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Turyova E, Mikolajcik P, Grendar M, Kudelova E, Holubekova V, Kalman M, Marcinek J, Hrnciar M, Kovac M, Miklusica J, Laca L, Lasabova Z. Expression of OCT4 isoforms is reduced in primary colorectal cancer. Front Oncol 2023; 13:1166835. [PMID: 37409260 PMCID: PMC10319064 DOI: 10.3389/fonc.2023.1166835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 05/02/2023] [Indexed: 07/07/2023] Open
Abstract
Introduction Colorectal cancer (CRC) is one of the most common types of cancer worldwide. The carcinogenesis of CRC is indeed complex, and there are many different mechanisms and pathways that contribute to the development of malignancy and the progression from primary to metastatic tumors. The OCT4A, encoded by the POU5F1 gene, is a transcription factor responsible for the phenotype of stem cells, maintaining pluripotency and regulation of differentiation. The POU5F1 gene is made up of five exons that can create numerous isoforms through alternative promoter or alternative splicing. In addition to OCT4A, other isoforms called OCT4B are also translated into protein; however, their role in cells has been unclear. The aim of our work was to investigate the expression patterns of OCT4 isoforms in primary and metastatic CRC, providing us with useful information about their role in the development and progression of CRC. Methods Surgical specimens from a total of 78 patients were collected and isolated from primary tumors (n = 47) and metastases (n = 31). The relative gene expression of OCT4 isoforms was investigated using the RT-qPCR method together with the TaqMan probes for particular OCT4 isoforms. Results Our results suggest significantly downregulated expression of the OCT4A and OCT4Bs isoforms in both primary (p = 0.0002 and p < 0.0001, respectively) and metastatic tumors (p = 0.0006 and p = 0.00051, respectively) when compared with the control samples. We also observed a correlation between reduced expression of all OCT4 isoforms and both primary and left-sided tumors (p = 0.001 and p = 0.030, respectively). On the other hand, the expression of all OCT4 isoforms was significantly upregulated in metastases compared with primary tumors (p < 0.0001). Discussion Unlike previous reports, we found out that the expression of OCT4A, OCT4Bs, and all OCT4 isoforms was significantly reduced in primary tumors and metastases compared with control samples. On the other hand, we supposed that the expression rate of all OCT4 isoforms may be related to the cancer type and side, as well as to liver metastases. However, further studies are required to investigate the detailed expression patterns and significance of individual OCT4 isoforms in carcinogenesis.
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Affiliation(s)
- Eva Turyova
- Department of Molecular Biology and Genomics, Jessenius Faculty of Medicine in Martin, Comenius University Bratislava, Martin, Slovakia
| | - Peter Mikolajcik
- Clinic of Surgery and Transplant Center, Jessenius Faculty of Medicine in Martin and University Hospital Martin, Comenius University Bratislava, Martin, Slovakia
| | - Marian Grendar
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University Bratislava, Martin, Slovakia
| | - Eva Kudelova
- Clinic of Surgery and Transplant Center, Jessenius Faculty of Medicine in Martin and University Hospital Martin, Comenius University Bratislava, Martin, Slovakia
| | - Veronika Holubekova
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University Bratislava, Martin, Slovakia
| | - Michal Kalman
- Department of Pathological Anatomy, Jessenius Faculty of Medicine in Martin and University Hospital Martin, Comenius University Bratislava, Martin, Slovakia
| | - Juraj Marcinek
- Department of Pathological Anatomy, Jessenius Faculty of Medicine in Martin and University Hospital Martin, Comenius University Bratislava, Martin, Slovakia
| | - Matej Hrnciar
- Department of Informatics, Information Systems and Software Engineering, Faculty of Informatics and Information Technologies, Slovak University of Technology, Bratislava, Slovakia
| | - Michal Kovac
- Department of Informatics, Information Systems and Software Engineering, Faculty of Informatics and Information Technologies, Slovak University of Technology, Bratislava, Slovakia
| | - Juraj Miklusica
- Clinic of Surgery and Transplant Center, Jessenius Faculty of Medicine in Martin and University Hospital Martin, Comenius University Bratislava, Martin, Slovakia
| | - Ludovit Laca
- Clinic of Surgery and Transplant Center, Jessenius Faculty of Medicine in Martin and University Hospital Martin, Comenius University Bratislava, Martin, Slovakia
| | - Zora Lasabova
- Department of Molecular Biology and Genomics, Jessenius Faculty of Medicine in Martin, Comenius University Bratislava, Martin, Slovakia
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Fouani Y, Gholipour A, Oveisee M, Shahryari A, Saberi H, Mowla SJ, Malakootian M. Distinct gene expression patterns of SOX2 and SOX2OT variants in different types of brain tumours. J Genet 2023. [DOI: 10.1007/s12041-023-01423-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
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Bagheri Moghaddam M, Maleki M, Oveisee M, Bagheri Moghaddam M, Arabian M, Malakootian M. Circular RNAs: New Players in Cardiomyopathy. Genes (Basel) 2022; 13:genes13091537. [PMID: 36140705 PMCID: PMC9498503 DOI: 10.3390/genes13091537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/20/2022] [Accepted: 08/22/2022] [Indexed: 11/16/2022] Open
Abstract
Cardiomyopathies comprise a heterogeneous group of cardiac diseases identified by myocardium disorders and diminished cardiac function. They often lead to heart failure or heart transplantation and constitute one of the principal causes of morbidity and mortality worldwide. Circular RNAs (circRNAs) are a novel type of noncoding RNAs. They are covalently closed and single-stranded and derived from the exons and introns of genes by alternative splicing. This specific structure renders them resistant to exonuclease digestion. Many recent studies have demonstrated that circRNAs are highly abundant and conserved and can play central roles in biological functions such as microRNA (miRNA) sponging, splicing, and transcription regulation. Emerging evidence indicates that circRNAs can play significant roles in cardiovascular diseases, including cardiomyopathies. In this review, we briefly describe the current understanding regarding the classification, nomenclature, characteristics, and function of circRNAs and report recent significant findings concerning the roles of circRNAs in cardiomyopathies. Furthermore, we discuss the clinical application potential of circRNAs as the therapeutic targets and diagnostic biomarkers of cardiomyopathies.
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Affiliation(s)
- Maedeh Bagheri Moghaddam
- Molecular Genetics Department, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 141171311, Iran
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran 1995614331, Iran
| | - Majid Maleki
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran 1995614331, Iran
| | - Maziar Oveisee
- School of Medicine, Bam University of Medical Sciences, Bam 7661771967, Iran
| | - Mahrokh Bagheri Moghaddam
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran 1995614331, Iran
| | - Maedeh Arabian
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran 1995614331, Iran
| | - Mahshid Malakootian
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran 1995614331, Iran
- Correspondence: ; Tel.: +98-2123923033; Fax: +98-2122663213
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Zhou RT, Ni YR, Zeng FJ. The roles of long noncoding RNAs in the regulation of OCT4 expression. Stem Cell Res Ther 2022; 13:383. [PMID: 35907897 PMCID: PMC9338536 DOI: 10.1186/s13287-022-03059-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 07/19/2022] [Indexed: 12/13/2022] Open
Abstract
OCT4 is a major transcription factor that maintains the pluripotency of stem cells, including embryonic stem cells, induced pluripotent stem cells and cancer stem cells. An increasing number of long noncoding RNAs have been reported to participate in the regulation of OCT4 expression through various mechanisms, including binding with the OCT4 gene promoter to regulate local methylation; promoting chromosomal spatial folding to form an inner ring, thereby aggregating OCT4 cis-acting elements scattered in discontinuous sites of the chromosome; competitively binding microRNAs with OCT4 to upregulate OCT4 expression at the posttranscriptional level; and sharing a promoter with OCT4. Moreover, the transcription of some long noncoding RNAs is regulated by OCT4, and certain long noncoding RNAs form feedback regulatory loops with OCT4. In this review, we summarized the research progress of the long noncoding RNAs involved in the regulation of OCT4 expression.
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Affiliation(s)
- Rui-Ting Zhou
- The First College of Clinical Medical Science, China Three Gorges University, Yichang, 443003, Hubei, China.,Yichang Central People's Hospital, Yichang, 443003, Hubei, China.,Medical College, China Three Gorges University, Yichang, 443002, Hubei, China
| | - Yi-Ran Ni
- Medical College, China Three Gorges University, Yichang, 443002, Hubei, China.,Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, 443002, Hubei, China
| | - Fan-Jun Zeng
- The First College of Clinical Medical Science, China Three Gorges University, Yichang, 443003, Hubei, China. .,Yichang Central People's Hospital, Yichang, 443003, Hubei, China.
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Yasui R, Matsui A, Sekine K, Okamoto S, Taniguchi H. Highly Sensitive Detection of Human Pluripotent Stem Cells by Loop-Mediated Isothermal Amplification. Stem Cell Rev Rep 2022; 18:2995-3007. [PMID: 35661077 PMCID: PMC9622575 DOI: 10.1007/s12015-022-10402-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/20/2022] [Indexed: 11/24/2022]
Abstract
For safe regenerative medicines, contaminated or remaining tumorigenic undifferentiated cells in cell-derived products must be rigorously assessed through sensitive assays. Although in vitro nucleic acid tests offer particularly sensitive tumorigenicity-associated assays, the human pluripotent stem cell (hPSC) detectability is partly constrained by the small input amount of RNA per test. To overcome this limitation, we developed reverse transcription loop-mediated isothermal amplification (RT-LAMP) assays that are highly gene specific and robust against interfering materials. LAMP could readily assay microgram order of input sample per test and detected an equivalent model of 0.00002% hiPSC contamination in a simple one-pot reaction. For the evaluation of cell-derived total RNA, RT-LAMP detected spiked-in hPSCs among hPSC-derived trilineage cells utilizing multiple pluripotency RNAs. We also developed multiplex RT-LAMP assays and further applied for in situ cell imaging, achieving specific co-staining of pluripotency proteins and RNAs. Our attempts uncovered the utility of RT-LAMP approaches for tumorigenicity-associated assays, supporting practical applications of regenerative medicine.
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Affiliation(s)
- Ryota Yasui
- Department of Regenerative Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, 236-0004, Japan
- Fundamental Research Laboratory, Eiken Chemical Co., Ltd., Nogi, Tochigi, 329-0114, Japan
| | - Atsuka Matsui
- Biochemical Research Laboratory, Eiken Chemical Co., Ltd., Ohtawara, Tochigi, 324-0036, Japan
| | - Keisuke Sekine
- Department of Regenerative Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, 236-0004, Japan.
- Laboratory of Cancer Cell Systems, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.
| | - Satoshi Okamoto
- Department of Regenerative Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, 236-0004, Japan
- Division of Regenerative Medicine, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Hideki Taniguchi
- Department of Regenerative Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, 236-0004, Japan.
- Division of Regenerative Medicine, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan.
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6
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Taheri Bajgan E, Gholipour A, Faghihi M, Mowla SJ, Malakootian M. Linc-ROR has a Potential ceRNA Activity for OCT4A by Sequestering miR-335-5p in the HEK293T Cell Line. Biochem Genet 2021; 60:1007-1024. [PMID: 34669056 DOI: 10.1007/s10528-021-10140-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 10/07/2021] [Indexed: 12/26/2022]
Abstract
Linc-ROR has a regulatory role in reprogramming, and the core stem cell transcription factors, OCT4, SOX2, and NANOG, regulate its expression. MicroRNAs (miRNAs) are also a critical constituent of pivotal posttranscriptional regulatory pathways. One of such interactions is a competing endogenous RNA interaction that connects small and long non-coding RNAs with coding transcripts. Here, we aimed to investigate the existence of such associations between OCT4A, Linc-ROR, hsa-miR-335-5p, and hsa-miR-544. Bioinformatic analysis was performed to evaluate the expression status of OCT4A, Linc-ROR, miR-335, and miR-544 throughout differentiation as well as in various differentiated cells. The complete lengths of OCT4A and Linc-ROR, and OCT4A 3'-UTR were cloned in the luciferase reporter vector, and the precursors of miR-335 and miR-544 were cloned in expression vectors. Following the overexpression of miR-335 and miR-544 in the 5637 cell line, the endogenous expression of OCT4A and Linc-ROR was evaluated. Afterward, the expression vectors of miRNAs and the reporter vectors of OCT4A/Linc-ROR were co-transfected in the HEK293T cell line. Via the Dual-Luciferase assay, the effect of the overexpression of miRNAs on their two possible targets (Linc-ROR and OCT4A) was investigated. The bioinformatic analysis demonstrated a relatively similar expression pattern for OCT4A and Linc-ROR, while miR-335 showed a different expression status. Both miR-335 and miR-544 inhibited the endogenous expression of OCT4A. The Dual-Luciferase assay likewise confirmed the inhibitory effect of miR-335 and miR-544 on OCT4A expression. In contrast, the miR-335 inhibitory effect was reversed in the presence of Linc-ROR, resulting in the upregulation of OCT4A. Such evidence suggests that Linc-ROR may compete with OCT4A to interact with miR-335.
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Affiliation(s)
- Elham Taheri Bajgan
- Molecular Genetics Department, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Akram Gholipour
- Department of Biology, Islamic Azad University Tehran Science and Research Branch, Tehran, Iran
| | - Mohammadali Faghihi
- Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, 33136, USA
| | - Seyed Javad Mowla
- Molecular Genetics Department, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mahshid Malakootian
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran.
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Mehravar M, Ghaemimanesh F, Poursani EM. An Overview on the Complexity of OCT4: at the Level of DNA, RNA and Protein. Stem Cell Rev Rep 2021; 17:1121-1136. [PMID: 33389631 DOI: 10.1007/s12015-020-10098-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/25/2020] [Indexed: 10/22/2022]
Abstract
OCT4 plays critical roles in self-renewal and pluripotency maintenance of embryonic stem cells, and is considered as one of the main stemness markers. It also has pivotal roles in early stages of embryonic development. Most studies on OCT4 have focused on the expression and function of OCT4A, which is the biggest isoform of OCT4 known so far. Recently, many studies have shown that OCT4 has various transcript variants, protein isoforms, as well as pseudogenes. Distinguishing the expression and function of these variants and isoforms is a big challenge in expression profiling studies of OCT4. Understanding how OCT4 is functioning in different contexts, depends on knowing of where and when each of OCT4 transcripts, isoforms and pseudogenes are expressed. Here, we review OCT4 known transcripts, isoforms and pseudogenes, as well as its interactions with other proteins, and emphasize the importance of discriminating each of them in order to understand the exact function of OCT4 in stem cells, normal development and development of diseases.
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Affiliation(s)
- Majid Mehravar
- Department of Anatomy and Developmental Biology, Development and Stem Cells Program, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Fatemeh Ghaemimanesh
- Monoclonal Antibody Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Ensieh M Poursani
- Hematology, Oncology and Stem Cell Transplantation Research Center, Tehran University of Medical Sciences, Tehran, Iran.
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8
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Mehravar M, Poursani EM. Novel Variant of OCT4, Named OCT4B5, is Highly Expressed in Human Pluripotent Cells. Stem Cell Rev Rep 2020; 17:1068-1073. [PMID: 33241484 DOI: 10.1007/s12015-020-10093-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/19/2020] [Indexed: 10/22/2022]
Abstract
Alternative promoter and alternative splicing are two important mechanisms of gene regulation and protein diversity in different physiological contexts of eukaryotes, especially in stem cells and developmental stages. Pou5f1 gene which codes the stemness marker OCT4, utilizes alternative splicing and promoter mechanisms, which result in generation of multiple spliced variants and subsequently multiple protein isoforms. By far, nine variants of OCT4 (OCT4A, OCT4B, OCT4B1, OCT4B2, OCT4B3, OCT4B4, OCT4C, OCT4C1, and OCT4D) have been introduced. It has been well established that OCT4A plays essential roles in early developmental stages as well as maintenance of stemness in embryonic stem cells (ESCs). However, the roles and functions of other variants and isoforms of OCT4 in biological systems are less appreciated. In this study, we report a new OCT4 variant, designated as OCT4B5. RT-PCR assay on different human cell lines including pluripotent, normal and cancer cells showed that OCT4B5 is expressed at variable level in different cell lines. By semi-quantifying of OCT4B5 expression in pluripotent and differentiated states of NT2 cell lines, we reveal that this variant of OCT4 is highly expressed in undifferentiated state and its expression is down-regulated upon differentiation. Compared to OCT4A which is sharply down-regulated in retinoic acid induced differentiation of NT2 cell line, the expression of OCT4B5 remains at low level in differentiated state. Overall, this study emphasizes the complexity of OCT4 gene expression and regulation in different states of stem cells and physiological contexts. Graphical Abstract.
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Affiliation(s)
- Majid Mehravar
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Ensieh M Poursani
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran. .,Hematology/Oncology and Stem Cell Transplantation Research Center, Tehran University of Medical Sciences, Tehran, Iran.
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Clemente-Periván SI, Gómez-Gómez Y, Leyva-Vázquez MA, Lagunas-Martínez A, Organista-Nava J, Illades-Aguiar B. Role of Oct3/4 in Cervical Cancer Tumorigenesis. Front Oncol 2020; 10:247. [PMID: 32219062 PMCID: PMC7079573 DOI: 10.3389/fonc.2020.00247] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 02/13/2020] [Indexed: 12/16/2022] Open
Abstract
Cervical cancer (CC) is the fourth most common type of cancer that affects women. Compared to other types of cancer, CC has a high mortality rate in women worldwide. Several factors contribute to the development of CC, but persistent high-risk human papillomavirus infection is the main etiologic agent associated with the development of CC. Moreover, several studies reported that alterations in the expression of transcription factors present in a small subpopulation of cells within tumors called cancer stem cells (CSCs), which contribute to the development of CC by promoting tumorigenicity and metastasis. These transcription factors affect self-renewal and maintenance of pluripotency and differentiation in stem cells. OCT3/4 belongs to the family of transcription factors with the POU domain. It consists of five exons and can be edited by alternative splicing into three main transcripts: OCT3/4A, OCT3/4B, and OCT3/4B1. The OCT3/4 expression in CSCs promotes carcinogenesis and the development of malignant tumors, and the loss of expression leads to the loss of self-renewal and proliferation and favors apoptosis. This review describes the main roles of OCT3/4 in CC and its importance in several biological processes that contribute to the development of CC and may serve as molecular targets to improve prognosis of CC.
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Affiliation(s)
- Sayuri Itzel Clemente-Periván
- Laboratorio de Biomedicina Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo, Mexico
| | - Yazmín Gómez-Gómez
- Laboratorio de Biomedicina Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo, Mexico
| | - Marco Antonio Leyva-Vázquez
- Laboratorio de Biomedicina Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo, Mexico
| | - Alfredo Lagunas-Martínez
- Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Mexico
| | - Jorge Organista-Nava
- Laboratorio de Biomedicina Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo, Mexico
| | - Berenice Illades-Aguiar
- Laboratorio de Biomedicina Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo, Mexico
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Mirzadeh Azad F, Arabian M, Maleki M, Malakootian M. Small Molecules with Big Impacts on Cardiovascular Diseases. Biochem Genet 2020; 58:359-383. [PMID: 31997044 DOI: 10.1007/s10528-020-09948-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Accepted: 01/13/2020] [Indexed: 12/22/2022]
Abstract
Cardiovascular diseases (CVDs) are the leading cause of morbidity and mortality worldwide. Although in recent years there has been a significant progress in the diagnosis, treatment, and prognosis of CVD, but due to their complex pathobiology, developing novel biomarkers and therapeutic interventions are still in need. MicroRNAs (miRNAs) are a fraction of non-coding RNAs that act as micro-regulators of gene expression. Mounting evidences over the last decade confirmed that microRNAs were deregulated in several CVDs and manipulating their expression could affect homeostasis, differentiation, and function of cardiovascular system. Here, we review the current knowledge concerning the roles of miRNAs in cardiovascular diseases with more details on cardiac remodeling, arrhythmias, and atherosclerosis. In addition, we discuss the latest findings on the potential therapeutic applications of miRNAs in cardiovascular diseases.
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Affiliation(s)
- Fatemeh Mirzadeh Azad
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Maedeh Arabian
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Majid Maleki
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Mahshid Malakootian
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran.
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lncRNA PSORS1C3 is regulated by glucocorticoids and fine-tunes OCT4 expression in non-pluripotent cells. Sci Rep 2019; 9:8370. [PMID: 31182783 PMCID: PMC6557835 DOI: 10.1038/s41598-019-44827-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 05/20/2019] [Indexed: 11/29/2022] Open
Abstract
OCT4 is a transcription factor known for its regulatory roles in stemness, tumorigenesis and stress response. Considering its versatile functions, expression of OCT4 is regulated at different levels. PSORS1C3, a long non-coding RNA overlapped with OCT4, has a putative association with immune mediated diseases; however, its exact functions remained to be elucidated. Here, we demonstrated that PSORS1C3 is regulated by glucocorticoids (GC), has two endogenously active promoters, promoter 0 and 1, and two sets of transcripts, short and long variants. According to our findings, PSORS1C3 promoters behaved differently during neural differentiation of NT2 cells and glucocorticoid receptor (GR) activation. In both processes the expression pattern of short variants differed from that of long variants and was similar to OCT4 expression. Furthermore, our data revealed that PSORS1C3’s promoter 0 could act as an enhancer for OCT4 in non-pluripotent cells, where its deletion caused a significant decrease in OCT4 expression. Meanwhile, during GR activation promoter 0 functioned as a negative regulator and alleviated transcription induction of OCT4 after GC treatment. Altogether, our work clarified the structure and regulation of PSORS1C3, explained its relation to immune-related disease through GR signaling and introduced it as a novel fine-tuner of OCT4 expression in non-pluripotent cells.
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12
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Siebenthall KT, Miller CP, Vierstra JD, Mathieu J, Tretiakova M, Reynolds A, Sandstrom R, Rynes E, Haugen E, Johnson A, Nelson J, Bates D, Diegel M, Dunn D, Frerker M, Buckley M, Kaul R, Zheng Y, Himmelfarb J, Ruohola-Baker H, Akilesh S. Integrated epigenomic profiling reveals endogenous retrovirus reactivation in renal cell carcinoma. EBioMedicine 2019; 41:427-442. [PMID: 30827930 PMCID: PMC6441874 DOI: 10.1016/j.ebiom.2019.01.063] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Revised: 01/30/2019] [Accepted: 01/31/2019] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Transcriptional dysregulation drives cancer formation but the underlying mechanisms are still poorly understood. Renal cell carcinoma (RCC) is the most common malignant kidney tumor which canonically activates the hypoxia-inducible transcription factor (HIF) pathway. Despite intensive study, novel therapeutic strategies to target RCC have been difficult to develop. Since the RCC epigenome is relatively understudied, we sought to elucidate key mechanisms underpinning the tumor phenotype and its clinical behavior. METHODS We performed genome-wide chromatin accessibility (DNase-seq) and transcriptome profiling (RNA-seq) on paired tumor/normal samples from 3 patients undergoing nephrectomy for removal of RCC. We incorporated publicly available data on HIF binding (ChIP-seq) in a RCC cell line. We performed integrated analyses of these high-resolution, genome-scale datasets together with larger transcriptomic data available through The Cancer Genome Atlas (TCGA). FINDINGS Though HIF transcription factors play a cardinal role in RCC oncogenesis, we found that numerous transcription factors with a RCC-selective expression pattern also demonstrated evidence of HIF binding near their gene body. Examination of chromatin accessibility profiles revealed that some of these transcription factors influenced the tumor's regulatory landscape, notably the stem cell transcription factor POU5F1 (OCT4). Elevated POU5F1 transcript levels were correlated with advanced tumor stage and poorer overall survival in RCC patients. Unexpectedly, we discovered a HIF-pathway-responsive promoter embedded within a endogenous retroviral long terminal repeat (LTR) element at the transcriptional start site of the PSOR1C3 long non-coding RNA gene upstream of POU5F1. RNA transcripts are induced from this promoter and read through PSOR1C3 into POU5F1 producing a novel POU5F1 transcript isoform. Rather than being unique to the POU5F1 locus, we found that HIF binds to several other transcriptionally active LTR elements genome-wide correlating with broad gene expression changes in RCC. INTERPRETATION Integrated transcriptomic and epigenomic analysis of matched tumor and normal tissues from even a small number of primary patient samples revealed remarkably convergent shared regulatory landscapes. Several transcription factors appear to act downstream of HIF including the potent stem cell transcription factor POU5F1. Dysregulated expression of POU5F1 is part of a larger pattern of gene expression changes in RCC that may be induced by HIF-dependent reactivation of dormant promoters embedded within endogenous retroviral LTRs.
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Affiliation(s)
- Kyle T Siebenthall
- Altius Institute for Biomedical Sciences, Seattle, WA 98121, United States
| | - Chris P Miller
- Department of Pathology, University of Washington, Seattle, WA 98195, United States
| | - Jeff D Vierstra
- Altius Institute for Biomedical Sciences, Seattle, WA 98121, United States
| | - Julie Mathieu
- Institute for Stem Cell and Regenerative Medicine, Seattle, WA 98109, United States; Department of Comparative Medicine, University of Washington, Seattle, WA 98195, United States
| | - Maria Tretiakova
- Department of Pathology, University of Washington, Seattle, WA 98195, United States
| | - Alex Reynolds
- Altius Institute for Biomedical Sciences, Seattle, WA 98121, United States
| | - Richard Sandstrom
- Altius Institute for Biomedical Sciences, Seattle, WA 98121, United States
| | - Eric Rynes
- Altius Institute for Biomedical Sciences, Seattle, WA 98121, United States
| | - Eric Haugen
- Altius Institute for Biomedical Sciences, Seattle, WA 98121, United States
| | - Audra Johnson
- Altius Institute for Biomedical Sciences, Seattle, WA 98121, United States
| | - Jemma Nelson
- Altius Institute for Biomedical Sciences, Seattle, WA 98121, United States
| | - Daniel Bates
- Altius Institute for Biomedical Sciences, Seattle, WA 98121, United States
| | - Morgan Diegel
- Altius Institute for Biomedical Sciences, Seattle, WA 98121, United States
| | - Douglass Dunn
- Altius Institute for Biomedical Sciences, Seattle, WA 98121, United States
| | - Mark Frerker
- Altius Institute for Biomedical Sciences, Seattle, WA 98121, United States
| | - Michael Buckley
- Altius Institute for Biomedical Sciences, Seattle, WA 98121, United States
| | - Rajinder Kaul
- Altius Institute for Biomedical Sciences, Seattle, WA 98121, United States
| | - Ying Zheng
- Department of Bioengineering, University of Washington, Seattle, WA 98195, United States; Kidney Research Institute, Seattle, WA 98104, United States
| | - Jonathan Himmelfarb
- Division of Nephrology, Department of Medicine, University of Washington, Seattle, WA 98195, United States; Kidney Research Institute, Seattle, WA 98104, United States
| | - Hannele Ruohola-Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195, United States; Institute for Stem Cell and Regenerative Medicine, Seattle, WA 98109, United States
| | - Shreeram Akilesh
- Department of Pathology, University of Washington, Seattle, WA 98195, United States; Kidney Research Institute, Seattle, WA 98104, United States.
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13
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Abel EV, Goto M, Magnuson B, Abraham S, Ramanathan N, Hotaling E, Alaniz AA, Kumar-Sinha C, Dziubinski ML, Urs S, Wang L, Shi J, Waghray M, Ljungman M, Crawford HC, Simeone DM. HNF1A is a novel oncogene that regulates human pancreatic cancer stem cell properties. eLife 2018; 7:e33947. [PMID: 30074477 PMCID: PMC6122955 DOI: 10.7554/elife.33947] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 08/01/2018] [Indexed: 12/20/2022] Open
Abstract
The biological properties of pancreatic cancer stem cells (PCSCs) remain incompletely defined and the central regulators are unknown. By bioinformatic analysis of a human PCSC-enriched gene signature, we identified the transcription factor HNF1A as a putative central regulator of PCSC function. Levels of HNF1A and its target genes were found to be elevated in PCSCs and tumorspheres, and depletion of HNF1A resulted in growth inhibition, apoptosis, impaired tumorsphere formation, decreased PCSC marker expression, and downregulation of POU5F1/OCT4 expression. Conversely, HNF1A overexpression increased PCSC marker expression and tumorsphere formation in pancreatic cancer cells and drove pancreatic ductal adenocarcinoma (PDA) cell growth. Importantly, depletion of HNF1A in xenografts impaired tumor growth and depleted PCSC marker-positive cells in vivo. Finally, we established an HNF1A-dependent gene signature in PDA cells that significantly correlated with reduced survivability in patients. These findings identify HNF1A as a central transcriptional regulator of PCSC properties and novel oncogene in PDA.
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Affiliation(s)
- Ethan V Abel
- Department of Molecular and Integrative PhysiologyUniversity of Michigan Health SystemAnn ArborUnited States
- Translational Oncology ProgramUniversity of Michigan Health SystemAnn ArborUnited States
| | - Masashi Goto
- Translational Oncology ProgramUniversity of Michigan Health SystemAnn ArborUnited States
| | - Brian Magnuson
- Translational Oncology ProgramUniversity of Michigan Health SystemAnn ArborUnited States
- Department of Biostatistics, School of Public HealthUniversity of Michigan Health SystemAnn ArborUnited States
| | - Saji Abraham
- Translational Oncology ProgramUniversity of Michigan Health SystemAnn ArborUnited States
| | - Nikita Ramanathan
- Translational Oncology ProgramUniversity of Michigan Health SystemAnn ArborUnited States
| | - Emily Hotaling
- Translational Oncology ProgramUniversity of Michigan Health SystemAnn ArborUnited States
| | - Anthony A Alaniz
- Translational Oncology ProgramUniversity of Michigan Health SystemAnn ArborUnited States
| | - Chandan Kumar-Sinha
- Department of PathologyUniversity of Michigan Health SystemAnn ArborUnited States
| | - Michele L Dziubinski
- Department of Molecular and Integrative PhysiologyUniversity of Michigan Health SystemAnn ArborUnited States
- Translational Oncology ProgramUniversity of Michigan Health SystemAnn ArborUnited States
| | - Sumithra Urs
- Translational Oncology ProgramUniversity of Michigan Health SystemAnn ArborUnited States
| | - Lidong Wang
- Department of SurgeryNew York University Langone HealthNew YorkUnited States
- Perlmutter Cancer CenterNew York University Langone HealthNew YorkUnited states
| | - Jiaqi Shi
- Translational Oncology ProgramUniversity of Michigan Health SystemAnn ArborUnited States
- Department of PathologyUniversity of Michigan Health SystemAnn ArborUnited States
| | - Meghna Waghray
- Translational Oncology ProgramUniversity of Michigan Health SystemAnn ArborUnited States
| | - Mats Ljungman
- Translational Oncology ProgramUniversity of Michigan Health SystemAnn ArborUnited States
- Department of Radiation OncologyUniversity of Michigan Health SystemAnn ArborUnited States
| | - Howard C Crawford
- Department of Molecular and Integrative PhysiologyUniversity of Michigan Health SystemAnn ArborUnited States
- Translational Oncology ProgramUniversity of Michigan Health SystemAnn ArborUnited States
| | - Diane M Simeone
- Department of SurgeryNew York University Langone HealthNew YorkUnited States
- Perlmutter Cancer CenterNew York University Langone HealthNew YorkUnited states
- Department of PathologyNew York University Langone HealthNew YorkUnited States
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