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Rahmati A, Mafi A, Vakili O, Soleymani F, Alishahi Z, Yahyazadeh S, Gholinezhad Y, Rezaee M, Johnston TP, Sahebkar A. Non-coding RNAs in leukemia drug resistance: new perspectives on molecular mechanisms and signaling pathways. Ann Hematol 2024; 103:1455-1482. [PMID: 37526673 DOI: 10.1007/s00277-023-05383-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 07/22/2023] [Indexed: 08/02/2023]
Abstract
Like almost all cancer types, timely diagnosis is needed for leukemias to be effectively cured. Drug efflux, attenuated drug uptake, altered drug metabolism, and epigenetic alterations are just several of the key mechanisms by which drug resistance develops. All of these mechanisms are orchestrated by up- and downregulators, in which non-coding RNAs (ncRNAs) do not encode specific proteins in most cases; albeit, some of them have been found to exhibit the potential for protein-coding. Notwithstanding, ncRNAs are chiefly known for their contribution to the regulation of physiological processes, as well as the pathological ones, such as cell proliferation, apoptosis, and immune responses. Specifically, in the case of leukemia chemo-resistance, ncRNAs have been recognized to be responsible for modulating the initiation and progression of drug resistance. Herein, we comprehensively reviewed the role of ncRNAs, specifically its effect on molecular mechanisms and signaling pathways, in the development of leukemia drug resistance.
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Affiliation(s)
- Atefe Rahmati
- Department of Hematology and Blood Banking, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Basic Sciences, Faculty of Medicine, Neyshabur University of Medical Sciences, Neyshabur, Iran
| | - Alireza Mafi
- Department of Clinical Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Omid Vakili
- Department of Clinical Biochemistry, Autophagy Research Center, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Firooze Soleymani
- Department of Medical Biotechnology and Nanotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Zahra Alishahi
- Department of Basic Sciences, Faculty of Medicine, Neyshabur University of Medical Sciences, Neyshabur, Iran
| | - Sheida Yahyazadeh
- Department of Immunology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Yasaman Gholinezhad
- Department of Pharmacology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Malihe Rezaee
- School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Tehran Heart Center, Cardiovascular Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Thomas P Johnston
- Division of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Missouri-Kansas City, Kansas City, MO, USA
| | - Amirhossein Sahebkar
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, the, Islamic Republic of Iran.
- Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, the, Islamic Republic of Iran.
- Department of Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, the, Islamic Republic of Iran.
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2
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Katkevics M, MacKay JA, Rozners E. Triplex-forming peptide nucleic acids as emerging ligands to modulate structure and function of complex RNAs. Chem Commun (Camb) 2024; 60:1999-2008. [PMID: 38259187 PMCID: PMC10922694 DOI: 10.1039/d3cc05409h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Over the last three decades, our view of RNA has changed from a simple intermediate supporting protein synthesis to a major regulator of biological processes. In the expanding area of RNA research, peptide nucleic acid (PNA) is emerging as a promising ligand for triple-helical recognition of complex RNAs. As discussed in this feature article, the key advantages of PNAs are high sequence specificity and affinity for RNA (>10 fold higher than for DNA) that are difficult to achieve with small molecule ligands. Emerging studies demonstrate that triple-helical binding of PNAs can modulate biological function and control dynamic conformational equilibria of complex folded RNAs. These results suggest that PNA has a unique potential as a research tool and therapeutic compound targeting RNA. The remaining problems hampering advances in these directions are limitations of sequences that can be recognized by Hoogsteen triplexes (typically purine rich tracts), poor cellular uptake and bioavailability of PNA, and potential off-target effects in biological systems. Recent exciting studies are discussed that illustrate how synthetic nucleic acid chemistry provides innovative solutions for these problems.
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Affiliation(s)
- Martins Katkevics
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, LV-1006, Latvia
| | - James A MacKay
- Department of Chemistry and Biochemistry, Elizabethtown College, Elizabethtown, PA 17022, USA
| | - Eriks Rozners
- Department of Chemistry, Binghamton University, Binghamton, NY 13902, USA.
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3
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Ghafouri-Fard S, Harsij A, Hussen BM, Pourmoshtagh H, Taheri M. A review on the role of FOXD2-AS1 in human disorders. Pathol Res Pract 2024; 254:155101. [PMID: 38211387 DOI: 10.1016/j.prp.2024.155101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/03/2024] [Accepted: 01/05/2024] [Indexed: 01/13/2024]
Abstract
FOXD2 adjacent opposite strand RNA 1 (FOXD2-AS1) is a long non-coding RNA being transcribed from a locus on chromosome 1p33. This transcript has been found to be up-regulated in tumor samples of almost all types of malignancies in association with a significant increase in malignant features. FOXD2-AS1 can affect activity of PI3K/AKT, AKT/mTOR, Hippo/YAP, Notch, NRf2, Wnt/β-catenin, NF-ƙB and ERK/MAPK pathways. Furthermore, it can enhance stem cell properties in cancer cells and prompt epithelial-mesenchymal transition. It is also involved in induction of resistance to a variety of anticancer agents such as adriamycin, cisplatin, 5-fluorouracil, temozolomide and gemcitabine. This article summarizes the impact of FOXD2-AS1 in diverse human disorders.
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Affiliation(s)
- Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Atefeh Harsij
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Bashdar Mahmud Hussen
- Department of Biomedical Sciences, College of Science, Cihan University-Erbil, Erbil, Kurdistan Region, Iraq; Department of Clinical Analysis, College of Pharmacy, Hawler Medical University, Erbil, Kurdistan Region, Iraq
| | - Hasan Pourmoshtagh
- Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Mohammad Taheri
- Institute of Human Genetics, Jena University Hospital, Jena, Germany; Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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4
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Chorostecki U, Bologna NG, Ariel F. The plant noncoding transcriptome: a versatile environmental sensor. EMBO J 2023; 42:e114400. [PMID: 37735935 PMCID: PMC10577639 DOI: 10.15252/embj.2023114400] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 08/11/2023] [Accepted: 08/21/2023] [Indexed: 09/23/2023] Open
Abstract
Plant noncoding RNA transcripts have gained increasing attention in recent years due to growing evidence that they can regulate developmental plasticity. In this review article, we comprehensively analyze the relationship between noncoding RNA transcripts in plants and their response to environmental cues. We first provide an overview of the various noncoding transcript types, including long and small RNAs, and how the environment modulates their performance. We then highlight the importance of noncoding RNA secondary structure for their molecular and biological functions. Finally, we discuss recent studies that have unveiled the functional significance of specific long noncoding transcripts and their molecular partners within ribonucleoprotein complexes during development and in response to biotic and abiotic stress. Overall, this review sheds light on the fascinating and complex relationship between dynamic noncoding transcription and plant environmental responses, and highlights the need for further research to uncover the underlying molecular mechanisms and exploit the potential of noncoding transcripts for crop resilience in the context of global warming.
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Affiliation(s)
- Uciel Chorostecki
- Faculty of Medicine and Health SciencesUniversitat Internacional de CatalunyaBarcelonaSpain
| | - Nicolas G. Bologna
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UBBarcelonaSpain
| | - Federico Ariel
- Instituto de Agrobiotecnologia del Litoral, CONICET, FBCBUniversidad Nacional del LitoralSanta FeArgentina
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5
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Khalilian S, Mohajer Z, Hosseini Imani SZ, Ghafouri-Fard S. circWHSC1: A circular RNA piece in the human cancer puzzle. Pathol Res Pract 2023; 249:154730. [PMID: 37549517 DOI: 10.1016/j.prp.2023.154730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 07/29/2023] [Indexed: 08/09/2023]
Abstract
Circular RNAs (circRNAs) are a group of non-coding RNAs with a closed loop shape, which are transcribed via non-canonical splicing. They are mainly formed by reverse splicing of a precursor mRNA. circWHSC1 (Hsa_circ_0001387), is a cancer-related circRNA that originated from the Wolf-Hirschhorn syndrome candidate 1 (WHSC1) gene on chromosome 4. circWHSC1 has been found to be overexpressed in different neoplastic conditions. circWHSC1 acts as a sponge for many different miRNAs, including miR-195-5p, miR-532-3p, miR-646, miR-142-3p, miR-7, miR-296-3p, miR-145, miR-1182, miR-212-5p, etc. It can also moderate several signaling pathways, including FASN/AMPK/mTOR, LTBP2, NPM1, HOXA1, TAB2, AKT3, hTERT, and MUC1. Studies have shown that circWHSC1 may leads to an increase in cell growth, tumor size, cell migration, invasion, and metastasis, but a reduction in apoptosis rates. Moreover, upregulation of CircWHSC1 has been associated with reduced patient's survival in different cancers, representing the function of this circRNA as a novel prognostic marker. Nevertheless, there are no reviews focusing on the relationship between circWHSC1 and cancers. Therefore, in the current review, we will first describe the oncogenic effect of circWHSC1 in various tissues according to the evidence from in vitro, in vivo, and human studies.
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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
| | - Zahra Mohajer
- Student Research Committee, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran; USERN Office, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Seyedeh Zahra Hosseini Imani
- Division of Genetics, Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Sciences and Technologies, University of Isfahan, Isfahan, Iran
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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6
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Khalilian S, Mohajer Z, Khazeei Tabari MA, Ghobadinezhad F, Ghafouri-Fard S. circGFRA1: A circular RNA with important roles in human carcinogenesis. Pathol Res Pract 2023; 248:154588. [PMID: 37285736 DOI: 10.1016/j.prp.2023.154588] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 05/29/2023] [Accepted: 05/30/2023] [Indexed: 06/09/2023]
Abstract
Circular RNAs (circRNAs) are a type of covalently closed RNA molecules, which are mainly formed by back splicing of a precursor mRNA upstream exon into a downstream exon. Abnormally expressed circRNAs can modulate gene transcription by indirectly interacting with microRNAs (miRNAs). According to the current studies, circGFRA1 has been suggested to be upregulated in various cancers. circGFRA1 (hsa_circ_005239) is a type of cancer-related circRNA, which is predicted to be originated from the GFRA1 on chromosome 10. circGFRA1 can act as a sponge for several miRNAs, including miR-34a, miR-1228, miR-361-5p, miR-149, miR-498, miR-188-3p, miR-3064-5p, miR-449a. Additionally, it can regulate signaling pathways such as TGF-β and PI3K/ AKT. circGFRA1 upregulation has been correlated with patients' poor overall survival in diverse cancers. In the present review, we have summarized the oncogenic effect of circGFRA1 in various cancers according to the adopted criteria from in vitro, in vivo, and clinical research. Moreover, functional enrichment analysis was performed on the circGFRA1 host gene and its protein interaction network to detect gene ontology and related pathways.
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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
| | - Zahra Mohajer
- 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
| | - Farbod Ghobadinezhad
- Student Research Committee, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran; USERN Office, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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7
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Kaczynski TJ, Husami NJ, Au ED, Farkas MH. Dysregulation of a lncRNA within the TNFRSF10A locus activates cell death pathways. Cell Death Discov 2023; 9:242. [PMID: 37443108 DOI: 10.1038/s41420-023-01544-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 05/23/2023] [Accepted: 07/04/2023] [Indexed: 07/15/2023] Open
Abstract
TNFRSF10A (tumor necrosis factor receptor superfamily member 10A) encodes a cell surface receptor protein involved in apoptotic, necroptotic, and inflammatory pathways. Dysregulation of TNFRSF10A has been implicated in sensitization to apoptosis and to the development of multiple diseases, yet little is known of the AC100861.1 long noncoding RNA (lncRNA) that lies head-to-head with TNFRSF10A. Given its genomic positioning, we sought to investigate the function of AC100861.1, focusing on its potential relationship with TNFRSF10A and the role it may play in death receptor signaling. Using knockdown and overexpression strategies, we probed cell viability and examined transcript and protein-level changes in key genes involved in apoptosis, necroptosis, and inflammation. Decreased cell viability was observed upon TNFRSF10A overexpression, regardless of whether the cells were subjected to the chemical stressor tunicamycin. Similarly, overexpression of AC100861.1 led to increased cell death, with a further increase observed under conditions of cellular stress. Knockdown of TNFRSF10A increased cell death only when the cells were stressed, and AC100861.1 knockdown exhibited no effect on cell death. Neither knockdown nor overexpression of either of these genes greatly affected the expression of the other. Manipulating AC100861.1, however, led to marked changes in the expression of genes involved in necroptosis and inflammatory cell-signaling pathways. Additionally, RNA fluorescence in situ hybridization (RNA-FISH) revealed that the AC100861.1 transcript is localized primarily to the cytoplasm. Together, these data suggest that AC100861.1 may have a role in regulating necroptotic and inflammatory signaling pathways and that this function is separate from changes in TNFRSF10A expression. Given the importance of this genomic locus for cell survival, these data provide insight into the function of a poorly understood lncRNA with potential implications regarding disease pathology and treatment.
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Affiliation(s)
- Tadeusz J Kaczynski
- Research Service, VA Medical Center, Buffalo, NY, USA
- Department of Ophthalmology, State University of New York at Buffalo, Buffalo, NY, USA
| | - Nadine J Husami
- Research Service, VA Medical Center, Buffalo, NY, USA
- Department of Ophthalmology, State University of New York at Buffalo, Buffalo, NY, USA
- Department of Biochemistry, State University of New York at Buffalo, Buffalo, NY, USA
| | - Elizabeth D Au
- Department of Ophthalmology, State University of New York at Buffalo, Buffalo, NY, USA
| | - Michael H Farkas
- Research Service, VA Medical Center, Buffalo, NY, USA.
- Department of Ophthalmology, State University of New York at Buffalo, Buffalo, NY, USA.
- Department of Biochemistry, State University of New York at Buffalo, Buffalo, NY, USA.
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8
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Mosca N, Russo A, Potenza N. Making Sense of Antisense lncRNAs in Hepatocellular Carcinoma. Int J Mol Sci 2023; 24:8886. [PMID: 37240232 PMCID: PMC10219390 DOI: 10.3390/ijms24108886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 05/14/2023] [Accepted: 05/15/2023] [Indexed: 05/28/2023] Open
Abstract
Transcriptome complexity is emerging as an unprecedented and fascinating domain, especially by high-throughput sequencing technologies that have unveiled a plethora of new non-coding RNA biotypes. This review covers antisense long non-coding RNAs, i.e., lncRNAs transcribed from the opposite strand of other known genes, and their role in hepatocellular carcinoma (HCC). Several sense-antisense transcript pairs have been recently annotated, especially from mammalian genomes, and an understanding of their evolutionary sense and functional role for human health and diseases is only beginning. Antisense lncRNAs dysregulation is significantly involved in hepatocarcinogenesis, where they can act as oncogenes or oncosuppressors, thus playing a key role in tumor onset, progression, and chemoradiotherapy response, as deduced from many studies discussed here. Mechanistically, antisense lncRNAs regulate gene expression by exploiting various molecular mechanisms shared with other ncRNA molecules, and exploit special mechanisms on their corresponding sense gene due to sequence complementarity, thus exerting epigenetic, transcriptional, post-transcriptional, and translational controls. The next challenges will be piecing together the complex RNA regulatory networks driven by antisense lncRNAs and, ultimately, assigning them a function in physiological and pathological contexts, in addition to defining prospective novel therapeutic targets and innovative diagnostic tools.
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Affiliation(s)
| | | | - Nicoletta Potenza
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, 81100 Caserta, Italy; (N.M.); (A.R.)
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Xu Q, Luo Y, Chao Z, Zhang J, Liu X, Tang Q, Wang K, Tan S, Fang M. Integrated Analysis of Transcriptome Expression Profiles Reveals miRNA-326-NKX3.2-Regulated Porcine Chondrocyte Differentiation. Int J Mol Sci 2023; 24:ijms24087257. [PMID: 37108419 PMCID: PMC10138716 DOI: 10.3390/ijms24087257] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 03/20/2023] [Accepted: 03/22/2023] [Indexed: 04/29/2023] Open
Abstract
The porcine body length trait is an essential factor affecting meat production and reproductive performance. It is evident that the development/lengthening of individual vertebrae is one of the main reasons for increases in body length; however, the underlying molecular mechanism remains unclear. In this study, RNA-seq analysis was used to profile the transcriptome (lncRNA, mRNA, and miRNA) of the thoracic intervertebral cartilage (TIC) at two time points (1 and 4 months) during vertebral column development in Yorkshire (Y) and Wuzhishan pigs (W). There were four groups: 1- (Y1) and 4-month-old (Y4) Yorkshire pigs and 1- (W1) and 4-month-old (W4) Wuzhishan pigs. In total, 161, 275, 86, and 126 differentially expressed (DE) lncRNAs, 1478, 2643, 404, and 750 DE genes (DEGs), and 74,51, 34, and 23 DE miRNAs (DE miRNAs) were identified in the Y4 vs. Y1, W4 vs. W1, Y4 vs. W4, and Y1 vs. W1 comparisons, respectively. Functional analysis of these DE transcripts (DETs) demonstrated that they had participated in various biological processes, such as cellular component organization or biogenesis, the developmental process, the metabolic process, bone development, and cartilage development. The crucial bone development-related candidate genes NK3 Homeobox 2 (NKX3.2), Wnt ligand secretion mediator (WLS), gremlin 1 (GREM1), fibroblast growth factor receptor 3 (FGFR3), hematopoietically expressed homeobox (HHEX), (collagen type XI alpha 1 chain (COL11A1), and Wnt Family Member 16 (WNT16)) were further identified by functional analysis. Moreover, lncRNA, miRNA, and gene interaction networks were constructed; a total of 55 lncRNAs, 6 miRNAs, and 7 genes formed lncRNA-gene, miRNA-gene, and lncRNA-miRNA-gene pairs, respectively. The aim was to demonstrate that coding and non-coding genes may co-regulate porcine spine development through interaction networks. NKX3.2 was identified as being specifically expressed in cartilage tissues, and it delayed chondrocyte differentiation. miRNA-326 regulated chondrocyte differentiation by targeting NKX3.2. The present study provides the first non-coding RNA and gene expression profiles in the porcine TIC, constructs the lncRNA-miRNA-gene interaction networks, and confirms the function of NKX3.2 in vertebral column development. These findings contribute to the understanding of the potential molecular mechanisms regulating pig vertebral column development. They expand our knowledge about the differences in body length between different pig species and provide a foundation for future studies.
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Affiliation(s)
- Qiao Xu
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Yabiao Luo
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Zhe Chao
- Institute of Animal Sciences and Veterinary, Hainan Academy of Agricultural Sciences, Haikou 571100, China
| | - Jibin Zhang
- Department of Molecular and Cellular Biology, Beckman Research Institute, City of Hope, Duarte, CA 91006, USA
| | - Ximing Liu
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Qiguo Tang
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Kejun Wang
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Shuyi Tan
- Institute of Animal Sciences and Veterinary, Hainan Academy of Agricultural Sciences, Haikou 571100, China
| | - Meiying Fang
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
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10
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Bekkouche I, Shishonin AY, Vetcher AA. Recent Development in Biomedical Applications of Oligonucleotides with Triplex-Forming Ability. Polymers (Basel) 2023; 15:polym15040858. [PMID: 36850142 PMCID: PMC9964087 DOI: 10.3390/polym15040858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 01/31/2023] [Accepted: 02/02/2023] [Indexed: 02/12/2023] Open
Abstract
A DNA structure, known as triple-stranded DNA, is made up of three oligonucleotide chains that wind around one another to form a triple helix (TFO). Hoogsteen base pairing describes how triple-stranded DNA may be built at certain conditions by the attachment of the third strand to an RNA, PNA, or DNA, which might all be employed as oligonucleotide chains. In each of these situations, the oligonucleotides can be employed as an anchor, in conjunction with a specific bioactive chemical, or as a messenger that enables switching between transcription and replication through the triplex-forming zone. These data are also considered since various illnesses have been linked to the expansion of triplex-prone sequences. In light of metabolic acidosis and associated symptoms, some consideration is given to the impact of several low-molecular-weight compounds, including pH on triplex production in vivo. The review is focused on the development of biomedical oligonucleotides with triplexes.
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Affiliation(s)
- Incherah Bekkouche
- Nanotechnology Scientific and Educational Center, Institute of Biochemical Technology and Nanotechnology, Peoples’ Friendship University of Russia (RUDN), Miklukho-Maklaya Str. 6, Moscow 117198, Russia
| | - Alexander Y. Shishonin
- Complementary and Integrative Health Clinic of Dr. Shishonin, 5, Yasnogorskaya Str., Moscow 117588, Russia
| | - Alexandre A. Vetcher
- Nanotechnology Scientific and Educational Center, Institute of Biochemical Technology and Nanotechnology, Peoples’ Friendship University of Russia (RUDN), Miklukho-Maklaya Str. 6, Moscow 117198, Russia
- Complementary and Integrative Health Clinic of Dr. Shishonin, 5, Yasnogorskaya Str., Moscow 117588, Russia
- Correspondence:
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11
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Xiong L, He X, Wang L, Dai P, Zhao J, Zhou X, Tang H. Hypoxia-associated prognostic markers and competing endogenous RNA coexpression networks in lung adenocarcinoma. Sci Rep 2022; 12:21340. [PMID: 36494419 PMCID: PMC9734750 DOI: 10.1038/s41598-022-25745-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022] Open
Abstract
Lung adenocarcinoma (LUAD) is the most common form of non-small cell lung cancer (NSCLC). Hypoxia has been found in 50-60% of locally advanced solid tumors and is associated with poor prognosis in various tumors, including NSCLC. This study focused on hypoxia-associated molecular hallmarks in LUAD. Fifteen hypoxia-related genes were selected to define the hypoxia status of LUAD by ConsensusClusterPlus based on data from The Cancer Genome Atlas (TCGA). Then, we investigated the immune status under different hypoxia statuses. Subsequently, we constructed prognostic models based on hypoxia-related differentially expressed genes (DEGs), identified hypoxia-related microRNAs, lncRNAs and mRNAs, and built a network based on the competing endogenous RNA (ceRNA) theory. Two clusters (Cluster 1 and Cluster 2) were identified with different hypoxia statuses. Cluster 1 was defined as the hypoxia subgroup, in which all 15 hypoxia-associated genes were upregulated. The infiltration of CD4+ T cells and Tfh cells was lower, while the infiltration of regulatory T (Treg) cells, the expression of PD-1/PD-L1 and TMB scores were higher in Cluster 1, indicating an immunosuppressive status. Based on the DEGs, a risk signature containing 7 genes was established. Furthermore, three differentially expressed microRNAs (hsa-miR-9, hsa-miR-31, hsa-miR-196b) associated with prognosis under different hypoxia clusters and their related mRNAs and lncRNAs were identified, and a ceRNA network was built. This study showed that hypoxia was associated with poor prognosis in LUAD and explored the potential mechanism from the perspective of the gene signature and ceRNA theory.
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Affiliation(s)
- Lecai Xiong
- grid.413247.70000 0004 1808 0969Department of Cardiovascular Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071 China
| | - Xueyu He
- grid.413247.70000 0004 1808 0969Department of Thoracic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071 China
| | - Le Wang
- grid.413247.70000 0004 1808 0969Department of Cardiovascular Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071 China
| | - Peng Dai
- grid.413247.70000 0004 1808 0969Department of Thoracic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071 China
| | - Jinping Zhao
- grid.413247.70000 0004 1808 0969Department of Cardiovascular Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071 China
| | - Xuefeng Zhou
- grid.413247.70000 0004 1808 0969Department of Thoracic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071 China
| | - Hexiao Tang
- grid.413247.70000 0004 1808 0969Department of Thoracic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071 China
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12
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Nadhan R, Isidoro C, Song YS, Dhanasekaran DN. Signaling by LncRNAs: Structure, Cellular Homeostasis, and Disease Pathology. Cells 2022; 11:2517. [PMID: 36010595 PMCID: PMC9406440 DOI: 10.3390/cells11162517] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 08/09/2022] [Accepted: 08/11/2022] [Indexed: 12/11/2022] Open
Abstract
The cellular signaling network involves co-ordinated regulation of numerous signaling molecules that aid the maintenance of cellular as well as organismal homeostasis. Aberrant signaling plays a major role in the pathophysiology of many diseases. Recent studies have unraveled the superfamily of long non-coding RNAs (lncRNAs) as critical signaling nodes in diverse signaling networks. Defective signaling by lncRNAs is emerging as a causative factor underlying the pathophysiology of many diseases. LncRNAs have been shown to be involved in the multiplexed regulation of diverse pathways through both genetic and epigenetic mechanisms. They can serve as decoys, guides, scaffolds, and effector molecules to regulate cell signaling. In comparison with the other classes of RNAs, lncRNAs possess unique structural modifications that contribute to their diversity in modes of action within the nucleus and cytoplasm. In this review, we summarize the structure and function of lncRNAs as well as their vivid mechanisms of action. Further, we provide insights into the role of lncRNAs in the pathogenesis of four major disease paradigms, namely cardiovascular diseases, neurological disorders, cancers, and the metabolic disease, diabetes mellitus. This review serves as a succinct treatise that could open windows to investigate the role of lncRNAs as novel therapeutic targets.
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Affiliation(s)
- Revathy Nadhan
- Stephenson Cancer Center, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Ciro Isidoro
- Laboratory of Molecular Pathology and NanoBioImaging, Department of Health Sciences, Università del Piemonte Orientale, Via Solaroli 17, 28100 Novara, Italy
| | - Yong Sang Song
- Department of Obstetrics and Gynecology, Cancer Research Institute, College of Medicine, Seoul National University, Seoul 151-921, Korea
| | - Danny N. Dhanasekaran
- Stephenson Cancer Center, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
- Department of Cell Biology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
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13
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He Z, Ye L, Yang D, Ma Z, Deng F, He Z, Hu J, Chen H, Zheng L, Pu Y, Jiao Y, Chen Q, Gao K, Xiong J, Lai B, Gu X, Huang X, Yang S, Zhang M, Yan T. Identification, characterization and functional analysis of gonadal long noncoding RNAs in a protogynous hermaphroditic teleost fish, the ricefield eel (Monopterus albus). BMC Genomics 2022; 23:450. [PMID: 35725373 PMCID: PMC9208217 DOI: 10.1186/s12864-022-08679-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 06/09/2022] [Indexed: 11/11/2022] Open
Abstract
Background An increasing number of long noncoding RNAs (lncRNAs) have been found to play important roles in sex differentiation and gonad development by regulating gene expression at the epigenetic, transcriptional and posttranscriptional levels. The ricefield eel, Monopterus albus, is a protogynous hermaphroditic fish that undergoes a sequential sex change from female to male. However, the roles of lncRNA in the sex change is unclear. Results Herein, we performed RNA sequencing to analyse lncRNA expression patterns in five different stages of M. albus development to investigate the roles of lncRNAs in the sex change process. A total of 12,746 lncRNAs (1503 known lncRNAs and 11,243 new lncRNAs) and 2901 differentially expressed lncRNAs (DE-lncRNAs) were identified in the gonads. The target genes of the DE-lncRNAs included foxo1, foxm1, smad3, foxr1, camk4, ar and tgfb3, which were mainly enriched in signalling pathways related to gonadal development, such as the insulin signalling pathway, MAPK signalling pathway, and calcium signalling pathway. We selected 5 highly expressed DE-lncRNAs (LOC109952131, LOC109953466, LOC109954337, LOC109954360 and LOC109958454) for full length amplification and expression pattern verification. They were all expressed at higher levels in ovaries and intersex gonads than in testes, and exhibited specific time-dependent expression in ovarian tissue incubated with follicle-stimulating hormone (FSH) and human chorionic gonadotropin (hCG). The results of quantitative real-time PCR (qRT-PCR) analysis and a dual-luciferase assay showed that znf207, as the gene targeted by LOC109958454, was expressed in multiple tissues and gonadal developmental stages of M. albus, and its expression was also inhibited by the hormones FSH and hCG. Conclusions These results provide new insights into the role of lncRNAs in gonad development, especially regarding natural sex changes in fish, which will be useful for enhancing our understanding of sequential hermaphroditism and sex changes in the ricefield eel (M. albus) and other teleosts. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08679-2.
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Affiliation(s)
- Zhi He
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Lijuan Ye
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Deying Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Zhijun Ma
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Faqiang Deng
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Zhide He
- Luzhou Municipal Bureau of Agriculture and Rural Affairs, Luzhou, 646000, Sichuan, China
| | - Jiaxiang Hu
- Sichuan Water Conservancy Vocational College, Chengdu, 611231, Sichuan, China
| | - Hongjun Chen
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Li Zheng
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yong Pu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yuanyuan Jiao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Qiqi Chen
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Kuo Gao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Jinxin Xiong
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Bolin Lai
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xiaobin Gu
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xiaoli Huang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Shiyong Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Mingwang Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Taiming Yan
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
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14
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Wang J, Hou F, Tang L, Xiao K, Yang T, Wang Z, Liu G. The interaction between long non-coding RNA LINC01564 and POU2F1 promotes the proliferation and metastasis of gastric cancer. J Transl Med 2022; 20:220. [PMID: 35562740 PMCID: PMC9101833 DOI: 10.1186/s12967-022-03391-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 02/23/2022] [Indexed: 12/24/2022] Open
Abstract
Background An increasing number of studies have demonstrated that long non-coding RNAs (lncRNAs) serve as key regulators in tumor development and progression. However, only a few lncRNAs have been functionally characterized in gastric cancer (GC). Methods Bioinformatics analysis was conducted to find lncRNAs that are associated with GC metastasis. RNA FISH, RIP, and RNA pull down assays were used to study the complementary binding of LINC01564 complementary to the 3′UTR of transcription factor POU2F1. The transcription activation of LINC01564 by POU2F1 as a transcription factor was examined by ChIP assay. In vitro assays such as MTT, cell invasion assay, and clonogenic assay were conducted to examined the impacts of LINC01564 and POU2F1 on GC cell proliferation and invasion. Experiments in vivo were performed to access the impacts of LINC01564 and POU2F1 on GC metastasis. Results The results showed that LINC01564 complementary bound to the 3′UTR of POU2F1 to form an RNA duplex, whereby stabilizing POU2F1 mRNA and increasing the enrichment in cells. The level of LINC01564 was also increased by POU2F1 through transcription activation. In vitro assays showed that LINC01564 promoted the proliferation, invasion and migration of GC cells through increasing POU2F1. In vivo experiments indicate the promotion of GC proliferation and metastasis by the interaction between LINC01564 and POU2F1. Conclusion Taken together, our results indicate that the interaction between LINC01564 and POU2F1 promotes the proliferation, migration and invasion of GC cells. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-022-03391-x.
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Affiliation(s)
- Jixu Wang
- Department of Interventional Vascular Surgery, Affiliated Hospital (Clinical College) of Xiangnan University and Key Laboratory of Medical Imaging and Artificial Intelligence of Hunan Province, Xiangnan University, 25 Renmin West Road, Chenzhou, 423000, Hunan, China
| | - Futao Hou
- Department of General Surgery, Hunan Provincial People's Hospital, First Affiliated Hospital of Hunan Normal University, 61 the West Jiefang Road, Furong District, Changsha, 410003, Hunan, China
| | - Lusheng Tang
- Department of Interventional Vascular Surgery, Affiliated Hospital (Clinical College) of Xiangnan University and Key Laboratory of Medical Imaging and Artificial Intelligence of Hunan Province, Xiangnan University, 25 Renmin West Road, Chenzhou, 423000, Hunan, China
| | - Ke Xiao
- Department of Gastroduodenal and Pancreatic Surgery, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Tengfei Yang
- Department of Interventional Vascular Surgery, Affiliated Hospital (Clinical College) of Xiangnan University and Key Laboratory of Medical Imaging and Artificial Intelligence of Hunan Province, Xiangnan University, 25 Renmin West Road, Chenzhou, 423000, Hunan, China
| | - Zhiqiang Wang
- Department of Interventional Vascular Surgery, Affiliated Hospital (Clinical College) of Xiangnan University and Key Laboratory of Medical Imaging and Artificial Intelligence of Hunan Province, Xiangnan University, 25 Renmin West Road, Chenzhou, 423000, Hunan, China.
| | - Gu Liu
- Department of Gastrointestinal Surgery, Chenzhou First People's Hospital and The First Affiliated Hospital of Xiangnan University, 102 Luojiajing, Chenzhou, 423000, Hunan, China.
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15
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Wang JP, Li C, Ding WC, Peng G, Xiao GL, Chen R, Cheng Q. Research Progress on the Inflammatory Effects of Long Non-coding RNA in Traumatic Brain Injury. Front Mol Neurosci 2022; 15:835012. [PMID: 35359568 PMCID: PMC8961287 DOI: 10.3389/fnmol.2022.835012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 02/08/2022] [Indexed: 11/29/2022] Open
Abstract
Globally, traumatic brain injury (TBI) is an acute clinical event and an important cause of death and long-term disability. However, the underlying mechanism of the pathophysiological has not been fully elucidated and the lack of effective treatment a huge burden to individuals, families, and society. Several studies have shown that long non-coding RNAs (lncRNAs) might play a crucial role in TBI; they are abundant in the central nervous system (CNS) and participate in a variety of pathophysiological processes, including oxidative stress, inflammation, apoptosis, blood-brain barrier protection, angiogenesis, and neurogenesis. Some lncRNAs modulate multiple therapeutic targets after TBI, including inflammation, thus, these lncRNAs have tremendous therapeutic potential for TBI, as they are promising biomarkers for TBI diagnosis, treatment, and prognosis prediction. This review discusses the differential expression of different lncRNAs in brain tissue during TBI, which is likely related to the physiological and pathological processes involved in TBI. These findings may provide new targets for further scientific research on the molecular mechanisms of TBI and potential therapeutic interventions.
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Affiliation(s)
- Jian-peng Wang
- Department of Neurosurgery, The Affiliated Nanhua Hospital, Hengyang Medical School, University of South China, Hengyang, China
| | - Chong Li
- Department of Neurosurgery, The Affiliated Nanhua Hospital, Hengyang Medical School, University of South China, Hengyang, China
| | - Wen-cong Ding
- Department of Neurosurgery, The Affiliated Nanhua Hospital, Hengyang Medical School, University of South China, Hengyang, China
| | - Gang Peng
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Ge-lei Xiao
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Rui Chen
- Department of Neurosurgery, The Affiliated Nanhua Hospital, Hengyang Medical School, University of South China, Hengyang, China
- *Correspondence: Rui Chen,
| | - Quan Cheng
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- Quan Cheng,
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16
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Abstract
As sequencing technologies improved, new classes of genes were uncovered. Initially, many of these were considered non-functional given their low protein-coding potential but have now emerged as important regulators of biological processes. One of the new classes of genes are called long noncoding RNAs (lncRNAs). LncRNAs are the largest group of transcribed RNA. As their name suggests, they are non-protein coding genes. To differentiate them from other smaller, noncoding RNAs, lncRNAs are transcripts whose length are greater than 200 nucleotides. According to GENCODE Release 38, there are approximately 18,000 lncRNAs, of which only 4% have a known function. Of the lncRNAs characterized, many of them play regulatory roles in many biological processes, including regulation of gene expression, alternative splicing, chromatin modification, protein activity, and posttranscriptional mechanisms. Compared to protein coding genes, lncRNAs show high cell type specificity. Many lncRNAs have been shown to be expressed in distinct immune cell populations and play RNA-mediated immune-regulatory roles. Many aspects of the immune response, including the duration, magnitude, and subsequent return to homeostasis are carefully controlled. Dysregulation of lncRNAs can result in an uncontrolled immune response, which can lead to a variety of immune-related diseases. This introduction aims to summarize the chapters highlighting the discovery of lncRNAs, their role in the immune response, and their functional characterization, either through interaction with DNA, RNA, and/or proteins in distinct immune cell populations or cells implicated in immune-related diseases. Additionally, the immune regulatory role of lncRNAs will be covered, and how lncRNA localization, sequence and secondary structure can inform function. Delving into this largely unexplored field can identify lncRNAs as potential therapeutic targets.
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17
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Felix R, Muñoz-Herrera D, Corzo-López A, Fernández-Gallardo M, Leyva-Leyva M, González-Ramírez R, Sandoval A. Ion channel long non-coding RNAs in neuropathic pain. Pflugers Arch 2022; 474:457-468. [PMID: 35235008 DOI: 10.1007/s00424-022-02675-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 02/17/2022] [Accepted: 02/18/2022] [Indexed: 02/01/2023]
Abstract
Neuropathic pain is one of the primary forms of chronic pain and is the consequence of the somatosensory system's direct injury or disease. It is a relevant public health problem that affects about 10% of the world's general population. In neuropathic pain, alteration in neurotransmission occurs at various levels, including the dorsal root ganglia, the spinal cord, and the brain, resulting from the malfunction of diverse molecules such as receptors, ion channels, and elements of specific intracellular signaling pathways. In this context, there have been exciting advances in elucidating neuropathic pain's cellular and molecular mechanisms in the last decade, including the possible role that long non-coding RNAs (lncRNAs) may play, which open up new alternatives for the development of diagnostic and therapeutic strategies for this condition. This review focuses on recent studies associated with the possible relevance of lncRNAs in the development and maintenance of neuropathic pain through their actions on the functional expression of ion channels. Recognizing the changes in the function and spatio-temporal patterns of expression of these membrane proteins is crucial to understanding the control of neuronal excitability in chronic pain syndromes.
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Affiliation(s)
- Ricardo Felix
- Department of Cell Biology, Centre for Research and Advanced Studies (Cinvestav), 07360, Mexico City, Mexico.
| | - David Muñoz-Herrera
- Department of Cell Biology, Centre for Research and Advanced Studies (Cinvestav), 07360, Mexico City, Mexico
| | - Alejandra Corzo-López
- Department of Cell Biology, Centre for Research and Advanced Studies (Cinvestav), 07360, Mexico City, Mexico
| | | | - Margarita Leyva-Leyva
- Department of Molecular Biology and Histocompatibility, "Dr. Manuel Gea González" General Hospital, Mexico City, Mexico
| | - Ricardo González-Ramírez
- Department of Molecular Biology and Histocompatibility, "Dr. Manuel Gea González" General Hospital, Mexico City, Mexico
| | - Alejandro Sandoval
- School of Medicine FES Iztacala, National Autonomous University of Mexico (UNAM), Tlalnepantla, Mexico
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18
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Feng N, Wang Z, Wu Y, Zheng H, Jiang X, Wang Z, Qu F, Zhang Z. ADAMTS9-AS2 Promotes Angiogenesis of Brain Microvascular Endothelial Cells Through Regulating miR-185-5p/IGFBP-2 Axis in Ischemic Stroke. Mol Neurobiol. [DOI: 10.1007/s12035-021-02641-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 11/07/2021] [Indexed: 12/21/2022]
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19
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Yu K, Hidaka K, Sugiyama H, Endo M, Matsumura S, Ikawa Y. A hexameric ribozyme nanostructure formed by double-decker assembly of a pair of triangular ribozyme trimers. Chembiochem 2022; 23:e202100573. [PMID: 35088928 DOI: 10.1002/cbic.202100573] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 12/29/2021] [Indexed: 11/12/2022]
Abstract
The modular architecture of naturally occurring ribozymes makes them a promising class of structural platforms to design and assemble three-dimensional (3D) RNA nanostructures, into which the catalytic ability of the platform ribozyme can be installed. We have constructed and analyzed RNA nanostructures with polygonal-shaped (closed) ribozyme oligomers by assembling unit RNAs derived from the Tetrahymena group I intron with a typical modular architecture. In this study, we dimerized ribozyme trimers with a triangular shape by introducing three pillar units. The resulting double-decker nanostructures containing six ribozyme units were characterized biochemically and their structures were observed by atomic force microscopy. The double-decker hexamers exhibited higher catalytic activity than the parent ribozyme trimers.
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Affiliation(s)
- Kai Yu
- University of Toyama: Toyama Daigaku, Department of Chemistry, JAPAN
| | - Kumi Hidaka
- Kyoto University: Kyoto Daigaku, Department of Chemistry, JAPAN
| | | | | | | | - Yoshiya Ikawa
- University of Toyama, Chemistry, Gofuku 3190, 930-8555, Toyama, JAPAN
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20
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Li J, Wang H. H3K27ac-activated EGFR-AS1 promotes cell growth in cervical cancer through ACTN4-mediated WNT pathway. Biol Direct 2022; 17:3. [PMID: 34998421 PMCID: PMC8742952 DOI: 10.1186/s13062-021-00315-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 11/29/2021] [Indexed: 01/09/2023] Open
Abstract
Background Recently, extensive studies unveiled that lncRNAs exert critical function in the development and progression of cervical cancer (CC). EGFR-AS1 is a novel lncRNA which has not been well-explored in CC. Aims Our study aimed to research the function and molecular mechanism of EGFR-AS1 in CC cells. qRT-PCR analysis was performed to detect gene expression. Colony formation, EdU, flow cytometry, TUNEL, western blot and transwell assays were performed to assess the effect of EGFR-AS1 on CC cell growth. The regulatory mechanism of EGFR-AS1 was dug out through mechanism experiments. Results EGFR-AS1 was notably overexpressed in CC cell lines. Loss-of-functional experiments revealed that EGFR-AS1 promoted CC cell proliferation, migration and invasion, and suppressed cell apoptosis. Mechanistically, up-regulation of EGFR-AS1 was attributed to the activation of H3K27 acetylation (H3K27ac). Further, EGFR-AS1 was revealed to function as miR-2355-5p sponge. Additionally, miR-2355-5p was down-regulated in CC cells and ACTN4 was identified as a target gene of miR-2355-5p. Ultimately, overexpressed ACTN4 could reserve the suppressive role of EGFR-AS1 silencing in CC cell growth. Last but not least, EGFR-AS1 facilitated CC cell growth via ACTN4-mediated WNT pathway. Conclusions H3K27ac-activated EGFR-AS1 sponged miR-2355-5p and promoted CC cell growth through ACTN4-mediated WNT pathway. Supplementary Information The online version contains supplementary material available at 10.1186/s13062-021-00315-5.
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Affiliation(s)
- Jingyan Li
- Zibo Maternal and Child Health Hospital of Shandong Province, Zibo, 255000, Shandong, China
| | - Hongbing Wang
- Department of Gynecology and Oncology, Hubei Cancer Hospital Affiliated to Tongji Medical College of Huazhong University of Science and Technology, Hongshan District, No. 116 Zhuodaoquan South Road, Wuhan, 430079, Hubei, China.
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21
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Siniscalchi C, Di Palo A, Russo A, Potenza N. The lncRNAs at X Chromosome Inactivation Center: Not Just a Matter of Sex Dosage Compensation. Int J Mol Sci 2022; 23:611. [PMID: 35054794 DOI: 10.3390/ijms23020611] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 12/30/2021] [Accepted: 01/05/2022] [Indexed: 02/06/2023] Open
Abstract
Non-coding RNAs (ncRNAs) constitute the majority of the transcriptome, as the result of pervasive transcription of the mammalian genome. Different RNA species, such as lncRNAs, miRNAs, circRNA, mRNAs, engage in regulatory networks based on their reciprocal interactions, often in a competitive manner, in a way denominated “competing endogenous RNA (ceRNA) networks” (“ceRNET”): miRNAs and other ncRNAs modulate each other, since miRNAs can regulate the expression of lncRNAs, which in turn regulate miRNAs, titrating their availability and thus competing with the binding to other RNA targets. The unbalancing of any network component can derail the entire regulatory circuit acting as a driving force for human diseases, thus assigning “new” functions to “old” molecules. This is the case of XIST, the lncRNA characterized in the early 1990s and well known as the essential molecule for X chromosome inactivation in mammalian females, thus preventing an imbalance of X-linked gene expression between females and males. Currently, literature concerning XIST biology is becoming dominated by miRNA associations and they are also gaining prominence for other lncRNAs produced by the X-inactivation center. This review discusses the available literature to explore possible novel functions related to ceRNA activity of lncRNAs produced by the X-inactivation center, beyond their role in dosage compensation, with prospective implications for emerging gender-biased functions and pathological mechanisms.
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22
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Sanbonmatsu K. Towards Molecular Mechanism in Long Non-coding RNAs: Linking Structure and Function. Long Noncoding RNA 2022; 1363:23-32. [DOI: 10.1007/978-3-030-92034-0_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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23
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Abstract
While long non-coding RNAs are known to play key roles in disease and development, relatively few structural studies have been performed for this important class of RNAs. Here, we review functional studies of long non-coding RNAs and expose the need for high-resolution 3-D structural studies, discussing the roles of long non-coding RNAs in the cell and how structure–function relationships might be used to elucidate further understanding. We then describe structural studies of other classes of RNAs using chemical probing, nuclear magnetic resonance, small-angle X-ray scattering, X-ray crystallography, and cryogenic electron microscopy (cryo-EM). Next, we review early structural studies of long non-coding RNAs to date and describe the way forward for the structural biology of long non-coding RNAs in terms of cryo-EM.
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Abstract
Pituitary adenomas (PAs) are common cranial tumors that affect the quality of life in patients. Early detection of PA is beneficial for avoiding clinical complications of this disease and increasing the quality of life. Noncoding RNAs, including long noncoding RNA, miRNA and circRNA, regulate protein expression, mostly by inhibiting the translation process. Studies have shown that dysregulation of noncoding RNAs is associated with PA. Hence understanding the expression pattern of noncoding RNAs can be considered a promising method for developing biomarkers. This article reviews data on the expression pattern of dysregulated noncoding RNAs involved in PA. Possible molecular mechanisms by which the dysregulated noncoding RNA could possibly induce PA are also described.
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Affiliation(s)
- Farbod Bahreini
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.,Network of Immunity in Infection, Malignancy & Autoimmunity (NIIMA), Universal Scientific Education & Research Network (USERN), Tehran, Iran
| | - Parnian Jabbari
- Network of Immunity in Infection, Malignancy & Autoimmunity (NIIMA), Universal Scientific Education & Research Network (USERN), Tehran, Iran.,Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran.,Department of Genetics, Genomics & Bioinformatics, University of California, Riverside, CA, USA
| | - Wilhelm Gossing
- Division Molecular Biotechnology & Functional Genomics, Technical University of Applied Sciences Wildau, Hochschulring 1, 15745, Wildau, Germany
| | - Fatemeh Aziziyan
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Marcus Frohme
- Division Molecular Biotechnology & Functional Genomics, Technical University of Applied Sciences Wildau, Hochschulring 1, 15745, Wildau, Germany
| | - Nima Rezaei
- Network of Immunity in Infection, Malignancy & Autoimmunity (NIIMA), Universal Scientific Education & Research Network (USERN), Tehran, Iran.,Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran.,Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
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25
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Baulin EF. Features and Functions of the A-Minor Motif, the Most Common Motif in RNA Structure. Biochemistry (Mosc) 2021; 86:952-961. [PMID: 34488572 DOI: 10.1134/s000629792108006x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
A-minor motifs are RNA tertiary structure motifs that generally involve a canonical base pair and an adenine base forming hydrogen bonds with the minor groove of the base pair. Such motifs are among the most common tertiary interactions in known RNA structures, comparable in number with the non-canonical base pairs. They are often found in functionally important regions of non-coding RNAs and, in particular, play a central role in protein synthesis. Here, we review local variations of the A-minor geometry and discuss difficulties associated with their annotation, as well as various structural contexts and common A-minor co-motifs, and diverse functions of A-minors in various processes in a living cell.
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Affiliation(s)
- Eugene F Baulin
- Institute of Mathematical Problems of Biology RAS - the Branch of Keldysh Institute of Applied Mathematics of the Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia. .,Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
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26
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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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27
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Chorostecki U, Saus E, Gabaldón T. Structural characterization of NORAD reveals a stabilizing role of spacers and two new repeat units. Comput Struct Biotechnol J 2021; 19:3245-3254. [PMID: 34141143 PMCID: PMC8192489 DOI: 10.1016/j.csbj.2021.05.045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 05/25/2021] [Accepted: 05/25/2021] [Indexed: 12/19/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) can perform a variety of key cellular functions by interacting with proteins and other RNAs. Recent studies have shown that the functions of lncRNAS are largely mediated by their structures. However, our structural knowledge for most lncRNAS is limited to sequence-based computational predictions. Non-coding RNA activated by DNA damage (NORAD) is an atypical lncRNA due to its abundant expression and high sequence conservation. NORAD regulates genomic stability by interacting with proteins and microRNAs. Previous sequence-based characterization has identified a modular organization of NORAD composed of several NORAD repeat units (NRUs). These units comprise the protein-binding elements and are separated by regular spacers. Here, we experimentally determine for the first time the secondary structure of NORAD using the nextPARS approach. Our results suggest that the spacer regions provide structural stability to NRUs. Furthermore, we uncover two previously unreported NRUs, and determine the core structural motifs conserved across NRUs. Overall, these findings will help to elucidate the function and evolution of NORAD.
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Affiliation(s)
- Uciel Chorostecki
- Barcelona Supercomputing Centre (BSC-CNS). Jordi Girona, 29. 08034 Barcelona, Spain.,Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Ester Saus
- Barcelona Supercomputing Centre (BSC-CNS). Jordi Girona, 29. 08034 Barcelona, Spain.,Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Toni Gabaldón
- Barcelona Supercomputing Centre (BSC-CNS). Jordi Girona, 29. 08034 Barcelona, Spain.,Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
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28
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Brodyagin N, Kumpina I, Applegate J, Katkevics M, Rozners E. Pyridazine Nucleobase in Triplex-Forming PNA Improves Recognition of Cytosine Interruptions of Polypurine Tracts in RNA. ACS Chem Biol 2021; 16:872-881. [PMID: 33881836 DOI: 10.1021/acschembio.1c00044] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Sequence specific recognition of regulatory noncoding RNAs would open new possibilities for fundamental science and medicine. However, molecular recognition of such complex double-stranded RNA (dsRNA) structures remains a formidable problem. Recently, we discovered that peptide nucleic acids (PNAs) form an unusually stable and sequence-specific triple helix with dsRNA. Triplex-forming PNAs could become universal tools for recognition of noncoding dsRNAs but are limited by the requirement of polypurine tracts in target RNAs as only purines form stable Hoogsteen hydrogen bonded base triplets. Herein, we systematically surveyed simple nitrogen heterocycles PN as modified nucleobases for recognition of cytosine in PN*C-G triplets. We found that a 3-pyridazinyl nucleobase formed significantly more stable PN*C-G triplets than other heterocycles including the pyrimidin-2-one previously used by us and others for recognition of cytosine interruptions in polypurine tracts of PNA-dsRNA triplexes. Our results improve triple helical recognition of dsRNA and provide insights for future development of new nucleobases to expand the sequence scope of noncoding dsRNAs that can be targeted by triplex-forming PNAs.
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Affiliation(s)
- Nikita Brodyagin
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
| | - Ilze Kumpina
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, LV-1006, Latvia
| | - Justin Applegate
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
| | - Martins Katkevics
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, LV-1006, Latvia
| | - Eriks Rozners
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
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29
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Guo Y, Feng X, Wang D, Kang X, Zhang L, Ren H, Yuan G. Long Non-coding RNA: A Key Regulator in the Pathogenesis of Diabetic Cardiomyopathy. Front Cardiovasc Med 2021; 8:655598. [PMID: 33889601 PMCID: PMC8057523 DOI: 10.3389/fcvm.2021.655598] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 03/09/2021] [Indexed: 12/31/2022] Open
Abstract
In recent years, diabetes mellitus has become a global issue with increasing incidence rate worldwide. Diabetic cardiomyopathy (DCM), one of the important complications of diabetes, refers to patients with type 1 and type 2 diabetes who have ventricular hypertrophy, fibrosis and even diastolic dysfunction. The pathogenesis of DCM is related to oxidative stress, inflammatory response, apoptosis, autophagy, myocardial fibrosis and, diabetic microangiopathy. Long non-coding RNAs (lncRNA) is a non-coding RNA with a length longer than 200 nucleotides which lack the ability of protein coding. With the development of molecular technology, massive evidence demonstrates that lncRNA play a critical role in the molecular mechanism of DCM. Moreover, it can also be used as potential diagnostic markers for DCM. In this review, we intend to summarize the pathological roles and molecular mechanism of lncRNA in the progression of diabetic cardiomyopathy, which may provide promising diagnosis and treatment strategies for DCM.
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Affiliation(s)
- Yaoyao Guo
- Department of Endocrinology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaohui Feng
- Department of Endocrinology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Dan Wang
- Department of Endocrinology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaonan Kang
- Department of Endocrinology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lu Zhang
- Department of Endocrinology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Huihui Ren
- Department of Endocrinology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Branch of National Clinical Research Center for Metabolic Disease, Wuhan, China
| | - Gang Yuan
- Department of Endocrinology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Branch of National Clinical Research Center for Metabolic Disease, Wuhan, China
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30
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Zhang D, Xia T, Li H, Li Z, Sun G, Li G, Tian Y, Liu X, Xu D, Kang X. Estrogen enhances the expression of a growth-associated long noncoding RNA in chicken liver via ERα. Br Poult Sci 2021; 62:336-345. [PMID: 33390024 DOI: 10.1080/00071668.2020.1868405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
1. The long noncoding RNA lncGLM is significantly differentially expressed in the livers of peak-laying hens compared with that in the livers of pre-laying hens, but its potential biological role and expression regulation are unclear.2. To explore the potential biological function of lncGLM, single nucleotide polymorphism (SNP) detection and association analysis were carried out in the Gushi×Anka F2 resource population.3. The tissues and spatiotemporal expression characteristics of lncGLM were analysed by real-time quantitative PCR. The effects of 17β-oestradiol on the expression of lncGLM expression were analysed through in vitro and in vivo experiments.4. The results showed that a g.19069338 T > C SNP was present in lncGLM. Association analysis revealed that lncGLM was significantly associated with body slanting length at 12 weeks, body weight at 12 weeks, shank length at four weeks, chest depth at eight weeks, pelvic width at 12 weeks, eviscerated weight, head weight, pancreas weight, pectoralis weight, leg muscle weight, muscular stomach weight rate, pancreas weight rate, carcase weight, aspartate aminotransferase, creatinine and pectoral muscle water loss rate.5. The expression of lncGLM in the liver was higher than that in other sampled tissues. In addition, the expression of lncGLM in the liver was significantly higher in the peak-laying period than at the pre-laying period. Both in vitro and in vivo experiments showed that lncGLM expression was regulated by 17β-oestradiol via oestrogen receptor alpha (ER-α). These results demonstrated that the chicken lncGLM gene is highly expressed in liver tissue and regulated by oestrogen through ER-α.
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Affiliation(s)
- D Zhang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - T Xia
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - H Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Henan Agricultural University, Zhengzhou, China.,International Joint Research Laboratory for Poultry Breeding of Henan, Henan Agricultural University, Zhengzhou, China
| | - Z Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Henan Agricultural University, Zhengzhou, China.,International Joint Research Laboratory for Poultry Breeding of Henan, Henan Agricultural University, Zhengzhou, China
| | - G Sun
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Henan Agricultural University, Zhengzhou, China.,International Joint Research Laboratory for Poultry Breeding of Henan, Henan Agricultural University, Zhengzhou, China
| | - G Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Henan Agricultural University, Zhengzhou, China.,International Joint Research Laboratory for Poultry Breeding of Henan, Henan Agricultural University, Zhengzhou, China
| | - Y Tian
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Henan Agricultural University, Zhengzhou, China.,International Joint Research Laboratory for Poultry Breeding of Henan, Henan Agricultural University, Zhengzhou, China
| | - X Liu
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Henan Agricultural University, Zhengzhou, China.,International Joint Research Laboratory for Poultry Breeding of Henan, Henan Agricultural University, Zhengzhou, China
| | - D Xu
- Henan Liujiang Ecological Animal Husbandry Co., Ltd, Hebi, China
| | - X Kang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Henan Agricultural University, Zhengzhou, China.,International Joint Research Laboratory for Poultry Breeding of Henan, Henan Agricultural University, Zhengzhou, China
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31
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Brodyagin N, Maryniak AL, Kumpina I, Talbott JM, Katkevics M, Rozners E, MacKay JA. Extended Peptide Nucleic Acid Nucleobases Based on Isoorotic Acid for the Recognition of A-U Base Pairs in Double-Stranded RNA. Chemistry 2021; 27:4332-4335. [PMID: 33439519 DOI: 10.1002/chem.202005401] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/12/2021] [Indexed: 02/06/2023]
Abstract
Peptide nucleic acids (PNA) with extended isoorotamide containing nucleobases (Io ) were designed for binding A-U base pairs in double-stranded RNA. Isothermal titration calorimetry and UV thermal melting experiments revealed improved affinity for A-U using the Io scaffold in PNA. PNAs having four sequential Io extended nucleobases maintained high binding affinity.
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Affiliation(s)
- Nikita Brodyagin
- Department of Chemistry, Binghamton University, Binghamton, New York, 13902, USA
| | - Aubrey L Maryniak
- Department of Chemistry and Biochemistry, Elizabethtown College, Elizabethtown, Pennsylvania, 17022, USA
| | - Ilze Kumpina
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, LV-1006, Latvia
| | - John M Talbott
- Department of Chemistry and Biochemistry, Elizabethtown College, Elizabethtown, Pennsylvania, 17022, USA
| | - Martins Katkevics
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, LV-1006, Latvia
| | - Eriks Rozners
- Department of Chemistry, Binghamton University, Binghamton, New York, 13902, USA
| | - James A MacKay
- Department of Chemistry and Biochemistry, Elizabethtown College, Elizabethtown, Pennsylvania, 17022, USA
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32
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Liu A, Liu M, Li Y, Chen X, Zhang L, Tian S. Differential expression and prediction of function of lncRNAs in the ovaries of low and high fecundity Hanper sheep. Reprod Domest Anim 2021; 56:604-620. [PMID: 33475207 DOI: 10.1111/rda.13898] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 01/18/2021] [Indexed: 12/13/2022]
Abstract
Litter size is an important trait that determines the production efficiency of sheep bred for meat. Its detailed investigation can reveal the molecular mechanisms that control the fecundity of sheep and possibly accelerate the breeding process of new varieties of sheep that have high prolificacy. Long non-coding RNAs (lncRNAs) have proven to be an important factor in the regulation of follicular development. However, the mechanisms by which lncRNAs regulate litter size in sheep remain unclear. In the present study, ovarian tissues from the follicular (F) or luteal phase (L) of Hanper sheep that were either monotocous (M) or polytocous (P; FM, FP, LM and LP groups) were collected and sequenced to identify differentially expressed lncRNAs and predict their function. The results indicate that the number of up- and down-regulated lncRNAs in the follicular phase (FM vs. FP) was 95 and 111 and 109 and 49, respectively, in the luteal phase (LM vs. LP). The functional enrichment of the different lncRNAs coexpressed with mRNA was analysed. The results demonstrated that the KISS1-GnRH-LH/FSH-E2 and EGF-EGFR-RAS-PI3K signalling pathways promoted the initiation of the primordial period, follicular development and ovulation in the follicular phase (FM vs. FP). During the luteal phase (LM vs. LP), the production and development of the corpus luteum in ewes was influenced by the KITLG-KIT/FGF-FGFR/HGF-MET-RAS-ERK signalling pathway. STEM clustering functional enrichment analysis of the differentially expressed lncRNAs indicated that profile11 was principally enriched in the Cytokine-Jak-STAT, PDGF-PDGFR-PI3K and KITLG-KIT-RAS-ERK signalling pathways. By analysis of the differential expression of the lncRNAs and their expression in each group, lncRNAs Xist (loc101112291) and Gtl2 (loc101123329) were found to be highly expressed, suggesting that regulation of follicular development was mediated through methylation processes.
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Affiliation(s)
- Aiju Liu
- College of Animal Science and Technology, Hebei Agricultural University, Baoding, China
| | - Menghe Liu
- Discipline of Obstetrics and Gynaecology, School of Medicine, Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia
| | - Yuexin Li
- College of Animal Science and Technology, Hebei Agricultural University, Baoding, China
| | - Xiaoyong Chen
- College of Animal Science and Technology, Hebei Agricultural University, Baoding, China
| | - Limeng Zhang
- Laboratory of Molecular Biology, Zhengzhou Normal University, Zhengzhou, China
| | - Shujun Tian
- College of Animal Science and Technology, Hebei Agricultural University, Baoding, China.,The Research Center of Cattle and Sheep, Embryonic Technique of Hebei Province, Baoding, China
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33
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Gurnari C, Pagliuca S, Visconte V. Deciphering the Therapeutic Resistance in Acute Myeloid Leukemia. Int J Mol Sci 2020; 21:ijms21228505. [PMID: 33198085 PMCID: PMC7697160 DOI: 10.3390/ijms21228505] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/05/2020] [Accepted: 11/10/2020] [Indexed: 02/06/2023] Open
Abstract
Acute myeloid leukemia (AML) is a clonal hematopoietic disorder characterized by abnormal proliferation, lack of cellular differentiation, and infiltration of bone marrow, peripheral blood, or other organs. Induction failure and in general resistance to chemotherapeutic agents represent a hindrance for improving survival outcomes in AML. Here, we review the latest insights in AML biology concerning refractoriness to therapies with a specific focus on cytarabine and daunorubicin which still represent milestones agents for inducing therapeutic response and disease eradication. However, failure to achieve complete remission in AML is still high especially in elderly patients (40-60% in patients >65 years old). Several lines of basic and clinical research have been employed to improve the achievement of complete remission. These lines of research include molecular targeted therapy and more recently immunotherapy. In terms of molecular targeted therapies, specific attention is given to DNMT3A and TP53 mutant AML by reviewing the mechanisms underlying epigenetic therapies' (e.g., hypomethylating agents) resistance and providing critical points and hints for possible future therapies overcoming AML refractoriness.
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Affiliation(s)
- Carmelo Gurnari
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH 44195, USA; (C.G.); (S.P.)
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Simona Pagliuca
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH 44195, USA; (C.G.); (S.P.)
| | - Valeria Visconte
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH 44195, USA; (C.G.); (S.P.)
- Correspondence: ; Tel.: +1-216-445-6895
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34
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Abstract
RNAs have emerged as a major target for diagnostics and therapeutics approaches. Regulatory nonprotein-coding RNAs (ncRNAs) in particular display remarkable versatility. They can fold into complex structures and interact with proteins, DNA, and other RNAs, thus modulating activity, localization, or interactome of multi-protein complexes. Thus, ncRNAs confer regulatory plasticity and represent a new layer of regulatory control. Interestingly, long noncoding RNAs (lncRNAs) tend to acquire complex secondary and tertiary structures and their function-in many cases-is dependent on structural conservation rather than primary sequence conservation. Whereas for many proteins, structure and its associated function are closely connected, for lncRNAs, the structural domains that determine functionality and its interactome are still not well understood. Numerous approaches for analyzing the structural configuration of lncRNAs have been developed recently. Here, will provide an overview of major experimental approaches used in the field, and discuss the potential benefit of using combinatorial strategies to analyze lncRNA modes of action based on structural information.
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Affiliation(s)
- Johannes Graf
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, Regensburg, Germany
| | - Markus Kretz
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, Regensburg, Germany
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35
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Wei Z, Chen L, Meng L, Han W, Huang L, Xu A. LncRNA HOTAIR promotes the growth and metastasis of gastric cancer by sponging miR-1277-5p and upregulating COL5A1. Gastric Cancer 2020; 23:1018-1032. [PMID: 32583079 DOI: 10.1007/s10120-020-01091-3] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 05/21/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND Emerging studies have shown that HOTAIR acts as an oncogene in gastric cancer (GC). However, its role in the extracellular matrix and in tumor immune infiltration remains unknown. METHODS HOTAIR and COL5A1 levels were analyzed by bioinformatics analysis and validated by qRT-PCR, western blotting and immunohistochemistry assays. The regulatory relationships between components of the HOTAIR/miR-1277-5p/COL5A1 axis and the role of this axis in GC were predicted by bioinformatics analysis, and validated by in vitro and in vivo experiments. The correlation between COL5A1 and GC immune infiltration was assessed by bioinformatics analysis and a COL5A1-based predictive nomogram was established using the Stomach Adenocarcinoma dataset from The Cancer Genome Atlas. RESULTS We found that HOTAIR and COL5A1 were overexpressed in GC compared to normal controls, which predicted poor prognosis. The regulatory relationship of the HOTAIR/miR-1277-5p/COL5A1 axis in GC was demonstrated, and HOTAIR and COL5A1 were found to promote GC growth while miR-1277-5p exerted the reverse effects. In addition, COL5A1 was negatively associated with tumor purity but positively associated with immune infiltration, which suggested that COL5A1-mediated GC growth may be partially mediated by the regulation of immune infiltration. Additionally, the established COL5A1-based nomogram showed that COL5A1 can serve as a prognostic biomarker in GC. CONCLUSIONS HOTAIR regulates GC growth by sponging miR-1277-5p and upregulating COL5A1, and COL5A1-mediated GC cell proliferation may be mediated by effects on the tumor microenvironment, which provides novel targets for GC treatment.
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Affiliation(s)
- Zhijian Wei
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, 218 JiXi Avenue, Hefei, 230022, Anhui, PR China
| | - Lei Chen
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, 218 JiXi Avenue, Hefei, 230022, Anhui, People's Republic of China.,Institute of Urology, Anhui Medical University, 218 JiXi Avenue, Hefei, 230022, Anhui, People's Republic of China
| | - Lei Meng
- Department of General Surgery, The Fourth Affiliated Hospital of Anhui Medical University, 100 HuaiHe Avenue, Hefei, 230002, Anhui, People's Republic of China
| | - Wenxiu Han
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, 218 JiXi Avenue, Hefei, 230022, Anhui, PR China.
| | - Lei Huang
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, 218 JiXi Avenue, Hefei, 230022, Anhui, PR China.
| | - Aman Xu
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, 218 JiXi Avenue, Hefei, 230022, Anhui, PR China.
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36
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Badmalia MD, Siddiqui MQ, Mrozowich T, Gemmill DL, Patel TR. Analytical ultracentrifuge: an ideal tool for characterization of non-coding RNAs. Eur Biophys J 2020; 49:809-18. [PMID: 33067686 DOI: 10.1007/s00249-020-01470-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 09/26/2020] [Accepted: 10/05/2020] [Indexed: 12/25/2022]
Abstract
Analytical ultracentrifugation (AUC) has emerged as a robust and reliable technique for biomolecular characterization with extraordinary sensitivity. AUC is widely used to study purity, conformational changes, biomolecular interactions, and stoichiometry. Furthermore, AUC is used to determine the molecular weight of biomolecules such as proteins, carbohydrates, and DNA and RNA. Due to the multifaceted role(s) of non-coding RNAs from viruses, prokaryotes, and eukaryotes, research aimed at understanding the structure-function relationships of non-coding RNAs is rapidly increasing. However, due to their large size, flexibility, complicated secondary structures, and conformations, structural studies of non-coding RNAs are challenging. In this review, we are summarizing the application of AUC to evaluate the homogeneity, interactions, and conformational changes of non-coding RNAs from adenovirus as well as from Murray Valley, Powassan, and West Nile viruses. We also discuss the application of AUC to characterize eukaryotic long non-coding RNAs, Xist, and HOTAIR. These examples highlight the significant role AUC can play in facilitating the structural determination of non-coding RNAs and their complexes.
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37
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Wang Y, Wang J, Hao H, Luo X. lncRNA KCNQ1OT1 promotes the proliferation, migration and invasion of retinoblastoma cells by upregulating HIF-1α via sponging miR-153-3p. J Investig Med 2020; 68:1349-1356. [DOI: 10.1136/jim-2020-001431] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/12/2020] [Indexed: 12/19/2022]
Abstract
It is reported that lncRNA KCNQ1 opposite strand/antisense transcript 1 (KCNQ1OT1) is oncogenic in many cancers. This work aimed at probing into its expression and biological functions in retinoblastoma (RB) as well as its regulatory effects on miR-153-3p and hypoxia-inducible factor-1α (HIF-1α). In our study, RB samples in pair were collected, and quantitative real-time PCR (qRT-PCR) was employed for examining the expression levels of KCNQ1OT1, miR-153-3p and HIF-1α. KCNQ1OT1 short hairpin RNAs were transfected into SO-Rb50 and HXO-RB44 cell to inhibit the expression of KCNQ1OT1. The proliferative activity, colony formation ability and apoptosis were examined through cell counting kit-8 assay, colony formation assays, Transwell assay and flow cytometry, respectively. qRT-PCR and western blot analysis were used for analyzing the changes of miR-153-3p and HIF-1α induced by KCNQ1OT1. The regulatory relationships between miR-153-3p and KCNQ1OT1, miR-153-3p and HIF-1α were examined by dual luciferase reporter gene assay and RNA-binding protein immunoprecipitation assay. The results of our study showed that KCNQ1OT1 expression was markedly enhanced in RB tissue samples, and KCNQ1OT1 knockdown had an inhibitory effect on the proliferation, migration, invasion and viability of RB cells. There were two validated binding sties between KCNQ1OT1 and miR-153-3p, and KCNQ1OT1 negatively regulated the expression of miR-153-3p in RB cells. HIF-1α was a target gene of miR-153-3p, and could be positively regulated by KCNQ1OT1. In conclusion, our study indicates that KCNQ1OT1 can increase the malignancy of RB cells via regulating miR-153-3p/HIF-1α axis.
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Wang Y, Kathiresan V, Chen Y, Hu Y, Jiang W, Bai G, Liu G, Qin PZ, Fang X. Posttranscriptional site-directed spin labeling of large RNAs with an unnatural base pair system under non-denaturing conditions. Chem Sci 2020; 11:9655-9664. [PMID: 33224460 PMCID: PMC7667596 DOI: 10.1039/d0sc01717e] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 08/19/2020] [Indexed: 12/25/2022] Open
Abstract
Site-directed spin labeling (SDSL) of large RNAs for electron paramagnetic resonance (EPR) spectroscopy has remained challenging to date.
Site-directed spin labeling (SDSL) of large RNAs for electron paramagnetic resonance (EPR) spectroscopy has remained challenging to date. We here demonstrate an efficient and generally applicable posttranscriptional SDSL method for large RNAs using an expanded genetic alphabet containing the NaM-TPT3 unnatural base pair (UBP). An alkyne-modified TPT3 ribonucleotide triphosphate (rTPT3COTP) is synthesized and site-specifically incorporated into large RNAs by in vitro transcription, which allows attachment of the azide-containing nitroxide through click chemistry. We validate this strategy by SDSL of a 419-nucleotide ribonuclease P (RNase P) RNA from Bacillus stearothermophilus under non-denaturing conditions. The effects of site-directed UBP incorporation and subsequent spin labeling on the global structure and function of RNase P are marginal as evaluated by Circular Dichroism spectroscopy, Small Angle X-ray Scattering, Sedimentation Velocity Analytical Ultracentrifugation and enzymatic assay. Continuous-Wave EPR analyses reveal that the labeling reaction is efficient and specific, and Pulsed Electron–Electron Double Resonance measurements yield an inter-spin distance distribution that agrees with the crystal structure. The labeling strategy as presented overcomes the size constraint of RNA labeling, opening new avenues of spin labeling and EPR spectroscopy for investigating the structure and dynamics of large RNAs.
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Affiliation(s)
- Yan Wang
- Beijing Advanced Innovation Center for Structural Biology , School of Life Sciences , Tsinghua University , Beijing 100084 , China .
| | - Venkatesan Kathiresan
- Department of Chemistry , University of Southern California , Los Angeles , California 90089 , USA .
| | - Yaoyi Chen
- Beijing Advanced Innovation Center for Structural Biology , School of Life Sciences , Tsinghua University , Beijing 100084 , China .
| | - Yanping Hu
- Beijing Advanced Innovation Center for Structural Biology , School of Life Sciences , Tsinghua University , Beijing 100084 , China .
| | - Wei Jiang
- Department of Chemistry , University of Southern California , Los Angeles , California 90089 , USA .
| | - Guangcan Bai
- State Key Laboratory of Natural and Biomimetic Drugs , School of Pharmaceutical Sciences , Peking University , Beijing 100191 , China
| | - Guoquan Liu
- State Key Laboratory of Natural and Biomimetic Drugs , School of Pharmaceutical Sciences , Peking University , Beijing 100191 , China
| | - Peter Z Qin
- Department of Chemistry , University of Southern California , Los Angeles , California 90089 , USA .
| | - Xianyang Fang
- Beijing Advanced Innovation Center for Structural Biology , School of Life Sciences , Tsinghua University , Beijing 100084 , China .
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Jones AN, Sattler M. Challenges and perspectives for structural biology of lncRNAs-the example of the Xist lncRNA A-repeats. J Mol Cell Biol 2020; 11:845-859. [PMID: 31336384 PMCID: PMC6917512 DOI: 10.1093/jmcb/mjz086] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 06/30/2019] [Accepted: 07/02/2019] [Indexed: 12/21/2022] Open
Abstract
Following the discovery of numerous long non-coding RNA (lncRNA) transcripts in the human genome, their important roles in biology and human disease are emerging. Recent progress in experimental methods has enabled the identification of structural features of lncRNAs. However, determining high-resolution structures is challenging as lncRNAs are expected to be dynamic and adopt multiple conformations, which may be modulated by interaction with protein binding partners. The X-inactive specific transcript (Xist) is necessary for X inactivation during dosage compensation in female placental mammals and one of the best-studied lncRNAs. Recent progress has provided new insights into the domain organization, molecular features, and RNA binding proteins that interact with distinct regions of Xist. The A-repeats located at the 5′ end of the transcript are of particular interest as they are essential for mediating silencing of the inactive X chromosome. Here, we discuss recent progress with elucidating structural features of the Xist lncRNA, focusing on the A-repeats. We discuss the experimental and computational approaches employed that have led to distinct structural models, likely reflecting the intrinsic dynamics of this RNA. The presence of multiple dynamic conformations may also play an important role in the formation of the associated RNPs, thus influencing the molecular mechanism underlying the biological function of the Xist A-repeats. We propose that integrative approaches that combine biochemical experiments and high-resolution structural biology in vitro with chemical probing and functional studies in vivo are required to unravel the molecular mechanisms of lncRNAs.
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Affiliation(s)
- Alisha N Jones
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, 85764, Germany.,Center for Integrated Protein Science Munich and Bavarian NMR Center at Department of Chemistry, Technical University of Munich, Garching, 85747, Germany
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, 85764, Germany.,Center for Integrated Protein Science Munich and Bavarian NMR Center at Department of Chemistry, Technical University of Munich, Garching, 85747, Germany
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Abstract
It is said that "hindsight is 20-20", so, given the current year, it is an opportune time to review and learn from experiences studying long noncoding RNAs. Investigation of the Saccharomyces cerevisiae telomerase RNA, TLC1, has unveiled striking flexibility in terms of both structural and functional features. Results support the "flexible scaffold" hypothesis for this 1157-nt telomerase RNA. This model describes TLC1 acting as a tether for holoenzyme protein subunits, and it also may apply to a plethora of RNAs beyond telomerase, such as types of lncRNAs. In this short perspective review, I summarize findings from studying the large yeast telomerase ribonucleoprotein (RNP) complex in the hope that this hindsight will sharpen foresight as so many of us seek to mechanistically understand noncoding RNA molecules from vast transcriptomes.
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Affiliation(s)
- David C Zappulla
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA
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Li Z, Xie X, Fan X, Li X. Long Non-coding RNA MINCR Regulates miR-876-5p/GSPT1 Axis to Aggravate Glioma Progression. Neurochem Res 2020; 45:1690-1699. [PMID: 32333234 DOI: 10.1007/s11064-020-03029-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 04/03/2020] [Accepted: 04/07/2020] [Indexed: 12/16/2022]
Abstract
Emerging evidence underlined the crucial roles played by long non-coding RNAs (lncRNAs) in glioma. MINCR has been reported in multiple malignancies. Here, we studied its function and potential mechanism in glioma, which remain unclear. Gene expressions were analyzed by qRT-PCR assay. Both in vitro and in vivo assays were conducted to evaluate the cellular function of MINCR in glioma. The subcellular situation of MINCR was detected by subcellular fractionation and FISH assays. Luciferase reporter, RNA pull-down and RNA immunoprecipitation (RIP) assays were combined to investigate potential mechanisms of relevant genes. MINCR was up-regulated in glioma. MINCR depletion markedly refrained glioma cell proliferation, migration and invasion via sponging miR-876-5p. MiR-876-5p suppressed the malignant behaviors of glioma via binding to GSPT1. MINCR shared the binding sites with the 3'-untranslated region of GSPT1 and prevented the binding of miR-876-5p to GSPT1 mRNA, thus up-regulating the level of GSPT1. Moreover, miR-876 inhibition and GSPT1 up-regulation counteracted the functional effect induced by silencing MINCR on glioma progression. Our findings uncovered that MINCR might aggravated glioma cell proliferation and migration via acting as competing endogenous RNA (ceRNA), indicating prospective novel therapeutic target for glioma.
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Affiliation(s)
- Zheng Li
- Department of Neurosurgery, Deyang People's Hospital, Deyang, 618000, Sichuan, China
| | - Xiaoxia Xie
- Department of Emergency, Deyang People's Hospital, Deyang, 618000, Sichuan, China
| | - Xiangyun Fan
- General Medical Wards (A), The People's Hospital of Binzhou City, Binzhou, 25660, Shandong, China
| | - Xing Li
- Department of Neurosurgery, Taizhou First People's Hospital, No. 218 Hengjie Road, Dongcheng Street, Huangyan District, Zhejiang, 318020, Taizhou, China.
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Yao J, Xu G, Zhu L, Zheng H. circGFRA1 Enhances NSCLC Progression by Sponging miR-188-3p. Onco Targets Ther 2020; 13:549-558. [PMID: 32021297 PMCID: PMC6980840 DOI: 10.2147/ott.s230795] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 12/30/2019] [Indexed: 12/13/2022] Open
Abstract
Background Lung cancer continues to be one of the most dangerous tumors around the world. It is an urgency to explore the molecular mechanism of non-small cell lung cancer (NSCLC) progression for developing novel therapeutic approaches. Circular RNA (circRNA) is a novel type of non-coding RNA with a stable closed loop structure. Abnormally expressed circRNAs have been found in many kinds of cancer including NSCLC. Methods and Results The expression of circGFRA1 and miR-188-3p was detected in NSCLC tissues by RT-qPCR and it was found that circGFRA1 was highly expressed and miR-183-3p was lowly expressed in NSCLC tissues. In NSCLC cell lines, we confirmed that circGFRA1 acted as an miR-188-3p sponge using dual-luciferase reporter assay and RNA immunoprecipitation (RIP) analysis. Overexpression of cirGFRA1 enhanced NSCLC progression while miR-188-3p overexpression inhibited it by CCK8 and colony formation analysis. In vivo tumor xenograft model, circGFRA1 and miR-188-3p synergistically regulated the proliferation of NSCLC tumors. Mechanistic study indicated that circGFRA1 and miR-188-3p regulated the proliferation of NSCLC cells at least through PI3K/AKT signaling pathway. Conclusion Our study elaborated a novel circGFRA-miR-188-3p-PI3K/AKT regulatory pathway, providing a potential diagnostic biomarker and therapeutic target for NSCLC.
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Affiliation(s)
- Jie Yao
- Department of Thoracic Surgery, Second Affiliated Hospital of Zhejiang University, School of Medicine, Hangzhou 310009, People's Republic of China
| | - Guanxin Xu
- Department of Thoracic Surgery, Second Affiliated Hospital of Zhejiang University, School of Medicine, Hangzhou 310009, People's Republic of China
| | - Ling Zhu
- Department of Thoracic Surgery, Second Affiliated Hospital of Zhejiang University, School of Medicine, Hangzhou 310009, People's Republic of China
| | - Heqing Zheng
- Department of Thoracic Surgery, Yueqing People's Hospital, Wenzhou, People's Republic of China
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Kim DN, Thiel BC, Mrozowich T, Hennelly SP, Hofacker IL, Patel TR, Sanbonmatsu KY. Zinc-finger protein CNBP alters the 3-D structure of lncRNA Braveheart in solution. Nat Commun 2020; 11:148. [PMID: 31919376 PMCID: PMC6952434 DOI: 10.1038/s41467-019-13942-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Accepted: 12/09/2019] [Indexed: 02/08/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) constitute a significant fraction of the transcriptome, playing important roles in development and disease. However, our understanding of structure-function relationships for this emerging class of RNAs has been limited to secondary structures. Here, we report the 3-D atomistic structural study of epigenetic lncRNA, Braveheart (Bvht), and its complex with CNBP (Cellular Nucleic acid Binding Protein). Using small angle X-ray scattering (SAXS), we elucidate the ensemble of Bvht RNA conformations in solution, revealing that Bvht lncRNA has a well-defined, albeit flexible 3-D structure that is remodeled upon CNBP binding. Our study suggests that CNBP binding requires multiple domains of Bvht and the RHT/AGIL RNA motif. We show that RHT/AGIL, previously shown to interact with CNBP, contains a highly flexible loop surrounded by more ordered helices. As one of the largest RNA-only 3-D studies, the work lays the foundation for future structural studies of lncRNA-protein complexes.
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Affiliation(s)
- Doo Nam Kim
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Bernhard C Thiel
- Department of Theoretical Chemistry, University of Vienna, Vienna, Austria
| | - Tyler Mrozowich
- Alberta RNA Research & Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Scott P Hennelly
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
- New Mexico Consortium, Los Alamos, New Mexico, USA
| | - Ivo L Hofacker
- Department of Theoretical Chemistry, University of Vienna, Vienna, Austria
- Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria
| | - Trushar R Patel
- Alberta RNA Research & Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada.
- Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta, Canada.
| | - Karissa Y Sanbonmatsu
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, USA.
- New Mexico Consortium, Los Alamos, New Mexico, USA.
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Yang Y, Li S, Cao J, Li Y, Hu H, Wu Z. RRM2 Regulated By LINC00667/miR-143-3p Signal Is Responsible For Non-Small Cell Lung Cancer Cell Progression. Onco Targets Ther 2019; 12:9927-9939. [PMID: 31819489 PMCID: PMC6876211 DOI: 10.2147/ott.s221339] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Accepted: 10/04/2019] [Indexed: 12/12/2022] Open
Abstract
Background Non-small cell lung cancer (NSCLC) is a common and fatal cancer worldwide with a very low 5-year overall survival rate. Ribonucleotide reductase M2 subunit (RRM2), a small subunit of the ribonucleotide reductase complex, has been found to be an oncogenic role in a variety of tumors including NSCLC. However, the regulatory mechanism of RRM2 in NSCLC is not clear. Increasing evidence suggests that non-coding RNAs (ncRNAs) including miRNAs and lincRNAs may promote or inhibit tumor initiation and development through regulating the expression of oncogenic genes. It is interesting to find ncRNAs which play important role in regulating RRM2 expression. Materials and methods The expression levels of RRM2, LINC0066 and miR-143-3p in NSCLC tumor tissues and cell lines were detected using qRT-PCR. The regulatory relationships among RRM2, LINC0066 and miR-143-3p were predicted using database analysis and verified by luciferase reporter assay and RIP analysis. The proliferation ability of NSCLC cells was assessed using CCK8 and colony formation assays. The expression of related proteins was determined by Western blot. In vivo effect of RRM2, LINC0066 and miR-143-3p to NSCLC were detected through xenograft experiments. Results In this study, we found RRM2 was upregulated in NSCLC tumor and cell lines, and the aberrant upregulation predicted a poor prognosis. Then, we predicted and confirmed that RRM2 was negatively regulated by miR-143-3p. Further study implied that LINC00667 acted as a ceRNA by sponging miR-143-3p and regulated RRM2 expression indirectly. Moreover, we found that the growth of NSCLC was regulated by LINC00667/miR-143-3p/RRM2 signal pathway both in vitro and in vivo. LINC00667 and RRM2 promoted the tumor growth while miR-143-3p inhibited it. Conclusion Our study revealed a LINC00667/miR-143-3p/RRM2 signal pathway that played an important role in the progress of NSCLC, which might be potential therapeutic targets for NSCLC.
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Affiliation(s)
- Yanbing Yang
- Department of Respiratory Medicine, Luohe Central Hospital, The First Affiliated Hospital of Luohe Medical College, Luohe, Henan 462000, People's Republic of China
| | - Sensen Li
- Department of Pharmacy, Luohe Central Hospital, The First Affiliated Hospital of Luohe Medical College, Luohe, Henan 462000, People's Republic of China
| | - Juan Cao
- Department of Respiratory Medicine, Luohe Central Hospital, The First Affiliated Hospital of Luohe Medical College, Luohe, Henan 462000, People's Republic of China
| | - Yaojun Li
- Department of Respiratory Medicine, Luohe Central Hospital, The First Affiliated Hospital of Luohe Medical College, Luohe, Henan 462000, People's Republic of China
| | - Haiying Hu
- Department of Respiratory Medicine, Luohe Central Hospital, The First Affiliated Hospital of Luohe Medical College, Luohe, Henan 462000, People's Republic of China
| | - Zhuyu Wu
- Department of Respiratory Medicine, Luohe Central Hospital, The First Affiliated Hospital of Luohe Medical College, Luohe, Henan 462000, People's Republic of China
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Zhang Y, Zhang Y, Liu Z, Cheng M, Ma J, Wang Y, Qin C, Fang X. Long non-coding subgenomic flavivirus RNAs have extended 3D structures and are flexible in solution. EMBO Rep 2019; 20:e47016. [PMID: 31502753 PMCID: PMC6832101 DOI: 10.15252/embr.201847016] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 08/14/2019] [Accepted: 08/21/2019] [Indexed: 01/05/2023] Open
Abstract
Most mosquito-borne flaviviruses, including Zika virus (ZIKV), Dengue virus (DENV), and West Nile virus (WNV), produce long non-coding subgenomic RNAs (sfRNAs) in infected cells that link to pathogenicity and immune evasion. Until now, the structural characterization of these lncRNAs remains limited. Here, we studied the 3D structures of individual and combined subdomains of sfRNAs, and visualized the accessible 3D conformational spaces of complete sfRNAs from DENV2, ZIKV, and WNV by small angle X-ray scattering (SAXS) and computational modeling. The individual xrRNA1s and xrRNA2s adopt similar structures in solution as the crystal structure of ZIKV xrRNA1, and all xrRNA1-2s form compact structures with reduced flexibility. While the DB12 of DENV2 is extended, the DB12s of ZIKV and WNV are compact due to the formation of intertwined double pseudoknots. All 3' stem-loops (3'SLs) share similar rod-like structures. Complete sfRNAs are extended and sample a large conformational space in solution. Our work not only provides structural insight into the function of flavivirus sfRNAs, but also highlights strategies of visualizing other lncRNAs in solution by SAXS and computational methods.
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Affiliation(s)
- Yupeng Zhang
- Beijing Advanced Innovation Center for Structural BiologySchool of Life SciencesTsinghua UniversityBeijingChina
| | - Yikan Zhang
- Beijing Advanced Innovation Center for Structural BiologySchool of Life SciencesTsinghua UniversityBeijingChina
| | - Zhong‐Yu Liu
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyBeijingChina
- Guangzhou Eighth People's HospitalGuangzhou Medical UniversityGuangzhouChina
- School of Medicine (Shenzhen)Sun Yat‐sen UniversityGuangzhouChina
| | - Meng‐Li Cheng
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyBeijingChina
| | - Junfeng Ma
- Beijing Advanced Innovation Center for Structural BiologySchool of Life SciencesTsinghua UniversityBeijingChina
| | - Yan Wang
- Beijing Advanced Innovation Center for Structural BiologySchool of Life SciencesTsinghua UniversityBeijingChina
| | - Cheng‐Feng Qin
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyBeijingChina
| | - Xianyang Fang
- Beijing Advanced Innovation Center for Structural BiologySchool of Life SciencesTsinghua UniversityBeijingChina
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Jabbari H, Wark I, Montemagno C, Will S. Knotty: efficient and accurate prediction of complex RNA pseudoknot structures. Bioinformatics 2019; 34:3849-3856. [PMID: 29868872 DOI: 10.1093/bioinformatics/bty420] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 05/24/2018] [Indexed: 12/14/2022] Open
Abstract
Motivation The computational prediction of RNA secondary structure by free energy minimization has become an important tool in RNA research. However in practice, energy minimization is mostly limited to pseudoknot-free structures or rather simple pseudoknots, not covering many biologically important structures such as kissing hairpins. Algorithms capable of predicting sufficiently complex pseudoknots (for sequences of length n) used to have extreme complexities, e.g. Pknots has O(n6) time and O(n4) space complexity. The algorithm CCJ dramatically improves the asymptotic run time for predicting complex pseudoknots (handling almost all relevant pseudoknots, while being slightly less general than Pknots), but this came at the cost of large constant factors in space and time, which strongly limited its practical application (∼200 bases already require 256 GB space). Results We present a CCJ-type algorithm, Knotty, that handles the same comprehensive pseudoknot class of structures as CCJ with improved space complexity of Θ(n3+Z)-due to the applied technique of sparsification, the number of 'candidates', Z, appears to grow significantly slower than n4 on our benchmark set (which include pseudoknotted RNAs up to 400 nt). In terms of run time over this benchmark, Knotty clearly outperforms Pknots and the original CCJ implementation, CCJ 1.0; Knotty's space consumption fundamentally improves over CCJ 1.0, being on a par with the space-economic Pknots. By comparing to CCJ 2.0, our unsparsified Knotty variant, we demonstrate the isolated effect of sparsification. Moreover, Knotty employs the state-of-the-art energy model of 'HotKnots DP09', which results in superior prediction accuracy over Pknots. Availability and implementation Our software is available at https://github.com/HosnaJabbari/Knotty. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Hosna Jabbari
- Department of Computer Science, University of Vermont, Burlington, VT, USA
| | - Ian Wark
- Ingenuity Lab, Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Canada
| | - Carlo Montemagno
- Department of Electrical and Computer Engineering, Southern Illinois University, Carbondale, IL, USA
| | - Sebastian Will
- Theoretical Biochemistry Group (TBI), Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria
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Li C, Zheng H, Hou W, Bao H, Xiong J, Che W, Gu Y, Sun H, Liang P. Long non-coding RNA linc00645 promotes TGF-β-induced epithelial-mesenchymal transition by regulating miR-205-3p-ZEB1 axis in glioma. Cell Death Dis 2019; 10:717. [PMID: 31558707 PMCID: PMC6763487 DOI: 10.1038/s41419-019-1948-8] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 07/06/2019] [Accepted: 09/02/2019] [Indexed: 02/07/2023]
Abstract
Accumulating evidence indicates long noncoding RNAs (lncRNA) play a vital role in tumor progression. However, the role of linc00645-induced accelerated malignant behavior in glioblastoma (GBM) remains unknown. In the present study, linc00645 expression was significantly upregulated in GBM tissues and cell lines. High level of linc00645 was associated with poor overall survival in GBM patients. Knockdown of linc00645 suppressed the proliferation, stemness, migration, invasion, and reversed transforming growth factor (TGF)-β-induced motility of glioma cell lines. Furthermore, linc00645 directly interacted with miR-205-3p and upregulated of miR-205-3p impeded efficiently the increase of ZEB1 induced by linc00645 overexpression. Moreover, knockdown of linc00645 significantly suppressed the progression of glioma cells in vivo. miR-205-3p was a target of linc00645 and linc00645 modulates TGF-β-induced glioma cell migration and invasion via miR-205-3p. Taken together, our findings identified the linc00645/miR-205-3p/ZEB1 signaling axis as a key player in EMT of glioma cells triggered by TGF-β. These data elucidated that linc00645 plays an oncogenic role in glioma and it may serve as a prognostic biomarker and a potential therapeutic target for the treatment of glioma in humans.
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Affiliation(s)
- Chenlong Li
- Department of Neurosurgery, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, 150001, P.R. China
| | - Hongshan Zheng
- Department of Neurosurgery, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, 150001, P.R. China
| | - Weiliang Hou
- Department of Neurosurgery, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, 150001, P.R. China
| | - Hongbo Bao
- Department of Neurosurgery, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, 150001, P.R. China
| | - Jinsheng Xiong
- Department of Neurosurgery, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, 150001, P.R. China
| | - Wanli Che
- Department of Neurosurgery, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, 150001, P.R. China
| | - Yifei Gu
- Department of Neurosurgery, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, 150001, P.R. China
| | - Haiming Sun
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, Heilongjiang, 150001, P.R. China.
- Key Laboratory of Medical Genetics (Harbin Medical University), Heilongjiang Higher Education Institutions, Harbin, Heilongjiang, 150001, P.R. China.
| | - Peng Liang
- Department of Neurosurgery, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, 150001, P.R. China.
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Abstract
Alterations and personal variations of RNA interactions have been mechanistically coupled with disease etiology and phenotypical variations. RNA biomarkers, RNA mimics, and RNA antagonists have been developed for diagnostic, prognostic, and therapeutic uses. Long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) are two major types of RNA molecules with regulatory roles, deregulation of which has been implicated in the initiation and progression of many human malignancies. Accumulating evidence indicated the clinical roles of regulatory RNAs in cancer control, stimulating a surge in exploring the functionalities of regulatory RNAs for improved understanding on disease pathogenesis and management. In this review, we highlight the critical roles of lncRNAs and miRNAs played in tumorigenesis, scrutinize their potential functionalities as diagnostic/prognostic biomarkers and/or therapeutic targets in clinics, outline opportunities that ncRNAs may bring to complement current clinical practice for improved cancer management and identify challenges faced by translating frontier knowledge on non-coding RNAs (ncRNAs) to bedside clinics as well as possible solutions.
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Affiliation(s)
- Xiaofeng Dai
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Aman Chandra Kaushik
- Wuxi School of Medicine, Jiangnan University, Wuxi, China.,School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jianying Zhang
- Henan Key Laboratory of Tumor Epidemiology, Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
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49
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Xie Y, Wang M, Tian J, Li X, Yang M, Zhang K, Tan S, Luo L, Luo C, Peng L, Tang A. Long non-coding RNA expressed in macrophage co-varies with the inflammatory phenotype during macrophage development and polarization. J Cell Mol Med 2019; 23:6530-6542. [PMID: 31419045 PMCID: PMC6787567 DOI: 10.1111/jcmm.14557] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 06/19/2019] [Accepted: 07/02/2019] [Indexed: 12/13/2022] Open
Abstract
Advances in microarray, RNA‐seq and omics techniques, thousands of long non‐coding RNAs (lncRNAs) with unknown functions have been discovered. LncRNAs have presented a diverse perspective on gene regulation in diverse biological processes, especially in human immune response. Macrophages participate in the whole phase of immune inflammatory response. They are able to shape their phenotype and arouse extensive functional activation after receiving physiological and pathological stimuli. Emerging studies indicated that lncRNAs participated in the gene regulatory network during complex biological processes of macrophage, including macrophage‐induced inflammatory responses. Here, we reviewed the existing knowledges of lncRNAs in the processes of macrophage development and polarization, and their roles in several different inflammatory diseases. Specifically, we focused on how lncRNAs function in macrophage, which might help to discover some potential therapeutic targets and diagnostic biomarkers.
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Affiliation(s)
- Yixin Xie
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China.,Department of Urological Organ Transplantation, Center of Organ Transplantation, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Min Wang
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jingjing Tian
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xianping Li
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Min Yang
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Kan Zhang
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Shan Tan
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Lingli Luo
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Can Luo
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Longkai Peng
- Department of Urological Organ Transplantation, Center of Organ Transplantation, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Aiguo Tang
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
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50
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Kubota M, Nainar S, Parker SM, England W, Furche F, Spitale RC. Expanding the Scope of RNA Metabolic Labeling with Vinyl Nucleosides and Inverse Electron-Demand Diels-Alder Chemistry. ACS Chem Biol 2019; 14:1698-1707. [PMID: 31310712 PMCID: PMC8061575 DOI: 10.1021/acschembio.9b00079] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Optimized and stringent chemical methods to profile nascent RNA expression are still in demand. Herein, we expand the toolkit for metabolic labeling of RNA through application of inverse electron demand Diels-Alder (IEDDA) chemistry. Structural examination of metabolic enzymes guided the design and synthesis of vinyl-modified nucleosides, which we systematically tested for their ability to be installed through cellular machinery. Further, we tested these nucleosides against a panel of tetrazines to identify those which are able to react with a terminal alkene, but are stable enough for selective conjugation. The selected pairings then facilitated RNA functionalization with biotin and fluorophores. We found that this chemistry not only is amenable to preserving RNA integrity but also endows the ability to both tag and image RNA in cells. These key findings represent a significant advancement in methods to profile the nascent transcriptome using chemical approaches.
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