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Fischer M. Gene regulation by the tumor suppressor p53 - The omics era. Biochim Biophys Acta Rev Cancer 2024; 1879:189111. [PMID: 38740351 DOI: 10.1016/j.bbcan.2024.189111] [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: 11/27/2023] [Revised: 05/08/2024] [Accepted: 05/10/2024] [Indexed: 05/16/2024]
Abstract
The transcription factor p53 is activated in response to a variety of cellular stresses and serves as a prominent and potent tumor suppressor. Since its discovery, we have sought to understand how p53 functions as both a transcription factor and a tumor suppressor. Two decades ago, the field of gene regulation entered the omics era and began to study the regulation of entire genomes. The omics perspective has greatly expanded our understanding of p53 functions and has begun to reveal its gene regulatory network. In this mini-review, I discuss recent insights into the p53 transcriptional program from high-throughput analyses.
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Affiliation(s)
- Martin Fischer
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany.
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Kamikokura M, Tange S, Nakase H, Tokino T, Idogawa M. Long Noncoding RNA RP11-278A23.1, a Potential Modulator of p53 Tumor Suppression, Contributes to Colorectal Cancer Progression. Cancers (Basel) 2024; 16:882. [PMID: 38473243 DOI: 10.3390/cancers16050882] [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: 01/09/2024] [Revised: 02/15/2024] [Accepted: 02/19/2024] [Indexed: 03/14/2024] Open
Abstract
Recently, many studies revealed that long noncoding RNAs (lncRNAs) play important roles in cancers. To identify lncRNAs contributing to colorectal cancers, we screened lncRNAs through expression and survival analyses in datasets from The Cancer Genome Atlas (TCGA). The screen revealed that RP11-278A23.1 expression is significantly increased in colorectal cancer tissues compared with normal tissues and that high RP11-278A23.1 expression correlates with poor prognosis. The knockdown of RP11-278A23.1 inhibited the growth of and promoted apoptosis in colorectal cancer cells. Next, to comprehensively examine differentially expressed genes after RP11-278A23.1 knockdown, RNA sequencing was performed in HCT116 cells. The expression of p21, a p53 target gene, was significantly upregulated, and the expression of several p53 target proapoptotic genes was also altered. RP11-278A23.1 knockdown increased p53 expression at the translational level but not at the transcriptional level. Interestingly, RP11-278A23.1 knockdown also altered the expression of these proapoptotic genes in DLD1 cells with mutated p53 and in p53-knockout HCT116 cells. These results suggest that RP11-278A23.1 modifies the expression of these apoptosis-related genes in p53-dependent and p53-independent manners. In summary, lncRNA RP11-278A23.1 contributes to colorectal cancer progression by promoting cell growth and inhibiting apoptosis, suggesting that this lncRNA may be a useful therapeutic target.
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Affiliation(s)
- Masayo Kamikokura
- Department of Medical Genome Sciences, Cancer Research Institute, Sapporo Medical University School of Medicine, Sapporo 060-8556, Japan
| | - Shoichiro Tange
- Department of Medical Genome Sciences, Cancer Research Institute, Sapporo Medical University School of Medicine, Sapporo 060-8556, Japan
| | - Hiroshi Nakase
- Department of Gastroenterology and Hepatology, Sapporo Medical University School of Medicine, Sapporo 060-8556, Japan
| | - Takashi Tokino
- Department of Medical Genome Sciences, Cancer Research Institute, Sapporo Medical University School of Medicine, Sapporo 060-8556, Japan
| | - Masashi Idogawa
- Department of Medical Genome Sciences, Cancer Research Institute, Sapporo Medical University School of Medicine, Sapporo 060-8556, Japan
- Department of Gastroenterology and Hepatology, Sapporo Medical University School of Medicine, Sapporo 060-8556, Japan
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Liu B, Song A, Gui P, Wang J, Pan Y, Li C, Li S, Zhang Y, Jiang T, Xu Y, Pei D, Song J. Long noncoding RNA LINC01594 inhibits the CELF6-mediated splicing of oncogenic CD44 variants to promote colorectal cancer metastasis. Cell Death Dis 2023; 14:427. [PMID: 37452042 PMCID: PMC10349055 DOI: 10.1038/s41419-023-05924-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 06/16/2023] [Accepted: 06/23/2023] [Indexed: 07/18/2023]
Abstract
Long noncoding RNAs (lncRNAs) play critical roles in tumorigenesis and tumor metastasis. However, the underlying mechanisms of lncRNAs in colorectal cancer (CRC) need further exploration. By using data from The Cancer Genome Atlas (TCGA) and GEO databases, we identified a novel CRC-related lncRNA, LINC01594, that is significantly upregulated in CRC and associated with poor prognosis. In vitro and in vivo, gain- and loss-of-function experiments demonstrated that LINC01594 promotes metastasis in CRC. LINC01594 functions as a DNMT1 scaffold, increasing the level of CELF6 promoter methylation. LINC01594 also competitively binds the transcription factor p53, decreasing CELF6 expression. This inhibited the exon skipping of CD44 V4-V7 induced by CELF6. In summary, this study highlights a novel CRC biomarker and therapeutic target, LINC01594, and the findings suggest that the LINC01594-CELF6-CD44 axis might serve as a biomarker and therapeutic target in CRC.
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Affiliation(s)
- Bowen Liu
- Department of General Surgery, The Affiliated Hospital of Xuzhou Medical University. No. 99, Huaihai West Road, Quanshan District, Xuzhou, 221006, China
- Institute of Digestive Diseases, Xuzhou Medical University. No. 84, Huaihai West Road, Quanshan District, Xuzhou, 221002, China
| | - Angxi Song
- Institute of Digestive Diseases, Xuzhou Medical University. No. 84, Huaihai West Road, Quanshan District, Xuzhou, 221002, China
| | - Pengkun Gui
- Institute of Digestive Diseases, Xuzhou Medical University. No. 84, Huaihai West Road, Quanshan District, Xuzhou, 221002, China
| | - Jin Wang
- Department of Pathology, Xuzhou Medical University. No. 209, Tongshan Road, Yunlong District, Xuzhou, 221004, China
| | - Yaojie Pan
- Department of Medical Oncology, Zhejiang Provincial People's Hospital. No. 158, Shangtang Road, Xiacheng District, Zhejiang, 310000, China
| | - Chao Li
- Department of General Surgery, The Affiliated Hospital of Xuzhou Medical University. No. 99, Huaihai West Road, Quanshan District, Xuzhou, 221006, China
- Institute of Digestive Diseases, Xuzhou Medical University. No. 84, Huaihai West Road, Quanshan District, Xuzhou, 221002, China
| | - Shuai Li
- Department of General Surgery, The Affiliated Hospital of Xuzhou Medical University. No. 99, Huaihai West Road, Quanshan District, Xuzhou, 221006, China
- Institute of Digestive Diseases, Xuzhou Medical University. No. 84, Huaihai West Road, Quanshan District, Xuzhou, 221002, China
| | - Yi Zhang
- Department of General Surgery, The Affiliated Hospital of Xuzhou Medical University. No. 99, Huaihai West Road, Quanshan District, Xuzhou, 221006, China
- Institute of Digestive Diseases, Xuzhou Medical University. No. 84, Huaihai West Road, Quanshan District, Xuzhou, 221002, China
| | - Tao Jiang
- Department of General Surgery, The Affiliated Hospital of Xuzhou Medical University. No. 99, Huaihai West Road, Quanshan District, Xuzhou, 221006, China
- Institute of Digestive Diseases, Xuzhou Medical University. No. 84, Huaihai West Road, Quanshan District, Xuzhou, 221002, China
| | - Yixin Xu
- Department of General Surgery, The Affiliated Hospital of Xuzhou Medical University. No. 99, Huaihai West Road, Quanshan District, Xuzhou, 221006, China
- Institute of Digestive Diseases, Xuzhou Medical University. No. 84, Huaihai West Road, Quanshan District, Xuzhou, 221002, China
| | - Dongsheng Pei
- Department of Pathology, Xuzhou Medical University. No. 209, Tongshan Road, Yunlong District, Xuzhou, 221004, China.
| | - Jun Song
- Department of General Surgery, The Affiliated Hospital of Xuzhou Medical University. No. 99, Huaihai West Road, Quanshan District, Xuzhou, 221006, China.
- Institute of Digestive Diseases, Xuzhou Medical University. No. 84, Huaihai West Road, Quanshan District, Xuzhou, 221002, China.
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Tange S, Hirano T, Idogawa M, Hirata E, Imoto I, Tokino T. MYEOV overexpression induced by demethylation of its promoter contributes to pancreatic cancer progression via activation of the folate cycle/c-Myc/mTORC1 pathway. BMC Cancer 2023; 23:85. [PMID: 36698109 PMCID: PMC9875418 DOI: 10.1186/s12885-022-10433-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 12/12/2022] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND While molecular targeted drugs and other therapies are being developed for many tumors, pancreatic cancer is still considered to be the malignant tumor with the worst prognosis. We started this study to identify prognostic genes and therapeutic targets of pancreatic cancer. METHODS To comprehensively identify prognostic genes in pancreatic cancer, we investigated the correlation between gene expression and cancer-specific prognosis using transcriptome and clinical information datasets from The Cancer Genome Atlas (TCGA). In addition, we examined the effects of the suppression of candidate prognostic genes in pancreatic cancer cell lines. RESULT We found that patients with high expression levels of MYEOV, a primate-specific gene with unknown function, had significantly shorter disease-specific survival times than those with low expression levels. Cox proportional hazards analysis revealed that high expression of MYEOV was significantly associated with poor survival and was an independent prognostic factor for disease-specific survival in pancreatic cancer patients. Analysis of multiple cancer samples revealed that the MYEOV promoter region is methylated in noncancer tissues but is demethylated in tumors, causing MYEOV overexpression in tumors. Notably, the knockdown of MYEOV suppressed the expression of MTHFD2 and other folate metabolism-related enzyme genes required for the synthesis of amino acids and nucleic acids and also restored the expression of c-Myc and mTORC1 repressors. CONCLUSION There is a significant correlation between elevated MYEOV expression and poor disease-specific survival in pancreatic cancer patients. MYEOV enhances the activation of several oncogenic pathways, resulting in the induction of pancreatic cancer cell proliferation. Overall, MYEOV acts as an oncogene in pancreatic cancer. Furthermore, MYEOV may be a prognostic biomarker and serve as an 'actionable' therapeutic target for pancreatic cancers.
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Affiliation(s)
- Shoichiro Tange
- grid.263171.00000 0001 0691 0855Department of Medical Genome Sciences, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, S1W17, Chuo-ku, Sapporo, 060-8556 Japan
| | - Tomomi Hirano
- grid.263171.00000 0001 0691 0855Department of Medical Genome Sciences, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, S1W17, Chuo-ku, Sapporo, 060-8556 Japan
| | - Masashi Idogawa
- grid.263171.00000 0001 0691 0855Department of Medical Genome Sciences, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, S1W17, Chuo-ku, Sapporo, 060-8556 Japan ,grid.263171.00000 0001 0691 0855Department of Gastroenterology and Hepatology, Sapporo Medical University School of Medicine, S1W16, Chuo-ku, Sapporo, 060-8543 Japan
| | - Eishu Hirata
- grid.9707.90000 0001 2308 3329Division of Tumor Cell Biology and Bioimaging, Cancer Research Institute, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192 Japan
| | - Issei Imoto
- grid.410800.d0000 0001 0722 8444Aichi Cancer Center Research Institute, 1-1 Kanokoden, Chikusa-ku, Nagoya, 464-8681 Japan
| | - Takashi Tokino
- grid.263171.00000 0001 0691 0855Department of Medical Genome Sciences, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, S1W17, Chuo-ku, Sapporo, 060-8556 Japan
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Critical role of HOX transcript antisense intergenic RNA (HOTAIR) in gliomas. J Mol Med (Berl) 2020; 98:1525-1546. [PMID: 32978667 DOI: 10.1007/s00109-020-01984-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 09/17/2020] [Accepted: 09/22/2020] [Indexed: 02/07/2023]
Abstract
Despite extensive research, gliomas are associated with high morbidity and mortality, mainly attributed to the rapid growth rate, excessive invasiveness, and molecular heterogeneity, as well as regenerative potential of cancer stem cells. Therefore, elucidation of the underlying molecular mechanisms and the identification of potential molecular diagnostic and prognostic biomarkers are of paramount importance. HOX transcript antisense intergenic RNA (HOTAIR) is a well-studied long noncoding RNA, playing an emerging role in tumorigenesis of several human cancers. A growing amount of preclinical and clinical evidence highlights the pro-oncogenic role of HOTAIR in gliomas, mainly attributed to the enhancement of proliferation and migration, as well as inhibition of apoptosis. In vitro and in vivo studies demonstrate that HOTAIR modulates the activity of specific transcription factors, such as MXI1, E2F1, ATF5, and ASCL1, and regulates the expression of cell cycle-associated genes along with related signaling pathways, like the Wnt/β-catenin axis. Moreover, it can interact with specific miRNAs, including miR-326, miR-141, miR-148b-3p, miR-15b, and miR-126-5p. Of importance, HOTAIR has been demonstrated to enhance angiogenesis and affect the permeability of the blood-tumor barrier, thus modulating the efficacy of chemotherapeutic agents. Herein, we provide evidence on the functional role of HOTAIR in gliomas and discuss the benefits of its targeting as a novel approach toward glioma treatment.
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