 PMCID: PMC8004037 DOI: 10.3390/cancers13061433] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/12/2021] [Accepted: 03/16/2021] [Indexed: 02/06/2023] Open
Abstract
Simple Summary The ZNF518B gene, which is up-regulated in colorectal cancer, plays a role in metastasis, but neither the mechanisms involved in this process nor the role of the different isoforms of the gene are known. Here we show that the ratio of these isoforms is related to the relapsing of the disease, and that the protein ZNF518B interacts with enzymes able to introduce epigenetic changes, which may affect the activity of many genes. We also report a list of genes affected in common by ZNF518B and by two of those related enzymes, namely, G9A and EZH2. An in-depth analysis of five of those genes revealed that ZNF518B is involved in the recruitment of the enzymes and in the deposition of the corresponding epigenetic marks. The results highlight the relevance of epigenetic changes in cancer development, and open the possibility of developing therapeutic approaches, as the introduction of epigenetic modifications is reversible. Abstract The ZNF518B gene, which is up-regulated in colorectal cancer, plays a role in cell dissemination and metastasis. It encodes a zinc-finger protein, which interacts with histone methyltransferases G9A and EZH2. The expression of the two major mRNA isoforms 1 (coding for the full protein) and 2 was quantified by RT-qPCR in a cohort of 66 patients. The effects of silencing ZNF518B on the transcriptome of DLD1 and HCT116 cells were analysed by Clariom-S assays and validated by RT-qPCR. The recruitment of methyltransferases and the presence of H3K27me3 were studied by chromatin immunoprecipitation (ChIP). The ratio (isoform 2)/(isoform 1) negatively correlated with the relapsing of disease. The study of the transcriptome of DLD1 and HCT116 cells revealed that many genes affected by silencing ZNF518B are related to cancer. After crossing these results with the list of genes affected by silencing the histone methyltransferases (retrieved in silico), five genes were selected. ChIP analysis revealed that the recruitment of EZH2 is ZNF518B-dependent in KAT2B, RGS4 and EFNA5; the level of H3K27me3 changes in accordance. G9A also binds RGS4 and PADI3 in a ZNF518B-dependent manner. The results highlight the importance of epigenetics in cancer and open a novel therapeutic possibility, as inhibition of histone methyltransferases may reverse the disease-linked histone marks.
Collapse
|
28
|
Bakhtina VI, Veprintsev DV, Zamay TN, Demko IV, Mironov GG, Berezovski MV, Petrova MM, Kichkailo AS, Glazyrin YE. Proteomics-Based Regression Model for Assessing the Development of Chronic Lymphocytic Leukemia. Proteomes 2021; 9:proteomes9010003. [PMID: 33498752 PMCID: PMC7924318 DOI: 10.3390/proteomes9010003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/09/2021] [Accepted: 01/20/2021] [Indexed: 11/16/2022] Open
Abstract
The clinical course of chronic lymphocytic leukemia (CLL) is very ambiguous, showing either an indolent nature of the disease or having latent dangerous progression, which, if diagnosed, will require an urgent therapy. The prognosis of the course of the disease and the estimation of the time of therapy initiation are crucial for the selection of a successful treatment strategy. A reliable estimating index is needed to assign newly diagnosed CLL patients to the prognostic groups. In this work, we evaluated the comparative expressions of proteins in CLL blood cells using a label-free quantification by mass spectrometry and calculated the integrated proteomic indexes for a group of patients who received therapy after the blood sampling over different periods of time. Using a two-factor linear regression analysis based on these data, we propose a new pipeline for evaluating model development for estimation of the moment of therapy initiation for newly diagnosed CLL patients.
Collapse
Affiliation(s)
- Varvara I. Bakhtina
- Department of Hematology, Krasnoyarsk Regional Clinical Hospital, 660022 Krasnoyarsk, Russia; (V.I.B.); (I.V.D.)
| | - Dmitry V. Veprintsev
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Science”, 660036 Krasnoyarsk, Russia; (D.V.V.); (A.S.K.)
| | - Tatiana N. Zamay
- Laboratory for Biomolecular and Medical Technologies, Krasnoyarsk State Medical University Named after Prof. V.F. Voyno-Yasenetsky, 660022 Krasnoyarsk, Russia;
| | - Irina V. Demko
- Department of Hematology, Krasnoyarsk Regional Clinical Hospital, 660022 Krasnoyarsk, Russia; (V.I.B.); (I.V.D.)
- Faculty of Medicine, Krasnoyarsk State Medical University Named after Prof. V.F. Voyno-Yasenetsky, 660022 Krasnoyarsk, Russia;
| | - Gleb G. Mironov
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N6N5, Canada; (G.G.M.); (M.V.B.)
| | - Maxim V. Berezovski
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N6N5, Canada; (G.G.M.); (M.V.B.)
| | - Marina M. Petrova
- Faculty of Medicine, Krasnoyarsk State Medical University Named after Prof. V.F. Voyno-Yasenetsky, 660022 Krasnoyarsk, Russia;
| | - Anna S. Kichkailo
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Science”, 660036 Krasnoyarsk, Russia; (D.V.V.); (A.S.K.)
- Laboratory for Biomolecular and Medical Technologies, Krasnoyarsk State Medical University Named after Prof. V.F. Voyno-Yasenetsky, 660022 Krasnoyarsk, Russia;
| | - Yury E. Glazyrin
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Science”, 660036 Krasnoyarsk, Russia; (D.V.V.); (A.S.K.)
- Laboratory for Biomolecular and Medical Technologies, Krasnoyarsk State Medical University Named after Prof. V.F. Voyno-Yasenetsky, 660022 Krasnoyarsk, Russia;
- Correspondence:
| |
Collapse
|
29
|
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.
Collapse
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.)
| |
Collapse
|
30
|
Abstract
Objective Alternative splicing can generate various structural and functional protein isoforms. Recently, accumulating evidence shows a relationship between alternative splicing and cancer. Cancer is a complex and chronic disease that involves malignant transformation. In this review, we consider alternative splicing events in relation to the hallmarks of cancer cells, and discuss current therapies to treat cancer-related to alternative splicing. Data sources Data cited in this article are from the PubMed and Embase database, primarily focusing on research published from 2000 to 2018. Study selection Articles were selected with the search terms “alternative splicing,” “cancer cell,” “tumor microenvironment,” and “therapy.” Results Alternative splicing plays an important role in tumorigenesis, development, and escape from cell death. Taking this trait of cancer cells into consideration will allow more definite diagnoses of cancer, and allow the development of more effective medicines to intervene in cancer that could focus on controlling alternative splicing or competitively binding to the final products. Conclusions Alternative splicing is common in cancer cells. Consideration of alternative splicing may allow different strategies for cancer therapy or the identification of novel biomarkers for cancer diagnosis.
Collapse
|
31
|
Rahman MA, Nasrin F, Bhattacharjee S, Nandi S. Hallmarks of Splicing Defects in Cancer: Clinical Applications in the Era of Personalized Medicine. Cancers (Basel) 2020; 12:cancers12061381. [PMID: 32481522 PMCID: PMC7352608 DOI: 10.3390/cancers12061381] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 05/25/2020] [Accepted: 05/25/2020] [Indexed: 12/14/2022] Open
Abstract
Alternative splicing promotes proteome diversity by using limited number of genes, a key control point of gene expression. Splicing is carried out by large macromolecular machineries, called spliceosome, composed of small RNAs and proteins. Alternative splicing is regulated by splicing regulatory cis-elements in RNA and trans-acting splicing factors that are often tightly regulated in a tissue-specific and developmental stage-specific manner. The biogenesis of ribonucleoprotein (RNP) complexes is strictly regulated to ensure that correct complements of RNA and proteins are coordinated in the right cell at the right time to support physiological functions. Any perturbations that impair formation of functional spliceosomes by disrupting the cis-elements, or by compromising RNA-binding or function of trans-factors can be deleterious to cells and result in pathological consequences. The recent discovery of oncogenic mutations in splicing factors, and growing evidence of the perturbed splicing in multiple types of cancer, underscores RNA processing defects as a critical driver of oncogenesis. These findings have resulted in a growing interest in targeting RNA splicing as a therapeutic approach for cancer treatment. This review summarizes our current understanding of splicing alterations in cancer, recent therapeutic efforts targeting splicing defects in cancer, and future potentials to develop novel cancer therapies.
Collapse
|
32
|
Fochi S, Lorenzi P, Galasso M, Stefani C, Trabetti E, Zipeto D, Romanelli MG. The Emerging Role of the RBM20 and PTBP1 Ribonucleoproteins in Heart Development and Cardiovascular Diseases. Genes (Basel) 2020; 11:genes11040402. [PMID: 32276354 PMCID: PMC7230170 DOI: 10.3390/genes11040402] [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: 03/09/2020] [Revised: 04/04/2020] [Accepted: 04/06/2020] [Indexed: 12/17/2022] Open
Abstract
Alternative splicing is a regulatory mechanism essential for cell differentiation and tissue organization. More than 90% of human genes are regulated by alternative splicing events, which participate in cell fate determination. The general mechanisms of splicing events are well known, whereas only recently have deep-sequencing, high throughput analyses and animal models provided novel information on the network of functionally coordinated, tissue-specific, alternatively spliced exons. Heart development and cardiac tissue differentiation require thoroughly regulated splicing events. The ribonucleoprotein RBM20 is a key regulator of the alternative splicing events required for functional and structural heart properties, such as the expression of TTN isoforms. Recently, the polypyrimidine tract-binding protein PTBP1 has been demonstrated to participate with RBM20 in regulating splicing events. In this review, we summarize the updated knowledge relative to RBM20 and PTBP1 structure and molecular function; their role in alternative splicing mechanisms involved in the heart development and function; RBM20 mutations associated with idiopathic dilated cardiovascular disease (DCM); and the consequences of RBM20-altered expression or dysfunction. Furthermore, we discuss the possible application of targeting RBM20 in new approaches in heart therapies.
Collapse
|
33
|
Cheng S, Ray D, Lee RTH, Naripogu KB, Yusoff PABM, Goh PBL, Liu Y, Suzuki Y, Das K, Chan HS, Wong WK, Chan WH, Chow PKH, Ong HS, Raj P, Soo KC, Tan P, Epstein DM, Rozen SG. A functional network of gastric-cancer-associated splicing events controlled by dysregulated splicing factors. NAR Genom Bioinform 2020; 2:lqaa013. [PMID: 33575575 PMCID: PMC7671336 DOI: 10.1093/nargab/lqaa013] [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: 09/09/2019] [Revised: 12/26/2019] [Accepted: 02/14/2020] [Indexed: 12/11/2022] Open
Abstract
Comprehensive understanding of aberrant splicing in gastric cancer is lacking. We RNA-sequenced 19 gastric tumor–normal pairs and identified 118 high-confidence tumor-associated (TA) alternative splicing events (ASEs) based on high-coverage sequencing and stringent filtering, and also identified 8 differentially expressed splicing factors (SFs). The TA ASEs occurred in genes primarily involved in cytoskeletal organization. We constructed a correlative network between TA ASE splicing ratios and SF expression, replicated it in independent gastric cancer data from The Cancer Genome Atlas and experimentally validated it by knockdown of the nodal SFs (PTBP1, ESRP2 and MBNL1). Each SF knockdown drove splicing alterations in several corresponding TA ASEs and led to alterations in cellular migration consistent with the role of TA ASEs in cytoskeletal organization. We have therefore established a robust network of dysregulated splicing associated with tumor invasion in gastric cancer. Our work is a resource for identifying oncogenic splice forms, SFs and splicing-generated tumor antigens as biomarkers and therapeutic targets.
Collapse
Affiliation(s)
- Shanshan Cheng
- Department of Epidemiology and Biostatistics, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Rd, Wuhan, Hubei 430030, China.,Centre for Computational Biology, Duke-NUS Medical School, 8 College Rd, Singapore 169857, Singapore.,Cancer & Stem Cell Biology Programme, Duke-NUS Medical School, 8 College Rd, Singapore 169857, Singapore
| | - Debleena Ray
- Cancer & Stem Cell Biology Programme, Duke-NUS Medical School, 8 College Rd, Singapore 169857, Singapore
| | - Raymond Teck Ho Lee
- Cancer & Stem Cell Biology Programme, Duke-NUS Medical School, 8 College Rd, Singapore 169857, Singapore
| | - Kishore Babu Naripogu
- Cancer & Stem Cell Biology Programme, Duke-NUS Medical School, 8 College Rd, Singapore 169857, Singapore
| | | | - Pamela Bee Leng Goh
- Cancer & Stem Cell Biology Programme, Duke-NUS Medical School, 8 College Rd, Singapore 169857, Singapore
| | - Yujing Liu
- Centre for Computational Biology, Duke-NUS Medical School, 8 College Rd, Singapore 169857, Singapore.,Cancer & Stem Cell Biology Programme, Duke-NUS Medical School, 8 College Rd, Singapore 169857, Singapore.,Singapore MIT Alliance, 4 Engineering Dr 3, Singapore 117576, Singapore
| | - Yuka Suzuki
- Centre for Computational Biology, Duke-NUS Medical School, 8 College Rd, Singapore 169857, Singapore.,Cancer & Stem Cell Biology Programme, Duke-NUS Medical School, 8 College Rd, Singapore 169857, Singapore
| | - Kakoli Das
- Cancer & Stem Cell Biology Programme, Duke-NUS Medical School, 8 College Rd, Singapore 169857, Singapore
| | - Hsiang Sui Chan
- Department of General Surgery, Gleneagles Medical Centre, 6A Napier Rd, Singapore 258500, Singapore
| | - Wai Keong Wong
- Department of Upper Gastrointestinal & Bariatric Surgery, Singapore General Hospital, 1 Hospital Dr, Singapore 169608, Singapore
| | - Weng Hoong Chan
- Department of Upper Gastrointestinal & Bariatric Surgery, Singapore General Hospital, 1 Hospital Dr, Singapore 169608, Singapore
| | - Pierce Kah-Hoe Chow
- Division of Surgical Oncology, National Cancer Center Singapore, 11 Hospital Dr, Singapore 169610, Singapore.,Department of HPB and Transplant, Singapore General Hospital, 1 Hospital Dr, Singapore 169608, Singapore.,Clinical, Academic & Faculty Affairs, Duke-NUS Medical School, 8 College Rd, Singapore 169857, Singapore
| | - Hock Soo Ong
- Department of General Surgery, Singapore General Hospital, 1 Hospital Dr, Singapore 169608, Singapore
| | - Prema Raj
- General Surgery, Mount Elizabeth Medical Center, 3 Mount Elizabeth, Singapore 228510, Singapore
| | - Khee Chee Soo
- Division of Surgical Oncology, National Cancer Center Singapore, 11 Hospital Dr, Singapore 169610, Singapore.,Clinical, Academic & Faculty Affairs, Duke-NUS Medical School, 8 College Rd, Singapore 169857, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, 21 Lower Kent Ridge Rd, Singapore 119077, Singapore
| | - Patrick Tan
- Cancer & Stem Cell Biology Programme, Duke-NUS Medical School, 8 College Rd, Singapore 169857, Singapore
| | - David M Epstein
- Cancer & Stem Cell Biology Programme, Duke-NUS Medical School, 8 College Rd, Singapore 169857, Singapore
| | - Steven G Rozen
- Centre for Computational Biology, Duke-NUS Medical School, 8 College Rd, Singapore 169857, Singapore.,Cancer & Stem Cell Biology Programme, Duke-NUS Medical School, 8 College Rd, Singapore 169857, Singapore
| |
Collapse
|
34
|
Zhu W, Zhou BL, Rong LJ, Ye L, Xu HJ, Zhou Y, Yan XJ, Liu WD, Zhu B, Wang L, Jiang XJ, Ren CP. Roles of PTBP1 in alternative splicing, glycolysis, and oncogensis. J Zhejiang Univ Sci B 2020; 21:122-136. [PMID: 32115910 DOI: 10.1631/jzus.b1900422] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Polypyrimidine tract-binding protein 1 (PTBP1) plays an essential role in splicing and is expressed in almost all cell types in humans, unlike the other proteins of the PTBP family. PTBP1 mediates several cellular processes in certain types of cells, including the growth and differentiation of neuronal cells and activation of immune cells. Its function is regulated by various molecules, including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and RNA-binding proteins. PTBP1 plays roles in various diseases, particularly in some cancers, including colorectal cancer, renal cell cancer, breast cancer, and glioma. In cancers, it acts mainly as a regulator of glycolysis, apoptosis, proliferation, tumorigenesis, invasion, and migration. The role of PTBP1 in cancer has become a popular research topic in recent years, and this research has contributed greatly to the formulation of a useful therapeutic strategy for cancer. In this review, we summarize recent findings related to PTBP1 and discuss how it regulates the development of cancer cells.
Collapse
Affiliation(s)
- Wei Zhu
- NHC Key Laboratory of Carcinogenesis (Central South University) and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Bo-Lun Zhou
- NHC Key Laboratory of Carcinogenesis (Central South University) and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Li-Juan Rong
- NHC Key Laboratory of Carcinogenesis (Central South University) and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Li Ye
- NHC Key Laboratory of Carcinogenesis (Central South University) and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Hong-Juan Xu
- NHC Key Laboratory of Carcinogenesis (Central South University) and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Yao Zhou
- NHC Key Laboratory of Carcinogenesis (Central South University) and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Xue-Jun Yan
- NHC Key Laboratory of Carcinogenesis (Central South University) and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Wei-Dong Liu
- NHC Key Laboratory of Carcinogenesis (Central South University) and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Bin Zhu
- NHC Key Laboratory of Carcinogenesis (Central South University) and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Lei Wang
- NHC Key Laboratory of Carcinogenesis (Central South University) and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Xing-Jun Jiang
- NHC Key Laboratory of Carcinogenesis (Central South University) and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Cai-Ping Ren
- NHC Key Laboratory of Carcinogenesis (Central South University) and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, China
| |
Collapse
|
35
|
Huan L, Guo T, Wu Y, Xu L, Huang S, Xu Y, Liang L, He X. Hypoxia induced LUCAT1/PTBP1 axis modulates cancer cell viability and chemotherapy response. Mol Cancer 2020; 19:11. [PMID: 31964396 PMCID: PMC6971890 DOI: 10.1186/s12943-019-1122-z] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 12/23/2019] [Indexed: 01/08/2023] Open
Abstract
Background Hypoxic tumors are refractory to DNA damage drugs. However, the underlying mechanism has yet to be elucidated. We aimed to identify lncRNAs that upregulated under hypoxia and their effects on colorectal cancer (CRC). Methods CRC cells were treated with 1% O2 to identify lncRNAs that upregulated under hypoxia. We integrated these lncRNAs with RNA-seq of 4 paired CRC tissues and TCGA data to get candidate lncRNAs. Multiple in vitro and in vivo assays were used to explore the role of LUCAT1 in CRC. Results We identified a hypoxia-induced lncRNA LUCAT1 that facilitated the growth of CRC cells and contributed to drug resistance of CRC cells both in vitro and in vivo. Mechanically, LUCAT1 interacts with polypyrimidine tract binding protein 1 (PTBP1) in CRC cells, facilitates the association of a set of DNA damage related genes with PTBP1, thus resulting in altered alternative splicing of these genes. Moreover, ectopic expression of PTBP1 in CRC cells with knockdown of LUCAT1 abrogated the effects induced by LUCAT1 knockdown. Chemotherapeutics drug combined with LUCAT1 knockdown via antisense oligonucleotides (ASO) would get a better outcome in vivo, compared with group treated with chemotherapeutic drug only. Notably, LUCAT1 is upregulated in CRC tissues, compared to adjacent normal tissues; and CRC patients with higher LUCAT1 have a worse prognosis and poorly responded to chemotherapy in the clinic. Conclusions Our data suggested CRC cells utilizes LUCAT1 to develop resistance to DNA damage drugs, and disrupting the LUCAT1/PTBP1 axis might be a promising therapeutic strategy for refractory hypoxic tumors.
Collapse
Affiliation(s)
- Lin Huan
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Tianan Guo
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Yangjun Wu
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Linguo Xu
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Shenglin Huang
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Ye Xu
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
| | - Linhui Liang
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China. .,Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032, China.
| | - Xianghuo He
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China. .,Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032, China.
| |
Collapse
|
36
|
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.
Collapse
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
| |
Collapse
|
37
|
Role of polypyrimidine tract-binding protein 1/yin yang 2 signaling in regulating vascular smooth muscle cell proliferation and neointima hyperplasia. Toxicol Appl Pharmacol 2019; 383:114747. [DOI: 10.1016/j.taap.2019.114747] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 08/22/2019] [Accepted: 09/05/2019] [Indexed: 11/21/2022]
|
38
|
Ferreira D, Martins B, Soares M, Correia J, Adega F, Ferreira F, Chaves R. Gene expression association study in feline mammary carcinomas. PLoS One 2019; 14:e0221776. [PMID: 31461477 PMCID: PMC6713336 DOI: 10.1371/journal.pone.0221776] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 08/14/2019] [Indexed: 12/15/2022] Open
Abstract
Works on cancer-related genes expression using feline mammary carcinomas (FMCs) are scarce but crucial, not only to validate these tumours as models for human breast cancer studies but also to improve small animal practice. Here, the expression of the cancer-related genes TP53, CCND1, FUS, YBX1, PTBP1, c-MYC and PKM2 was evaluated by real-time RT-qPCR, in a population of FMCs clinically characterized and compared with the disease-free tissue of the same individual. In most of the FMCs analysed, RNA quantification revealed normal expression levels for TP53, c-MYC, YBX1 and FUS, but overexpression in the genes CCND1, PTBP1 and PKM2. The expression levels of these cancer-related genes are strongly correlated with each other, with exception of c-MYC and PKM2 genes. The integration of clinicopathological data with the transcriptional levels revealed several associations. The oral contraceptive administration showed to be positively related with the TP53, YBX1, CCND1, FUS and PTBP1 RNA levels. Positive associations were found between tumour size and YBX1 RNA, and lymph node metastasis with c-MYC RNA levels. This work allowed to verify that many of these cancer-related genes are associated but may also, indirectly, influence other genes, creating a complex molecular cancer network that in the future can provide new cancer biomarkers.
Collapse
Affiliation(s)
- Daniela Ferreira
- CAG - Laboratory of Cytogenomics and Animal Genomics, Department of Genetics and Biotechnology, University of Trás-os-Montes e Alto Douro, Vila Real, Portugal
- BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Bárbara Martins
- CAG - Laboratory of Cytogenomics and Animal Genomics, Department of Genetics and Biotechnology, University of Trás-os-Montes e Alto Douro, Vila Real, Portugal
| | - Maria Soares
- CBiOS - Research Center for Biosciences & Health Technologies, Faculdade de Medicina Veterinária, Universidade Lusófona de Humanidades e Tecnologias, Lisbon, Portugal
| | - Jorge Correia
- CIISA - Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, Lisboa, Portugal
| | - Filomena Adega
- CAG - Laboratory of Cytogenomics and Animal Genomics, Department of Genetics and Biotechnology, University of Trás-os-Montes e Alto Douro, Vila Real, Portugal
- BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Fernando Ferreira
- CIISA - Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, Lisboa, Portugal
| | - Raquel Chaves
- CAG - Laboratory of Cytogenomics and Animal Genomics, Department of Genetics and Biotechnology, University of Trás-os-Montes e Alto Douro, Vila Real, Portugal
- BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| |
Collapse
|
39
|
Kang H, Heo S, Shin JJ, Ji E, Tak H, Ahn S, Lee KJ, Lee EK, Kim W. A miR‐194/PTBP1/CCND3 axis regulates tumor growth in human hepatocellular carcinoma. J Pathol 2019; 249:395-408. [DOI: 10.1002/path.5325] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Revised: 06/16/2019] [Accepted: 07/11/2019] [Indexed: 01/05/2023]
Affiliation(s)
- Hoin Kang
- Department of BiochemistryThe Catholic University of Korea, College of Medicine Seoul South Korea
- Institute of Aging and Metabolic DiseasesThe Catholic University of Korea, College of Medicine Seoul South Korea
| | - Sungeun Heo
- Department of Molecular Science and TechnologyAjou University Suwon South Korea
| | - Jung Jae Shin
- Department of Molecular Science and TechnologyAjou University Suwon South Korea
| | - Eunbyul Ji
- Department of BiochemistryThe Catholic University of Korea, College of Medicine Seoul South Korea
| | - Hyosun Tak
- Department of BiochemistryThe Catholic University of Korea, College of Medicine Seoul South Korea
| | - Sojin Ahn
- Department of BiochemistryThe Catholic University of Korea, College of Medicine Seoul South Korea
| | - Kyung Jin Lee
- Department of Convergence Medicine, Asan Institute for Life SciencesUniversity of Ulsan College of Medicine Seoul South Korea
| | - Eun Kyung Lee
- Department of BiochemistryThe Catholic University of Korea, College of Medicine Seoul South Korea
- Institute of Aging and Metabolic DiseasesThe Catholic University of Korea, College of Medicine Seoul South Korea
| | - Wook Kim
- Department of Molecular Science and TechnologyAjou University Suwon South Korea
| |
Collapse
|
40
|
Escobar-Hoyos L, Knorr K, Abdel-Wahab O. Aberrant RNA Splicing in Cancer. ANNUAL REVIEW OF CANCER BIOLOGY-SERIES 2018; 3:167-185. [PMID: 32864546 DOI: 10.1146/annurev-cancerbio-030617-050407] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
RNA splicing, the enzymatic process of removing segments of premature RNA to produce mature RNA, is a key mediator of proteome diversity and regulator of gene expression. Increased systematic sequencing of the genome and transcriptome of cancers has identified a variety of means by which RNA splicing is altered in cancer relative to normal cells. These findings, in combination with the discovery of recurrent change-of-function mutations in splicing factors in a variety of cancers, suggest that alterations in splicing are drivers of tumorigenesis. Greater characterization of altered splicing in cancer parallels increasing efforts to pharmacologically perturb splicing and early-phase clinical development of small molecules that disrupt splicing in patients with cancer. Here we review recent studies of global changes in splicing in cancer, splicing regulation of mitogenic pathways critical in cancer transformation, and efforts to therapeutically target splicing in cancer.
Collapse
Affiliation(s)
- Luisa Escobar-Hoyos
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Department of Pathology, Stony Brook University, Stony Brook, NY 11794, USA
| | | | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Weill Cornell Medical College, New York, NY 10065, USA.,Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| |
Collapse
|
41
|
Masuda K, Kuwano Y. Diverse roles of RNA-binding proteins in cancer traits and their implications in gastrointestinal cancers. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 10:e1520. [PMID: 30479000 DOI: 10.1002/wrna.1520] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 10/31/2018] [Accepted: 11/01/2018] [Indexed: 02/06/2023]
Abstract
Gene expression patterns in cancer cells are strongly influenced by posttranscriptional mechanisms. RNA-binding proteins (RBPs) play key roles in posttranscriptional gene regulation; they can interact with target mRNAs in a sequence- and structure-dependent manner, and determine cellular behavior by manipulating the processing of these mRNAs. Numerous RBPs are aberrantly deregulated in many human cancers and hence, affect the functioning of mRNAs that encode proteins, implicated in carcinogenesis. Here, we summarize the key roles of RBPs in posttranscriptional gene regulation, describe RBPs disrupted in cancer, and lastly focus on RBPs that are responsible for implementing cancer traits in the digestive tract. These evidences may reveal a potential link between changes in expression/function of RBPs and malignant transformation, and a framework for new insights and potential therapeutic applications. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
Collapse
Affiliation(s)
- Kiyoshi Masuda
- Kawasaki Medical School at Kurashiki-City, Okayama, Japan
| | - Yuki Kuwano
- Department of Pathophysiology, Institute of Biomedical Sciences, Tokushima University Graduate School at Tokushima-City, Tokushima, Japan
| |
Collapse
|
42
|
Dual functions for OVAAL in initiation of RAF/MEK/ERK prosurvival signals and evasion of p27-mediated cellular senescence. Proc Natl Acad Sci U S A 2018; 115:E11661-E11670. [PMID: 30478051 PMCID: PMC6294934 DOI: 10.1073/pnas.1805950115] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Here, we report that the long noncoding RNA (lncRNA) ovarian adenocarcinoma-amplified lncRNA (OVAAL) is a mediator of cancer cell resistance, counteracting the effects of apoptosis-inducing agents acting through both the extrinsic and intrinsic pathways. Building upon previous reports associating OVAAL amplification with ovarian and endometrial cancers, we now show that OVAAL overexpression occurs during the pathogenesis of colorectal cancer and melanoma. Mechanistically, our findings also establish that OVAAL expression more generally contributes a prosurvival role to cancer cells under steady-state conditions. OVAAL accomplishes these actions utilizing distinct functional modalities: one promoting activation of RAF/MEK/ERK signaling and the other blocking cell entry into senescence. Our study demonstrates that expression of a single OVAAL in cancer cells drives two distinct but coordinated actions contributing to cancer pathology. Long noncoding RNAs (lncRNAs) function through a diverse array of mechanisms that are not presently fully understood. Here, we sought to find lncRNAs differentially regulated in cancer cells resistant to either TNF-related apoptosis-inducing ligand (TRAIL) or the Mcl-1 inhibitor UMI-77, agents that act through the extrinsic and intrinsic apoptotic pathways, respectively. This work identified a commonly up-regulated lncRNA, ovarian adenocarcinoma-amplified lncRNA (OVAAL), that conferred apoptotic resistance in multiple cancer types. Analysis of clinical samples revealed OVAAL expression was significantly increased in colorectal cancers and melanoma in comparison to the corresponding normal tissues. Functional investigations showed that OVAAL depletion significantly inhibited cancer cell proliferation and retarded tumor xenograft growth. Mechanically, OVAAL physically interacted with serine/threonine-protein kinase 3 (STK3), which, in turn, enhanced the binding between STK3 and Raf-1. The ternary complex OVAAL/STK3/Raf-1 enhanced the activation of the RAF protooncogene serine/threonine-protein kinase (RAF)/mitogen-activated protein kinase kinase 1 (MEK)/ERK signaling cascade, thus promoting c-Myc–mediated cell proliferation and Mcl-1–mediated cell survival. On the other hand, depletion of OVAAL triggered cellular senescence through polypyrimidine tract-binding protein 1 (PTBP1)–mediated p27 expression, which was regulated by competitive binding between OVAAL and p27 mRNA to PTBP1. Additionally, c-Myc was demonstrated to drive OVAAL transcription, indicating a positive feedback loop between c-Myc and OVAAL in controlling tumor growth. Taken together, these results reveal that OVAAL contributes to the survival of cancer cells through dual mechanisms controlling RAF/MEK/ERK signaling and p27-mediated cell senescence.
Collapse
|
43
|
Sriram A, Bohlen J, Teleman AA. Translation acrobatics: how cancer cells exploit alternate modes of translational initiation. EMBO Rep 2018; 19:embr.201845947. [PMID: 30224410 DOI: 10.15252/embr.201845947] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 07/09/2018] [Accepted: 08/16/2018] [Indexed: 12/11/2022] Open
Abstract
Recent work has brought to light many different mechanisms of translation initiation that function in cells in parallel to canonical cap-dependent initiation. This has important implications for cancer. Canonical cap-dependent translation initiation is inhibited by many stresses such as hypoxia, nutrient limitation, proteotoxic stress, or genotoxic stress. Since cancer cells are often exposed to these stresses, they rely on alternate modes of translation initiation for protein synthesis and cell growth. Cancer mutations are now being identified in components of the translation machinery and in cis-regulatory elements of mRNAs, which both control translation of cancer-relevant genes. In this review, we provide an overview on the various modes of non-canonical translation initiation, such as leaky scanning, translation re-initiation, ribosome shunting, IRES-dependent translation, and m6A-dependent translation, and then discuss the influence of stress on these different modes of translation. Finally, we present examples of how these modes of translation are dysregulated in cancer cells, allowing them to grow, to proliferate, and to survive, thereby highlighting the importance of translational control in cancer.
Collapse
Affiliation(s)
- Ashwin Sriram
- German Cancer Research Center (DKFZ), Heidelberg, Germany.,Heidelberg University, Heidelberg, Germany
| | - Jonathan Bohlen
- German Cancer Research Center (DKFZ), Heidelberg, Germany.,Heidelberg University, Heidelberg, Germany
| | - Aurelio A Teleman
- German Cancer Research Center (DKFZ), Heidelberg, Germany .,Heidelberg University, Heidelberg, Germany
| |
Collapse
|
44
|
Fukata T, Mizushima T, Nishimura J, Okuzaki D, Wu X, Hirose H, Yokoyama Y, Kubota Y, Nagata K, Tsujimura N, Inoue A, Miyoshi N, Haraguchi N, Takahashi H, Hata T, Matsuda C, Kayama H, Takeda K, Doki Y, Mori M, Yamamoto H. The Supercarbonate Apatite-MicroRNA Complex Inhibits Dextran Sodium Sulfate-Induced Colitis. MOLECULAR THERAPY. NUCLEIC ACIDS 2018; 12:658-671. [PMID: 30092402 PMCID: PMC6083010 DOI: 10.1016/j.omtn.2018.07.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Revised: 07/07/2018] [Accepted: 07/10/2018] [Indexed: 01/02/2023]
Abstract
The incidence of inflammatory bowel disease (IBD) is increasing. Nucleic acid-based medicine has potential as a next-generation treatment, but it is rarely successful with IBD. The aim of this study was to establish a microRNA-based therapy in an IBD model. For this purpose, we used microRNA-29 (miR-29) and a supercarbonate apatite (sCA) nanoparticle as a drug delivery system. Injection of sCA-miR-29a-3p or sCA-miR-29b-3p into mouse tail veins markedly prevented and restored inflammation because of dextran sulfate sodium (DSS)-induced colitis. RNA sequencing analysis revealed that miR-29a and miR-29b could inhibit the interferon-associated inflammatory cascade. Subcutaneous injection of sCA-miR-29b also potently inhibited inflammation, and it efficiently targeted CD11c+ dendritic cells (DCs) among various types of immune cells in the inflamed mucosa. RT-PCR analysis indicated that the miR-29 RNAs in CD11c+ DCs suppressed the production of interleukin-6 (IL-6), transforming growth factor β (TGF-β), and IL-23 subunits in DSS-treated mice. This may inhibit Th17 differentiation and subsequent activation, which is critical in IBD pathogenesis. In vivo experiments using a non-natural artificial microRNA sequence revealed that targeting of DCs in the inflamed colon is an exceptional feature of sCA. This study suggests that sCA-miR-29s may open a new avenue in nucleic acid-based medicine for IBD treatment.
Collapse
Affiliation(s)
- Tadafumi Fukata
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Yamadaoka 2-2, Suita City, Osaka, Japan
| | - Tsunekazu Mizushima
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Yamadaoka 2-2, Suita City, Osaka, Japan
| | - Junichi Nishimura
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Yamadaoka 2-2, Suita City, Osaka, Japan
| | - Daisuke Okuzaki
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Yamadaoka 3-1, Suita City, Osaka, Japan
| | - Xin Wu
- Department of Molecular Pathology, Division of Health Sciences, Graduate School of Medicine, Osaka University, Yamadaoka 1-7, Suita City, Osaka, Japan
| | - Haruka Hirose
- Department of Molecular Pathology, Division of Health Sciences, Graduate School of Medicine, Osaka University, Yamadaoka 1-7, Suita City, Osaka, Japan
| | - Yuhki Yokoyama
- Department of Molecular Pathology, Division of Health Sciences, Graduate School of Medicine, Osaka University, Yamadaoka 1-7, Suita City, Osaka, Japan
| | - Yui Kubota
- Department of Molecular Pathology, Division of Health Sciences, Graduate School of Medicine, Osaka University, Yamadaoka 1-7, Suita City, Osaka, Japan
| | - Kazuya Nagata
- Department of Molecular Pathology, Division of Health Sciences, Graduate School of Medicine, Osaka University, Yamadaoka 1-7, Suita City, Osaka, Japan
| | - Naoto Tsujimura
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Yamadaoka 2-2, Suita City, Osaka, Japan
| | - Akira Inoue
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Yamadaoka 2-2, Suita City, Osaka, Japan
| | - Norikatsu Miyoshi
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Yamadaoka 2-2, Suita City, Osaka, Japan
| | - Naotsugu Haraguchi
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Yamadaoka 2-2, Suita City, Osaka, Japan
| | - Hidekazu Takahashi
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Yamadaoka 2-2, Suita City, Osaka, Japan
| | - Taishi Hata
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Yamadaoka 2-2, Suita City, Osaka, Japan
| | - Chu Matsuda
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Yamadaoka 2-2, Suita City, Osaka, Japan
| | - Hisako Kayama
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Graduate School of Medicine, Yamadaoka 2-2, Suita City, Osaka, Japan; Laboratory of Mucosal Immunology, WPI Immunology Frontier Research Center, Osaka University, Yamadaoka3-1, Suita City, Osaka, Japan
| | - Kiyoshi Takeda
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Graduate School of Medicine, Yamadaoka 2-2, Suita City, Osaka, Japan; Laboratory of Mucosal Immunology, WPI Immunology Frontier Research Center, Osaka University, Yamadaoka3-1, Suita City, Osaka, Japan
| | - Yuichiro Doki
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Yamadaoka 2-2, Suita City, Osaka, Japan
| | - Masaki Mori
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Yamadaoka 2-2, Suita City, Osaka, Japan
| | - Hirofumi Yamamoto
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Yamadaoka 2-2, Suita City, Osaka, Japan; Department of Molecular Pathology, Division of Health Sciences, Graduate School of Medicine, Osaka University, Yamadaoka 1-7, Suita City, Osaka, Japan.
| |
Collapse
|
45
|
Fu X, Xie F, Gong F, Yang Z, Lv X, Li X, Jiao H, Wang Q, Liu X, Yan L, Xiao R. Suppression of PTBP1 signaling is responsible for mesenchymal stem cell induced invasion of low malignancy cancer cells. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2018; 1865:1552-1565. [PMID: 30327198 DOI: 10.1016/j.bbamcr.2018.08.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 08/03/2018] [Accepted: 08/07/2018] [Indexed: 12/30/2022]
Abstract
Mesenchymal stem cells (MSCs) hold great promise as attractive vehicles to deliver therapeutic agents against cancer, while the cross-talk between MSCs and cancer cells remains controversial. Here in an indirect co-culture system we observed that MSCs induced the malignancy transformation of low malignancy cancer cells HT29 and MCF7, whereas MSCs were reprogrammed by high malignancy cancer cells HCT116 and MDA-MB-231 without exerting an obvious influence on them. We further demonstrated that the RNA-binding protein polypyrimidine tract-binding protein 1 (PTBP1) was suppressed in low malignancy cancer cells co-cultured with MSCs. Moreover, shRNA mediated silencing of PTBP1 could promote the invasiveness of HT29 cells while over-expression of PTBP1 attenuate the MSC-induced invasion of HT29 cells. Our results suggested that differential effects of MSCs on the invasion of cancer cells partially corresponded to PTBP1 expression in cancer cells and the maintenance of biological characteristics in MSCs, which insight could provide a theoretical basis for evaluating the safety of MSC application and PTBP1 targeting in cancer treatment.
Collapse
Affiliation(s)
- Xin Fu
- Research Center of Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 33 Ba-Da-Chu Road, Beijing 100144, PR China
| | - Fangnan Xie
- Research Center of Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 33 Ba-Da-Chu Road, Beijing 100144, PR China
| | - Fuxing Gong
- Research Center of Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 33 Ba-Da-Chu Road, Beijing 100144, PR China
| | - Zhigang Yang
- Research Center of Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 33 Ba-Da-Chu Road, Beijing 100144, PR China
| | - Xiaoyan Lv
- Research Center of Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 33 Ba-Da-Chu Road, Beijing 100144, PR China
| | - Xintian Li
- Research Center of Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 33 Ba-Da-Chu Road, Beijing 100144, PR China
| | - Hu Jiao
- Research Center of Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 33 Ba-Da-Chu Road, Beijing 100144, PR China
| | - Qian Wang
- Research Center of Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 33 Ba-Da-Chu Road, Beijing 100144, PR China
| | - Xia Liu
- Research Center of Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 33 Ba-Da-Chu Road, Beijing 100144, PR China
| | - Li Yan
- Research Center of Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 33 Ba-Da-Chu Road, Beijing 100144, PR China
| | - Ran Xiao
- Research Center of Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 33 Ba-Da-Chu Road, Beijing 100144, PR China.
| |
Collapse
|
46
|
Urbanski L, Leclair N, Anczuków O. Alternative-splicing defects in cancer: Splicing regulators and their downstream targets, guiding the way to novel cancer therapeutics. WILEY INTERDISCIPLINARY REVIEWS. RNA 2018; 9:e1476. [PMID: 29693319 PMCID: PMC6002934 DOI: 10.1002/wrna.1476] [Citation(s) in RCA: 221] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 02/27/2018] [Accepted: 03/01/2018] [Indexed: 12/14/2022]
Abstract
Defects in alternative splicing are frequently found in human tumors and result either from mutations in splicing-regulatory elements of specific cancer genes or from changes in the regulatory splicing machinery. RNA splicing regulators have emerged as a new class of oncoproteins and tumor suppressors, and contribute to disease progression by modulating RNA isoforms involved in the hallmark cancer pathways. Thus, dysregulation of alternative RNA splicing is fundamental to cancer and provides a potentially rich source of novel therapeutic targets. Here, we review the alterations in splicing regulatory factors detected in human tumors, as well as the resulting alternatively spliced isoforms that impact cancer hallmarks, and discuss how they contribute to disease pathogenesis. RNA splicing is a highly regulated process and, as such, the regulators are themselves tightly regulated. Differential transcriptional and posttranscriptional regulation of splicing factors modulates their levels and activities in tumor cells. Furthermore, the composition of the tumor microenvironment can also influence which isoforms are expressed in a given cell type and impact drug responses. Finally, we summarize current efforts in targeting alternative splicing, including global splicing inhibition using small molecules blocking the spliceosome or splicing-factor-modifying enzymes, as well as splice-switching RNA-based therapeutics to modulate cancer-specific splicing isoforms. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Processing > Splicing Regulation/Alternative Splicing.
Collapse
|
47
|
Wang X, Li Y, Fan Y, Yu X, Mao X, Jin F. PTBP1 promotes the growth of breast cancer cells through the PTEN/Akt pathway and autophagy. J Cell Physiol 2018; 233:8930-8939. [PMID: 29856478 PMCID: PMC6175200 DOI: 10.1002/jcp.26823] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Accepted: 04/30/2018] [Indexed: 12/22/2022]
Abstract
Invasion and migration is the hallmark of malignant tumors as well as the major cause for breast cancer death. The polypyrimidine tract binding, PTB, protein serves as an important model for understanding how RNA binding proteins affect proliferation and invasion and how changes in the expression of these proteins can control complex programs of tumorigenesis. We have investigated some roles of polypyrimidine tract binding protein 1 (PTBP1) in human breast cancer. We found that PTBP1 was upregulated in breast cancer tissues compared with normal tissues and the same result was confirmed in breast cancer cell lines. Knockdown of PTBP1 substantially inhibited tumor cell growth, migration, and invasion. These results suggest that PTBP1 is associated with breast tumorigenesis and appears to be required for tumor cell growth and maintenance of metastasis. We further analyzed the relationship between PTBP1 and clinicopathological parameters and found that PTBP1 was correlated with her‐2 expression, lymph node metastasis, and pathological stage. This will be a novel target for her‐2(+) breast cancer. PTBP1 exerts these effects, in part, by regulating the phosphatase and tensin homolog‐phosphatidylinositol‐4,5‐bisphosphate 3‐kinase/protein kinase B (PTEN‐PI3K/Akt) pathway and autophagy, and consequently alters cell growth and contributes to the invasion and metastasis.
Collapse
Affiliation(s)
- Xu Wang
- Department of Breast Surgery, The First Affiliated Hospital of China Medical University, Shenyang City, Liaoning, China
| | - Yang Li
- Department of Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health, and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang, China
| | - Yan Fan
- Department of Pediatrics, The First Affiliated Hospital of China Medical University, Shenyang City, Liaoning, China
| | - Xinmiao Yu
- Department of Breast Surgery, The First Affiliated Hospital of China Medical University, Shenyang City, Liaoning, China
| | - Xiaoyun Mao
- Department of Breast Surgery, The First Affiliated Hospital of China Medical University, Shenyang City, Liaoning, China
| | - Feng Jin
- Department of Breast Surgery, The First Affiliated Hospital of China Medical University, Shenyang City, Liaoning, China
| |
Collapse
|
48
|
PTBP1 enhances miR-101-guided AGO2 targeting to MCL1 and promotes miR-101-induced apoptosis. Cell Death Dis 2018; 9:552. [PMID: 29748555 PMCID: PMC5945587 DOI: 10.1038/s41419-018-0551-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 03/16/2018] [Accepted: 03/22/2018] [Indexed: 12/22/2022]
Abstract
Myeloid cell leukemia 1 (MCL1) is a key anti-apoptotic protein belonging to the BCL-2 protein family. To preserve normal cellular homeostasis, cells must maintain strict control over MCL1 expression. Overexpression of MCL1 has been identified as a key contributor to tumorigenesis, and further enables resistance to a number of anti-cancer chemotherapies. Thus, there is an ongoing interest to develop selective MCL1 inhibitors. In order to better target MCL1, it is essential to understand the molecular mechanisms that regulate MCL1 expression in cells. While MCL1 expression is tightly controlled by multiple mechanisms, the post-transcriptional regulation of MCL1 mRNA is poorly studied. Our previous work identified that polypyrimidine tract binding protein 1 (PTBP1) binds to MCL1 mRNA and represses MCL1 expression by destabilizing MCL1 mRNA. In this report, we show that PTBP1 modulates MCL1 expression by regulating the microRNA (miRNA) direction of the miRNA-induced silencing complex (miRISC) to MCL1. We demonstrate that PTBP1 enhances miR-101-guided AGO2 interaction with MCL1, thereby regulating miR-101-induced apoptosis and clonogenic cell survival inhibition in cells. Taken together, not only do these studies expand our understanding on the regulation of MCL1, they also demonstrate that PTBP1 and miRNAs can function cooperatively on a shared target mRNA.
Collapse
|
49
|
Li T, Liu Q, Garza N, Kornblau S, Jin VX. Integrative analysis reveals functional and regulatory roles of H3K79me2 in mediating alternative splicing. Genome Med 2018; 10:30. [PMID: 29665865 PMCID: PMC5902843 DOI: 10.1186/s13073-018-0538-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 03/29/2018] [Indexed: 01/26/2023] Open
Abstract
Background Accumulating evidence suggests alternative splicing (AS) is a co-transcriptional splicing process not only controlled by RNA-binding splicing factors, but also mediated by epigenetic regulators, such as chromatin structure, nucleosome density, and histone modification. Aberrant AS plays an important role in regulating various diseases, including cancers. Methods In this study, we integrated AS events derived from RNA-seq with H3K79me2 ChIP-seq data across 34 different normal and cancer cell types and found the higher enrichment of H3K79me2 in two AS types, skipping exon (SE) and alternative 3′ splice site (A3SS). Results Interestingly, by applying self-organizing map (SOM) clustering, we unveiled two clusters mainly comprised of blood cancer cell types with a strong correlation between H3K79me2 and SE. Remarkably, the expression of transcripts associated with SE was not significantly different from that of those not associated with SE, indicating the involvement of H3K79me2 in splicing has little impact on full mRNA transcription. We further showed that the deletion of DOT1L1, the sole H3K79 methyltransferase, impeded leukemia cell proliferation as well as switched exon skipping to the inclusion isoform in two MLL-rearranged acute myeloid leukemia cell lines. Our data demonstrate H3K79me2 was involved in mediating SE processing, which might in turn influence transformation and disease progression in leukemias. Conclusions Collectively, our work for the first time reveals that H3K79me2 plays functional and regulatory roles through a co-transcriptional splicing mechanism. Electronic supplementary material The online version of this article (10.1186/s13073-018-0538-1) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Tianbao Li
- College of Life Science, Jilin University, Changchun, 130012, China.,Department of Molecular Medicine, University of Texas Health, 8403 Floyd Curl, San Antonio, TX, 78229, USA
| | - Qi Liu
- Department of Molecular Medicine, University of Texas Health, 8403 Floyd Curl, San Antonio, TX, 78229, USA
| | - Nick Garza
- Department of Molecular Medicine, University of Texas Health, 8403 Floyd Curl, San Antonio, TX, 78229, USA.,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Steven Kornblau
- Department of Leukemia, UT MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Victor X Jin
- Department of Molecular Medicine, University of Texas Health, 8403 Floyd Curl, San Antonio, TX, 78229, USA.
| |
Collapse
|
50
|
Tamai K, Mizushima T, Wu X, Inoue A, Ota M, Yokoyama Y, Miyoshi N, Haraguchi N, Takahashi H, Nishimura J, Hata T, Matsuda C, Doki Y, Mori M, Yamamoto H. Photodynamic Therapy Using Indocyanine Green Loaded on Super Carbonate Apatite as Minimally Invasive Cancer Treatment. Mol Cancer Ther 2018; 17:1613-1622. [PMID: 29654066 DOI: 10.1158/1535-7163.mct-17-0788] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 12/26/2017] [Accepted: 04/06/2018] [Indexed: 11/16/2022]
Abstract
Minimally invasive treatment is getting more and more important in an aging society. The purpose of this study was to explore the possibility of ICG loaded on super carbonate apatite (sCA) nanoparticles as a novel photodynamic therapy (PDT) against cancers. Using colon cancer cells, ICG uptake and anti-tumor effects were examined between the treatments of ICG and sCA-ICG. Reactive oxygen species (ROS) production and temperature rise were also evaluated to explore the underlying mechanism. Atomic force microscopy revealed that the size of sCA-ICG ranged from 10 to 20 nm. In aqueous solution with 0.5% albumin, the temperature increase after laser irradiation was 27.1°C and 23.1°C in sCA-ICG and ICG, respectively (control DW: 5.7°C). A significant increase in ROS generation was noted in cell cultures treated with sCA-ICG plus irradiation compared with those treated with ICG plus irradiation (P < 0.01). Uptake of ICG in the tumor cells significantly increased in sCA-ICG compared with ICG in vitro and in vivo The fluorescence signals of ICG in the tumor, liver, and kidney faded away in both treatments by 24 hours. Finally, the HT29 tumors treated with sCA-ICG followed by irradiation exhibited drastic tumor growth retardation (P < 0.01), whereas irradiation of tumors after injection of ICG did not inhibit tumor growth. This study shows that sCA is a useful vehicle for ICG-based PDT. Quick withdrawal of ICG from normal organs is unique to sCA-ICG and contrasts with the other nanoparticles remaining in normal organs for a long time. Mol Cancer Ther; 17(7); 1613-22. ©2018 AACR.
Collapse
Affiliation(s)
- Koki Tamai
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Suita city, Osaka, Japan
| | - Tsunekazu Mizushima
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Suita city, Osaka, Japan
| | - Xin Wu
- Division of Health Sciences, Department of Molecular Pathology, Graduate School of Medicine, Osaka University, Suita City, Osaka, Japan
| | - Akira Inoue
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Suita city, Osaka, Japan
| | - Minori Ota
- Division of Health Sciences, Department of Molecular Pathology, Graduate School of Medicine, Osaka University, Suita City, Osaka, Japan
| | - Yuhki Yokoyama
- Division of Health Sciences, Department of Molecular Pathology, Graduate School of Medicine, Osaka University, Suita City, Osaka, Japan
| | - Norikatsu Miyoshi
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Suita city, Osaka, Japan
| | - Naotsugu Haraguchi
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Suita city, Osaka, Japan
| | - Hidekazu Takahashi
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Suita city, Osaka, Japan
| | - Junichi Nishimura
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Suita city, Osaka, Japan
| | - Taishi Hata
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Suita city, Osaka, Japan
| | - Chu Matsuda
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Suita city, Osaka, Japan
| | - Yuichiro Doki
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Suita city, Osaka, Japan
| | - Masaki Mori
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Suita city, Osaka, Japan
| | - Hirofumi Yamamoto
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Suita city, Osaka, Japan. .,Division of Health Sciences, Department of Molecular Pathology, Graduate School of Medicine, Osaka University, Suita City, Osaka, Japan
| |
Collapse
|