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Acharya P, Parkins S, Tranter M. RNA binding proteins as mediators of pathological cardiac remodeling. Front Cell Dev Biol 2024; 12:1368097. [PMID: 38818408 PMCID: PMC11137256 DOI: 10.3389/fcell.2024.1368097] [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] [Accepted: 05/01/2024] [Indexed: 06/01/2024] Open
Abstract
RNA binding proteins (RBPs) play a central in the post-transcriptional regulation of gene expression, which can account for up to 50% of all variations in protein expression within a cell. Following their binding to target RNAs, RBPs most typically confer changes in gene expression through modulation of alternative spicing, RNA stabilization/degradation, or ribosome loading/translation rate. All of these post-transcriptional regulatory processes have been shown to play a functional role in pathological cardiac remodeling, and a growing body of evidence is beginning to identify the mechanistic contribution of individual RBPs and their cardiac RNA targets. This review highlights the mechanisms of RBP-dependent post-transcriptional gene regulation in cardiomyocytes and fibroblasts and our current understanding of how RNA binding proteins functionally contribute to pathological cardiac remodeling.
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Affiliation(s)
- Pooja Acharya
- Department of Molecular Medicine and Therapeutics, The Ohio State University Wexner Medical Center, Columbus, OH, United States
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, Columbus, OH, United States
| | - Sharon Parkins
- Department of Molecular Medicine and Therapeutics, The Ohio State University Wexner Medical Center, Columbus, OH, United States
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, Columbus, OH, United States
- Department of Internal Medicine, Division of Cardiovascular Health and Disease, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Michael Tranter
- Department of Molecular Medicine and Therapeutics, The Ohio State University Wexner Medical Center, Columbus, OH, United States
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, Columbus, OH, United States
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2
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Khalilian S, Tabari MAK, Omrani MA, Ghafouri-Fard S. Emerging functions and significance of circCDYL in human disorders. Mol Biol Rep 2023; 51:7. [PMID: 38085365 DOI: 10.1007/s11033-023-08993-2] [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: 08/16/2023] [Accepted: 10/13/2023] [Indexed: 12/18/2023]
Abstract
Circular RNAs (circRNAs) are a group of non-coding transcripts in which a loop structure is shaped via a back splicing procedure. They have central roles in the regulation of gene expression. hsa_circ_0008285, alternatively named as circCDYL, is a circular RNA originated from the exon 4 of CDYL gene. It is produced by a back-splice incident and is mainly located in the cytoplasm. It has no internal ribosome entry site, open reading frame and intronic sequences. CircCDYL dysregulation has been reported in the malignant conditions including multiple myeloma, mantle cell lymphoma, breast cancer, non-small cell lung cancer, Wilms tumor, bladder cancer, colon cancer, and hepatocellular carcinoma. It also has an emerging role in the pathophysiology of non-malignant conditions including myocardial infarction, gestational diabetes mellitus, membranous nephropathy, and abdominal aortic aneurysm. In the current study, we summarize the emerging roles of circCDYL in malignant and non-malignant conditions.
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Affiliation(s)
- Sheyda Khalilian
- Student Research Committee, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- USERN Office, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Amin Khazeei Tabari
- Student Research Committee, Mazandaran University of Medical Sciences, Sari, Iran
- USERN Office, Mazandaran University of Medical Sciences, Sari, Iran
| | | | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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3
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Dong X, Bai Y, Liao Z, Gritsch D, Liu X, Wang T, Borges-Monroy R, Ehrlich A, Serrano GE, Feany MB, Beach TG, Scherzer CR. Circular RNAs in the human brain are tailored to neuron identity and neuropsychiatric disease. Nat Commun 2023; 14:5327. [PMID: 37723137 PMCID: PMC10507039 DOI: 10.1038/s41467-023-40348-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 07/20/2023] [Indexed: 09/20/2023] Open
Abstract
Little is known about circular RNAs (circRNAs) in specific brain cells and human neuropsychiatric disease. Here, we systematically identify over 11,039 circRNAs expressed in vulnerable dopamine and pyramidal neurons laser-captured from 190 human brains and non-neuronal cells using ultra-deep, total RNA sequencing. 1526 and 3308 circRNAs are custom-tailored to the cell identity of dopamine and pyramidal neurons and enriched in synapse pathways. 29% of Parkinson's and 12% of Alzheimer's disease-associated genes produced validated circRNAs. circDNAJC6, which is transcribed from a juvenile-onset Parkinson's gene, is already dysregulated during prodromal, onset stages of common Parkinson's disease neuropathology. Globally, addiction-associated genes preferentially produce circRNAs in dopamine neurons, autism-associated genes in pyramidal neurons, and cancers in non-neuronal cells. This study shows that circular RNAs in the human brain are tailored to neuron identity and implicate circRNA-regulated synaptic specialization in neuropsychiatric diseases.
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Affiliation(s)
- Xianjun Dong
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women's Hospital, Boston, MA, USA
- Precision Neurology Program, Harvard Medical School and Brigham & Women's Hospital, Boston, MA, USA
- Genomics and Bioinformatics Hub, Harvard Medical School and Brigham & Women's Hospital, Boston, MA, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
| | - Yunfei Bai
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women's Hospital, Boston, MA, USA
- Precision Neurology Program, Harvard Medical School and Brigham & Women's Hospital, Boston, MA, USA
- State Key Lab of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Zhixiang Liao
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women's Hospital, Boston, MA, USA
- Precision Neurology Program, Harvard Medical School and Brigham & Women's Hospital, Boston, MA, USA
| | - David Gritsch
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women's Hospital, Boston, MA, USA
- Precision Neurology Program, Harvard Medical School and Brigham & Women's Hospital, Boston, MA, USA
| | - Xiaoli Liu
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women's Hospital, Boston, MA, USA
- Precision Neurology Program, Harvard Medical School and Brigham & Women's Hospital, Boston, MA, USA
- Department of Neurology, Zhejiang Hospital, Zhejiang, China
| | - Tao Wang
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women's Hospital, Boston, MA, USA
- Precision Neurology Program, Harvard Medical School and Brigham & Women's Hospital, Boston, MA, USA
- School of Computer Science, Northwestern Polytechnical University, Xi'an, Shaanxi, China
| | - Rebeca Borges-Monroy
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women's Hospital, Boston, MA, USA
- Precision Neurology Program, Harvard Medical School and Brigham & Women's Hospital, Boston, MA, USA
| | - Alyssa Ehrlich
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women's Hospital, Boston, MA, USA
- Precision Neurology Program, Harvard Medical School and Brigham & Women's Hospital, Boston, MA, USA
- Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Mel B Feany
- Departement of Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Clemens R Scherzer
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women's Hospital, Boston, MA, USA.
- Precision Neurology Program, Harvard Medical School and Brigham & Women's Hospital, Boston, MA, USA.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA.
- Program in Neuroscience, Harvard Medical School, Boston, MA, USA.
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4
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Qadir J, Wen SY, Yuan H, Yang BB. CircRNAs regulate the crosstalk between inflammation and tumorigenesis: The bilateral association and molecular mechanisms. Mol Ther 2023; 31:1514-1532. [PMID: 36518080 PMCID: PMC10278049 DOI: 10.1016/j.ymthe.2022.12.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/16/2022] [Accepted: 12/09/2022] [Indexed: 12/15/2022] Open
Abstract
Inflammation, a hallmark of cancer, has been associated with tumor progression, transition into malignant phenotype and efficacy of the chemotherapeutic agents in cancer. Chronic inflammation provides a favorable environment for tumorigenesis by inducing immunosuppression, whereas acute inflammation prompts tumor suppression by generating anti-tumor immune responses. Inflammatory factors derived from interstitial cells or tumor cells can stimulate cell proliferation and survival by modulating oncogenes and/or tumor suppressors. Recently, a new class of RNAs, i.e., circular RNAs (circRNAs), has been implicated in inflammatory diseases. Although there are reports on circRNAs imparting functions in inflammatory insults, whether these circularized transcripts hold the potential to regulate inflammation-induced cancer or tumor-related inflammation, and modulate the interactions between tumor microenvironment (TME) and the inflammatory stromal/immune cells, awaits further elucidation. Contextually, the current review describes the molecular association between inflammation and cancer, and spotlights the regulatory mechanisms by which circRNAs can moderate TME in response to inflammatory signals/triggers. We also present comprehensive information about the immune cell(s)-specific expression and functions of the circRNAs in TME, modulation of inflammatory signaling pathways to drive tumorigenesis, and their plausible roles in inflammasomes and tumor development. Moreover, the therapeutic potential of these circRNAs in harnessing inflammatory responses in cancer is also discussed.
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Affiliation(s)
- Javeria Qadir
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, ON, Canada; Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Shuo-Yang Wen
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Hui Yuan
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Burton B Yang
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, ON, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.
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5
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Dong X, Bai Y, Liao Z, Gritsch D, Liu X, Wang T, Borges-Monroy R, Ehrlich A, Serano GE, Feany MB, Beach TG, Scherzer CR. Circular RNAs in the human brain are tailored to neuron identity and neuropsychiatric disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.01.535194. [PMID: 37066229 PMCID: PMC10103951 DOI: 10.1101/2023.04.01.535194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Little is known about circular RNAs (circRNAs) in specific brain cells and human neuropsychiatric disease. Here, we systematically identified over 11,039 circRNAs expressed in vulnerable dopamine and pyramidal neurons laser-captured from 190 human brains and non-neuronal cells using ultra-deep, total RNA sequencing. 1,526 and 3,308 circRNAs were custom-tailored to the cell identity of dopamine and pyramidal neurons and enriched in synapse pathways. 88% of Parkinson's and 80% of Alzheimer's disease-associated genes produced circRNAs. circDNAJC6, produced from a juvenile-onset Parkinson's gene, was already dysregulated during prodromal, onset stages of common Parkinson's disease neuropathology. Globally, addiction-associated genes preferentially produced circRNAs in dopamine neurons, autism-associated genes in pyramidal neurons, and cancers in non-neuronal cells. This study shows that circular RNAs in the human brain are tailored to neuron identity and implicate circRNA- regulated synaptic specialization in neuropsychiatric diseases.
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Affiliation(s)
- Xianjun Dong
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women’s Hospital, Boston, MA, USA
- Precision Neurology Program, Harvard Medical School and Brigham & Women’s Hospital, Boston, MA, USA
- Genomics and Bioinformatics Hub, Harvard Medical School and Brigham & Women’s Hospital, Boston, MA, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815
| | - Yunfei Bai
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women’s Hospital, Boston, MA, USA
- Precision Neurology Program, Harvard Medical School and Brigham & Women’s Hospital, Boston, MA, USA
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Zhixiang Liao
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women’s Hospital, Boston, MA, USA
- Precision Neurology Program, Harvard Medical School and Brigham & Women’s Hospital, Boston, MA, USA
| | - David Gritsch
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women’s Hospital, Boston, MA, USA
- Precision Neurology Program, Harvard Medical School and Brigham & Women’s Hospital, Boston, MA, USA
| | - Xiaoli Liu
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women’s Hospital, Boston, MA, USA
- Precision Neurology Program, Harvard Medical School and Brigham & Women’s Hospital, Boston, MA, USA
- Department of Neurology, Zhejiang Hospital, Zhejiang, China
| | - Tao Wang
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women’s Hospital, Boston, MA, USA
- Precision Neurology Program, Harvard Medical School and Brigham & Women’s Hospital, Boston, MA, USA
- School of Computer Science, Northwestern Polytechnical University, Xi’an, Shaanxi, China
| | - Rebeca Borges-Monroy
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women’s Hospital, Boston, MA, USA
- Precision Neurology Program, Harvard Medical School and Brigham & Women’s Hospital, Boston, MA, USA
| | - Alyssa Ehrlich
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women’s Hospital, Boston, MA, USA
- Precision Neurology Program, Harvard Medical School and Brigham & Women’s Hospital, Boston, MA, USA
- Department of Psychiatry, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Mel B. Feany
- Departement of Pathology, Brigham & Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Clemens R. Scherzer
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women’s Hospital, Boston, MA, USA
- Precision Neurology Program, Harvard Medical School and Brigham & Women’s Hospital, Boston, MA, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815
- Program in Neuroscience, Harvard Medical School, Boston, MA, USA
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6
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Lee KY, Liu CM, Chen LH, Lee CY, Lu TP, Chuang LL, Lai LC. Hypoxia-responsive circular RNA circAAGAB reduces breast cancer malignancy by activating p38 MAPK and sponging miR-378 h. Cancer Cell Int 2023; 23:45. [PMID: 36899354 PMCID: PMC10007766 DOI: 10.1186/s12935-023-02891-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 03/04/2023] [Indexed: 03/12/2023] Open
Abstract
BACKGROUND Breast cancer is a prevalent disease in women, with high prevalence worldwide. The hypoxic microenvironment of solid tumors develops during the progress of carcinogenesis and leads to greater malignancy and treatment resistance. Recently, accumulating evidence indicates that non-coding RNAs, such as circular RNAs (circRNAs), play a pivotal role in altering cellular functions. However, the underlying mechanisms of circRNAs in breast cancer are still unclear. Therefore, the purpose of this study was to investigate the role of a tumor-suppressive circRNA, circAAGAB, in breast cancer by assuming down-regulation of circAAGAB under hypoxia and the properties of a tumor suppressor. METHODS Firstly, circAAGAB was identified from expression profiling by next generation sequencing. Next, the stability of circAAGAB increased by interacting with the RNA binding protein FUS. Moreover, cellular and nuclear fractionation showed that most circAAGAB resided in the cytoplasm and that it up-regulated KIAA1522, NKX3-1, and JADE3 by sponging miR-378 h. Lastly, the functions of circAAGAB were explored by identifying its down-stream genes using Affymetrix microarrays and validated by in vitro assays. RESULTS The results showed that circAAGAB reduced cell colony formation, cell migration, and signaling through p38 MAPK pathway, as well as increased radiosensitivity. CONCLUSION These findings suggest that the oxygen-responsive circAAGAB acts as a tumor suppressor in breast cancer, and may contribute to the development of a more specific therapeutic regimen for breast cancer.
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Affiliation(s)
- Kuan-Yi Lee
- Graduate Institute of Physiology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chia-Ming Liu
- Graduate Institute of Physiology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Li-Han Chen
- Institute of Fisheries Science, College of Life Science, National Taiwan University, Taipei, Taiwan.,Department of Life Science, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Chien-Yueh Lee
- Master Program for Biomedical Engineering, College of Biomedical Engineering, China Medical University, Taichung, Taiwan
| | - Tzu-Pin Lu
- Institute of Epidemiology and Preventive Medicine, Department of Public Health, National Taiwan University, Taipei, Taiwan
| | - Li-Ling Chuang
- School of Physical Therapy and Graduate Institute of Rehabilitation Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan. .,Department of Physical Medicine and Rehabilitation, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan.
| | - Liang-Chuan Lai
- Graduate Institute of Physiology, College of Medicine, National Taiwan University, Taipei, Taiwan. .,Bioinformatics and Biostatistics Core, Center of Genomic and Precision Medicine, National Taiwan University, Taipei, Taiwan.
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7
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Sun K, Yao H, Zhang P, Sun Y, Ma J, Xia Q. Emerging landscape of circFNDC3B and its role in human malignancies. Front Oncol 2023; 13:1097956. [PMID: 36793611 PMCID: PMC9924128 DOI: 10.3389/fonc.2023.1097956] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 01/06/2023] [Indexed: 01/31/2023] Open
Abstract
In recent years, more attention has been paid to expanding the abundance of Circular RNAs (circRNAs), while the circRNAs that have been found to have significant functions have not been studied in different diseases. CircFNDC3B is one of the most researched circRNAs generated from fibronectin type III domain-containing protein 3B (FNDC3B) gene. Accumulating researches have reported the multiple functions of circFNDC3B in different cancer types and other non-neoplastic diseases, and predicted that circFNDC3B might be a potential biomarker. Notably, circFNDC3B can play roles in different diseases by binding to various microRNAs (miRNAs), binding to RNA-binding proteins (RBPs), or encoding functional peptides. This paper systematically summarizes the biogenesis and function of circRNAs, reviews and discusses the roles and molecular mechanisms of circFNDC3B and its target genes in different cancers and non-neoplastic diseases, which will do favor to broaden our comprehension of the function of circRNAs and facilitate subsequent research on circFNDC3B.
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Affiliation(s)
- Kai Sun
- Department of Urology, Shandong Province Hospital, Shandong University, Jinan, China
| | - Huibao Yao
- Department of Urology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, Shandong, China
| | - Peizhi Zhang
- Department of Urology, Shandong Province Hospital, Shandong University, Jinan, China
| | - Yanning Sun
- Department of Urology, Shandong Province Hospital, Shandong University, Jinan, China
| | - Jian Ma
- Department of Urology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, Shandong, China
| | - Qinghua Xia
- Department of Urology, Shandong Province Hospital, Shandong University, Jinan, China
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8
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The malignancy of chordomas is enhanced via a circTLK1/miR-16-5p/Smad3 positive feedback axis. Cell Death Discov 2023; 9:64. [PMID: 36792585 PMCID: PMC9932141 DOI: 10.1038/s41420-023-01332-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 01/08/2023] [Accepted: 01/12/2023] [Indexed: 02/17/2023] Open
Abstract
CircRNAs play crucial roles in various malignancies via an increasing number of reported regulatory mechanisms, including the classic sponging mechanism between circRNAs and micro RNAs (miRNAs). We performed bioinformatic analyses and identified circTLK1 as a regulator of malignant chordoma progression. Moreover, we observed that circTLK1 showed high expression in chordoma cells and tissues, while circTLK1 interference suppressed chordoma cell proliferation and invasion. In addition, circTLK1 directly interacted with miR-16-5p, which has previously been shown to repress chordoma, and circTLK1 knockdown suppressed Smad3 expression. Chromatin immunoprecipitation sequencing further demonstrated that Smad3 acts as a positive regulator by interacting with TLK1, thereby mediating the circTLK1/miR-16-5p/Smad3 positive feedback axis. Taken together, our findings suggested that the disruption of the circTLK1/miR-16-5p/Smad3 positive feedback pathway, particularly via the Smad3 inhibitor SIS3, could be a promising therapeutic strategy.
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9
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Castro-Muñoz LJ, Vázquez Ulloa E, Sahlgren C, Lizano M, De La Cruz-Hernández E, Contreras-Paredes A. Modulating epigenetic modifications for cancer therapy (Review). Oncol Rep 2023; 49:59. [PMID: 36799181 PMCID: PMC9942256 DOI: 10.3892/or.2023.8496] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 11/08/2022] [Indexed: 02/12/2023] Open
Abstract
Cancer is a global public health concern. Alterations in epigenetic processes are among the earliest genomic aberrations occurring during cancer development and are closely related to progression. Unlike genetic mutations, aberrations in epigenetic processes are reversible, which opens the possibility for novel pharmacological treatments. Non‑coding RNAs (ncRNAs) represent an essential epigenetic mechanism, and emerging evidence links ncRNAs to carcinogenesis. Epigenetic drugs (epidrugs) are a group of promising target therapies for cancer treatment acting as coadjuvants to reverse drug resistance in cancer. The present review describes central epigenetic aberrations during malignant transformation and explains how epidrugs target DNA methylation, histone modifications and ncRNAs. Furthermore, clinical trials focused on evaluating the effect of these epidrugs alone or in combination with other anticancer therapies and other ncRNA‑based therapies are discussed. The use of epidrugs promises to be an effective tool for reversing drug resistance in some patients with cancer.
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Affiliation(s)
| | - Elenaé Vázquez Ulloa
- Faculty of Science and Engineering/Cell Biology, University of Turku and Åbo Akademi University, Turku 20500, Finland,Turku Bioscience, University of Turku and Åbo Akademi University, Turku 20500, Finland
| | - Cecilia Sahlgren
- Faculty of Science and Engineering/Cell Biology, University of Turku and Åbo Akademi University, Turku 20500, Finland,Turku Bioscience, University of Turku and Åbo Akademi University, Turku 20500, Finland,Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven 5600 MB, The Netherlands,Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven 5600 MB, The Netherlands
| | - Marcela Lizano
- Unidad de Investigacion Biomedica en Cancer, Instituto Nacional de Cancerología-Universidad Nacional Autonoma de Mexico, Ciudad de Mexico 14080, Mexico,Departamento de Medicina Genomica y Toxicologia Ambiental, Instituto de Investigaciones Biomedicas, Universidad Nacional Autonoma de Mexico, Mexico 04510, Mexico
| | - Erick De La Cruz-Hernández
- Laboratory of Research in Metabolic and Infectious Diseases, Multidisciplinary Academic Division of Comalcalco, Juarez Autonomous University of Tabasco, Comalcalco, Tabasco 86650, Mexico
| | - Adriana Contreras-Paredes
- Unidad de Investigacion Biomedica en Cancer, Instituto Nacional de Cancerología-Universidad Nacional Autonoma de Mexico, Ciudad de Mexico 14080, Mexico,Correspondence to: Professor Adriana Contreras-Paredes, Unidad de Investigacion Biomedica en Cancer, Instituto Nacional de Cancerología-Universidad Nacional Autonoma de Mexico, Avenue San Fernando, Col. Sección XVI, Tlalpan, Ciudad de Mexico 14080, Mexico, E-mail:
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10
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Circular RNAs and tuberculosis infection. Int J Biol Macromol 2023; 226:1218-1225. [PMID: 36442574 DOI: 10.1016/j.ijbiomac.2022.11.235] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 08/13/2022] [Accepted: 11/18/2022] [Indexed: 11/27/2022]
Abstract
Tuberculosis (TB) is a deadly infectious disease caused by Mycobacterium tuberculosis (Mtb) that affects the immune system chronically. Therefore, effective control and treatment of tuberculosis requires rapid and accurate diagnostic strategies. Tuberculosis has always been a global burden on health, social and economic systems due to the lack of standard curative and diagnostic (bio)markers. Accordingly, the management and monitoring of patients with active TB at the primary care level may be possible through new, rapid and cost-effective non-sputum-based diagnostic procedures. Biomarkers can help diagnose various diseases, including circular RNA (circRNA), which has recently been introduced as an endogenous, abundant and stable RNA in the cytoplasm with unique tissue specificity. There are frequent reports of circRNA involvement in many pathological and physiological processes in human beings. Recent studies have highlighted the presence of circRNAs in serum and their role as promising biomarkers in the diagnosis of the disease, potentially due to the continuous, stable, closed covalent circular structures and lack of easy degradation by nucleases. The purpose of this review article is to scrutinize the behavior of circulating plasma RNAs in relation to the pathogenesis and diagnosis of tuberculosis.
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11
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Razpotnik R, Vidmar R, Fonović M, Rozman D, Režen T. Circular RNA hsa_circ_0062682 Binds to YBX1 and Promotes Oncogenesis in Hepatocellular Carcinoma. Cancers (Basel) 2022; 14:cancers14184524. [PMID: 36139684 PMCID: PMC9497178 DOI: 10.3390/cancers14184524] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/11/2022] [Accepted: 09/11/2022] [Indexed: 11/23/2022] Open
Abstract
Simple Summary Circular RNA (circRNA) have a role in carcinogenesis in different cancers, also in hepatocellular carcinoma (HCC). The transcriptome analyses of HCC tumours identified an upregulated circRNA hsa_circ_0062682. We show that this circRNA affects several aspects of oncogenesis, which are cell proliferation, migration, and invasion. Using transcriptome analyses we identified modulated signalling pathways and transcription factors, confirming the observed phenotype in cells. We identified Y-box-binding protein 1 (YBX1), a known oncogene and RNA-binding protein, as a binding partner, which was in line with transcriptome analyses. We also identified a cell-specific response to sorafenib after circRNA modulation, which is in line with a heterogeneous molecular pathology of HCC subtypes. Abstract Circular RNAs (circRNAs) have been shown to play an important role in the pathogenesis of hepatocellular carcinoma (HCC). By implementing available transcriptomic analyses of HCC patients, we identified an upregulated circRNA hsa_circ_0062682. Stable perturbations of hsa_circ_0062682 in Huh-7 and SNU-449 cell lines influenced colony formation, migration, cell proliferation, sorafenib sensitivity, and additionally induced morphological changes in cell lines, indicating an important role of hsa_circ_0062682 in oncogenesis. Pathway enrichment analysis and gene set enrichment analysis of the transcriptome data from hsa_circ_0062682 knockdown explained the observed phenotypes and exposed transcription factors E2F1, Sp1, HIF-1α, and NFκB1 as potential downstream targets. Biotinylated oligonucleotide pulldown combined with proteomic analyses identified protein interaction partners of which YBX1, a known oncogene, was confirmed by RNA immunoprecipitation. Furthermore, we discovered a complex cell-type-specific phenotype in response to the oncogenic potential of hsa_circ_0062682. This finding is in line with different classes of HCC tumours, and more studies are needed to shed a light on the molecular complexity of liver cancer.
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Affiliation(s)
- Rok Razpotnik
- Centre for Functional Genomics and Bio-Chips, Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Robert Vidmar
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, 1000 Ljubljana, Slovenia
| | - Marko Fonović
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, 1000 Ljubljana, Slovenia
| | - Damjana Rozman
- Centre for Functional Genomics and Bio-Chips, Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Tadeja Režen
- Centre for Functional Genomics and Bio-Chips, Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
- Correspondence: ; Tel.: +386-1-543-7592 or +386-1-543-7588
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12
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Xia J, Wu C, Tang Y, Tang J, Zhu D, Zhang F, Xu Z, Sun D, Tan Z, Zhuo H. CircMYH9 increases KPNA2 mRNA stability to promote hepatocellular carcinoma progression in an EIF4A3-dependent manner. Am J Cancer Res 2022; 12:4361-4372. [PMID: 36225644 PMCID: PMC9548019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 09/01/2022] [Indexed: 06/16/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is the most commonly diagnosed cancer worldwide with a high incidence of recurrence and metastasis; however, the molecular mechanisms underlying HCC development remain to be fully understood. In this study, we identified circMYH9 as an important regulator of HCC. Overexpression of circMYH9 induced, while knockdown of circMYH9 inhibited, the proliferation, migration, and invasion of HCC cells. Mechanistically, circMYH9 bound to eukaryotic translation initiation factor 4A3 (EIF4A3) and increased karyopherin subunit alpha 2 (KPNA2) mRNA stability. circMYH9 knockdown in HCC cells reduced the stability of KPNA2 mRNA. Importantly, circMYH9 regulation of HCC required the activity of KPNA2. In support with this, circMYH9 level was positively correlated with the expression of KPNA2 in HCC patient samples. Taken together, our study was the first to uncover the oncogenic role of circMYH9 in HCC and further elucidated the functional mechanism of circMYH9 by interacting with EIF4A3 to increase KPNA2 mRNA stability. Our findings might provide a novel potential target for the diagnose and treatment of HCC.
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Affiliation(s)
- Jinguo Xia
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical UniversityNanjing, Jiangsu, P. R. China
| | - Chen Wu
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical UniversityNanjing, Jiangsu, P. R. China
| | - Yanhui Tang
- Qidong Hospital of Traditional Chinese MedicineNantong, Jiangsu, P. R. China
| | - Junwei Tang
- General Surgery, The First Affiliated Hospital of Nanjing Medical UniversityNanjing, Jiangsu, P. R. China
| | - Deming Zhu
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical UniversityNanjing, Jiangsu, P. R. China
| | - Feihong Zhang
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical UniversityNanjing, Jiangsu, P. R. China
| | - Zhenggang Xu
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical UniversityNanjing, Jiangsu, P. R. China
| | - Dongwei Sun
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical UniversityNanjing, Jiangsu, P. R. China
| | - Zhongming Tan
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical UniversityNanjing, Jiangsu, P. R. China
| | - Han Zhuo
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical UniversityNanjing, Jiangsu, P. R. China
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13
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Yarmishyn AA, Ishola AA, Chen CY, Verusingam ND, Rengganaten V, Mustapha HA, Chuang HK, Teng YC, Phung VL, Hsu PK, Lin WC, Ma HI, Chiou SH, Wang ML. Circular RNAs Modulate Cancer Hallmark and Molecular Pathways to Support Cancer Progression and Metastasis. Cancers (Basel) 2022; 14:cancers14040862. [PMID: 35205610 PMCID: PMC8869994 DOI: 10.3390/cancers14040862] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/22/2022] [Accepted: 01/26/2022] [Indexed: 02/05/2023] Open
Abstract
Simple Summary Circular RNAs (circRNA) are a type of RNA molecule of circular shape that are now being extensively studied due to the important roles they play in different biological processes. In addition, they were also shown to be implicated in disease such as cancer. Cancer is a complex process which is often defined by a combination of specific processes called cancer hallmarks. In this review, we summarize the literature on circRNAs in cancer and classify them as being implicated in specific cancer hallmarks. Abstract Circular RNAs (circRNAs) are noncoding products of backsplicing of pre-mRNAs which have been established to possess potent biological functions. Dysregulated circRNA expression has been linked to diseases including different types of cancer. Cancer progression is known to result from the dysregulation of several molecular mechanisms responsible for the maintenance of cellular and tissue homeostasis. The dysregulation of these processes is defined as cancer hallmarks, and the molecular pathways implicated in them are regarded as the targets of therapeutic interference. In this review, we summarize the literature on the investigation of circRNAs implicated in cancer hallmark molecular signaling. First, we present general information on the properties of circRNAs, such as their biogenesis and degradation mechanisms, as well as their basic molecular functions. Subsequently, we summarize the roles of circRNAs in the framework of each cancer hallmark and finally discuss the potential as therapeutic targets.
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Affiliation(s)
- Aliaksandr A. Yarmishyn
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 112, Taiwan; (A.A.Y.); (A.A.I.); (C.-Y.C.); (N.D.V.); (V.R.); (H.A.M.); (H.-K.C.); (Y.-C.T.); (V.L.P.); (S.-H.C.)
| | - Afeez Adekunle Ishola
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 112, Taiwan; (A.A.Y.); (A.A.I.); (C.-Y.C.); (N.D.V.); (V.R.); (H.A.M.); (H.-K.C.); (Y.-C.T.); (V.L.P.); (S.-H.C.)
- Taiwan International Graduate Program in Molecular Medicine, National Yang Ming Chiao Tung University and Academia Sinica, Taipei 112, Taiwan
| | - Chieh-Yu Chen
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 112, Taiwan; (A.A.Y.); (A.A.I.); (C.-Y.C.); (N.D.V.); (V.R.); (H.A.M.); (H.-K.C.); (Y.-C.T.); (V.L.P.); (S.-H.C.)
- Taiwan International Graduate Program in Molecular Medicine, National Yang Ming Chiao Tung University and Academia Sinica, Taipei 112, Taiwan
| | - Nalini Devi Verusingam
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 112, Taiwan; (A.A.Y.); (A.A.I.); (C.-Y.C.); (N.D.V.); (V.R.); (H.A.M.); (H.-K.C.); (Y.-C.T.); (V.L.P.); (S.-H.C.)
- Institute of Pharmacology, School of Medicine, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
- Centre for Stem Cell Research, Faculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, Kajang 43000, Malaysia
| | - Vimalan Rengganaten
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 112, Taiwan; (A.A.Y.); (A.A.I.); (C.-Y.C.); (N.D.V.); (V.R.); (H.A.M.); (H.-K.C.); (Y.-C.T.); (V.L.P.); (S.-H.C.)
- Institute of Pharmacology, School of Medicine, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
- Postgraduate Programme, Department of Preclinical Sciences, Faculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, Kajang 43000, Malaysia
| | - Habeebat Aderonke Mustapha
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 112, Taiwan; (A.A.Y.); (A.A.I.); (C.-Y.C.); (N.D.V.); (V.R.); (H.A.M.); (H.-K.C.); (Y.-C.T.); (V.L.P.); (S.-H.C.)
- Institute of Pharmacology, School of Medicine, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
| | - Hao-Kai Chuang
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 112, Taiwan; (A.A.Y.); (A.A.I.); (C.-Y.C.); (N.D.V.); (V.R.); (H.A.M.); (H.-K.C.); (Y.-C.T.); (V.L.P.); (S.-H.C.)
| | - Yuan-Chi Teng
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 112, Taiwan; (A.A.Y.); (A.A.I.); (C.-Y.C.); (N.D.V.); (V.R.); (H.A.M.); (H.-K.C.); (Y.-C.T.); (V.L.P.); (S.-H.C.)
| | - Van Long Phung
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 112, Taiwan; (A.A.Y.); (A.A.I.); (C.-Y.C.); (N.D.V.); (V.R.); (H.A.M.); (H.-K.C.); (Y.-C.T.); (V.L.P.); (S.-H.C.)
- Institute of Pharmacology, School of Medicine, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
| | - Po-Kuei Hsu
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 112, Taiwan;
- Division of Thoracic Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei 112, Taiwan
| | - Wen-Chang Lin
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan;
| | - Hsin-I Ma
- Department of Neurological Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei 114, Taiwan;
| | - Shih-Hwa Chiou
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 112, Taiwan; (A.A.Y.); (A.A.I.); (C.-Y.C.); (N.D.V.); (V.R.); (H.A.M.); (H.-K.C.); (Y.-C.T.); (V.L.P.); (S.-H.C.)
- Taiwan International Graduate Program in Molecular Medicine, National Yang Ming Chiao Tung University and Academia Sinica, Taipei 112, Taiwan
- Institute of Pharmacology, School of Medicine, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
- Genomic Research Center, Academia Sinica, Taipei 112, Taiwan
| | - Mong-Lien Wang
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 112, Taiwan; (A.A.Y.); (A.A.I.); (C.-Y.C.); (N.D.V.); (V.R.); (H.A.M.); (H.-K.C.); (Y.-C.T.); (V.L.P.); (S.-H.C.)
- Institute of Pharmacology, School of Medicine, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
- Institute of Food Safety and Health Risk Assessment, School of Pharmaceutical Sciences, National Yang-Ming Chiao Tung University, Taipei 112, Taiwan
- Correspondence: ; Tel.: +886-2-5568-1156; Fax: +886-2-2875-7435
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14
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Lu P, Jiang Y, Xia Z. Hsa_circ_0003221 facilitates the malignant development of bladder cancer cells via resulting in the upregulation of DHCR24 by targeting miR-892b. Investig Clin Urol 2022; 63:577-588. [PMID: 36068004 PMCID: PMC9448672 DOI: 10.4111/icu.20220153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 06/23/2022] [Accepted: 07/10/2022] [Indexed: 11/18/2022] Open
Affiliation(s)
- Peng Lu
- Department of Urology, Chongqing University Three Gorges Hospital, Chongqing, China
| | - Yingchun Jiang
- Department of Scientific Research and Foreign Affairs, Chongqing University Three Gorges Hospital, Chongqing, China
| | - Zongyu Xia
- Department of Urology, Chongqing University Three Gorges Hospital, Chongqing, China
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15
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Wang X, Ma R, Zhang X, Cui L, Ding Y, Shi W, Guo C, Shi Y. Crosstalk between N6-methyladenosine modification and circular RNAs: current understanding and future directions. Mol Cancer 2021; 20:121. [PMID: 34560891 PMCID: PMC8461955 DOI: 10.1186/s12943-021-01415-6] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 08/31/2021] [Indexed: 02/07/2023] Open
Abstract
N6-methyladenosine (m6A) is a prevalent internal modification in eukaryotic RNAs regulated by the so-called "writers", "erasers", and "readers". m6A has been demonstrated to exert critical molecular functions in modulating RNA maturation, localization, translation and metabolism, thus playing an essential role in cellular, developmental, and disease processes. Circular RNAs (circRNAs) are a class of non-coding RNAs with covalently closed single-stranded structures generated by back-splicing. CircRNAs also participate in physiological and pathological processes through unique mechanisms. Despite their discovery several years ago, m6A and circRNAs has drawn increased research interest due to advances in molecular biology techniques these years. Recently, several scholars have investigated the crosstalk between m6A and circRNAs. In this review, we provide an overview of the current knowledge of m6A and circRNAs, as well as summarize the crosstalk between these molecules based on existing research. In addition, we present some suggestions for future research perspectives.
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Affiliation(s)
- Xin Wang
- Department of Dermatology, Shanghai Skin Disease Hospital, Tongji University School of Medicine, 1278 Baode Road, Jing'an District, Shanghai, 200443, China.,Institute of Psoriasis, Tongji University School of Medicine, Shanghai, China
| | - Rui Ma
- Ministry of Education-Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xilin Zhang
- Department of Dermatology, Shanghai Skin Disease Hospital, Tongji University School of Medicine, 1278 Baode Road, Jing'an District, Shanghai, 200443, China.,Institute of Psoriasis, Tongji University School of Medicine, Shanghai, China
| | - Lian Cui
- Department of Dermatology, Shanghai Skin Disease Hospital, Tongji University School of Medicine, 1278 Baode Road, Jing'an District, Shanghai, 200443, China.,Institute of Psoriasis, Tongji University School of Medicine, Shanghai, China
| | - Yangfeng Ding
- Department of Dermatology, Shanghai Skin Disease Hospital, Tongji University School of Medicine, 1278 Baode Road, Jing'an District, Shanghai, 200443, China.,Institute of Psoriasis, Tongji University School of Medicine, Shanghai, China
| | - Weimin Shi
- Department of Dermatology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chunyuan Guo
- Department of Dermatology, Shanghai Skin Disease Hospital, Tongji University School of Medicine, 1278 Baode Road, Jing'an District, Shanghai, 200443, China. .,Institute of Psoriasis, Tongji University School of Medicine, Shanghai, China.
| | - Yuling Shi
- Department of Dermatology, Shanghai Skin Disease Hospital, Tongji University School of Medicine, 1278 Baode Road, Jing'an District, Shanghai, 200443, China. .,Institute of Psoriasis, Tongji University School of Medicine, Shanghai, China.
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