1
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Leng X, Liu J, Jin A, Zheng H, Wu J, Zhong L, Li Q, Li D. Multi-omics Analyses Reveal Function of Apolipoprotein E in Alternative Splicing and Tumor Immune Microenvironment in Kidney Renal Clear Cell Carcinoma via Pan-cancer Analysis. Cell Biochem Biophys 2024; 82:1-13. [PMID: 38182861 DOI: 10.1007/s12013-023-01211-7] [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: 03/30/2023] [Accepted: 12/22/2023] [Indexed: 01/07/2024]
Abstract
Apolipoprotein E (APOE) regulates lipid metabolism, associated with the development of various cancers. However, its precise prognostic significance and functions in alternative splicing and the tumor immune microenvironment remain unclear. In this study, we extracted APOE expression in pan-cancer from TCGA and analyzed mRNA transcriptome, cell lines, and protein levels. Furthermore, we analyzed the alternative splicing expression of the APOE gene transcript with prognostic profiles using the OncoSplicing database. We obtained 73 common APOE genes to perform functional enrichment analysis, assess the correlation between genes and immune cells using TIMER, EPIC, and ssGSEA methods, and examine the prognostic significance using the UALCAN database. Finally, single-cell data was employed to assess the correlation between APOE genes and cell functions. Our findings revealed that APOE expression varies across different tumor types and cancer cell lines. The alternative splicing analysis demonstrated that APOE transcript expression levels have prognostic value in cancers such as LGG, KIRC, and KIRP. Functional enrichment analysis indicated significant associations between APOE and various immune cells, such as macrophages, CD8 T cells, and NK cells, with significant implications for prognosis. Moreover, single-cell data indicated that APOE was primarily expressed in renal epithelial cells among stromal cells and in macrophages among immune cells, significantly negatively correlated with five functional states. Our study represents the first comprehensive exploration of APOE's function in pan-cancers and identifies APOE as a potential biomarker in cancer pathogenesis, prognosis, and immune therapeutic target.
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Affiliation(s)
- Xin Leng
- Department of Urology, Affiliated Kunshan Hospital of Jiangsu University, Suzhou, 215300, China
| | - Jianhu Liu
- Department of Urology, Affiliated Kunshan Hospital of Jiangsu University, Suzhou, 215300, China
| | - Anqi Jin
- The BioBank, Affiliated Kunshan Hospital of Jiangsu University, Suzhou, 215300, China
| | - Hongfang Zheng
- Department of Urology, Affiliated Kunshan Hospital of Jiangsu University, Suzhou, 215300, China
| | - Jiulong Wu
- Department of Urology, Affiliated Kunshan Hospital of Jiangsu University, Suzhou, 215300, China
| | - Longfei Zhong
- Department of Urology, Affiliated Kunshan Hospital of Jiangsu University, Suzhou, 215300, China
| | - Qiaoxin Li
- Department of Urology, Affiliated Kunshan Hospital of Jiangsu University, Suzhou, 215300, China
| | - Dongfeng Li
- Department of Urology, The Third People's Hospital of Kunshan, Suzhou, 215300, China.
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2
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A Novel Nomogram Combining Alternative Splicing Events and Clinical Factors for Prognosis Prediction in Head and Neck Squamous Cell Carcinoma. JOURNAL OF ONCOLOGY 2022; 2022:4552445. [PMID: 35103061 PMCID: PMC8800633 DOI: 10.1155/2022/4552445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/04/2022] [Accepted: 01/07/2022] [Indexed: 11/18/2022]
Abstract
Due to limitations of sensitive biomarkers, the clinical prognosis of patients with head and neck squamous cell carcinoma (HNSCC) remains poor. Alternative splicing (AS) is the basis of both transcriptome and proteome richness, so more and more evidence indicates an important relationship between AS and tumor progression. The aim of this study was to offer a comprehensive analysis on AS events and then investigate its potentials as a new biomarker for patients with squamous cell carcinoma of the head and neck. In this study, univariate assays were conducted to examine the prognosis-associated AS events, and we screened 4068 survival-related AS events in 2573 genes. Then, the AS events related to survival were further determined and analyzed using LASSO regression and multivariate assays, and an eleven-AS signature was developed. Kaplan–Meier assays indicated patients with high-risk scores exhibited a shorter OS than those with low-risk scores. Multivariate assays further demonstrated that the signature’s risk score was independent of HNSCC survivals. Meanwhile, we analyzed the clinical association of AS-based prognostic signature in HNSCC patients and observed that tumor specimens with advanced stages and grades exhibited a high risk score. In addition, the results of survival nomogram revealed that predicted outcomes and actual outcomes were highly consistent. Overall, our group showed an eleven-AS signature of HNSCC, which could be regarded as a separate prognostic factor.
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3
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Cai Z, Wei Y, Chen S, Gong Y, Fu Y, Dai X, Zhou Y, Yang H, Tang L, Liu H. Screening and identification of key biomarkers in alimentary tract cancers: A bioinformatic analysis. Cancer Biomark 2021; 29:221-233. [PMID: 32623389 DOI: 10.3233/cbm-201580] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
BACKGROUND Alimentary tract cancers (ATCs) are the most malignant cancers in the world. Numerous studies have revealed the tumorigenesis, diagnosis and treatment of ATCs, but many mechanisms remain to be explored. METHODS To identify the key genes of ATCs, microarray datasets of oesophageal cancer, gastric cancer and colorectal cancer were obtained from the Gene Expression Omnibus (GEO) database. In total, 207 differentially expressed genes (DEGs) were screened. KEGG and GO function enrichment analyses were conducted, and a protein-protein interaction (PPI) network was generated and gene modules analysis was performed using STRING and Cytoscape. RESULTS Five hub genes were screened, and the associated biological processes indicated that these genes were mainly enriched in cellular processes, protein binding and metabolic processes. Clinical survival analysis showed that COL10A1 and KIF14 may be significantly associated with the tumorigenesis or pathology grade of ATCs. In addition, relative human ATC cell lines along with blood samples and tumour tissues of ATC patients were obtained. The data proved that high expression of COL10A1 and KIF14 was associated with tumorigenesis and could be detected in blood. CONCLUSION In conclusion, the identification of hub genes in the present study helped us to elucidate the molecular mechanisms of tumorigenesis and identify potential diagnostic indicators and targeted treatment for ATCs.
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Affiliation(s)
- Zeling Cai
- Genter of General Surgery, The Affiliated Haimen People's Hospital of Nantong University, Nantong, Jiangsu, China.,Genter of General Surgery, The Affiliated Haimen People's Hospital of Nantong University, Nantong, Jiangsu, China
| | - Yi Wei
- Center of Gastrointestinal Disease, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, Jiangsu, China.,Genter of General Surgery, The Affiliated Haimen People's Hospital of Nantong University, Nantong, Jiangsu, China
| | - Shuai Chen
- Center of Gastrointestinal Disease, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, Jiangsu, China.,Genter of General Surgery, The Affiliated Haimen People's Hospital of Nantong University, Nantong, Jiangsu, China
| | - Yu Gong
- Center of Gastrointestinal Disease, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, Jiangsu, China
| | - Yue Fu
- Center of Gastrointestinal Disease, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, Jiangsu, China
| | - Xianghua Dai
- Genter of General Surgery, The Affiliated Haimen People's Hospital of Nantong University, Nantong, Jiangsu, China
| | - Yan Zhou
- Center of Gastrointestinal Disease, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, Jiangsu, China
| | - Haojun Yang
- Center of Gastrointestinal Disease, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, Jiangsu, China
| | - Liming Tang
- Center of Gastrointestinal Disease, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, Jiangsu, China
| | - Hanyang Liu
- Center of Gastrointestinal Disease, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, Jiangsu, China
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4
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Dlamini Z, Hull R, Mbatha SZ, Alaouna M, Qiao YL, Yu H, Chatziioannou A. Prognostic Alternative Splicing Signatures in Esophageal Carcinoma. Cancer Manag Res 2021; 13:4509-4527. [PMID: 34113176 PMCID: PMC8186946 DOI: 10.2147/cmar.s305464] [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: 02/05/2021] [Accepted: 04/06/2021] [Indexed: 01/10/2023] Open
Abstract
Alternative splicing (AS) is a method of increasing the number of proteins that the genome is capable of coding for, by altering the pre-mRNA during its maturation. This process provides the ability of a broad range of proteins to arise from a single gene. AS events are known to occur in up to 94% of human genes. Cumulative data have shown that aberrant AS functionality is a major factor in human diseases. This review focuses on the contribution made by aberrant AS functionality in the development and progression of esophageal cancer. The changes in the pattern of expression of alternately spliced isoforms in esophageal cancer can be used as diagnostic or prognostic biomarkers. Additionally, these can be used as targets for the development of new treatments for esophageal cancer.
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Affiliation(s)
- Zodwa Dlamini
- SAMRC Precision Prevention & Novel Drug Targets for HIV-Associated Cancers Extramural Unit, Pan African Cancer Research Institute, University of Pretoria, Pretoria, South Africa
| | - Rodney Hull
- SAMRC Precision Prevention & Novel Drug Targets for HIV-Associated Cancers Extramural Unit, Pan African Cancer Research Institute, University of Pretoria, Pretoria, South Africa
| | - Sikhumbuzo Z Mbatha
- Department of Surgery, Steve Biko Academic Hospital, University of Pretoria, Pretoria, South Africa
| | - Mohammed Alaouna
- SAMRC Precision Prevention & Novel Drug Targets for HIV-Associated Cancers Extramural Unit, Pan African Cancer Research Institute, University of Pretoria, Pretoria, South Africa.,Department of Internal Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - You-Lin Qiao
- SAMRC Precision Prevention & Novel Drug Targets for HIV-Associated Cancers Extramural Unit, Pan African Cancer Research Institute, University of Pretoria, Pretoria, South Africa.,Cancer Institute/Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, People's Republic of China
| | - Herbert Yu
- SAMRC Precision Prevention & Novel Drug Targets for HIV-Associated Cancers Extramural Unit, Pan African Cancer Research Institute, University of Pretoria, Pretoria, South Africa.,University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Aristotelis Chatziioannou
- SAMRC Precision Prevention & Novel Drug Targets for HIV-Associated Cancers Extramural Unit, Pan African Cancer Research Institute, University of Pretoria, Pretoria, South Africa.,Center of Systems Biology, Biomedical Research Foundation Academy of Athens, Athens, Greece.,e-NIOS Applications PC, Kallithea, Athens, 17676, Greece
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5
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Li H, Liu J, Shen S, Dai D, Cheng S, Dong X, Sun L, Guo X. Pan-cancer analysis of alternative splicing regulator heterogeneous nuclear ribonucleoproteins (hnRNPs) family and their prognostic potential. J Cell Mol Med 2020; 24:11111-11119. [PMID: 32915499 PMCID: PMC7576281 DOI: 10.1111/jcmm.15558] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 05/23/2020] [Accepted: 06/12/2020] [Indexed: 12/12/2022] Open
Abstract
As the most critical alternative splicing regulator, heterogeneous nuclear ribonucleoproteins (hnRNPs) have been reported to be implicated in various aspects of cancer. However, the comprehensive understanding of hnRNPs in cancer is still lacking. The molecular alterations and clinical relevance of hnRNP genes were systematically analysed in 33 cancer types based on next-generation sequence data. The expression, mutation, copy number variation, functional pathways, immune cell correlations and prognostic value of hnRNPs were investigated across different cancer types. HNRNPA1 and HNRNPAB were highly expressed in most tumours. HNRNPM, HNRNPUL1, and HNRNPL showed high mutation frequencies, and most hnRNP genes were frequently mutated in uterine corpus endometrial carcinoma (UCEC). HNRNPA2B1 showed widespread copy number amplification across various cancer types. HNRNPs participated in cancer-related pathways including protein secretion, mitotic spindle, G2/M checkpoint, DNA repair, IL6/JAK/STAT3 signal and coagulation, of which hnRNP genes of HNRNPF, HNRNPH2, HNRNPU and HNRNPUL1 are more likely to be implicated. Significant correlation of hnRNP genes with T help cells, NK cells, CD8 positive T cells and neutrophils was identified. Most hnRNPs were associated with worse survival of adrenocortical carcinoma (ACC), liver hepatocellular carcinoma (LIHC) and lung adenocarcinoma (LUAD), whereas hnRNPs predicted better prognosis in kidney renal clear cell carcinoma (KIRC) and thymoma (THYM). The prognosis analysis of KIRC suggested that hnRNPs gene cluster was significantly associated with overall survival (HR = 0.5, 95% CI = 0.35-0.73, P = 0.003). These findings provide novel evidence for further investigation of hnRNPs in the development and therapy of cancer in the future.
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Affiliation(s)
- Hao Li
- Department of Laboratory MedicineThe First Affiliated Hospital of China Medical UniversityShenyangChina
| | - Jingwei Liu
- Department of Anorectal Surgerythe First Affiliated Hospital of China Medical UniversityShenyangChina
| | - Shixuan Shen
- Tumor Etiology and Screening Department of Cancer Institute and General SurgeryKey Laboratory of Cancer Etiology and PreventionThe First Hospital of China Medical UniversityChina Medical UniversityShenyangChina
| | - Di Dai
- Department of Laboratory MedicineThe First Affiliated Hospital of China Medical UniversityShenyangChina
| | - Shitong Cheng
- Department of Laboratory MedicineThe First Affiliated Hospital of China Medical UniversityShenyangChina
| | - Xiaolong Dong
- Department of Laboratory MedicineThe First Affiliated Hospital of China Medical UniversityShenyangChina
| | - Liping Sun
- Tumor Etiology and Screening Department of Cancer Institute and General SurgeryKey Laboratory of Cancer Etiology and PreventionThe First Hospital of China Medical UniversityChina Medical UniversityShenyangChina
| | - Xiaolin Guo
- Department of Laboratory MedicineThe First Affiliated Hospital of China Medical UniversityShenyangChina
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6
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Zong Z, Li H, Yi C, Ying H, Zhu Z, Wang H. Genome-Wide Profiling of Prognostic Alternative Splicing Signature in Colorectal Cancer. Front Oncol 2018; 8:537. [PMID: 30524964 PMCID: PMC6262947 DOI: 10.3389/fonc.2018.00537] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 10/31/2018] [Indexed: 01/20/2023] Open
Abstract
Background: This study was to explore differential RNA splicing patterns and elucidate the function of the splice variants served as prognostic biomarkers in colorectal cancer (CRC). Methods: Genome-wide profiling of prognostic alternative splicing (AS) events using RNA-seq data from The Cancer Genome Atlas (TCGA) program was conducted to evaluate the roles of seven AS patterns in 330 colorectal cancer cohort. The prognostic predictors models were assessed by integrated Cox proportional hazards regression. Based on the correlations between survival associated AS events and splicing factors, splicing networks were built. Results: A total of 2,158 survival associated AS events in CRC were identified. Interestingly, most of these top 20 survival associated AS events were adverse prognostic factors. The prognostic models were built by each type of splicing patterns, performing well for risk stratification in CRC patients. The area under curve (AUC) of receiver operating characteristic (ROC) for the combined prognostic predictors model could reach 0.963. Splicing network also suggested distinguished correlation between the expression of splicing factors and AS events in CRC patients. Conclusion: The ideal prognostic predictors model for risk stratification in CRC patients was constructed by differential splicing patterns of 13 genes. Our findings enriched knowledge about differential RNA splicing patterns and the regulation of splicing, providing generous biomarker candidates and potential targets for the treatment of CRC.
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Affiliation(s)
- Zhen Zong
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Hui Li
- Department of Rheumatology, The first Affiliated Hospital of Nanchang University, Nanchang, China
| | - Chenghao Yi
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Houqun Ying
- Department of Clinical Laboratory, The Second Affiliated Hospital of Nanchang University (Jiangxi Province Key Laboratory of Laboratory Medicine), Nanchang, China
| | - Zhengming Zhu
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - He Wang
- Department of Cardiovascular Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, China
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7
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Ullah I, Sun W, Tang L, Feng J. Roles of Smads Family and Alternative Splicing Variants of Smad4 in Different Cancers. J Cancer 2018; 9:4018-4028. [PMID: 30410607 PMCID: PMC6218760 DOI: 10.7150/jca.20906] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Accepted: 08/20/2018] [Indexed: 12/15/2022] Open
Abstract
Transforming Growth Factor β (TGF-β) is one of the most common secretory proteins which are recognized by membrane receptors joined to transcription regulatory factor. TGF-β signals are transduced by the Smads family that regulate differentiation, proliferation, early growth, apoptosis, homeostasis, and tumor development. Functional study of TGF-β signaling pathway and Smads role is vital for certain diseases such as cancer. Alternative splicing produces a diverse range of protein isoforms with unique function and the ability to react differently with various pharmaceutical products. This review organizes to describe the general study of Smads family, the process of alternative splicing, the general aspect of alternative splicing of Smad4 in cancer and the possible use of spliceoforms for the diagnosis and therapeutic purpose. The main aim and objective of this article are to highlight some particular mechanisms involving in alternatives splicing of cancer and also to demonstrate new evidence about alternative splicing in different steps given cancer initiation and progression.
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Affiliation(s)
- Irfan Ullah
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China
| | - Weichao Sun
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China
| | - Liling Tang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China
| | - Jianguo Feng
- Department of Anesthesiology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan Province, China
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8
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Ogura Y, Hoshino T, Tanaka N, Ailiken G, Kobayashi S, Kitamura K, Rahmutulla B, Kano M, Murakami K, Akutsu Y, Nomura F, Itoga S, Matsubara H, Matsushita K. Disturbed alternative splicing of FIR (PUF60) directed cyclin E overexpression in esophageal cancers. Oncotarget 2018; 9:22929-22944. [PMID: 29796163 PMCID: PMC5955432 DOI: 10.18632/oncotarget.25149] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 03/22/2018] [Indexed: 02/06/2023] Open
Abstract
Overexpression of alternative splicing of far upstream element binding protein 1 (FUBP1) interacting repressor (FIR; poly(U) binding splicing factor 60 [PUF60]) and cyclin E were detected in esophageal squamous cell carcinomas (ESCC). Accordingly, the expression of FBW7 was examined by which cyclin E is degraded as a substrate via the proteasome system. Expectedly, FBW7 expression was decreased significantly in ESCC. Conversely, c-myc gene transcriptional repressor FIR (alias PUF60; U2AF-related protein) and its alternative splicing variant form (FIRΔexon2) were overexpressed in ESCC. Further, anticancer drugs (cis-diaminedichloroplatinum/cisplatin [CDDP] or 5-fluorouracil [5-FU]) and knockdown of FIR by small interfering RNA (siRNA) increased cyclin E while knockdown of FIRΔexon2 by siRNA decreased cyclin E expression in ESCC cell lines (TE1, TE2, and T.Tn) or cervical SCC cells (HeLa cells). Especially, knockdown of SAP155 (SF3b1), a splicing factor required for proper alternative splicing of FIR pre-mRNA, decreased cyclin E. Therefore, disturbed alternative splicing of FIR generated FIR/FIRΔexon2 with cyclin E overexpression in esophageal cancers, indicating that SAP155 siRNA potentially rescued FBW7 function by reducing expression of FIR and/or FIRΔexon2. Remarkably, Three-dimensional structure analysis revealed the hypothetical inhibitory mechanism of FBW7 function by FIR/FIRΔexon2, a novel mechanism of cyclin E overexpression by FIR/FIRΔexon2-FBW7 interaction was discussed. Clinically, elevated FIR expression potentially is an indicator of the number of lymph metastases and anti-FIR/FIRΔexon2 antibodies in sera as cancer diagnosis, indicating chemical inhibitors of FIR/FIRΔexon2-FBW7 interaction could be potential candidate drugs for cancer therapy. In conclusion, elevated cyclin E expression was, in part, induced owing to potential FIR/FIRΔexon2–FBW7 interaction in ESCC.
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Affiliation(s)
- Yukiko Ogura
- Department of Frontier Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Tyuji Hoshino
- Department of Physical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Nobuko Tanaka
- Department of Laboratory Medicine & Division of Clinical Genetics and Proteomics, Chiba University Hospital, Chiba, Japan
| | - Guzhanuer Ailiken
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Sohei Kobayashi
- Department of Frontier Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan.,Department of Laboratory Medicine & Division of Clinical Genetics and Proteomics, Chiba University Hospital, Chiba, Japan
| | - Kouichi Kitamura
- Department of Laboratory Medicine & Division of Clinical Genetics and Proteomics, Chiba University Hospital, Chiba, Japan.,Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Bahityar Rahmutulla
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Masayuki Kano
- Department of Frontier Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Kentarou Murakami
- Department of Frontier Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Yasunori Akutsu
- Department of Frontier Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Fumio Nomura
- Department of Laboratory Medicine & Division of Clinical Genetics and Proteomics, Chiba University Hospital, Chiba, Japan
| | - Sakae Itoga
- Department of Laboratory Medicine & Division of Clinical Genetics and Proteomics, Chiba University Hospital, Chiba, Japan
| | - Hisahiro Matsubara
- Department of Frontier Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Kazuyuki Matsushita
- Department of Laboratory Medicine & Division of Clinical Genetics and Proteomics, Chiba University Hospital, Chiba, Japan
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9
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Kobayashi S, Hoshino T, Hiwasa T, Satoh M, Rahmutulla B, Tsuchida S, Komukai Y, Tanaka T, Matsubara H, Shimada H, Nomura F, Matsushita K. Anti-FIRs (PUF60) auto-antibodies are detected in the sera of early-stage colon cancer patients. Oncotarget 2018; 7:82493-82503. [PMID: 27756887 PMCID: PMC5347708 DOI: 10.18632/oncotarget.12696] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 10/12/2016] [Indexed: 01/09/2023] Open
Abstract
Anti-PUF60, poly(U)-binding-splicing factor, autoantibodies are reported to be detected in the sera of dermatomyositis and Sjogren's syndrome that occasionally associated with malignancies. PUF60 is identical with far-upstream element-binding protein-interacting repressor (FIR) that is a transcriptional repressor of c-myc gene. In colorectal cancers, a splicing variant of FIR that lacks exon2 (FIRΔexon2) is overexpressed as a dominant negative form of FIR. In this study, to reveal the presence and the significance of anti-FIRs (FIR/FIRΔexon2) antibodies in cancers were explored in the sera of colorectal and other cancer patients. Anti-FIRs antibodies were surely detected in the preoperative sera of 28 colorectal cancer patients (32.2% of positive rates), and the detection rate was significantly higher than that in healthy control sera (Mann-Whitney U test, p < 0.01). The level of anti-FIRs antibodies significantly decreased after the operation (p < 0.01). Anti-FIRs antibodies were detected in the sera of early-stage and/or recurrent colon cancer patients in which anti-p53 antibodies, CEA, and CA19-9 were not detected as well as in the sera of other cancer patients. Furthermore, the area under the curve of receiver operating characteristic for anti-FIRs antibodies was significantly larger (0.85) than that for anti-p53 antibodies or CA19-9. In conclusions, the combination of anti-FIRs antibodies with other clinically available tumor markers further improved the specificity and accuracy of cancer diagnosis.
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Affiliation(s)
- Sohei Kobayashi
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba City, Chiba 260-8670, Japan
| | - Tyuji Hoshino
- Department of Physical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 260-8675, Japan
| | - Takaki Hiwasa
- Department of Biochemistry and Genetics, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Mamoru Satoh
- Divisions of Clinical Mass Spectrometry and Clinical Genetics, Chiba University Hospital, Chiba 260-8670, Japan
| | - Bahityar Rahmutulla
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba City, Chiba 260-8670, Japan.,Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba City, Chiba 260-8670, Japan
| | - Sachio Tsuchida
- Divisions of Clinical Mass Spectrometry and Clinical Genetics, Chiba University Hospital, Chiba 260-8670, Japan
| | - Yuji Komukai
- Department of Physical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 260-8675, Japan
| | - Tomoaki Tanaka
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba City, Chiba 260-8670, Japan
| | - Hisahiro Matsubara
- Department of Academic Surgery, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Hideaki Shimada
- Department of Gastroenterological Surgery, Toho University Omori Medical Center, Tokyo 143-8541, Japan
| | - Fumio Nomura
- Divisions of Clinical Mass Spectrometry and Clinical Genetics, Chiba University Hospital, Chiba 260-8670, Japan
| | - Kazuyuki Matsushita
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba City, Chiba 260-8670, Japan.,Department of Laboratory Medicine & Division of Clinical Genetics and Proteomics Chiba University Hospital, Chiba 260-8670, Japan
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10
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Kozlov AP. Expression of evolutionarily novel genes in tumors. Infect Agent Cancer 2016; 11:34. [PMID: 27437030 PMCID: PMC4949931 DOI: 10.1186/s13027-016-0077-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 05/18/2016] [Indexed: 01/29/2023] Open
Abstract
The evolutionarily novel genes originated through different molecular mechanisms are expressed in tumors. Sometimes the expression of evolutionarily novel genes in tumors is highly specific. Moreover positive selection of many human tumor-related genes in primate lineage suggests their involvement in the origin of new functions beneficial to organisms. It is suggested to consider the expression of evolutionarily young or novel genes in tumors as a new biological phenomenon, a phenomenon of TSEEN (tumor specifically expressed, evolutionarily novel) genes.
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Affiliation(s)
- A. P. Kozlov
- The Biomedical Center and Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
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11
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Adenovirus-mediated FIR demonstrated TP53-independent cell-killing effect and enhanced antitumor activity of carbon-ion beams. Gene Ther 2015; 23:50-6. [PMID: 26241176 DOI: 10.1038/gt.2015.84] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 05/27/2015] [Accepted: 06/18/2015] [Indexed: 12/16/2022]
Abstract
Combination therapy of carbon-ion beam with the far upstream element-binding protein (FBP)-interacting repressor, FIR, which interferes with DNA damage repair proteins, was proposed as an approach for esophageal cancer treatment with low side effects regardless of TP53 status. In vivo therapeutic antitumor efficacy of replication-defective adenovirus (E1 and E3 deleted adenovirus serotype 5) encoding human FIR cDNA (Ad-FIR) was demonstrated in the tumor xenograft model of human esophageal squamous cancer cells, TE-2. Bleomycin (BLM) is an anticancer agent that introduces DNA breaks. The authors reported that Ad-FIR involved in the BLM-induced DNA damage repair response and thus applicable for other DNA damaging agents. To examine the effect of Ad-FIR on DNA damage repair, BLM, X-ray and carbon-ion irradiation were used as DNA damaging agents. The biological effects of high linear energy transfer (LET) radiotherapy used with carbon-ion irradiation are more expansive than low-LET conventional radiotherapy, such as X-rays or γ rays. High LET radiotherapy is suitable for the local control of tumors because of its high relative biological effectiveness. Ad-FIR enhanced BLM-induced DNA damage indicated by γH2AX in vitro. BLM treatment increased endogenous nuclear FIR expression in TE-2 cells, and P27Kip1 expression was suppressed by TP53 siRNA and BLM treatment. Further, Ad-FIRΔexon2, a dominant-negative form of FIR that lacks exon2 transcriptional repression domain, decreased Ku86 expression. The combination of Ad-FIR and BLM in TP53 siRNA increased DNA damage. Additionally, Ad-FIR showed synergistic cell toxicity with X-ray in vitro and significantly increased the antitumor efficacy of carbon-ion irradiation in the xenograft mouse model of TE-2 cells (P=0.03, Mann-Whitney's U-test) and was synergistic with the sensitization enhancement ratio (SER) value of 1.15. Therefore, Ad-FIR increased the cell-killing activity of the carbon-ion beam that avoids late-phase severe adverse effects independently of the TP53 status in vitro. Our findings indicated the feasibility of the combination of Ad-FIR with DNA damaging agents for future esophageal cancer treatment.
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Matsushita K, Kitamura K, Rahmutulla B, Tanaka N, Ishige T, Satoh M, Hoshino T, Miyagi S, Mori T, Itoga S, Shimada H, Tomonaga T, Kito M, Nakajima-Takagi Y, Kubo S, Nakaseko C, Hatano M, Miki T, Matsuo M, Fukuyo M, Kaneda A, Iwama A, Nomura F. Haploinsufficiency of the c-myc transcriptional repressor FIR, as a dominant negative-alternative splicing model, promoted p53-dependent T-cell acute lymphoblastic leukemia progression by activating Notch1. Oncotarget 2015; 6:5102-17. [PMID: 25671302 PMCID: PMC4467136 DOI: 10.18632/oncotarget.3244] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 12/27/2014] [Indexed: 12/22/2022] Open
Abstract
FUSE-binding protein (FBP)-interacting repressor (FIR) is a c-myc transcriptional suppressor. A splice variant of FIR that lacks exon 2 in the transcriptional repressor domain (FIRΔexon2) upregulates c-myc transcription by inactivating wild-type FIR. The ratio of FIRΔexon2/FIR mRNA was increased in human colorectal cancer and hepatocellular carcinoma tissues. Because FIRΔexon2 is considered to be a dominant negative regulator of FIR, FIR heterozygous knockout (FIR⁺/⁻) C57BL6 mice were generated. FIR complete knockout (FIR⁻/⁻) was embryonic lethal before E9.5; therefore, it is essential for embryogenesis. This strongly suggests that insufficiency of FIR is crucial for carcinogenesis. FIR⁺/⁻ mice exhibited prominent c-myc mRNA upregulation, particularly in the peripheral blood (PB), without any significant pathogenic phenotype. Furthermore, elevated FIRΔexon2/FIR mRNA expression was detected in human leukemia samples and cell lines. Because the single knockout of TP53 generates thymic lymphoma, FIR⁺/⁻TP53⁻/⁻ generated T-cell type acute lymphocytic/lymphoblastic leukemia (T-ALL) with increased organ or bone marrow invasion with poor prognosis. RNA-sequencing analysis of sorted thymic lymphoma cells revealed that the Notch signaling pathway was activated significantly in FIR⁺/⁻TP53⁻/⁻ compared with that in FIR⁺/⁺TP53⁻/⁻ mice. Notch1 mRNA expression in sorted thymic lymphoma cells was confirmed using qRT-PCR. In addition, flow cytometry revealed that c-myc mRNA was negatively correlated with FIR but positively correlated with Notch1 in sorted T-ALL/thymic lymphoma cells. Moreover, the knockdown of TP53 or c-myc using siRNA decreased Notch1 expression in cancer cells. In addition, an adenovirus vector encoding FIRΔexon2 cDNA increased bleomycin-induced DNA damage. Taken together, these data suggest that the altered expression of FIRΔexon2 increased Notch1 at least partially by activating c-Myc via a TP53-independent pathway. In conclusion, the alternative splicing of FIR, which generates FIRΔexon2, may contribute to both colorectal carcinogenesis and leukemogenesis.
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Affiliation(s)
- Kazuyuki Matsushita
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Inohana, Chiba, Japan
- Division of Laboratory Medicine, Chiba University Hospital, Inohana, Chiba, Japan
| | - Kouichi Kitamura
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Inohana, Chiba, Japan
- Division of Laboratory Medicine, Chiba University Hospital, Inohana, Chiba, Japan
| | - Bahityar Rahmutulla
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Inohana, Chiba, Japan
| | - Nobuko Tanaka
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Inohana, Chiba, Japan
| | - Takayuki Ishige
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Inohana, Chiba, Japan
- Division of Laboratory Medicine, Chiba University Hospital, Inohana, Chiba, Japan
| | - Mamoru Satoh
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Inohana, Chiba, Japan
| | - Tyuji Hoshino
- Department of Physical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, Inohana, Chiba, Japan
| | - Satoru Miyagi
- Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Inohana, Chuo-ku, Chiba, Japan
| | - Takeshi Mori
- Department of Pediatrics, Graduate School of Medicine, Kobe University, Kusunoki-cho, Kobe, Japan
| | - Sakae Itoga
- Division of Laboratory Medicine, Chiba University Hospital, Inohana, Chiba, Japan
| | - Hideaki Shimada
- Department of Surgery, School of Medicine, Toho University, Omori-nishi, Ota-ku, Tokyo, Japan
| | - Takeshi Tomonaga
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Saito-Asagi, Ibaraki, Osaka, Japan
| | - Minoru Kito
- Oriental Yeast Co., Ltd. Azusawa, Itabashi-ku, Tokyo, Japan
| | - Yaeko Nakajima-Takagi
- Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Inohana, Chuo-ku, Chiba, Japan
| | - Shuji Kubo
- Department of Genetics, Hyogo College of Medicine, Mukogawa-cho, Nishinomiya, Hyogo Prefecture, Japan
| | - Chiaki Nakaseko
- Department of Haematology, Chiba University Hospital, Inohana, Chiba, Japan
| | - Masahiko Hatano
- Department of Biomedical Science, Graduate School of Medicine, Chiba University, Inohana, Chiba, Japan
| | - Takashi Miki
- Department of Medical Physiology, Graduate School of Medicine, Chiba University, Inohana, Chiba, Japan
| | - Masafumi Matsuo
- Department of Pediatrics, Graduate School of Medicine, Kobe University, Kusunoki-cho, Kobe, Japan
- Department of Medical Rehabilitation, Faculty of Rehabilitation, Kobegakuin University, Arise, Ikawadani, Nishi, Kobe, Japan
| | - Masaki Fukuyo
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Inohana, Chiba, Japan
| | - Atsushi Kaneda
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Inohana, Chiba, Japan
| | - Atsushi Iwama
- Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Inohana, Chuo-ku, Chiba, Japan
| | - Fumio Nomura
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Inohana, Chiba, Japan
- Division of Laboratory Medicine, Chiba University Hospital, Inohana, Chiba, Japan
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