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Sabalette KB, Campo VA, Sotelo-Silveira JR, Smircich P, De Gaudenzi JG. Transcriptomic analysis of N-terminal mutated Trypanosoma cruzi UBP1 knockdown underlines the importance of this RNA-binding protein in parasite development. PLoS Negl Trop Dis 2024; 18:e0012179. [PMID: 38758959 PMCID: PMC11139272 DOI: 10.1371/journal.pntd.0012179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 05/30/2024] [Accepted: 04/30/2024] [Indexed: 05/19/2024] Open
Abstract
BACKGROUND During its life cycle, the human pathogen Trypanosoma cruzi must quickly adapt to different environments, in which the variation in the gene expression of the regulatory U-rich RNA-binding protein 1 (TcUBP1) plays a crucial role. We have previously demonstrated that the overexpression of TcUBP1 in insect-dwelling epimastigotes orchestrates an RNA regulon to promote differentiation to infective forms. METHODS In an attempt to generate TcUBP1 knockout parasites by using CRISPR-Cas9 technology, in the present study, we obtained a variant transcript that encodes a protein with 95% overall identity and a modified N-terminal sequence. The expression of this mutant protein, named TcUBP1mut, was notably reduced compared to that of the endogenous form found in normal cells. TcUBP1mut-knockdown epimastigotes exhibited normal growth and differentiation into infective metacyclic trypomastigotes and were capable of infecting mammalian cells. RESULTS We analyzed the RNA-Seq expression profiles of these parasites and identified 276 up- and 426 downregulated genes with respect to the wildtype control sample. RNA-Seq comparison across distinct developmental stages revealed that the transcriptomic profile of these TcUBP1mut-knockdown epimastigotes significantly differs not only from that of epimastigotes in the stationary phase but also from the gene expression landscape characteristic of infective forms. This is both contrary to and consistent with the results of our recent study involving TcUBP1-overexpressing cells. CONCLUSION Together, our findings demonstrate that the genes exhibiting opposite changes under overexpression and knockdown conditions unveil key mRNA targets regulated by TcUBP1. These mostly encompass transcripts that encode for trypomastigote-specific surface glycoproteins and ribosomal proteins, supporting a role for TcUBP1 in determining the molecular characteristics of the infective stage.
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Affiliation(s)
- Karina B. Sabalette
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín—Consejo Nacional de Investigaciones Científicas y Técnicas, General San Martín, Prov. de Buenos Aires, Argentina
- Escuela de Bio y Nanotecnologías (EByN), Universidad Nacional de San Martín, General San Martín, Prov. de Buenos Aires, Argentina
| | - Vanina A. Campo
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín—Consejo Nacional de Investigaciones Científicas y Técnicas, General San Martín, Prov. de Buenos Aires, Argentina
- Escuela de Bio y Nanotecnologías (EByN), Universidad Nacional de San Martín, General San Martín, Prov. de Buenos Aires, Argentina
| | - José R. Sotelo-Silveira
- Department of Genomics, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
- Instituto de Biología, School of Sciences, Universidad de la República, Montevideo, Uruguay
| | - Pablo Smircich
- Department of Genomics, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
- Instituto de Biología, School of Sciences, Universidad de la República, Montevideo, Uruguay
| | - Javier G. De Gaudenzi
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín—Consejo Nacional de Investigaciones Científicas y Técnicas, General San Martín, Prov. de Buenos Aires, Argentina
- Escuela de Bio y Nanotecnologías (EByN), Universidad Nacional de San Martín, General San Martín, Prov. de Buenos Aires, Argentina
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Yu X, Bu C, Yang X, Jiang W, He X, Sun R, Guo H, Shang L, Ou C. Exosomal non-coding RNAs in colorectal cancer metastasis. Clin Chim Acta 2024; 556:117849. [PMID: 38417779 DOI: 10.1016/j.cca.2024.117849] [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: 06/08/2023] [Revised: 02/24/2024] [Accepted: 02/25/2024] [Indexed: 03/01/2024]
Abstract
Colorectal cancer (CRC) is a type of gastrointestinal cancer with high morbidity and mortality rates, and is often accompanied by distant metastases. Metastasis is a major cause of shortened survival time and poor treatment outcomes for patients with CRC. However, the molecular mechanisms underlying the metastasis of CRC remain unclear. Exosomes are a class of small extracellular vesicles that originate from almost all human cells and can transmit biological information (e.g., nucleic acids, lipids, proteins, and metabolites) from secretory cells to target recipient cells. Recent studies have revealed that non-coding RNAs (ncRNAs) can be released by exosomes into the tumour microenvironment or specific tissues, and play a pivotal role in tumorigenesis by regulating a series of key molecules or signalling pathways, particularly those involved in tumour metastasis. Exosomal ncRNAs have potential as novel therapeutic targets for CRC metastasis, and can also be used as liquid biopsy biomarkers because of their specificity and sensitivity. Therefore, further investigations into the biological function and clinical value of exosomal ncRNAs will be of great value for the prevention, early diagnosis, and treatment of CRC metastasis.
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Affiliation(s)
- Xiaoqian Yu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Chiwen Bu
- Department of General Surgery, People's Hospital of Guanyun County, Lianyungang 222200, Jiangsu, China
| | - Xuejie Yang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Wenying Jiang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Xiaoyun He
- Departments of Ultrasound Imaging, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Ru Sun
- Department of Blood Transfusion, Affiliated Hospital of North Sichuan Medical College, Xichang 637000, Sichuan, China
| | - Hongbin Guo
- Department of Orthopedics, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Li Shang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China.
| | - Chunlin Ou
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China.
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3
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Sherwood DR, Kenny-Ganzert IW, Balachandar Thendral S. Translational regulation of cell invasion through extracellular matrix-an emerging role for ribosomes. F1000Res 2023; 12:1528. [PMID: 38628976 PMCID: PMC11019292 DOI: 10.12688/f1000research.143519.1] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/22/2023] [Indexed: 04/19/2024] Open
Abstract
Many developmental and physiological processes require cells to invade and migrate through extracellular matrix barriers. This specialized cellular behavior is also misregulated in many diseases, such as immune disorders and cancer. Cell invasive activity is driven by pro-invasive transcriptional networks that activate the expression of genes encoding numerous different proteins that expand and regulate the cytoskeleton, endomembrane system, cell adhesion, signaling pathways, and metabolic networks. While detailed mechanistic studies have uncovered crucial insights into pro-invasive transcriptional networks and the distinct cell biological attributes of invasive cells, less is known about how invasive cells modulate mRNA translation to meet the robust, dynamic, and unique protein production needs of cell invasion. In this review we outline known modes of translation regulation promoting cell invasion and focus on recent studies revealing elegant mechanisms that expand ribosome biogenesis within invasive cells to meet the increased protein production requirements to invade and migrate through extracellular matrix barriers.
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Man HSJ, Moosa VA, Singh A, Wu L, Granton JT, Juvet SC, Hoang CD, de Perrot M. Unlocking the potential of RNA-based therapeutics in the lung: current status and future directions. Front Genet 2023; 14:1281538. [PMID: 38075698 PMCID: PMC10703483 DOI: 10.3389/fgene.2023.1281538] [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: 08/22/2023] [Accepted: 11/06/2023] [Indexed: 02/12/2024] Open
Abstract
Awareness of RNA-based therapies has increased after the widespread adoption of mRNA vaccines against SARS-CoV-2 during the COVID-19 pandemic. These mRNA vaccines had a significant impact on reducing lung disease and mortality. They highlighted the potential for rapid development of RNA-based therapies and advances in nanoparticle delivery systems. Along with the rapid advancement in RNA biology, including the description of noncoding RNAs as major products of the genome, this success presents an opportunity to highlight the potential of RNA as a therapeutic modality. Here, we review the expanding compendium of RNA-based therapies, their mechanisms of action and examples of application in the lung. The airways provide a convenient conduit for drug delivery to the lungs with decreased systemic exposure. This review will also describe other delivery methods, including local delivery to the pleura and delivery vehicles that can target the lung after systemic administration, each providing access options that are advantageous for a specific application. We present clinical trials of RNA-based therapy in lung disease and potential areas for future directions. This review aims to provide an overview that will bring together researchers and clinicians to advance this burgeoning field.
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Affiliation(s)
- H. S. Jeffrey Man
- Temerty Faculty of Medicine, Institute of Medical Science, Toronto, ON, Canada
- Department of Immunology, University of Toronto, Toronto, ON, Canada
- Latner Thoracic Research Laboratories, Toronto General Hospital Research Institute, Toronto, ON, Canada
- Division of Respirology and Critical Care Medicine, Department of Medicine, University Health Network, Toronto, ON, Canada
| | - Vaneeza A. Moosa
- Latner Thoracic Research Laboratories, Toronto General Hospital Research Institute, Toronto, ON, Canada
- Division of Thoracic Surgery, Toronto General Hospital, Toronto, ON, Canada
| | - Anand Singh
- Thoracic Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Licun Wu
- Latner Thoracic Research Laboratories, Toronto General Hospital Research Institute, Toronto, ON, Canada
- Division of Thoracic Surgery, Toronto General Hospital, Toronto, ON, Canada
| | - John T. Granton
- Division of Respirology and Critical Care Medicine, Department of Medicine, University Health Network, Toronto, ON, Canada
| | - Stephen C. Juvet
- Temerty Faculty of Medicine, Institute of Medical Science, Toronto, ON, Canada
- Department of Immunology, University of Toronto, Toronto, ON, Canada
- Latner Thoracic Research Laboratories, Toronto General Hospital Research Institute, Toronto, ON, Canada
- Division of Respirology and Critical Care Medicine, Department of Medicine, University Health Network, Toronto, ON, Canada
| | - Chuong D. Hoang
- Thoracic Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Marc de Perrot
- Department of Immunology, University of Toronto, Toronto, ON, Canada
- Latner Thoracic Research Laboratories, Toronto General Hospital Research Institute, Toronto, ON, Canada
- Division of Thoracic Surgery, Toronto General Hospital, Toronto, ON, Canada
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Chen Y, Chen C, Gao G, Zeng C, Chen Z, Lin G, Yao G, Nian S, Chen X, Weng S, Gu X, Lin C. Identification and validation of N6-methyladenosine (m6A)-related lncRNAs signature for predicting the prognosis of laryngeal carcinoma, especially for smoking patients. Front Genet 2023; 14:1292164. [PMID: 38028627 PMCID: PMC10666777 DOI: 10.3389/fgene.2023.1292164] [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: 09/11/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Laryngeal cancer (LC), a highly fatal tumor in the head and neck region, has been the focus of research in recent years. The study of LC has primarily focused on the role of long non-coding RNAs (lncRNAs) in regulating gene expression, as they have emerged as pivotal factors in this biological process. Additionally, a reversible RNA modification called N6-methyladenosine (m6A) has been observed to have a significant impact on gene expression as well. The purpose of this research is to investigate the impact of m6A-related lncRNAs on the prognosis of laryngeal squamous cell carcinoma (LSCC). Specifically, this investigation analyzed the m6A-related regulators' patterns of expression and mutation, encompassing a total of 15 regulators. Drawing upon the expression levels of prognostic m6A-regulated lncRNAs, two distinct lncRNA clusters were identified. Further analysis revealed differentially expressed lncRNAs between these clusters. In addition to studying the expression of lncRNAs, the researchers also examined the distribution of clinical characteristics and the tumor microenvironment (TME) in relation to the identified lncRNA clusters. This provided valuable insights into potential associations between lncRNA expression patterns and the clinical features of LSCC. Through the establishment of a risk model associated with lncRNAs, we were able to further investigate their clinical features, prognosis, and immune status. Additionally, we conducted a separate analysis of LINC00528, a lncRNA associated with smoking, examining its expression, overall survival time, correlated mRNAs, and conducting enrichment of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), as well as determining the sensitivity of related drugs. RT-qPCR results also indicated an increase in LINC00528 expression among smoking LSCC patients. The findings suggest that a high expression level of LINC00528 in LSCC patients may lead to a more favorable prognosis, providing new insights for the management and treatment of LSCC patients, particularly those with high expression of LINC00528. Overall, this research sheds light on the prognostic impact of m6A-regulated lncRNAs in LSCC. The implications of these findings for the advancement of innovative therapeutic approaches for LSCC patients are noteworthy.
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Affiliation(s)
- Yuqing Chen
- Department of Otorhinolaryngology, Head and Neck Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Department of Otorhinolaryngology, Head and Neck Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Fujian Provincial Clinical Medical Research Center for Ear, Nose and Throat Difficulty Diseases, Fuzhou, Fujian, China
| | - Chenyu Chen
- Department of Otorhinolaryngology, Head and Neck Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Department of Otorhinolaryngology, Head and Neck Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Fujian Provincial Clinical Medical Research Center for Ear, Nose and Throat Difficulty Diseases, Fuzhou, Fujian, China
| | - Gufeng Gao
- Department of Geriatrics, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
| | - Chaojun Zeng
- Department of Otorhinolaryngology, Head and Neck Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Department of Otorhinolaryngology, Head and Neck Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Fujian Provincial Clinical Medical Research Center for Ear, Nose and Throat Difficulty Diseases, Fuzhou, Fujian, China
| | - Zhifeng Chen
- Department of Otorhinolaryngology, Head and Neck Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Department of Otorhinolaryngology, Head and Neck Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Fujian Provincial Clinical Medical Research Center for Ear, Nose and Throat Difficulty Diseases, Fuzhou, Fujian, China
| | - Gongbiao Lin
- Department of Otorhinolaryngology, Head and Neck Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Department of Otorhinolaryngology, Head and Neck Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Fujian Provincial Clinical Medical Research Center for Ear, Nose and Throat Difficulty Diseases, Fuzhou, Fujian, China
| | - Guangnan Yao
- Department of Otorhinolaryngology, Head and Neck Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Department of Otorhinolaryngology, Head and Neck Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Fujian Provincial Clinical Medical Research Center for Ear, Nose and Throat Difficulty Diseases, Fuzhou, Fujian, China
| | - Shenqing Nian
- Department of Otorhinolaryngology, Head and Neck Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Department of Otorhinolaryngology, Head and Neck Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Fujian Provincial Clinical Medical Research Center for Ear, Nose and Throat Difficulty Diseases, Fuzhou, Fujian, China
| | - Xihang Chen
- Department of Otorhinolaryngology, Head and Neck Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Department of Otorhinolaryngology, Head and Neck Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Fujian Provincial Clinical Medical Research Center for Ear, Nose and Throat Difficulty Diseases, Fuzhou, Fujian, China
| | - Simin Weng
- Department of Otorhinolaryngology, Head and Neck Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Department of Otorhinolaryngology, Head and Neck Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Fujian Provincial Clinical Medical Research Center for Ear, Nose and Throat Difficulty Diseases, Fuzhou, Fujian, China
| | - Xi Gu
- Department of Otorhinolaryngology, Head and Neck Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Department of Otorhinolaryngology, Head and Neck Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Fujian Provincial Clinical Medical Research Center for Ear, Nose and Throat Difficulty Diseases, Fuzhou, Fujian, China
| | - Chang Lin
- Department of Otorhinolaryngology, Head and Neck Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Department of Otorhinolaryngology, Head and Neck Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Fujian Provincial Clinical Medical Research Center for Ear, Nose and Throat Difficulty Diseases, Fuzhou, Fujian, China
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Huang J, Su C, Lu P, Zhao X, Liu Y, Xie Q, Chen C. hsa_circ_0000417 downregulation suppresses androgen receptor expression and apoptotic signals in human foreskin fibroblasts via sponging miR-6756-5p. Mol Biol Rep 2023; 50:6769-6781. [PMID: 37389702 DOI: 10.1007/s11033-023-08628-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 06/22/2023] [Indexed: 07/01/2023]
Abstract
BACKGROUND Dysregulated apoptosis of penile mesenchymal cells during male urethragenesis has been previously demonstrated to underly hypospadiac urethral closure failure, and androgen receptor (AR) has been shown to play a central role in regulating penile mesenchyme cell proliferation and survival. However, the regulatory mechanisms upstream and downstream of AR remain poorly understood. Our clinical data and bioinformatics analysis previously indicated that hsa_circ_0000417, a circRNA significantly downregulated in hypospadias preputial specimens, may act as a ceRNA for AR via sequestering hsa_miR-6756-5p, and that the biological functions of hsa_circ_0000417 may significantly involve the PI3K/AKT pathway. In this study, we employed human foreskin fibroblasts (HFF-1) to experimentally validate this putative hsa_circ_0000417/miR-6756-5p/AR axis and its impact on penile mesenchymal cell proliferation and apoptosis. METHOD AND RESULTS We showed that hsa_circ_0000417 knockdown significantly promoted proliferation and suppressed apoptosis of HFF-1 cells. Mechanistically, hsa_circ_0000417 functioned as a molecular sponge for miR-6756-5p in HFF-1 cells and relieved the latter's translational repression on AR mRNA, leading to decreased AKT activation and increased expression of pro-apoptotic proteins BAX and cleaved-caspase 9. Conversely, elevated levels of miR-6756-5p resulted in diminished AR expression concomitant with enhanced AKT activation and HFF-1 cell proliferation. CONCLUSIONS Collectively, our data describe for the first time a circRNA-mediated post-transcriptional regulatory mechanism of AR and its functional consequences in penile mesenchymal cells in the context of hypospadias. These findings may contribute to advancing our current understanding of the roles of AR and mesenchymal cell fate decisions during penile morphogenesis.
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Affiliation(s)
- Junqiang Huang
- Department of Pediatric Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Cheng Su
- Department of Pediatric Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Pingan Lu
- Faculty of Medicine, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam, Netherlands
| | - Xiangyou Zhao
- Department of Pediatric Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yuling Liu
- Department of Pediatric Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Qike Xie
- Department of Pediatric Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Chao Chen
- Department of Pediatric Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China.
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RNA-seq reveals that overexpression of TcUBP1 switches the gene expression pattern towards that of the infective form of Trypanosoma cruzi. J Biol Chem 2023; 299:104623. [PMID: 36935010 PMCID: PMC10141520 DOI: 10.1016/j.jbc.2023.104623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/02/2023] [Accepted: 03/03/2023] [Indexed: 03/19/2023] Open
Abstract
Trypanosomes regulate gene expression mainly by using post-transcriptional mechanisms. Key factors responsible for carrying out this regulation are RNA-binding proteins (RBPs), affecting subcellular localization, translation, and/or transcript stability. Trypanosoma cruzi U-rich RBP 1 (TcUBP1) is a small protein that modulates the expression of several surface glycoproteins of the trypomastigote infective stage of the parasite. Its mRNA targets are known but the impact of its overexpression at the transcriptome level in the insect-dwelling epimastigote cells has not yet been investigated. Thus, in the present study, by using a tetracycline-inducible system, we generated a population of TcUBP1-overexpressing parasites and analyzed its effect by RNA-seq methodology. This allowed us to identify 793 up- and 371 down-regulated genes with respect to the wild-type control sample. Among the up-regulated genes, it was possible to identify members coding for the TcS superfamily, MASP, MUCI/II, and protein kinases, whereas among the down-regulated transcripts, we found mainly genes coding for ribosomal, mitochondrial, and synthetic pathway proteins. RNA-seq comparison with two previously published datasets revealed that the expression profile of this TcUBP1-overexpressing replicative epimastigote form resembles the transition to the infective metacyclic trypomastigote stage. We identified novel cis-regulatory elements in the 3'-untranslated region of the affected transcripts and confirmed that UBP1m -a signature TcUBP1 binding element previously characterized in our lab- is enriched in the list of stabilized genes. We can conclude that the overall effect of TcUBP1 overexpression on the epimastigote transcriptome is mainly the stabilization of mRNAs coding for proteins that are important for parasite infection.
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Man HSJ, Subramaniam N, Downs T, Sukumar AN, Saha AD, Nair R, Chen L, Teitelbaum D, Turgeon PJ, Ku KH, Tran E, de Perrot M, Marsden PA. Long noncoding RNA GATA2-AS1 augments endothelial Hypoxia Inducible Factor 1-α induction and regulates hypoxic signaling. J Biol Chem 2023; 299:103029. [PMID: 36806681 PMCID: PMC10148162 DOI: 10.1016/j.jbc.2023.103029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 01/18/2023] [Accepted: 01/20/2023] [Indexed: 02/18/2023] Open
Abstract
Vascular endothelial cells form the inner cellular lining of blood vessels and have myriad physiologic functions including angiogenesis and response to hypoxia. We recently identified a set of endothelial cell (EC)-enriched long noncoding RNAs (lncRNAs) in differentiated human primary cell types and described the role of the STEEL lncRNA in angiogenic patterning. We sought to further understand the role of EC-enriched lncRNAs in physiologic adaptation of the vascular endothelium. In this work, we describe an abundant, cytoplasmic, and EC-enriched lncRNA, GATA2-AS1, that is divergently transcribed from the EC-enriched developmental regulator, GATA2. While GATA2-AS1 is largely co-expressed with GATA2 in ECs, GATA2-AS1 and GATA2 appear to be complementary rather than synergistic as they have mostly distinct target genes. Common single nucleotide variants (SNVs) in GATA2-AS1 exons are associated with early onset coronary artery disease (CAD) and decreased expression of GATA2-AS1 in endothelial cell lines. In most cells, HIF1-α is central to the transcriptional response to hypoxia, while in ECs, both HIF1-α and HIF2-α are required to coordinate an acute and chronic response respectively. In this setting, GATA2-AS1 contributes to the "HIF switch" and augments HIF1-α induction in acute hypoxia to regulate HIF1-α/ HIF2-α balance. In hypoxia, GATA2-AS1 orchestrates HIF1-α-dependent induction of the glycolytic pathway, and HIF1-α-independent maintenance of mitochondrial biogenesis. Similarly, GATA2-AS1 coordinates both metabolism and "tip/stalk" cell signaling to regulate angiogenesis in hypoxic ECs. Furthermore, we find that GATA2-AS1 expression patterns are perturbed in atherosclerotic disease. Together, these results define a role for GATA2-AS1 in the EC-specific response to hypoxia.
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Affiliation(s)
- H S Jeffrey Man
- Institute of Medical Science, Toronto, Ontario, Canada; Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada; Latner Thoracic Surgery Research Laboratories, Toronto General Hospital Research Institute, Toronto, Ontario, Canada; Department of Respirology, University Health Network, Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Noeline Subramaniam
- Institute of Medical Science, Toronto, Ontario, Canada; Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada
| | - Tiana Downs
- Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Aravin N Sukumar
- Institute of Medical Science, Toronto, Ontario, Canada; Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada
| | - Aninda D Saha
- Institute of Medical Science, Toronto, Ontario, Canada; Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada
| | - Ranju Nair
- Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Lucy Chen
- Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Daniel Teitelbaum
- Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Paul J Turgeon
- Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Kyung Ha Ku
- Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Eileen Tran
- Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Marc de Perrot
- Latner Thoracic Surgery Research Laboratories, Toronto General Hospital Research Institute, Toronto, Ontario, Canada; Division of Thoracic Surgery, Toronto General Hospital, Toronto, Ontario, Canada
| | - Philip A Marsden
- Institute of Medical Science, Toronto, Ontario, Canada; Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, Department of Medicine, University of Toronto, Toronto, Ontario, Canada.
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Domingo-Muelas A, Duart-Abadia P, Morante-Redolat JM, Jordán-Pla A, Belenguer G, Fabra-Beser J, Paniagua-Herranz L, Pérez-Villalba A, Álvarez-Varela A, Barriga FM, Gil-Sanz C, Ortega F, Batlle E, Fariñas I. Post-transcriptional control of a stemness signature by RNA-binding protein MEX3A regulates murine adult neurogenesis. Nat Commun 2023; 14:373. [PMID: 36690670 PMCID: PMC9871011 DOI: 10.1038/s41467-023-36054-6] [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: 08/01/2022] [Accepted: 01/12/2023] [Indexed: 01/25/2023] Open
Abstract
Neural stem cells (NSCs) in the adult murine subependymal zone balance their self-renewal capacity and glial identity with the potential to generate neurons during the lifetime. Adult NSCs exhibit lineage priming via pro-neurogenic fate determinants. However, the protein levels of the neural fate determinants are not sufficient to drive direct differentiation of adult NSCs, which raises the question of how cells along the neurogenic lineage avoid different conflicting fate choices, such as self-renewal and differentiation. Here, we identify RNA-binding protein MEX3A as a post-transcriptional regulator of a set of stemness associated transcripts at critical transitions in the subependymal neurogenic lineage. MEX3A regulates a quiescence-related RNA signature in activated NSCs that is needed for their return to quiescence, playing a role in the long-term maintenance of the NSC pool. Furthermore, it is required for the repression of the same program at the onset of neuronal differentiation. Our data indicate that MEX3A is a pivotal regulator of adult murine neurogenesis acting as a translational remodeller.
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Grants
- EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)
- Ministerio de Ciencia e Innovación (MICINN, Spain) - PID2020-119917RB-I00.
- Regional Government of Valencia | Conselleria d'Educació, Investigació, Cultura i Esport (Conselleria d'Educació, Investigació, Cultura i Esport de la Generalitat Valenciana)
- Ministerio de Ciencia e Innovación (MICINN, Spain) - PID2020-117937GB-I00, PID2020-119917RB-I00, PID 2019-109155RB-I00, PID2020-114227RB-I00, RyC-2015-19058, PRE2018-084838. Centro de Investigación Biomédica en Red Enfermedades Neurodegenerativas (CIBERNED, Spain) - MICINN- CB06/05/0086.
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Affiliation(s)
- Ana Domingo-Muelas
- Departamento de Biología Celular, Biología Funcional y Antropología Física, Universidad de Valencia, Valencia, Spain
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Universidad de Valencia, Valencia, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Valencia, Spain
| | - Pere Duart-Abadia
- Departamento de Biología Celular, Biología Funcional y Antropología Física, Universidad de Valencia, Valencia, Spain
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Universidad de Valencia, Valencia, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Valencia, Spain
| | - Jose Manuel Morante-Redolat
- Departamento de Biología Celular, Biología Funcional y Antropología Física, Universidad de Valencia, Valencia, Spain
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Universidad de Valencia, Valencia, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Valencia, Spain
| | - Antonio Jordán-Pla
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Universidad de Valencia, Valencia, Spain
| | - Germán Belenguer
- Departamento de Biología Celular, Biología Funcional y Antropología Física, Universidad de Valencia, Valencia, Spain
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Universidad de Valencia, Valencia, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Valencia, Spain
| | - Jaime Fabra-Beser
- Departamento de Biología Celular, Biología Funcional y Antropología Física, Universidad de Valencia, Valencia, Spain
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Universidad de Valencia, Valencia, Spain
| | - Lucía Paniagua-Herranz
- Departamento de Bioquímica y Biología Molecular, Universidad Complutense de Madrid (UCM), Madrid, Spain
- Instituto Universitario de Investigación en Neuroquímica (IUIN), Madrid, Spain
- Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain
| | - Ana Pérez-Villalba
- Departamento de Biología Celular, Biología Funcional y Antropología Física, Universidad de Valencia, Valencia, Spain
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Universidad de Valencia, Valencia, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Valencia, Spain
| | - Adrián Álvarez-Varela
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - Francisco M Barriga
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - Cristina Gil-Sanz
- Departamento de Biología Celular, Biología Funcional y Antropología Física, Universidad de Valencia, Valencia, Spain
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Universidad de Valencia, Valencia, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Valencia, Spain
| | - Felipe Ortega
- Departamento de Bioquímica y Biología Molecular, Universidad Complutense de Madrid (UCM), Madrid, Spain
- Instituto Universitario de Investigación en Neuroquímica (IUIN), Madrid, Spain
- Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain
| | - Eduard Batlle
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain.
- ICREA, Barcelona, Spain.
| | - Isabel Fariñas
- Departamento de Biología Celular, Biología Funcional y Antropología Física, Universidad de Valencia, Valencia, Spain.
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Universidad de Valencia, Valencia, Spain.
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Valencia, Spain.
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10
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Zhang S, Yang X, Jiang M, Ma L, Hu J, Zhang HH. Post-transcriptional control by RNA-binding proteins in diabetes and its related complications. Front Physiol 2022; 13:953880. [PMID: 36277184 PMCID: PMC9582753 DOI: 10.3389/fphys.2022.953880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 09/20/2022] [Indexed: 11/25/2022] Open
Abstract
Diabetes mellitus (DM) is a fast-growing chronic metabolic disorder that leads to significant health, social, and economic problems worldwide. Chronic hyperglycemia caused by DM leads to multiple devastating complications, including macrovascular complications and microvascular complications, such as diabetic cardiovascular disease, diabetic nephropathy, diabetic neuropathy, and diabetic retinopathy. Numerous studies provide growing evidence that aberrant expression of and mutations in RNA-binding proteins (RBPs) genes are linked to the pathogenesis of diabetes and associated complications. RBPs are involved in RNA processing and metabolism by directing a variety of post-transcriptional events, such as alternative splicing, stability, localization, and translation, all of which have a significant impact on RNA fate, altering their function. Here, we purposed to summarize the current progression and underlying regulatory mechanisms of RBPs in the progression of diabetes and its complications. We expected that this review will open the door for RBPs and their RNA networks as novel therapeutic targets for diabetes and its related complications.
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Affiliation(s)
- Shiyu Zhang
- Department of Endocrinology, The Second Affiliated Hospital, Soochow University, Suzhou, China
| | - Xiaohua Yang
- The Affiliated Haian Hospital of Nantong University, Nantong, China
| | - Miao Jiang
- Department of Endocrinology, The Second Affiliated Hospital, Soochow University, Suzhou, China
| | - Lianhua Ma
- Department of Endocrinology, The Second Affiliated Hospital, Soochow University, Suzhou, China
| | - Ji Hu
- Department of Endocrinology, The Second Affiliated Hospital, Soochow University, Suzhou, China,*Correspondence: Ji Hu, ; Hong-Hong Zhang,
| | - Hong-Hong Zhang
- Department of Endocrinology, The Second Affiliated Hospital, Soochow University, Suzhou, China,*Correspondence: Ji Hu, ; Hong-Hong Zhang,
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11
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Palzer KA, Bolduan V, Käfer R, Kleinert H, Bros M, Pautz A. The Role of KH-Type Splicing Regulatory Protein (KSRP) for Immune Functions and Tumorigenesis. Cells 2022; 11:cells11091482. [PMID: 35563788 PMCID: PMC9104899 DOI: 10.3390/cells11091482] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/21/2022] [Accepted: 04/26/2022] [Indexed: 12/11/2022] Open
Abstract
Post-transcriptional control of gene expression is one important mechanism that enables stringent and rapid modulation of cytokine, chemokines or growth factors expression, all relevant for immune or tumor cell function and communication. The RNA-binding protein KH-type splicing regulatory protein (KSRP) controls the mRNA stability of according genes by initiation of mRNA decay and inhibition of translation, and by enhancing the maturation of microRNAs. Therefore, KSRP plays a pivotal role in immune cell function and tumor progression. In this review, we summarize the current knowledge about KSRP with regard to the regulation of immunologically relevant targets, and the functional role of KSRP on immune responses and tumorigenesis. KSRP is involved in the control of myeloid hematopoiesis. Further, KSRP-mediated mRNA decay of pro-inflammatory factors is necessary to keep immune homeostasis. In case of infection, functional impairment of KSRP is important for the induction of robust immune responses. In this regard, KSRP seems to primarily dampen T helper cell 2 immune responses. In cancer, KSRP has often been associated with tumor growth and metastasis. In summary, aside of initiation of mRNA decay, the KSRP-mediated regulation of microRNA maturation seems to be especially important for its diverse biological functions, which warrants further in-depth examination.
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Affiliation(s)
- Kim-Alicia Palzer
- Department of Pharmacology, University Medical Center of the Johannes Gutenberg University Mainz, 55131 Mainz, Germany; (K.-A.P.); (R.K.); (H.K.)
| | - Vanessa Bolduan
- Department of Dermatology, University Medical Center of the Johannes Gutenberg University Mainz, 55131 Mainz, Germany; (V.B.); (M.B.)
| | - Rudolf Käfer
- Department of Pharmacology, University Medical Center of the Johannes Gutenberg University Mainz, 55131 Mainz, Germany; (K.-A.P.); (R.K.); (H.K.)
| | - Hartmut Kleinert
- Department of Pharmacology, University Medical Center of the Johannes Gutenberg University Mainz, 55131 Mainz, Germany; (K.-A.P.); (R.K.); (H.K.)
| | - Matthias Bros
- Department of Dermatology, University Medical Center of the Johannes Gutenberg University Mainz, 55131 Mainz, Germany; (V.B.); (M.B.)
| | - Andrea Pautz
- Department of Pharmacology, University Medical Center of the Johannes Gutenberg University Mainz, 55131 Mainz, Germany; (K.-A.P.); (R.K.); (H.K.)
- Correspondence: ; Tel.: +49-6131-179276; Fax: +49-6131-179042
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12
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Millette MM, Holland ED, Tenpas TJ, Dent EW. A Single Transcript Knockdown-Replacement Strategy Employing 5' UTR Secondary Structures to Precisely Titrate Rescue Protein Translation. Front Genome Ed 2022; 4:803375. [PMID: 35419562 PMCID: PMC8995503 DOI: 10.3389/fgeed.2022.803375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 01/31/2022] [Indexed: 11/16/2022] Open
Abstract
One overarching goal of gene therapy is the replacement of faulty genes with functional ones. A significant hurdle is presented by the fact that under- or over-expression of a protein may cause disease as readily as coding mutations. There is a clear and present need for pipelines to translate experimentally validated gene therapy strategies to clinical application. To address this we developed a modular, single-transgene expression system for replacing target genes with physiologically expressed variants. In order to accomplish this, we first designed a range of 5' UTR "attenuator" sequences which predictably diminish translation of the paired gene. These sequences provide wide general utility by allowing control over translation from high expression, ubiquitous promoters. Importantly, we demonstrate that this permits an entirely novel knockdown and rescue application by pairing microRNA-adapted shRNAs alongside their respective replacement gene on a single transcript. A noteworthy candidate for this corrective approach is the degenerative and uniformly fatal motor neuron disease ALS. A strong proportion of non-idiopathic ALS cases are caused by varied mutations to the SOD1 gene, and as clinical trials to treat ALS are being initiated, it is important to consider that loss-of-function mechanisms contribute to its pathology as strongly as any other factor. As a generalized approach to treat monogenic diseases caused by heterogeneous mutations, we demonstrate complete and predictable control over replacement of SOD1 in stable cell lines by varying the strength of attenuators.
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Affiliation(s)
- Matthew M. Millette
- Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin, Madison, WI, United States
- Neuroscience Training Program, University of Wisconsin, Madison, WI, United States
| | - Elizabeth D. Holland
- Neuroscience Training Program, University of Wisconsin, Madison, WI, United States
| | - Tanner J. Tenpas
- Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin, Madison, WI, United States
| | - Erik W. Dent
- Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin, Madison, WI, United States
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13
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Nikonova E, Mukherjee A, Kamble K, Barz C, Nongthomba U, Spletter ML. Rbfox1 is required for myofibril development and maintaining fiber type-specific isoform expression in Drosophila muscles. Life Sci Alliance 2022; 5:5/4/e202101342. [PMID: 34996845 PMCID: PMC8742874 DOI: 10.26508/lsa.202101342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 12/22/2021] [Accepted: 12/23/2021] [Indexed: 11/24/2022] Open
Abstract
Protein isoform transitions confer muscle fibers with distinct properties and are regulated by differential transcription and alternative splicing. RNA-binding Fox protein 1 (Rbfox1) can affect both transcript levels and splicing, and is known to contribute to normal muscle development and physiology in vertebrates, although the detailed mechanisms remain obscure. In this study, we report that Rbfox1 contributes to the generation of adult muscle diversity in Drosophila Rbfox1 is differentially expressed among muscle fiber types, and RNAi knockdown causes a hypercontraction phenotype that leads to behavioral and eclosion defects. Misregulation of fiber type-specific gene and splice isoform expression, notably loss of an indirect flight muscle-specific isoform of Troponin-I that is critical for regulating myosin activity, leads to structural defects. We further show that Rbfox1 directly binds the 3'-UTR of target transcripts, regulates the expression level of myogenic transcription factors myocyte enhancer factor 2 and Salm, and both modulates expression of and genetically interacts with the CELF family RNA-binding protein Bruno1 (Bru1). Rbfox1 and Bru1 co-regulate fiber type-specific alternative splicing of structural genes, indicating that regulatory interactions between FOX and CELF family RNA-binding proteins are conserved in fly muscle. Rbfox1 thus affects muscle development by regulating fiber type-specific splicing and expression dynamics of identity genes and structural proteins.
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Affiliation(s)
- Elena Nikonova
- Department of Physiological Chemistry, Biomedical Center, Ludwig-Maximilians-Universität München, Martinsried-Planegg, Germany
| | - Amartya Mukherjee
- Department of Molecular Reproduction, Development and Genetics (MRDG), Indian Institute of Science, Bangalore, India
| | - Ketaki Kamble
- Department of Molecular Reproduction, Development and Genetics (MRDG), Indian Institute of Science, Bangalore, India
| | - Christiane Barz
- Muscle Dynamics Group, Max Planck Institute of Biochemistry, Martinsried-Planegg, Germany
| | - Upendra Nongthomba
- Department of Molecular Reproduction, Development and Genetics (MRDG), Indian Institute of Science, Bangalore, India
| | - Maria L Spletter
- Department of Physiological Chemistry, Biomedical Center, Ludwig-Maximilians-Universität München, Martinsried-Planegg, Germany
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14
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Weng C, Wang L, Liu G, Guan M, Lu L. Identification of a N6-Methyladenosine (m6A)-Related lncRNA Signature for Predicting the Prognosis and Immune Landscape of Lung Squamous Cell Carcinoma. Front Oncol 2021; 11:763027. [PMID: 34868980 PMCID: PMC8637334 DOI: 10.3389/fonc.2021.763027] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 10/26/2021] [Indexed: 12/21/2022] Open
Abstract
Background m6A-related lncRNAs emerged as potential targets for tumor diagnosis and treatment. This study aimed to identify m6A-regulated lncRNAs in lung squamous cell carcinoma (LUSC) patients. Materials and Methods RNA sequencing and the clinical data of LUSC patients were downloaded from The Cancer Genome Atlas (TCGA) database. The m6A-related lncRNAs were identified by using Pearson correlation assay. Univariate and multivariate Cox regression analyses were utilized to construct a risk model. The performance of the risk model was validated using Kaplan–Meier survival analysis and receiver operating characteristics (ROC). Immune estimation of LUSC was downloaded from TIMER, and the correlations between the risk score and various immune cells infiltration were analyzed using various methods. Differences in immune functions and expression of immune checkpoint inhibitors and m6A regulators between high-risk and low-risk groups were further explored. Finally, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were utilized to explore the biological functions of AL122125.1. Results A total of 351 m6A-related lncRNAs were obtained from TCGA. Seven lncRNAs demonstrated prognostic values. A further multivariate Cox regression assay constructed a risk model consisting of two lncRNAs (AL122125.1 and HORMAD2-AS1). The Kaplan–Meier analysis and area under the curve indicated that this risk model could be used to predict the prognosis of LUSC patients. The m6A-related lncRNAs were immune-associated. There were significant correlations between risk score and immune cell infiltration, immune functions, and expression of immune checkpoint inhibitors. Meanwhile, there were significant differences in the expression of m6A regulators between the high- and low-risk groups. Moreover, GO and KEGG analyses revealed that the upregulated expression of AL122125.1 was tumor-related. Conclusion In this study, we constructed an m6A-related lncRNA risk model to predict the survival of LUSC patients. This study could provide a novel insight to the prognosis and treatment of LUSC patients.
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Affiliation(s)
- Chengyin Weng
- Department of Medical Oncology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Lina Wang
- Department of Medical Oncology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Guolong Liu
- Department of Medical Oncology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Mingmei Guan
- Department of Medical Oncology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Lin Lu
- Department of Medical Oncology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
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15
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He W, Yang G, Liu S, Maghsoudloo M, Shasaltaneh MD, Kaboli PJ, Zhang C, Zhang J, Entezari M, Imani S, Wen Q. Comparative mRNA/micro-RNA co-expression network drives melanomagenesis by promoting epithelial-mesenchymal transition and vasculogenic mimicry signaling. Transl Oncol 2021; 14:101237. [PMID: 34626953 PMCID: PMC8512639 DOI: 10.1016/j.tranon.2021.101237] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 09/30/2021] [Indexed: 12/17/2022] Open
Abstract
This study aimed to identify a novel disease-associated differentially co-expressed mRNA-microRNA (miRNA) that is associated with vasculogenic mimicry (VM) and epithelial-to-mesenchymal transition (EMT) network at different stages of melanoma. By applying weighted gene co-expression network analysis, we constructed a VM+EMT biological network with the available microarray dataset downloaded from a public database. Quantitative real-time PCR, immunohistochemical staining, and CD31-periodic acid solution dual staining were performed to confirm the expression of genes associated with EMT and VM formation in subjects with malignant melanoma (n = 18) and primary melanoma (n = 13) and in healthy subjects (n = 10). Our findings suggested that phosphatidylserine-specific phospholipase A1-alpha (PLA1A) and dermokine (DMKN) genes function as oncogenes that trigger VM and EMT processes during melanomagenesis on interaction with miR-370, miR-563, and miR-770-5p. PLA1A and DMKN genes can be considered potential VM+EMT network-based diagnostic biomarkers for distinguishing between melanoma patients. We postulate that a network with altered PLA1A/miR-563 and DMNK/miR-770-5p/miR-370 may contribute to melanomagenesis by triggering the EMT signaling pathway and VM formation. This study provides a potentially valuable approach for the early diagnosis and prognosis of melanoma progression.
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Affiliation(s)
- WenFeng He
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Gang Yang
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China; Department of Oncology, Anyue Hospital of Traditional Chinese Medicine, Second Ziyang Hospital of Traditional Chinese Medicine, Ziyang, Sichuan, China
| | - Shuya Liu
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China; Department of Oncology, Chengdu Jinniu District People's Hospital, Chengdu, Sichuan, China
| | - Mazaher Maghsoudloo
- Laboratory of Systems Biology and Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran; Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | | | - Parham Jabbarzadeh Kaboli
- Graduate Institute of Biomedical Sciences, Research Center for Cancer Biology, and Center for Molecular Medicine, China Medical University, Taichung, Taiwan
| | - Cuiwei Zhang
- Department of Pathology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - JingHeng Zhang
- Oncology Department, Luzhou People's Hospital, Luzhou, Sichuan, China
| | - Maliheh Entezari
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Farhikhtegan Medical Convergence sciences Research Center, Farhikhtegan Hospital Tehran Medical sciences, Islamic Azad University, Tehran, Iran
| | - Saber Imani
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China.
| | - QingLian Wen
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China.
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16
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Reimagining the Power of Nucleic Acids as Therapeutic and Diagnostic Agents. Biomolecules 2021; 11:biom11111707. [PMID: 34827705 PMCID: PMC8615837 DOI: 10.3390/biom11111707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 11/06/2021] [Indexed: 11/24/2022] Open
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17
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Luo Y, Ge P, Wang M, Chen H, Liu J, Wei T, Jiang Y, Qu J, Chen H. Research progress of DLX6-AS1 in human cancers. Hum Cell 2021; 34:1642-1652. [PMID: 34508305 DOI: 10.1007/s13577-021-00613-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 09/06/2021] [Indexed: 12/21/2022]
Abstract
Long non-coding RNAs (lncRNAs) are a kind of translational-repressor RNAs composed of more than 200 nucleotides and formerly considered as "transcriptional noise". Recently studies have shown that lncRNAs could bind to multiple biomolecules such as DNA, transcription factors, RNA, chromatin complexes and proteins, and regulate target gene expression at multi-levels, thus playing an essential role in human tumors. DLX6-AS1, a recently discovered oncogenic lncRNA, is highly expressed in various human tumors, including lung cancer, liver cancer and pancreatic cancer. This paper mainly reviewed the regulatory mechanism of DLX6-AS1 as a competitive endogenous RNA (ceRNA) in tumor cell proliferation, cell apoptosis, angiogenesis, epithelial-mesenchymal transformation, chemotherapy resistance and metabolic changes. Furthermore, the translational value of DLX6-AS1 in cancer was also elucidated, which suggested its potential as a diagnostic or prognostic biomarker in cancer. In summary, this present article not only makes an in-depth analysis of the expression changes and carcinogenic mechanism of DLX6-AS1 in various human cancers, but also provides a new breakthrough for the diagnosis and treatment of cancers.
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Affiliation(s)
- Yalan Luo
- Department of General Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, 116011, People's Republic of China.,Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, 116044, People's Republic of China.,Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, 116011, People's Republic of China
| | - Peng Ge
- Department of General Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, 116011, People's Republic of China.,Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, 116044, People's Republic of China.,Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, 116011, People's Republic of China
| | - Mengfei Wang
- Department of General Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, 116011, People's Republic of China.,Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, 116044, People's Republic of China
| | - Haiyang Chen
- Department of General Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, 116011, People's Republic of China.,Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, 116044, People's Republic of China.,Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, 116011, People's Republic of China
| | - Jiayue Liu
- Department of General Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, 116011, People's Republic of China.,Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, 116044, People's Republic of China.,Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, 116011, People's Republic of China
| | - Tianfu Wei
- Department of General Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, 116011, People's Republic of China.,Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, 116044, People's Republic of China.,Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, 116011, People's Republic of China
| | - Yuankuan Jiang
- Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, 116044, People's Republic of China.,Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, 116011, People's Republic of China
| | - Jialin Qu
- Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, 116044, People's Republic of China. .,Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, 116011, People's Republic of China.
| | - Hailong Chen
- Department of General Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, 116011, People's Republic of China. .,Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, 116044, People's Republic of China. .,Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, 116011, People's Republic of China.
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Subramaniam N, Nair R, Marsden PA. Epigenetic Regulation of the Vascular Endothelium by Angiogenic LncRNAs. Front Genet 2021; 12:668313. [PMID: 34512715 PMCID: PMC8427604 DOI: 10.3389/fgene.2021.668313] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 05/17/2021] [Indexed: 12/15/2022] Open
Abstract
The functional properties of the vascular endothelium are diverse and heterogeneous between vascular beds. This is especially evident when new blood vessels develop from a pre-existing closed cardiovascular system, a process termed angiogenesis. Endothelial cells are key drivers of angiogenesis as they undergo a highly choreographed cascade of events that has both exogenous (e.g., hypoxia and VEGF) and endogenous regulatory inputs. Not surprisingly, angiogenesis is critical in health and disease. Diverse therapeutics target proteins involved in coordinating angiogenesis with varying degrees of efficacy. It is of great interest that recent work on non-coding RNAs, especially long non-coding RNAs (lncRNAs), indicates that they are also important regulators of the gene expression paradigms that underpin this cellular cascade. The protean effects of lncRNAs are dependent, in part, on their subcellular localization. For instance, lncRNAs enriched in the nucleus can act as epigenetic modifiers of gene expression in the vascular endothelium. Of great interest to genetic disease, they are undergoing rapid evolution and show extensive inter- and intra-species heterogeneity. In this review, we describe endothelial-enriched lncRNAs that have robust effects in angiogenesis.
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Affiliation(s)
- Noeline Subramaniam
- Marsden Lab, Institute of Medical Sciences, University of Toronto, Toronto, ON, Canada
- Marsden Lab, Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael’s Hospital, Toronto, ON, Canada
| | - Ranju Nair
- Marsden Lab, Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael’s Hospital, Toronto, ON, Canada
- Marsden Lab, Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Philip A. Marsden
- Marsden Lab, Institute of Medical Sciences, University of Toronto, Toronto, ON, Canada
- Marsden Lab, Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael’s Hospital, Toronto, ON, Canada
- Marsden Lab, Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Department of Medicine, University of Toronto, Toronto, ON, Canada
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