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Yu X, Bu C, Yang X, Jiang W, He X, Sun R, Guo H, Shang L, Ou C. Exosomal non-coding RNAs in colorectal cancer metastasis. Clin Chim Acta 2024; 556:117849. [PMID: 38417779 DOI: 10.1016/j.cca.2024.117849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 02/24/2024] [Accepted: 02/25/2024] [Indexed: 03/01/2024]
Abstract
Colorectal cancer (CRC) is a type of gastrointestinal cancer with high morbidity and mortality rates, and is often accompanied by distant metastases. Metastasis is a major cause of shortened survival time and poor treatment outcomes for patients with CRC. However, the molecular mechanisms underlying the metastasis of CRC remain unclear. Exosomes are a class of small extracellular vesicles that originate from almost all human cells and can transmit biological information (e.g., nucleic acids, lipids, proteins, and metabolites) from secretory cells to target recipient cells. Recent studies have revealed that non-coding RNAs (ncRNAs) can be released by exosomes into the tumour microenvironment or specific tissues, and play a pivotal role in tumorigenesis by regulating a series of key molecules or signalling pathways, particularly those involved in tumour metastasis. Exosomal ncRNAs have potential as novel therapeutic targets for CRC metastasis, and can also be used as liquid biopsy biomarkers because of their specificity and sensitivity. Therefore, further investigations into the biological function and clinical value of exosomal ncRNAs will be of great value for the prevention, early diagnosis, and treatment of CRC metastasis.
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Affiliation(s)
- Xiaoqian Yu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Chiwen Bu
- Department of General Surgery, People's Hospital of Guanyun County, Lianyungang 222200, Jiangsu, China
| | - Xuejie Yang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Wenying Jiang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Xiaoyun He
- Departments of Ultrasound Imaging, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Ru Sun
- Department of Blood Transfusion, Affiliated Hospital of North Sichuan Medical College, Xichang 637000, Sichuan, China
| | - Hongbin Guo
- Department of Orthopedics, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Li Shang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China.
| | - Chunlin Ou
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China.
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2
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Yang C, Hardy P. The Multifunctional Nature of the MicroRNA/AKT3 Regulatory Axis in Human Cancers. Cells 2023; 12:2594. [PMID: 37998329 PMCID: PMC10670075 DOI: 10.3390/cells12222594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 11/25/2023] Open
Abstract
Serine/threonine kinase (AKT) signaling regulates diverse cellular processes and is one of the most important aberrant cell survival mechanisms associated with tumorigenesis, metastasis, and chemoresistance. Targeting AKT has become an effective therapeutic strategy for the treatment of many cancers. AKT3 (PKBγ), the least studied isoform of the AKT family, has emerged as a major contributor to malignancy. AKT3 is frequently overexpressed in human cancers, and many regulatory oncogenic or tumor suppressor small non-coding RNAs (ncRNAs), including microRNAs (miRNAs), have recently been identified to be involved in regulating AKT3 expression. Therefore, a better understanding of regulatory miRNA/AKT3 networks may reveal novel biomarkers for the diagnosis of patients with cancer and may provide invaluable information for developing more effective therapeutic strategies. The aim of this review was to summarize current research progress in the isoform-specific functions of AKT3 in human cancers and the roles of dysregulated miRNA/AKT3 in specific types of human cancers.
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Affiliation(s)
- Chun Yang
- Research Center of CHU Sainte-Justine, University of Montréal, Montreal, QC H3T 1C5, Canada;
| | - Pierre Hardy
- Research Center of CHU Sainte-Justine, University of Montréal, Montreal, QC H3T 1C5, Canada;
- Department of Pharmacology and Physiology, Department of Pediatrics, University of Montréal, Montreal, QC H3T 1C5, Canada
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3
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Peng B, Li J, Yan Y, Liu Y, Liang Q, Liu W, Thakur A, Zhang K, Xu Z, Wang J, Zhang F. Non-coding RNAs: The recently accentuated molecules in the regulation of cell autophagy for ovarian cancer pathogenesis and therapeutic response. Front Pharmacol 2023; 14:1162045. [PMID: 37063265 PMCID: PMC10102359 DOI: 10.3389/fphar.2023.1162045] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 03/20/2023] [Indexed: 04/03/2023] Open
Abstract
Autophagy is a self-recycling and conserved process, in which the senescent cytoplasmic components are degraded in cells and then recycled to maintain homeostatic balance. Emerging evidence has suggested the involvement of autophagy in oncogenesis and progression of various cancers, such as ovarian cancer (OC). Meanwhile, the non-coding RNAs (ncRNAs) frequently regulate the mRNA transcription and other functional signaling pathways in cell autophagy, displaying promising roles in human cancer pathogenesis and therapeutic response. This article mainly reviews the cutting-edge research advances about the interactions between ncRNAs and autophagy in OC. This review not only summarizes the underlying mechanisms of dynamic ncRNA-autophagy association in OC, but also discusses their prognostic implications and therapeutic biomarkers. The aim of this review was to provide a more in-depth knowledge framework exploring the ncRNA-autophagy crosstalk and highlight the promising treatment strategies for OC patients.
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Affiliation(s)
- Bi Peng
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jing Li
- Department of Pharmacy, Shanghai Pudong New Area People’s Hospital, Shanghai, China
| | - Yuanliang Yan
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yuanhong Liu
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Qiuju Liang
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Wei Liu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Orthopedic Surgery, The Second Hospital University of South China, Hengyang, Hunan, China
| | - Abhimanyu Thakur
- Ben May Department for Cancer Research, Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, United States
| | - Kui Zhang
- State Key Laboratory of Silkworm Genome Biology, Medical Research Institute, Southwest University, Chongqing, China
| | - Zhijie Xu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jian Wang
- Department of Pharmacy, Shanghai Pudong New Area People’s Hospital, Shanghai, China
| | - Fan Zhang
- Department of Gynecology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- *Correspondence: Fan Zhang,
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4
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Khalafiyan A, Emadi-Baygi M, Wolfien M, Salehzadeh-Yazdi A, Nikpour P. Construction of a three-component regulatory network of transcribed ultraconserved regions for the identification of prognostic biomarkers in gastric cancer. J Cell Biochem 2023; 124:396-408. [PMID: 36748954 DOI: 10.1002/jcb.30373] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 01/04/2023] [Accepted: 01/09/2023] [Indexed: 02/08/2023]
Abstract
Altered expression and functional roles of the transcribed ultraconserved regions (T-UCRs), as genomic sequences with 100% conservation between the genomes of human, mouse, and rat, in the pathophysiology of neoplasms has already been investigated. Nevertheless, the relevance of the functions for T-UCRs in gastric cancer (GC) is still the subject of inquiry. In the current study, we first used a genome-wide profiling approach to analyze the expression of T-UCRs in GC patients. Then, we constructed a three-component regulatory network and investigated potential diagnostic and prognostic values of the T-UCRs. The Cancer Genome Atlas Stomach Adenocarcinoma (TCGA-STAD) dataset was used as a resource for the RNA-sequencing data. FeatureCounts was utilized to quantify the number of reads mapped to each T-UCR. Differential expression analysis was then conducted using DESeq2. In the following, interactions between T-UCRs, microRNAs (miRNAs), and messenger RNAs (mRNAs) were combined into a three-component network. Enrichment analyses were performed and a protein-protein interaction (PPI) network was constructed. The R Survival package was utilized to identify survival-related significantly differentially expressed T-UCRs (DET-UCRs). Using an in-house cohort of GC tissues, expression of two DET-UCRs was furthermore experimentally verified. Our results showed that several T-UCRs were dysregulated in TCGA-STAD tumoral samples compared to nontumoral counterparts. The three-component network was constructed which composed of DET-UCRs, miRNAs, and mRNAs nodes. Functional enrichment and PPI network analyses revealed important enriched signaling pathways and gene ontologies such as "pathway in cancer" and regulation of cell proliferation and apoptosis. Five T-UCRs were significantly correlated with the overall survival of GC patients. While no expression of uc.232 was observed in our in-house cohort of GC tissues, uc.343 showed an increased expression, although not statistically significant, in gastric tumoral tissues. The constructed three-component regulatory network of T-UCRs in GC presents a comprehensive understanding of the underlying gene expression regulation processes involved in tumor development and can serve as a basis to investigate potential prognostic biomarkers and therapeutic targets.
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Affiliation(s)
- Anis Khalafiyan
- Department of Genetics and Molecular Biology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Modjtaba Emadi-Baygi
- Department of Genetics, Faculty of Basic Sciences, Shahrekord University, Shahrekord, Iran
| | - Markus Wolfien
- Department of System Biology and Bioinformatics, University of Rostock, Rostock, Germany
- Center for Medical Informatics, Dresden, Germany
| | - Ali Salehzadeh-Yazdi
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen, Germany
| | - Parvaneh Nikpour
- Department of Genetics and Molecular Biology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
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5
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Rezaee M, Mohammadi F, Keshavarzmotamed A, Yahyazadeh S, Vakili O, Milasi YE, Veisi V, Dehmordi RM, Asadi S, Ghorbanhosseini SS, Rostami M, Alimohammadi M, Azadi A, Moussavi N, Asemi Z, Aminianfar A, Mirzaei H, Mafi A. The landscape of exosomal non-coding RNAs in breast cancer drug resistance, focusing on underlying molecular mechanisms. Front Pharmacol 2023; 14:1152672. [PMID: 37153758 PMCID: PMC10154547 DOI: 10.3389/fphar.2023.1152672] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 03/29/2023] [Indexed: 05/10/2023] Open
Abstract
Breast cancer (BC) is the most common malignancy among women worldwide. Like many other cancers, BC therapy is challenging and sometimes frustrating. In spite of the various therapeutic modalities applied to treat the cancer, drug resistance, also known as, chemoresistance, is very common in almost all BCs. Undesirably, a breast tumor might be resistant to different curative approaches (e.g., chemo- and immunotherapy) at the same period of time. Exosomes, as double membrane-bound extracellular vesicles 1) secreted from different cell species, can considerably transfer cell products and components through the bloodstream. In this context, non-coding RNAs (ncRNAs), including miRNAs, long ncRNAs (lncRNAs), and circular RNAs (circRNAs), are a chief group of exosomal constituents with amazing abilities to regulate the underlying pathogenic mechanisms of BC, such as cell proliferation, angiogenesis, invasion, metastasis, migration, and particularly drug resistance. Thereby, exosomal ncRNAs can be considered potential mediators of BC progression and drug resistance. Moreover, as the corresponding exosomal ncRNAs circulate in the bloodstream and are found in different body fluids, they can serve as foremost prognostic/diagnostic biomarkers. The current study aims to comprehensively review the most recent findings on BC-related molecular mechanisms and signaling pathways affected by exosomal miRNAs, lncRNAs, and circRNAs, with a focus on drug resistance. Also, the potential of the same exosomal ncRNAs in the diagnosis and prognosis of BC will be discussed in detail.
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Affiliation(s)
- Malihe Rezaee
- Department of Pharmacology, 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
| | - Fatemeh Mohammadi
- Afzalipour Faculty of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | | | - Sheida Yahyazadeh
- Department of Immunology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Omid Vakili
- Autophagy Research Center, Department of Clinical Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Clinical Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Yaser Eshaghi Milasi
- Department of Clinical Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Vida Veisi
- School of Medicine, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Rohollah Mousavi Dehmordi
- Department of Clinical Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
- Department of Clinical Biochemistry, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Sepideh Asadi
- Department of Life Science Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran, Iran
| | - Seyedeh Sara Ghorbanhosseini
- Department of Clinical Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mehdi Rostami
- Department of Clinical Biochemistry, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mina Alimohammadi
- Student Research Committee, Department of Immunology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- *Correspondence: Mina Alimohammadi, ; Abbas Azadi, ; Hamed Mirzaei, ; Alireza Mafi,
| | - Abbas Azadi
- Department of Internal Medicine, Lorestan University of Medical Sciences, Khorramabad, Iran
- *Correspondence: Mina Alimohammadi, ; Abbas Azadi, ; Hamed Mirzaei, ; Alireza Mafi,
| | - Nushin Moussavi
- Department of Surgery, Kashan University of Medical Sciences, Kashan, Iran
| | - Zatollah Asemi
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Kashan University of Medical Sciences, Kashan, Iran
| | - Azadeh Aminianfar
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Kashan University of Medical Sciences, Kashan, Iran
| | - Hamed Mirzaei
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Kashan University of Medical Sciences, Kashan, Iran
- *Correspondence: Mina Alimohammadi, ; Abbas Azadi, ; Hamed Mirzaei, ; Alireza Mafi,
| | - Alireza Mafi
- Department of Clinical Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
- Nutrition and Food Security Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
- *Correspondence: Mina Alimohammadi, ; Abbas Azadi, ; Hamed Mirzaei, ; Alireza Mafi,
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Affiliation(s)
- Xing Chen
- Artificial Intelligence Research Institute, China University of Mining and Technology, Xuzhou, 221116, China
| | - Li Huang
- The Future Laboratory, Tsinghua University, Beijing, 100084, China
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7
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Costábile A, Castellano M, Aversa-Marnai M, Quartiani I, Conijeski D, Perretta A, Villarino A, Silva-Álvarez V, Ferreira AM. A different transcriptional landscape sheds light on Russian sturgeon (Acipenser gueldenstaedtii) mechanisms to cope with bacterial infection and chronic heat stress. FISH & SHELLFISH IMMUNOLOGY 2022; 128:505-522. [PMID: 35985628 DOI: 10.1016/j.fsi.2022.08.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 08/09/2022] [Accepted: 08/11/2022] [Indexed: 06/15/2023]
Abstract
Sturgeons are chondrostean fish of high economic value and critically endangered due to anthropogenic activities, which has led to sturgeon aquaculture development. Russian sturgeon (Acipenser gueldenstaedtii), the second most important species reared for caviar, is successfully farmed in subtropical countries, including Uruguay. However, during the Uruguayan summer, sturgeons face intolerable warmer temperatures that weaken their defences and favour infections by opportunistic pathogens, increasing fish mortality and farm economic losses. Since innate immunity is paramount in fish, for which the liver plays a key role, we used deep RNA sequencing to analyse differentially expressed genes in the liver of Russian sturgeons exposed to chronic heat stress and challenged with Aeromonas hydrophila. We assembled 149.615 unigenes in the Russian sturgeon liver transcriptome and found that metabolism and immune defence pathways are among the top five biological processes taking place in the liver. Chronic heat stress provoked profound effects on liver biological functions, up-regulating genes related to protein folding, heat shock response and lipid and protein metabolism to meet energy demands for coping with heat stress. Besides, long-term exposure to heat stress led to cell damage triggering liver inflammation and diminishing liver ability to mount an innate response to A. hydrophila challenge. Accordingly, the reprogramming of liver metabolism over an extended period had detrimental effects on fish health, resulting in weight loss and mortality, with the latter increasing after A. hydrophila challenge. To our knowledge, this is the first transcriptomic study describing how chronic heat-stressed sturgeons respond to a bacterial challenge, suggesting that liver metabolism alterations have a negative impact on the innate anti-bacterial response.
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Affiliation(s)
- Alicia Costábile
- Sección Bioquímica y Biología Molecular, Facultad de Ciencias, Universidad de la República, CP 11400, Montevideo, Uruguay
| | - Mauricio Castellano
- Unidad de Inmunología, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, CP 11600, Montevideo, Uruguay; Área Inmunología, Departamento de Biociencias, Facultad de Química, Universidad de la República, Montevideo, CP 11600, Montevideo, Uruguay; Sección Bioquímica y Biología Molecular, Facultad de Ciencias, Universidad de la República, CP 11400, Montevideo, Uruguay
| | - Marcio Aversa-Marnai
- Unidad de Inmunología, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, CP 11600, Montevideo, Uruguay; Área Inmunología, Departamento de Biociencias, Facultad de Química, Universidad de la República, Montevideo, CP 11600, Montevideo, Uruguay
| | - Ignacio Quartiani
- Unidad de Patología, Biología y Cultivo de Organismos Acuáticos, Departamento de Ciencia y Tecnología de los Alimentos, Facultad de Veterinaria, Universidad de la República, CP 11300, Montevideo, Uruguay
| | | | - Alejandro Perretta
- Unidad de Patología, Biología y Cultivo de Organismos Acuáticos, Departamento de Ciencia y Tecnología de los Alimentos, Facultad de Veterinaria, Universidad de la República, CP 11300, Montevideo, Uruguay
| | - Andrea Villarino
- Sección Bioquímica y Biología Molecular, Facultad de Ciencias, Universidad de la República, CP 11400, Montevideo, Uruguay
| | - Valeria Silva-Álvarez
- Unidad de Inmunología, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, CP 11600, Montevideo, Uruguay; Área Inmunología, Departamento de Biociencias, Facultad de Química, Universidad de la República, Montevideo, CP 11600, Montevideo, Uruguay.
| | - Ana María Ferreira
- Unidad de Inmunología, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, CP 11600, Montevideo, Uruguay; Área Inmunología, Departamento de Biociencias, Facultad de Química, Universidad de la República, Montevideo, CP 11600, Montevideo, Uruguay.
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Dey SS, Sharma PK, Munshi AD, Jaiswal S, Behera TK, Kumari K, G. B, Iquebal MA, Bhattacharya RC, Rai A, Kumar D. Genome wide identification of lncRNAs and circRNAs having regulatory role in fruit shelf life in health crop cucumber ( Cucumis sativus L.). FRONTIERS IN PLANT SCIENCE 2022; 13:884476. [PMID: 35991462 PMCID: PMC9383263 DOI: 10.3389/fpls.2022.884476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
Cucumber is an extremely perishable vegetable; however, under room conditions, the fruits become unfit for consumption 2-3 days after harvesting. One natural variant, DC-48 with an extended shelf-life was identified, fruits of which can be stored up to 10-15 days under room temperature. The genes involved in this economically important trait are regulated by non-coding RNAs. The study aims to identify the long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) by taking two contrasting genotypes, DC-48 and DC-83, at two different fruit developmental stages. The upper epidermis of the fruits was collected at 5 days and 10 days after pollination (DAP) for high throughput RNA sequencing. The differential expression analysis was performed to identify differentially expressed (DE) lncRNAs and circRNAs along with the network analysis of lncRNA, miRNA, circRNA, and mRNA interactions. A total of 97 DElncRNAs were identified where 18 were common under both the developmental stages (8 down regulated and 10 upregulated). Based on the back-spliced reads, 238 circRNAs were found to be distributed uniformly throughout the cucumber genomes with the highest numbers (71) in chromosome 4. The majority of the circRNAs (49%) were exonic in origin followed by inter-genic (47%) and intronic (4%) origin. The genes related to fruit firmness, namely, polygalacturonase, expansin, pectate lyase, and xyloglucan glycosyltransferase were present in the target sites and co-localized networks indicating the role of the lncRNA and circRNAs in their regulation. Genes related to fruit ripening, namely, trehalose-6-phosphate synthase, squamosa promoter binding protein, WRKY domain transcription factors, MADS box proteins, abscisic stress ripening inhibitors, and different classes of heat shock proteins (HSPs) were also found to be regulated by the identified lncRNA and circRNAs. Besides, ethylene biosynthesis and chlorophyll metabolisms were also found to be regulated by DElncRNAs and circRNAs. A total of 17 transcripts were also successfully validated through RT PCR data. These results would help the breeders to identify the complex molecular network and regulatory role of the lncRNAs and circRNAs in determining the shelf-life of cucumbers.
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Affiliation(s)
- Shyam S. Dey
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Parva Kumar Sharma
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - A. D. Munshi
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Sarika Jaiswal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - T. K. Behera
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Khushboo Kumari
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Boopalakrishnan G.
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Mir Asif Iquebal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | | | - Anil Rai
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
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Giordo R, Wehbe Z, Posadino AM, Erre GL, Eid AH, Mangoni AA, Pintus G. Disease-Associated Regulation of Non-Coding RNAs by Resveratrol: Molecular Insights and Therapeutic Applications. Front Cell Dev Biol 2022; 10:894305. [PMID: 35912113 PMCID: PMC9326031 DOI: 10.3389/fcell.2022.894305] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 06/21/2022] [Indexed: 12/13/2022] Open
Abstract
There have been significant advances, particularly over the last 20 years, in the identification of non-coding RNAs (ncRNAs) and their pathophysiological role in a wide range of disease states, particularly cancer and other chronic conditions characterized by excess inflammation and oxidative stress such as atherosclerosis, diabetes, obesity, multiple sclerosis, osteoporosis, liver and lung fibrosis. Such discoveries have potential therapeutic implications as a better understanding of the molecular mechanisms underpinning the effects of ncRNAs on critical homeostatic control mechanisms and biochemical pathways might lead to the identification of novel druggable targets. In this context, increasing evidence suggests that several natural compounds can target ncRNAs at different levels and, consequently, influence processes involved in the onset and progression of disease states. The natural phenol resveratrol has been extensively studied for therapeutic purposes in view of its established anti-inflammatory and antioxidant effects, particularly in disease states such as cancer and cardiovascular disease that are associated with human aging. However, increasing in vitro and in vivo evidence also suggests that resveratrol can directly target various ncRNAs and that this mediates, at least in part, its potential therapeutic effects. This review critically appraises the available evidence regarding the resveratrol-mediated modulation of different ncRNAs in a wide range of disease states characterized by a pro-inflammatory state and oxidative stress, the potential therapeutic applications, and future research directions.
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Affiliation(s)
- Roberta Giordo
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Zena Wehbe
- Vascular Biology Research Centre, Molecular and Clinical Research Institute, University of London, London, United Kingdom
| | | | - Gian Luca Erre
- Rheumatology Unit, Department of Clinical and Experimental Medicine, University Hospital (AOUSS) and University of Sassari, Sassari, Italy
| | - Ali H. Eid
- Department of Basic Medical Sciences, College of Medicine, Q.U. Health. Qatar University, Doha, Qatar
| | - Arduino A. Mangoni
- Discipline of Clinical Pharmacology, College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
- Department of Clinical Pharmacology, Flinders Medical Centre, Adelaide, SA, Australia
- *Correspondence: Arduino A. Mangoni, ; Gianfranco Pintus,
| | - Gianfranco Pintus
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
- Department of Medical Laboratory Sciences, College of Health Sciences and Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
- *Correspondence: Arduino A. Mangoni, ; Gianfranco Pintus,
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10
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Wang Y, Liu Y, Zhang T, Guan G, Mao T, Liu H, Zhang J, Lu F, Chen X. LncCDCA3L inhibits cell proliferation via a novel RNA structure-based crosstalk with CDCA3 in hepatocellular carcinoma. Liver Int 2022; 42:1432-1446. [PMID: 35230745 DOI: 10.1111/liv.15225] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 11/25/2021] [Accepted: 01/25/2022] [Indexed: 12/31/2022]
Abstract
BACKGROUND & AIMS The molecular mechanisms underlying hepatocellular carcinoma (HCC) remain poorly understood. In this study, we investigated cell division cycle-associated 3 (CDCA3) expression status and characterized a CDCA3-related long non-coding RNA (lncRNA) in HCC. METHODS RT-qPCR and western blot were used to determine CDCA3 expression level in HCC clinical specimens. 5' and 3'-RACE, RNAscope, RNA pull-down, CRISPR/Cas9-based RNA immunoprecipitation (CRIP) and site-directed mutation experiments were used to characterize lncCDCA3L and investigate its function target. Chi-square test and Kaplan-Meier analysis were used to assess lncCDCA3L clinical significance. The effects of lncCDCA3L on HCC development were assessed by overexpression in vitro and in vivo. RESULTS In this study, we found CDCA3 was a potential oncogenic factor in HCC and characterized the lncCDCA3L, which could inhibit CDCA3. LncCDCA3L is significantly downregulated in HCC and its expression level is associated with tumour size and can act as an independent risk factor affecting postoperative survival time in HCC patients. Mechanistically, lncCDCA3L can repress CDCA3 protein level and inhibit hepatocarcinogenesis by directly binding to CDCA3 mRNA at 1423-1455 region via a novel manner based on a hairpin structure motif. CONCLUSIONS Our study collectively unveiled the molecular mechanisms of how lncCDCA3L repressed the tumourigenic properties of HCC cells and exhibited a tumour suppressor character in HCC in a CDCA3-dependent manner. The findings here support lncCDCA3L can be used as a candidate prognostic biomarker for HCC patients.
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Affiliation(s)
- Yongfeng Wang
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, P.R. China.,Department of Laboratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yongzhen Liu
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, P.R. China.,Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Ting Zhang
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, P.R. China
| | - Guiwen Guan
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, P.R. China
| | - Tianhao Mao
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, P.R. China
| | - Hui Liu
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, P.R. China
| | - Jing Zhang
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, P.R. China
| | - Fengmin Lu
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, P.R. China.,Precision Medicine Center of Zhengzhou University, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Xiangmei Chen
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, P.R. China
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11
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Žarković M, Hufsky F, Markert UR, Marz M. The Role of Non-Coding RNAs in the Human Placenta. Cells 2022; 11:cells11091588. [PMID: 35563893 PMCID: PMC9104507 DOI: 10.3390/cells11091588] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 05/01/2022] [Accepted: 05/03/2022] [Indexed: 12/11/2022] Open
Abstract
Non-coding RNAs (ncRNAs) play a central and regulatory role in almost all cells, organs, and species, which has been broadly recognized since the human ENCODE project and several other genome projects. Nevertheless, a small fraction of ncRNAs have been identified, and in the placenta they have been investigated very marginally. To date, most examples of ncRNAs which have been identified to be specific for fetal tissues, including placenta, are members of the group of microRNAs (miRNAs). Due to their quantity, it can be expected that the fairly larger group of other ncRNAs exerts far stronger effects than miRNAs. The syncytiotrophoblast of fetal origin forms the interface between fetus and mother, and releases permanently extracellular vesicles (EVs) into the maternal circulation which contain fetal proteins and RNA, including ncRNA, for communication with neighboring and distant maternal cells. Disorders of ncRNA in placental tissue, especially in trophoblast cells, and in EVs seem to be involved in pregnancy disorders, potentially as a cause or consequence. This review summarizes the current knowledge on placental ncRNA, their transport in EVs, and their involvement and pregnancy pathologies, as well as their potential for novel diagnostic tools.
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Affiliation(s)
- Milena Žarković
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Leutragraben 1, 07743 Jena, Germany; (M.Ž.); (F.H.)
- European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany
- Placenta Lab, Department of Obstetrics, University Hospital Jena, Am Klinikum 1, 07747 Jena, Germany;
| | - Franziska Hufsky
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Leutragraben 1, 07743 Jena, Germany; (M.Ž.); (F.H.)
- European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany
| | - Udo R. Markert
- Placenta Lab, Department of Obstetrics, University Hospital Jena, Am Klinikum 1, 07747 Jena, Germany;
| | - Manja Marz
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Leutragraben 1, 07743 Jena, Germany; (M.Ž.); (F.H.)
- European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany
- FLI Leibniz Institute for Age Research, Beutenbergstraße 11, 07745 Jena, Germany
- Aging Research Center (ARC), 07745 Jena, Germany
- Correspondence:
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12
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Omics and Male Infertility: Highlighting the Application of Transcriptomic Data. Life (Basel) 2022; 12:life12020280. [PMID: 35207567 PMCID: PMC8875138 DOI: 10.3390/life12020280] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 02/03/2022] [Accepted: 02/07/2022] [Indexed: 12/15/2022] Open
Abstract
Male infertility is a multifaceted disorder affecting approximately 50% of male partners in infertile couples. Over the years, male infertility has been diagnosed mainly through semen analysis, hormone evaluations, medical records and physical examinations, which of course are fundamental, but yet inefficient, because 30% of male infertility cases remain idiopathic. This dilemmatic status of the unknown needs to be addressed with more sophisticated and result-driven technologies and/or techniques. Genetic alterations have been linked with male infertility, thereby unveiling the practicality of investigating this disorder from the “omics” perspective. Omics aims at analyzing the structure and functions of a whole constituent of a given biological function at different levels, including the molecular gene level (genomics), transcript level (transcriptomics), protein level (proteomics) and metabolites level (metabolomics). In the current study, an overview of the four branches of omics and their roles in male infertility are briefly discussed; the potential usefulness of assessing transcriptomic data to understand this pathology is also elucidated. After assessing the publicly obtainable transcriptomic data for datasets on male infertility, a total of 1385 datasets were retrieved, of which 10 datasets met the inclusion criteria and were used for further analysis. These datasets were classified into groups according to the disease or cause of male infertility. The groups include non-obstructive azoospermia (NOA), obstructive azoospermia (OA), non-obstructive and obstructive azoospermia (NOA and OA), spermatogenic dysfunction, sperm dysfunction, and Y chromosome microdeletion. Findings revealed that 8 genes (LDHC, PDHA2, TNP1, TNP2, ODF1, ODF2, SPINK2, PCDHB3) were commonly differentially expressed between all disease groups. Likewise, 56 genes were common between NOA versus NOA and OA (ADAD1, BANF2, BCL2L14, C12orf50, C20orf173, C22orf23, C6orf99, C9orf131, C9orf24, CABS1, CAPZA3, CCDC187, CCDC54, CDKN3, CEP170, CFAP206, CRISP2, CT83, CXorf65, FAM209A, FAM71F1, FAM81B, GALNTL5, GTSF1, H1FNT, HEMGN, HMGB4, KIF2B, LDHC, LOC441601, LYZL2, ODF1, ODF2, PCDHB3, PDHA2, PGK2, PIH1D2, PLCZ1, PROCA1, RIMBP3, ROPN1L, SHCBP1L, SMCP, SPATA16, SPATA19, SPINK2, TEX33, TKTL2, TMCO2, TMCO5A, TNP1, TNP2, TSPAN16, TSSK1B, TTLL2, UBQLN3). These genes, particularly the above-mentioned 8 genes, are involved in diverse biological processes such as germ cell development, spermatid development, spermatid differentiation, regulation of proteolysis, spermatogenesis and metabolic processes. Owing to the stage-specific expression of these genes, any mal-expression can ultimately lead to male infertility. Therefore, currently available data on all branches of omics relating to male fertility can be used to identify biomarkers for diagnosing male infertility, which can potentially help in unravelling some idiopathic cases.
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13
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Qiao C, Qiao T, Yang S, Liu L, Zheng M. SNHG17/miR-384/ELF1 axis promotes cell growth by transcriptional regulation of CTNNB1 to activate Wnt/β-catenin pathway in oral squamous cell carcinoma. Cancer Gene Ther 2022; 29:122-132. [PMID: 33531646 DOI: 10.1038/s41417-021-00294-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 10/29/2020] [Accepted: 01/05/2021] [Indexed: 01/29/2023]
Abstract
Increasing evidence proved the abnormal expression of long non-coding RNAs (lncRNAs) in various human malignancies, including oral squamous cell carcinoma (OSCC). Nevertheless, limited explorations concern the role of lncRNA small nucleolar RNA host gene 17 (SNHG17) in OSCC. Herein, SNHG17 was disclosed to be remarkably upregulated in OSCC cell lines and promoted OSCC cell growth. Further mechanistic studies, including DNA/RNA pull down, RIP, ChIP, and luciferase reporter gene assays, were conducted. It was confirmed that Wnt/β-catenin signaling pathway was involved in the SNHG17-mediated OSCC cell growth. Moreover, E74 like ETS transcription factor 1 (ELF1) was identified as the transcription activator of CTNNB1 (β-catenin mRNA) in OSCC. Inspired by competing for endogenous RNAs (ceRNAs) network, we were pleasantly surprised to find that SNHG17 and ELF1 functioned as ceRNAs in OSCC via competitively binding to microRNA-384 (miR-384). By using rescue assays, we revealed that SNHG17 facilitated OSCC cell growth through modulating miR-384/ELF1 axis. Importantly, we certified that ELF1 was indispensable for SNHG17-affected OSCC progression. Collectively, it can be concluded that SNHG17/miR-384/ELF1 axis contributed to OSCC cell growth via promoting CTNNB1 expression, thus activating Wnt/β-catenin signaling pathway.
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Affiliation(s)
- Chunyan Qiao
- Department of Pathology, School and Hospital of Stomatology, Jilin University, Changchun, 130012, Jilin, China.
| | - Tianyi Qiao
- Department of Gastroenterology, the First Clinical Medical College and Hospital of Jilin University, Changchun, 130012, Jilin, China
| | - Shihui Yang
- Department of Dental Implantology, School and Hospital of Stomatology, Jilin University, Changchun, 130012, Jilin, China
| | - Lili Liu
- Department of Pathology, School and Hospital of Stomatology, Jilin University, Changchun, 130012, Jilin, China
| | - Mengdan Zheng
- Department of Pathology, School and Hospital of Stomatology, Jilin University, Changchun, 130012, Jilin, China
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14
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Golhani V, Ray SK, Mukherjee S. Role of MicroRNAs and Long Non-Coding RNAs in Regulating Angiogenesis in Human Breast Cancer- A Molecular Medicine Perspective. Curr Mol Med 2021; 22:882-893. [PMID: 34923940 DOI: 10.2174/1566524022666211217114527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 10/26/2021] [Accepted: 11/05/2021] [Indexed: 11/22/2022]
Abstract
MicroRNAs (miRNAs) and long non-coding RNAs (lncRNAs) are proficient in regulating gene expression post-transcriptionally. Considering the recent trend in exploiting non-coding RNAs (ncRNAs) as cancer therapeutics, the potential use of miRNAs and lncRNAs as biomarkers and novel therapeutic agents against angiogenesis is an important scientific aspect. An estimated 70% of the genome is actively transcribed, only 2% of which codes for known protein-coding genes. Long noncoding RNAs (lncRNAs) are a large and diverse class of RNAs > 200 nucleotides in length, and not translated into protein, and are of utmost importance and it governs the expression of genes in a temporal, spatial, and cell context-dependent manner. Angiogenesis is an essential process for organ morphogenesis and growth during development, and it is relevant during the repair of wounded tissue in adults. It is coordinated by an equilibrium of pro-and anti-angiogenic factors; nevertheless, when affected, it promotes several diseases, including breast cancer. Signaling pathways involved here are tightly controlled systems that regulate the appropriate timing of gene expression required for the differentiation of cells down a particular lineage essential for proper tissue development. Lately, scientific reports are indicating that ncRNAs, such as miRNAs, and lncRNAs, play critical roles in angiogenesis related to breast cancer. The specific roles of various miRNAs and lncRNAs in regulating angiogenesis in breast cancer, with particular focus on the downstream targets and signaling pathways regulated by these ncRNAs with molecular medicine perspective, are highlighted in this write-up.
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Affiliation(s)
- Vandana Golhani
- Department of Biochemistry. All India Institute of Medical Sciences. Bhopal, Madhya Pradesh-462020, India
| | | | - Sukhes Mukherjee
- Department of Biochemistry. All India Institute of Medical Sciences. Bhopal, Madhya Pradesh-462020, India
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15
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Novel approaches in cancer treatment: preclinical and clinical development of small non-coding RNA therapeutics. J Exp Clin Cancer Res 2021; 40:383. [PMID: 34863235 PMCID: PMC8642961 DOI: 10.1186/s13046-021-02193-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 11/23/2021] [Indexed: 11/20/2022] Open
Abstract
Short or small interfering RNAs (siRNAs) and microRNA (miRNAs) are molecules similar in size and function able to inhibit gene expression based on their complementarity with mRNA sequences, inducing the degradation of the transcript or the inhibition of their translation. siRNAs bind specifically to a single gene location by sequence complementarity and regulate gene expression by specifically targeting transcription units via posttranscriptional gene silencing. miRNAs can regulate the expression of different gene targets through their imperfect base pairing. This process - known as RNA interference (RNAi) - modulates transcription in order to maintain a correct physiological environment, playing a role in almost the totality of the cellular pathways. siRNAs have been evolutionary evolved for the protection of genome integrity in response to exogenous and invasive nucleic acids such as transgenes or transposons. Artificial siRNAs are widely used in molecular biology for transient silencing of genes of interest. This strategy allows to inhibit the expression of any target protein of known sequence and is currently used for the treatment of different human diseases including cancer. Modifications and rearrangements in gene regions encoding for miRNAs have been found in cancer cells, and specific miRNA expression profiles characterize the developmental lineage and the differentiation state of the tumor. miRNAs with different expression patterns in tumors have been reported as oncogenes (oncomirs) or tumor-suppressors (anti-oncomirs). RNA modulation has become important in cancer research not only for development of early and easy diagnosis tools but also as a promising novel therapeutic approach. Despite the emerging discoveries supporting the role of miRNAs in carcinogenesis and their and siRNAs possible use in therapy, a series of concerns regarding their development, delivery and side effects have arisen. In this review we report the biology of miRNAs and siRNAs in relation to cancer summarizing the recent methods described to use them as novel therapeutic drugs and methods to specifically deliver them to cancer cells and overcome the limitations in the use of these molecules.
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16
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Peng Q, Wang J. Non-coding RNAs in melanoma: Biological functions and potential clinical applications. MOLECULAR THERAPY-ONCOLYTICS 2021; 22:219-231. [PMID: 34514101 PMCID: PMC8424110 DOI: 10.1016/j.omto.2021.05.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Malignant melanoma (MM) is a malignant tumor that originates from melanocytes and has a high mortality rate. Therefore, early diagnosis and treatment are very important for survival. So far, the exact molecular mechanism leading to the occurrence of melanoma, especially the molecular metastatic mechanism, remains largely unknown. Non-coding RNAs (ncRNAs), such as microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNA (circRNAs), have been investigated and found to play vital roles in regulating tumor occurrence and development, including melanoma. In this review, we summarize the progress of recent research on the effects of ncRNAs on melanoma and attempt to elucidate the role of ncRNAs as molecular markers or potential targets that will provide promising application perspectives on melanoma.
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Affiliation(s)
- Qiu Peng
- Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, Hunan 410008, China
| | - Jia Wang
- Department of Immunology, Changzhi Medical College, Changzhi, Shanxi 046000 China
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17
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Xu J, Wu KJ, Jia QJ, Ding XF. Roles of miRNA and lncRNA in triple-negative breast cancer. J Zhejiang Univ Sci B 2021; 21:673-689. [PMID: 32893525 PMCID: PMC7519626 DOI: 10.1631/jzus.b1900709] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 05/28/2020] [Indexed: 12/11/2022]
Abstract
Triple-negative breast cancer (TNBC) is currently the most malignant subtype of breast cancer without effective targeted therapies, which makes its pathogenesis an important target for research. A growing number of studies have shown that non-coding RNA (ncRNA), including microRNA (miRNA) and long non-coding RNA (lncRNA), plays a significant role in tumorigenesis. This review summarizes the roles of miRNA and lncRNA in the progression, diagnosis, and neoadjuvant chemotherapy of TNBC. Aberrantly expressed miRNA and lncRNA are listed according to their roles. Further, it describes the multiple mechanisms that lncRNA shows for regulating gene expression in the nucleus and cytoplasm, and more importantly, describes lncRNA-regulated TNBC progression through complete combining with miRNA at the post-transcriptional level. Focusing on miRNA and lncRNA associated with TNBC can provide new insights for early diagnosis and treatment-they can be targeted in the future as a novel anticancer target of TNBC.
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18
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Wang J, Sun Y, Liu J, Yang B, Wang T, Zhang Z, Jiang X, Guo Y, Zhang Y. Roles of long non‑coding RNA in osteoarthritis (Review). Int J Mol Med 2021; 48:133. [PMID: 34013375 PMCID: PMC8148092 DOI: 10.3892/ijmm.2021.4966] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 05/05/2021] [Indexed: 02/01/2023] Open
Abstract
Osteoarthritis (OA) is a chronic bone and joint disease characterized by articular cartilage degeneration and joint inflammation and is the most common form of arthritis. The clinical manifestations of OA are chronic pain and joint activity disorder, which severely affect the patient quality of life. Long non-coding RNA (lncRNA) is a class of RNA molecules >200 nucleotides long that are expressed in animals, plants, yeast, prokaryotes and viruses. lncRNA molecules lack an open reading frame and are not translated into protein. The present review collated the results of recent studies on the role of lncRNA in the pathogenesis of OA to provide information for the prevention, diagnosis and treatment of OA.
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Affiliation(s)
- Jicheng Wang
- Department of Joint Surgery, Weifang People's Hospital, Weifang, Shandong 261000, P.R. China
| | - Yanshan Sun
- Department of Joint Surgery, Weifang People's Hospital, Weifang, Shandong 261000, P.R. China
| | - Jianyong Liu
- Department of Joint Surgery, Weifang People's Hospital, Weifang, Shandong 261000, P.R. China
| | - Bo Yang
- Department of Joint Surgery, Weifang People's Hospital, Weifang, Shandong 261000, P.R. China
| | - Tengyun Wang
- Department of Joint Surgery, Weifang People's Hospital, Weifang, Shandong 261000, P.R. China
| | - Zhen Zhang
- Department of Joint Surgery, Weifang People's Hospital, Weifang, Shandong 261000, P.R. China
| | - Xin Jiang
- Department of Joint Surgery, Weifang People's Hospital, Weifang, Shandong 261000, P.R. China
| | - Yongzhi Guo
- Department of Joint Surgery, Weifang People's Hospital, Weifang, Shandong 261000, P.R. China
| | - Yangyang Zhang
- Department of Joint Surgery, Weifang People's Hospital, Weifang, Shandong 261000, P.R. China
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19
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Yu AT, Berasain C, Bhatia S, Rivera K, Liu B, Rigo F, Pappin DJ, Spector DL. PHAROH lncRNA regulates Myc translation in hepatocellular carcinoma via sequestering TIAR. eLife 2021; 10:68263. [PMID: 34002693 PMCID: PMC8163507 DOI: 10.7554/elife.68263] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 05/02/2021] [Indexed: 12/26/2022] Open
Abstract
Hepatocellular carcinoma, the most common type of liver malignancy, is one of the most lethal forms of cancer. We identified a long non-coding RNA, Gm19705, that is overexpressed in hepatocellular carcinoma and mouse embryonic stem cells. We named this RNA Pluripotency and Hepatocyte Associated RNA Overexpressed in HCC, or PHAROH. Depletion of PHAROH impacts cell proliferation and migration, which can be rescued by ectopic expression of PHAROH. RNA-seq analysis of PHAROH knockouts revealed that a large number of genes with decreased expression contain a Myc motif in their promoter. MYC is decreased in knockout cells at the protein level, but not the mRNA level. RNA-antisense pulldown identified nucleolysin TIAR, a translational repressor, to bind to a 71-nt hairpin within PHAROH, sequestration of which increases MYC translation. In summary, our data suggest that PHAROH regulates MYC translation by sequestering TIAR and as such represents a potentially exciting diagnostic or therapeutic target in hepatocellular carcinoma.
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Affiliation(s)
- Allen T Yu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, United States.,Genetics Program, Stony Brook University, Stony Brook, United States
| | - Carmen Berasain
- Hepatology Program, Cima, University of Navarra, Pamplona, Spain.,Instituto de Investigaciones Sanitarias de Navarra-IdiSNA, Pamplona, Spain.,CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
| | - Sonam Bhatia
- Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
| | - Keith Rivera
- Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
| | - Bodu Liu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
| | - Frank Rigo
- Ionis Pharmaceuticals, Carlsbad, United States
| | - Darryl J Pappin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
| | - David L Spector
- Cold Spring Harbor Laboratory, Cold Spring Harbor, United States.,Genetics Program, Stony Brook University, Stony Brook, United States
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20
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Qu S, Jiao Z, Lu G, Yao B, Wang T, Rong W, Xu J, Fan T, Sun X, Yang R, Wang J, Yao Y, Xu G, Yan X, Wang T, Liang H, Zen K. PD-L1 lncRNA splice isoform promotes lung adenocarcinoma progression via enhancing c-Myc activity. Genome Biol 2021; 22:104. [PMID: 33849634 PMCID: PMC8042710 DOI: 10.1186/s13059-021-02331-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 03/25/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Although using a blockade of programmed death-ligand 1 (PD-L1) to enhance T cell immune responses shows great promise in tumor immunotherapy, the immune-checkpoint inhibition strategy is limited for patients with solid tumors. The mechanism and efficacy of such immune-checkpoint inhibition strategies in solid tumors remains unclear. RESULTS Employing qRT-PCR, Sanger sequencing, and RNA BaseScope analysis, we show that human lung adenocarcinoma (LUAD) all produce a long non-coding RNA isoform of PD-L1 (PD-L1-lnc) by alternative splicing, regardless if the tumor is positive or negative for the protein PD-L1. Similar to PD-L1 mRNA, PD-L1-lnc in various lung adenocarcinoma cells is significantly upregulated by IFNγ. Both in vitro and in vivo studies demonstrate that PD-L1-lnc increases proliferation and invasion but decreases apoptosis of lung adenocarcinoma cells. Mechanistically, PD-L1-lnc promotes lung adenocarcinoma progression through directly binding to c-Myc and enhancing c-Myc transcriptional activity. CONCLUSIONS In summary, the PD-L1 gene can generate a long non-coding RNA through alternative splicing to promote lung adenocarcinoma progression by enhancing c-Myc activity. Our results argue in favor of investigating PD-L1-lnc depletion in combination with PD-L1 blockade in lung cancer therapy.
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Affiliation(s)
- Shuang Qu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University, Nanjing, China
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Zichen Jiao
- Department of Thoracic Surgery, Nanjing Drum Tower Hospital, Medical School, Nanjing University, Nanjing, China
| | - Geng Lu
- Department of Emergency Medicine, Nanjing Drum Tower Hospital, Medical School, Nanjing University, Nanjing, China
| | - Bing Yao
- Department of Medical Genetics, Nanjing Medical University, Nanjing, China
| | - Ting Wang
- Department of Pathology, Nanjing Drum Tower Hospital, Medical School, Nanjing University, Nanjing, China
| | - Weiwei Rong
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University, Nanjing, China
| | - Jiahan Xu
- Department of General Surgery, Nanjing Drum Tower Hospital, Medical School, Nanjing University, Nanjing, China
| | - Ting Fan
- Department of Gastroenterology, Nanjing Drum Tower Hospital, Medical School, Nanjing University, Nanjing, China
| | - Xinlei Sun
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University, Nanjing, China
| | - Rong Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University, Nanjing, China
| | - Jun Wang
- Department of Emergency Medicine, Nanjing Drum Tower Hospital, Medical School, Nanjing University, Nanjing, China
| | - Yongzhong Yao
- Department of General Surgery, Nanjing Drum Tower Hospital, Medical School, Nanjing University, Nanjing, China
| | - Guifang Xu
- Department of Gastroenterology, Nanjing Drum Tower Hospital, Medical School, Nanjing University, Nanjing, China
| | - Xin Yan
- Department of Respiratory Medicine, Nanjing Drum Tower Hospital, Medical School, Nanjing University, Nanjing, China
| | - Tao Wang
- Department of Thoracic Surgery, Nanjing Drum Tower Hospital, Medical School, Nanjing University, Nanjing, China.
| | - Hongwei Liang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University, Nanjing, China.
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, China.
| | - Ke Zen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University, Nanjing, China.
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21
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Grady WM. Epigenetic alterations in the gastrointestinal tract: Current and emerging use for biomarkers of cancer. Adv Cancer Res 2021; 151:425-468. [PMID: 34148620 DOI: 10.1016/bs.acr.2021.02.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Colorectal cancer is a leading cause of cancer related deaths worldwide. One of the hallmarks of cancer and a fundamental trait of virtually all gastrointestinal cancers is genomic and epigenomic DNA alterations. Cancer cells acquire genetic and epigenetic alterations that drive the initiation and progression of the cancers by altering the molecular and cell biological process of the cells. These alterations, as well as other host and microenvironment factors, ultimately mediate the initiation and progression of cancers, including colorectal cancer. Epigenetic alterations, which include changes affecting DNA methylation, histone modifications, chromatin structure, and noncoding RNA expression, have emerged as a major class of molecular alteration in colon polyps and colorectal cancer. The classes of epigenetic alterations, their status in colorectal polyps and cancer, their effects on neoplasm biology, and their application to clinical care will be discussed.
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Affiliation(s)
- William M Grady
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States; Division of Gastroenterology, University of Washington School of Medicine, Seattle, WA, United States.
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22
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Huang S, Dong D, Zhang Y, Chen Z, Geng J, Zhao Y. Long non-coding RNA nuclear paraspeckle assembly transcript 1 promotes activation of T helper 2 cells via inhibiting STAT6 ubiquitination. Hum Cell 2021; 34:800-807. [PMID: 33550532 DOI: 10.1007/s13577-021-00496-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 01/23/2021] [Indexed: 11/25/2022]
Abstract
T helper (Th) 2 cell-medicated immune response participates in various immune diseases, including systemic lupus erythematosus (SLE). Long non-coding RNA nuclear paraspeckle assembly transcript 1 (NEAT1) has been reported to be associated with T helper 2 (Th2) cell activation. Here, we demonstrated the molecular mechanism of NEAT1 in regulating Th2 cell activation. We found that NEAT1 was located in nucleus. NEAT1 overexpression promoted the levels of Th2-related cytokines IL-4, IL-5 and IL-13 in CD4+ T cells. Moreover, NEAT1 up-regulation reduced Th1-related cytokine INF-γ production and enhanced the levels of Th17-related cytokines IL-17 in CD4+ T cells. STAT6 deficiency reduced the levels of IL-4, IL-5, IL-13 and IL-17 enhanced the levels of INF-γ in CD4+ T cells, which was rescued by NEAT1 overexpression. Moreover, NEAT1 promoted STAT6 protein expression, whereas NEAT1 had no effect on the expression of STAT6 mRNA. Furthermore, NEAT1 interacted with STAT6, inhibited the ubiquitination of STAT6 in CD4+ T cells. In conclusion, our work has confirmed that NEAT1 promotes STAT6 expression by inhibiting STAT6 ubiquitination, thereby promoting Th2 cell activation. Thus, our work may highlight novel insights into the molecular mechanism of NEAT1 in regulating Th2 cell activation.
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Affiliation(s)
- Shuman Huang
- The Rhinology Department, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Zhengzhou, 450052, China.,Academy of Medical Science, Zhengzhou University, Zhengzhou, 450052, China
| | - Dong Dong
- The Rhinology Department, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Zhengzhou, 450052, China
| | - Yaqian Zhang
- The Rhinology Department, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Zhengzhou, 450052, China
| | - Zhuo Chen
- The Rhinology Department, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Zhengzhou, 450052, China
| | - Jing Geng
- The Rhinology Department, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Zhengzhou, 450052, China.,Academy of Medical Science, Zhengzhou University, Zhengzhou, 450052, China
| | - Yulin Zhao
- The Rhinology Department, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Zhengzhou, 450052, China.
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Tülay Aydın P, Göz M, Kankılıç N, Aydın MS, Koyuncu İ. Micro-RNA gene expressions during cardiopulmonary bypass. J Card Surg 2021; 36:921-927. [PMID: 33484193 DOI: 10.1111/jocs.15329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 11/16/2020] [Accepted: 01/05/2021] [Indexed: 11/27/2022]
Abstract
INTRODUCTION Cardiopulmonary bypass (CBP) is the most widely used method in cardiac surgery. During the CPB procedure, studies are conducted to maintain myocardial perfusion adequacy, reduce oxidative stress caused by immune reactions, and understand the longevity of the procedure. Recently, microRNAs (miRNAs) have come to the fore to understand the changes in the CPB. In vivo studies have shown that many different miRNAs regulate critical signaling molecules including cytokines, growth factors, transcription factors, proapoptotic, and antiapoptotic proteins. Our study aims to investigate the changes of miR-34a, miR-15a, and miR-320a gene expression in extracorporeal circulation. METHODS Fifteen patients who underwent elective open-heart surgery were included in the study. Serum plasma samples were taken from the patients preoperatively, at the time of CPB, and at 24 h postoperatively. Gene expression of miR-34a, miR-15a, and miR-320a in plasma samples was studied. Differences in gene expression were compared. RESULTS miR-15a gene expression increased during CPB compared with preoperative levels (p < .001). This increase was decreased after the operation (p < .05). miR-34a gene expression increased significantly during CPB (p < .01). Similar to the other two gene expressions, miR-320a gene expression was significantly increased during CPB (p < .01). CONCLUSIONS miRNAs may play a key role in the initiation and maintenance of pathophysiological cascades during CPB. Our study showed the gene expression of miR-34a, miR-15a, and miR-320a in the CPB process. Our study will be a pioneer among future studies to investigate the molecular pathophysiology of the CPB process.
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Affiliation(s)
| | - Mustafa Göz
- Department of Cardiovascular Surgery, Medical School of Harran University, Şanlıurfa, Turkey
| | - Nazım Kankılıç
- Department of Cardiovascular Surgery, Medical School of Harran University, Şanlıurfa, Turkey
| | - Mehmet Salih Aydın
- Department of Cardiovascular Surgery, Medical School of Harran University, Şanlıurfa, Turkey
| | - İsmail Koyuncu
- Department of Biochemistry, Medical School of Harran University, Şanlıurfa, Turkey
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Zuo L, Su H, Zhang Q, Wu WY, Zeng Y, Li XM, Xiong J, Chen LF, Zhou Y. Comprehensive analysis of lncRNAs N 6-methyladenosine modification in colorectal cancer. Aging (Albany NY) 2021; 13:4182-4198. [PMID: 33493136 PMCID: PMC7906145 DOI: 10.18632/aging.202383] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 11/30/2020] [Indexed: 12/14/2022]
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) and their N6-methyladenosine (M6A) modifications are involved in cancer occurrence and development. METHODS lncRNA M6A modification in colorectal cancer (CRC) was comprehensively analyzed for the first time. RESULTS M6A levels of lnRNAs in CRC tissues were higher than those in tumor-adjacent normal tissues. A total of 8,332 M6A peaks were detected in 6,690 lncRNAs in CRC tissues. Approximately 91% of the modified lncRNAs had unique M6A modification peaks. A total of 383 lncRNAs were differentially methylated in CRC, of which 48.24% had a length of 1-1,000 bp. Most of these were located on chromosomes 1, 2, 7, 11, 16 and 19; 42.3% were within a sense-overlapping exon. RNA sequencing identified 163 differentially expressed lncRNAs in CRC. GO and KEGG analyses revealed that genes near differentially-methylated or -expressed lncRNAs were associated with CRC occurrence and development. Methylation was positively correlated with lncRNA expression levels in CRC and tumor-adjacent normal tissues. More unmethylated than M6A methylated lncRNA molecules were detected. A competing endogenous RNA (ceRNA) and lncRNA-mRNA expression-regulation network revealed a regulatory relationship between lncRNAs, microRNAs (miRNAs), and mRNAs. CONCLUSIONS The findings may help improve our understanding of lncRNA function in colorectal cancer.
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Affiliation(s)
- Luo Zuo
- The Gastroenterology Tumor and Microenvironment Laboratory, Department of Gastroenterology, The First Affiliated Hospital of Chengdu Medical College, Chengdu Medical College, Chengdu 610041, Sichuan, PR China
| | - Hui Su
- The Gastroenterology Tumor and Microenvironment Laboratory, Department of Gastroenterology, The First Affiliated Hospital of Chengdu Medical College, Chengdu Medical College, Chengdu 610041, Sichuan, PR China
| | - Qiao Zhang
- The Gastroenterology Tumor and Microenvironment Laboratory, Department of Gastroenterology, The First Affiliated Hospital of Chengdu Medical College, Chengdu Medical College, Chengdu 610041, Sichuan, PR China
| | - Wei-Yu Wu
- The Gastroenterology Tumor and Microenvironment Laboratory, Department of Gastroenterology, The First Affiliated Hospital of Chengdu Medical College, Chengdu Medical College, Chengdu 610041, Sichuan, PR China
| | - Yan Zeng
- The Gastroenterology Tumor and Microenvironment Laboratory, Department of Gastroenterology, The First Affiliated Hospital of Chengdu Medical College, Chengdu Medical College, Chengdu 610041, Sichuan, PR China
| | - Xue-Mei Li
- The Gastroenterology Tumor and Microenvironment Laboratory, Department of Gastroenterology, The First Affiliated Hospital of Chengdu Medical College, Chengdu Medical College, Chengdu 610041, Sichuan, PR China
| | - Jing Xiong
- The Gastroenterology Tumor and Microenvironment Laboratory, Department of Gastroenterology, The First Affiliated Hospital of Chengdu Medical College, Chengdu Medical College, Chengdu 610041, Sichuan, PR China
| | - Lan-Fang Chen
- The Gastroenterology Tumor and Microenvironment Laboratory, Department of Gastroenterology, The First Affiliated Hospital of Chengdu Medical College, Chengdu Medical College, Chengdu 610041, Sichuan, PR China
| | - Yan Zhou
- The Gastroenterology Tumor and Microenvironment Laboratory, Department of Gastroenterology, The First Affiliated Hospital of Chengdu Medical College, Chengdu Medical College, Chengdu 610041, Sichuan, PR China
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Toden S, Zumwalt TJ, Goel A. Non-coding RNAs and potential therapeutic targeting in cancer. Biochim Biophys Acta Rev Cancer 2021; 1875:188491. [PMID: 33316377 PMCID: PMC7856203 DOI: 10.1016/j.bbcan.2020.188491] [Citation(s) in RCA: 120] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 12/02/2020] [Accepted: 12/02/2020] [Indexed: 12/11/2022]
Abstract
Recent advances have begun to clarify the physiological and pathological roles of non-coding RNAs (ncRNAs) in various diseases, including cancer. Among these, microRNAs (miRNAs) have been the most studied and have emerged as key players that are involved in the regulation of important growth regulatory pathways in cancer pathogenesis. The ability of a single ncRNA to modulate the expression of multiple downstream gene targets and associated pathways, have provided a rationale to pursue them for therapeutic drug development in cancer. In this context, early data from pre-clinical studies have demonstrated that synthetic miRNA-based therapeutic molecules, along with various protective coating approaches, has allowed for their efficient delivery and anti-tumor activity. In fact, some of the miRNA-based cancer therapeutic strategies have shown promising results even in early-phase human clinical trials. While the enthusiasm for ncRNA-based cancer therapeutics continue to evolve, the field is still in the midst of unraveling a more precise understanding of the molecular mechanisms and specific downstream therapeutic targets of other lesser studied ncRNAs such as the long-non-coding RNAs, transfer RNAs, circular RNAs, small nucleolar RNAs, and piwi-interacting RNAs. This review article provides the current state of knowledge and the evolving principles for ncRNA-based therapeutic approaches in cancer, and specifically highlights the importance of data to date and the approaches that are being developed to overcome the challenges associated with their delivery and mitigating the off-target effects in human cancers.
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Affiliation(s)
- Shusuke Toden
- Center for Gastrointestinal Research; Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute and Charles A. Sammons Cancer Center, Baylor Research Institute and Sammons Cancer Center, Baylor University Medical Center, Dallas, Texas, USA
| | - Timothy J Zumwalt
- Center for Gastrointestinal Research; Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute and Charles A. Sammons Cancer Center, Baylor Research Institute and Sammons Cancer Center, Baylor University Medical Center, Dallas, Texas, USA
| | - Ajay Goel
- Center for Gastrointestinal Research; Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute and Charles A. Sammons Cancer Center, Baylor Research Institute and Sammons Cancer Center, Baylor University Medical Center, Dallas, Texas, USA; Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope Comprehensive Cancer Center, Duarte, CA, USA.
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26
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Wang J, Liu S, Shi J, Liu H, Li J, Zhao S, Yi Z. The Role of lncRNAs in Osteogenic Differentiation of Bone Marrow Mesenchymal Stem Cells. Curr Stem Cell Res Ther 2020; 15:243-249. [PMID: 31880266 DOI: 10.2174/1574888x15666191227113742] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 10/29/2019] [Accepted: 10/31/2019] [Indexed: 02/01/2023]
Abstract
Bone Marrow Mesenchymal Stem Cells (BMSCs) are one of the primary cells found in the bone marrow, and they can differentiate into osteoblasts, chondrocytes, adipocytes and even myoblasts, and are, therefore, considered pluripotent cells. Because of their multipotential differentiation, selfrenewal capability, immunomodulation and other potential activities, BMSCs have become an important source of seed cells for gene therapy, tissue engineering, cell replacement therapy and regenerative medicine. Long non-coding RNA (lncRNA) is an RNA molecule greater than 200 nucleotides in length that is expressed in a variety of species, including animals, plants, yeast, prokaryotes, and viruses, but lacks an apparent open reading frame, and does not have the function of translation into proteins. Many studies have shown that lncRNAs play an important role in the osteogenic differentiation of BMSCs. Here, we describe the role of lncRNAs in the osteogenic differentiation of BMSCs, in order to provide a new theoretical and experimental basis for bone tissue engineering and clinical treatment.
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Affiliation(s)
- Jicheng Wang
- Department of Orthopaedic, Shaanxi Provincial People's Hospital, Xi'an 710068, China.,Xi'an Medical University, Xi'an 710068, China
| | - Shizhang Liu
- Department of Orthopaedic, Shaanxi Provincial People's Hospital, Xi'an 710068, China
| | - Jiyuan Shi
- Department of Orthopaedic, Shaanxi Provincial People's Hospital, Xi'an 710068, China
| | - Huitong Liu
- Department of Orthopaedic, Shaanxi Provincial People's Hospital, Xi'an 710068, China
| | - Jingyuan Li
- Department of Orthopaedic, Shaanxi Provincial People's Hospital, Xi'an 710068, China
| | - Song Zhao
- Department of Orthopaedic, Shaanxi Provincial People's Hospital, Xi'an 710068, China.,Xi'an Medical University, Xi'an 710068, China
| | - Zhi Yi
- Department of Orthopaedic, Shaanxi Provincial People's Hospital, Xi'an 710068, China
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Novel Genetic and Epigenetic Biomarkers of Prognostic and Predictive Significance in Stage II/III Colorectal Cancer. Mol Ther 2020; 29:587-596. [PMID: 33333293 DOI: 10.1016/j.ymthe.2020.12.017] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 10/15/2020] [Accepted: 12/09/2020] [Indexed: 12/18/2022] Open
Abstract
The therapeutic strategies of stage II/III colorectal cancer (CRC) patients after curative surgery remain controversial. In the clinical decision-making process, oncologists need to answer questions such as whether adjuvant chemotherapy is necessary or which therapeutic regimen should be given to each patient. At present, whether adjuvant chemotherapy should be applied is primarily based on histopathological features and clinical risk factors. However, only a fraction of patients can benefit from it. More rigorous stratifying biomarkers are urgently needed to help further distinguishing these populations of patients. Recent progress in next-generation sequencing and high-throughput technologies has greatly promoted biomarker discovery as well as our understanding of the underlying mechanisms in CRC. Novel genetic and epigenetic biomarkers that are associated with prognosis or therapeutic responses have emerged. In this review, we discuss the strategies of biomarker discovery and summarize the status and assess the utility of previously published biomarkers in CRC.
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28
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Sun E, Liu X, Lu C, Liu K. Long non‑coding RNA TTN‑AS1 regulates the proliferation, invasion and migration of triple‑negative breast cancer by targeting miR‑211‑5p. Mol Med Rep 2020; 23:45. [PMID: 33179096 PMCID: PMC7684865 DOI: 10.3892/mmr.2020.11683] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Accepted: 07/06/2020] [Indexed: 12/17/2022] Open
Abstract
Increasing evidence has demonstrated that long non-coding RNAs (lncRNAs) serve important roles in numerous malignancies, including triple-negative breast cancer (TNBC). The lncRNA titin-antisense RNA1 (TTN-AS1) has previously been reported to promote tumorigenesis in various types of cancer. The present study aimed to investigate the potential role of TTN-AS1 in breast cancer and the associated underlying mechanisms. Following prediction by Starbase and confirmation by dual-luciferase reporter assay, TINCR was demonstrated to be a target gene for microRNA (miR)-211-5p. The expression levels of TTN-AS1 and miR-211-5p, which was predicted to be targeted by TTN-AS1, in TNBC tissues and in the breast cancer cell lines MDA-MB-453 and MDA-MB-231 were measured using reverse transcription-quantitative PCR. Following TTN-AS1-knockdown, cell proliferation was measured using a Cell Counting Kit-8 assay and colony formation assay, whereas cell invasion and migration were measured using Transwell and wound healing assays, respectively. Luciferase reporter assay was performed to verify the potential interaction between TTN-AS1 and miR-211-5p. In addition, rescue assays were conducted to investigate the effects of TTN-AS1 and miR-211-5p on TNBC development. The results demonstrated that TTN-AS1 expression was significantly upregulated, whereas that of miR-211-5p was found to be downregulated in TNBC tissues and cell lines compared with the matched adjacent normal tissues and normal breast epithelial cell line MCF-10A, respectively. Furthermore, TTN-AS1-knockdown inhibited the proliferation and invasive and migratory abilities of MDA-MB-453 and MDA-MB-231 cells, which was reversed following co-transfection with the miR-211-5p inhibitor. The results from luciferase reporter assay confirmed that miR-211-5p was a direct target of TTN-AS1, suggesting that TTN-AS1 may bind directly to miR-211-5p to negatively regulate its expression. In conclusion, the findings from the present study demonstrated that TTN-AS1 regulated the proliferation and invasive and migratory abilities of TNBC by targeting miR-211-5p. This study may provide some insights into the regulatory mechanism of TNBC and help the development of novel therapeutic interventions for TNBC.
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Affiliation(s)
- Erhu Sun
- Department of Breast, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu 210000, P.R. China
| | - Xiaofeng Liu
- Department of Breast, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu 210000, P.R. China
| | - Cheng Lu
- Department of Breast, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu 210000, P.R. China
| | - Kangsheng Liu
- Department of Clinical Laboratory, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu 210000, P.R. China
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29
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Zheng B, Wang H, Cui G, Guo Q, Si L, Yan H, Fang D, Jiang L, Jiang Z, Zhou J. ERG-Associated lncRNA (ERGAL) Promotes the Stability and Integrity of Vascular Endothelial Barrier During Dengue Viral Infection via Interaction With miR-183-5p. Front Cell Infect Microbiol 2020; 10:477. [PMID: 33014896 PMCID: PMC7506072 DOI: 10.3389/fcimb.2020.00477] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Accepted: 08/03/2020] [Indexed: 12/20/2022] Open
Abstract
Dengue virus (DENV) continues to be a major public health problem. DENV infection will cause mild dengue and severe dengue. Severe dengue is clinically manifested as serious complications, including dengue hemorrhagic fever and/or dengue shock syndrome (DHF/DSS), which is mainly characterized by vascular leakage. Currently, the pathogenesis of severe dengue is not elucidated thoroughly, and there are no known therapeutic targets for controlling the disease effectively. This study aimed to further reveal the potential molecular mechanism of severe dengue. In this study, the long non-coding RNA, ERG-associated lncRNA (lncRNA-ERGAL), was activated and significantly up-regulated in DENV-infected vascular endothelial cells. After knockdown of lncRNA-ERGAL, the expression of ERG, VE-cadherin, and claudin-5 was repressed; besides, cell apoptosis was enhanced, and cytoskeletal remodeling was disordered, leading to instability and increased permeability of vascular endothelial barrier during DENV infection. Fluorescence in situ hybridization (FISH) assay showed lncRNA-ERGAL to be mainly expressed in the cytoplasm. Moreover, the expression of miR-183-5p was found to increase during DENV infection and revealed to regulate ERG, junction-associated proteins, and the cytoskeletal structure after overexpression and knockdown. Then, ERGAL was confirmed to interact with miR-183-5p by luciferase reporter assay. Collectively, ERGAL acted as a miRNA sponge that can promote stability and integrity of vascular endothelial barrier during DENV infection via binding to miR-183-5p, thus revealing the potential molecular mechanism of severe dengue and providing a foundation for a promising clinical target in the future.
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Affiliation(s)
- Baojia Zheng
- Department of Microbiology and Immunology, School of Basic Medical Sciences, Jinan University, Guangzhou, China
| | - Hui Wang
- Department of Microbiology and Immunology, School of Basic Medical Sciences, Jinan University, Guangzhou, China
| | - Guohui Cui
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, China.,Department of Medical Microbiology, Zhongshan Medical College, Sun Yat-sen University, Guangzhou, China
| | - Qianfang Guo
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, China.,Department of Medical Microbiology, Zhongshan Medical College, Sun Yat-sen University, Guangzhou, China
| | - Lulu Si
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, China.,Department of Medical Microbiology, Zhongshan Medical College, Sun Yat-sen University, Guangzhou, China
| | - Huijun Yan
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, China.,Department of Medical Microbiology, Zhongshan Medical College, Sun Yat-sen University, Guangzhou, China
| | - Danyun Fang
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, China.,Department of Medical Microbiology, Zhongshan Medical College, Sun Yat-sen University, Guangzhou, China
| | - Lifang Jiang
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, China.,Department of Medical Microbiology, Zhongshan Medical College, Sun Yat-sen University, Guangzhou, China
| | - Zhenyou Jiang
- Department of Microbiology and Immunology, School of Basic Medical Sciences, Jinan University, Guangzhou, China
| | - Junmei Zhou
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, China.,Department of Medical Microbiology, Zhongshan Medical College, Sun Yat-sen University, Guangzhou, China
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Leite ML, Oliveira KBS, Cunha VA, Dias SC, da Cunha NB, Costa FF. Epigenetic Therapies in the Precision Medicine Era. ADVANCED THERAPEUTICS 2020. [DOI: 10.1002/adtp.201900184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Michel Lopes Leite
- Genomic Sciences and Biotechnology Program UCB ‐ Brasilia, SgAN 916, Modulo B, Bloco C, 70790‐160 Brasília DF Brazil
| | | | - Victor Albuquerque Cunha
- Genomic Sciences and Biotechnology Program UCB ‐ Brasilia, SgAN 916, Modulo B, Bloco C, 70790‐160 Brasília DF Brazil
| | - Simoni Campos Dias
- Genomic Sciences and Biotechnology Program UCB ‐ Brasilia, SgAN 916, Modulo B, Bloco C, 70790‐160 Brasília DF Brazil
- Animal Biology DepartmentUniversidade de Brasília UnB, Campus Darcy Ribeiro. Brasilia DF 70910‐900 Brazil
| | - Nicolau Brito da Cunha
- Genomic Sciences and Biotechnology Program UCB ‐ Brasilia, SgAN 916, Modulo B, Bloco C, 70790‐160 Brasília DF Brazil
| | - Fabricio F. Costa
- Cancer Biology and Epigenomics ProgramAnn & Robert H Lurie Children's Hospital of Chicago Research Center, Northwestern University's Feinberg School of Medicine 2430 N. Halsted St., Box 220 Chicago IL 60611 USA
- Northwestern University's Feinberg School of Medicine 2430 N. Halsted St., Box 220 Chicago IL 60611 USA
- MATTER Chicago 222 W. Merchandise Mart Plaza, Suite 12th Floor Chicago IL 60654 USA
- Genomic Enterprise (www.genomicenterprise.com) San Diego, CA 92008 and New York NY 11581 USA
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Zhang S, Shen S, Yang Z, Kong X, Liu F, Zhen Z. Coding and Non-coding RNAs: Molecular Basis of Forest-Insect Outbreaks. Front Cell Dev Biol 2020; 8:369. [PMID: 32596236 PMCID: PMC7300193 DOI: 10.3389/fcell.2020.00369] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 04/24/2020] [Indexed: 12/19/2022] Open
Abstract
Insect population dynamics are closely related to 'human' ecological and economic environments, and a central focus of research is outbreaks. However, the lack of molecular-based investigations restricts our understanding of the intrinsic mechanisms responsible for insect outbreaks. In this context, the moth Dendrolimus punctatus Walker can serve as an ideal model species for insect population dynamics research because it undergoes periodic outbreaks. Here, high-throughput whole-transcriptome sequencing was performed using D. punctatus, sampled during latent and outbreak periods, to systemically explore the molecular basis of insect outbreaks and to identify the involved non-coding RNA (ncRNA) regulators, namely microRNAs, long non-coding RNAs, and circular RNAs. Differentially expressed mRNAs of D. punctatus from different outbreak periods were involved in developmental, reproductive, immune, and chemosensory processes; results that were consistent with the physiological differences in D. punctatus during differing outbreak periods. Targets analysis of the non-coding RNAs indicated that long non-coding RNAs could be the primary ncRNA regulators of D. punctatus outbreaks, while circular RNAs mainly regulated synapses and cell junctions. The target genes of differentially expressed microRNAs mainly regulated the metabolic and reproductive pathways during the D. punctatus outbreaks. Developmental, multi-organismal, and reproductive processes, as well as biological adhesion, characterized the competing endogenous RNA network. Chemosensory and immune genes closely related to the outbreak of D. punctatus were further analyzed in detail: from their ncRNA regulators' analysis, we deduce that both lncRNA and miRNA may play significant roles. This is the first report to examine the molecular basis of coding and non-coding RNAs' roles in insect outbreaks. The results provide potential biomarkers for control targets in forest insect management, as well as fresh insights into underlying outbreak-related mechanisms, which could be used for improving insect control strategies in the future.
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Affiliation(s)
- Sufang Zhang
- Key Laboratory of Forest Protection of State Forestry and Grassland Administration, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
| | - Sifan Shen
- Key Laboratory of Forest Protection of State Forestry and Grassland Administration, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
| | - Zhongwu Yang
- Forestry Comprehensive Development Center of Guilin, Guilin, China
| | - Xiangbo Kong
- Key Laboratory of Forest Protection of State Forestry and Grassland Administration, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
| | - Fu Liu
- Key Laboratory of Forest Protection of State Forestry and Grassland Administration, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
| | - Zhang Zhen
- Key Laboratory of Forest Protection of State Forestry and Grassland Administration, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
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Yin Z, Wang Q, Yan X, Zhang L, Tang K, Cao Z, Qiu T. Reveal the Regulation Patterns of Prognosis-Related miRNAs and lncRNAs Across Solid Tumors in the Cancer Genome Atlas. Front Cell Dev Biol 2020; 8:368. [PMID: 32523951 PMCID: PMC7261917 DOI: 10.3389/fcell.2020.00368] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 04/24/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND The dysregulation of non-coding RNAs (ncRNAs) such as miRNAs and lncRNAs are associated with the pathogenesis and progression in multiple cancers including solid tumors. Comprehensive investigations of prognosis-related ncRNA markers could promote the development of therapeutic strategies for solid tumors, but rarely reported. METHODS By taking advantage of The Cancer Genome Atlas (TCGA), pan-cancer prognosis analysis (PCPA) models were firstly constructed based on miRNA and lncRNA expression profiles of 8,450 samples in 19 solid tumors. Further, the co-occurrence and exclusivity among ncRNA markers were systematically analyzed for different cancers. RESULTS In identified ncRNA makers, 71% of the miRNA markers were shared in multiple cancers, whereas 96% of the lncRNA markers were cancer-specific. Moreover, to analyze the regulation patterns of prognosis-related ncRNAs at the pan-cancer level, miRNA markers were further annotated into eight carcinogenic pathways. Results represented that approximately 86% of these miRNA markers could regulate the PI3K-Akt signaling pathway, while only 48% for the Notch signaling pathway. Finally, among 126 common genes that participated in eight carcinogenic pathways, BCL2, CSNK2A1, EGFR, PDGFRA, and VEGFA were proposed as potential drug targets for multiple cancers. CONCLUSION The prognosis analysis and regulation characteristics of ncRNAs presented in this study may help to facilitate the discovery of anti-cancer drugs for multiple solid tumors.
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Affiliation(s)
- Zuojing Yin
- Department of Gastroenterology, Shanghai Tenth People’s Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Qiming Wang
- Department of Gastroenterology, Shanghai Tenth People’s Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Xinmiao Yan
- Department of Gastroenterology, Shanghai Tenth People’s Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Lu Zhang
- Department of Gastroenterology, Shanghai Tenth People’s Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Kailin Tang
- Department of Gastroenterology, Shanghai Tenth People’s Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Zhiwei Cao
- Department of Gastroenterology, Shanghai Tenth People’s Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Tianyi Qiu
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
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Long non-coding RNA molecules in tuberculosis. Int J Biol Macromol 2020; 156:340-346. [PMID: 32283111 DOI: 10.1016/j.ijbiomac.2020.04.030] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 03/03/2020] [Accepted: 04/04/2020] [Indexed: 02/06/2023]
Abstract
Tuberculosis (TB), a chronic disease caused by Mycobacterium tuberculosis, is one of the deadliest infectious diseases in the world. Despite significant advances in detection techniques and therapeutic approaches for tuberculosis, there is still no suitable solution for early screening and reducing the number of individuals affected and their effective treatment. Various cellular events can disrupt the development of TB. The basis of these events is dysregulating of genes expression patterns related with specific molecules. Long non-coding RNAs (lncRNAs) are molecules discovered to regulate the expression of protein-coding genes and participate in gene silencing, cell cycle regulation and cellular differentiation processes. Dysregulation of lncRNAs has been found to be associated with many diseases, including cancers and infectious diseases. Thus, the recognition of lncRNAs as novel molecular biomarkers and therapeutic targets for tuberculosis is promising. In the present review, we try to summarize the current findings of lncRNA expression patterns and its role in tuberculosis infection process.
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Zhang Y, Fan LJ, Zhang Y, Jiang J, Qi XW. Long Non-coding Wilms Tumor 1 Antisense RNA in the Development and Progression of Malignant Tumors. Front Oncol 2020; 10:35. [PMID: 32117711 PMCID: PMC7033608 DOI: 10.3389/fonc.2020.00035] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 01/09/2020] [Indexed: 12/15/2022] Open
Abstract
A growing number of studies have shown that long non-coding RNAs (lncRNAs) play an important role in tumor development and progression and are key molecules affecting tumor progression. The lncRNA Wilms tumor 1 antisense RNA (WT1-AS) is specifically expressed in various malignant tumors. In particular, WT1-AS expression is upregulated in colon cancer and breast cancer but is significantly downregulated in cervical cancer, liver cancer, and kidney cancer. The level of WT1-AS expression is closely related to the size, stage, and patient survival rate of these cancers. In this article, we review the modes of action, expression, function, and mechanisms of WT1-AS in different tumors to provide new targets for tumor diagnosis and treatment.
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Affiliation(s)
- Ye Zhang
- Department of Breast and Thyroid Surgery, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Lin-Jun Fan
- Department of Breast and Thyroid Surgery, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Yi Zhang
- Department of Breast and Thyroid Surgery, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Jun Jiang
- Department of Breast and Thyroid Surgery, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Xiao-Wei Qi
- Department of Breast and Thyroid Surgery, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
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Abbasifard M, Kamiab Z, Bagheri-Hosseinabadi Z, Sadeghi I. The role and function of long non-coding RNAs in osteoarthritis. Exp Mol Pathol 2020; 114:104407. [PMID: 32088191 DOI: 10.1016/j.yexmp.2020.104407] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 01/03/2020] [Accepted: 02/19/2020] [Indexed: 12/20/2022]
Abstract
Osteoarthiritis (OA) is the most prevalent disease of articulating joints in human that frequently results in joint pain, movement limitations, inflammation, and progressive degradation of articular cartilage. The etiology of OA is not completely clear and there is no full treatment for this disease. Molecular investigations have revealed the involvement of non-coding RNAs such as Long non-coding RNAs (lncRNAs) in OA pathogenesis. LncRNAs play roles in multiple cellular and biological processes. Moreover, numerous lncRNAs are differentially expressed in human OA cartilage. In this review, we underlie the increasing evidence for the critical role of lncRNAs in OA pathogenesis reviewing the latest researches.
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Affiliation(s)
- Mitra Abbasifard
- Department of Internal Medicine, Ali-Ibn Abi-Talib Hospital, Rafsanjan University of Medical Sciences, Rafsanjan, Iran
| | - Zahra Kamiab
- Department of Family Medicine, School of Medicine, Rafsanjan University of Medical Sciences, Rafsanjan, Iran; Clinical Research Development Unit, Ali Ibn Abi Talib Hospital, Rafsanjan University of Medical Sciences, Rafsanjan, Iran
| | - Zahra Bagheri-Hosseinabadi
- Department of Clinical Biochemistry, School of Medicine, Rafsanjan University of Medical Sciences, Rafsanjan, Iran.
| | - Iman Sadeghi
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, Barcelona, E-08003 Catalonia, Spain; CEINGE-biotecnologie avanzate, Naples, Italy.
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36
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Li C, Shen C, Shang X, Tang L, Xiong W, Ge H, Zhang H, Lu S, Shen Y, Wang J, Fei J, Wang Z. Two novel testis-specific long noncoding RNAs produced by <i>1700121C10Rik</i> are dispensable for male fertility in mice. J Reprod Dev 2019; 66:57-65. [PMID: 31801914 PMCID: PMC7040208 DOI: 10.1262/jrd.2019-104] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Testis-specific genes are prone to affect spermatogenesis or sperm fertility, and thus may play pivotal roles in male reproduction. However, whether a gene really affects male reproduction
in vivo needs to be confirmed using a gene knock-out (KO) model, a ‘gold standard’ method. Increasing studies have found that some of the evolutionarily conserved
testis-enriched genes are not essential for male fertility. In this study, we report that 1700121C10Rik, a previously uncharacterized gene, is specifically expressed in the
testis and produces two long noncoding RNAs (lncRNAs) in mouse: Transcript 1 and Transcript 2. qRT-PCR, northern blotting, and in situ hybridization revealed that expression
of both the lncRNAs commenced at the onset of sexual maturity and was predominant in round and elongating spermatids during spermiogenesis. Moreover, we found different subcellular
localization of Transcript 1 and Transcript 2 that was predominant in the cytoplasm and nucleus, respectively. 1700121C10Rik-KO mouse model disrupting Transcript 1 and
Transcript 2 expression was generated by CRISPR/Cas9 to determine their role in male reproduction. Results showed that 1700121C10Rik-KO male mice were fully fertile with
approximately standard testis size, testicular histology, sperm production, sperm morphology, sperm motility, and induction of acrosome reaction. Thus, we conclude that both the
testis-specific 1700121C10Rik-produced lncRNAs are dispensable for male fertility in mice under standard laboratory conditions.
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Affiliation(s)
- Chaojie Li
- State Key Laboratory of Medical Genomics, Research Center for Experimental Medicine, Shanghai Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Chunling Shen
- State Key Laboratory of Medical Genomics, Research Center for Experimental Medicine, Shanghai Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xuan Shang
- State Key Laboratory of Medical Genomics, Research Center for Experimental Medicine, Shanghai Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Lingyun Tang
- State Key Laboratory of Medical Genomics, Research Center for Experimental Medicine, Shanghai Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Wenfeng Xiong
- State Key Laboratory of Medical Genomics, Research Center for Experimental Medicine, Shanghai Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Haoyang Ge
- State Key Laboratory of Medical Genomics, Research Center for Experimental Medicine, Shanghai Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Hongxin Zhang
- State Key Laboratory of Medical Genomics, Research Center for Experimental Medicine, Shanghai Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Shunyuan Lu
- State Key Laboratory of Medical Genomics, Research Center for Experimental Medicine, Shanghai Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yan Shen
- State Key Laboratory of Medical Genomics, Research Center for Experimental Medicine, Shanghai Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jinjin Wang
- Shanghai Research Center for Model Organisms, Shanghai 201203, China
| | - Jian Fei
- Shanghai Research Center for Model Organisms, Shanghai 201203, China
| | - Zhugang Wang
- State Key Laboratory of Medical Genomics, Research Center for Experimental Medicine, Shanghai Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.,Shanghai Research Center for Model Organisms, Shanghai 201203, China
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The importance of long non-coding RNAs in neuropsychiatric disorders. Mol Aspects Med 2019; 70:127-140. [DOI: 10.1016/j.mam.2019.07.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 06/10/2019] [Accepted: 07/14/2019] [Indexed: 12/20/2022]
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38
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Vishnubalaji R, Shaath H, Elango R, Alajez NM. Noncoding RNAs as potential mediators of resistance to cancer immunotherapy. Semin Cancer Biol 2019; 65:65-79. [PMID: 31733291 DOI: 10.1016/j.semcancer.2019.11.006] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 10/31/2019] [Accepted: 11/11/2019] [Indexed: 12/12/2022]
Abstract
Substantial evolution in cancer therapy has been witnessed lately, steering mainly towards immunotherapeutic approaches, replacing or in combination with classical therapies. Whereas the use of various immunotherapy approaches, such as adoptive T cell therapy, genetically-modified T cells, or immune checkpoint inhibitors, has been a triumph for cancer immunotherapy, the great challenge is the ability of the immune system to sustain long lasting anti-tumor response. Additionally, epigenetic changes in a suppressive tumor microenvironment can pertain to T cell exhaustion, limiting their functionality. Noncoding RNAs (ncRNAs) have emerged over the last years as key players in epigenetic regulation. Among those, microRNAs (miRNAs) and long noncoding RNAs (lncRNAs) have been studied extensively for their potential role in regulating tumor immunity through direct regulation of genes involved in immune activation or suppression. In this review, we will provide an overview of contemporary approaches for cancer immunotherapy and will present the current state of knowledge implicating miRNAs and lncRNAs in regulating immune response against human cancer and their potential implications in resistance to cancer immunotherapy, with main emphasis on immune checkpoints regulation.
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Affiliation(s)
- Radhakrishnan Vishnubalaji
- Cancer Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), PO Box 34110, Doha, Qatar
| | - Hibah Shaath
- Cancer Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), PO Box 34110, Doha, Qatar; College of Health & Life Sciences, Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar
| | - Ramesh Elango
- Cancer Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), PO Box 34110, Doha, Qatar
| | - Nehad M Alajez
- Cancer Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), PO Box 34110, Doha, Qatar; College of Health & Life Sciences, Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar.
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39
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Zhang B, Zhang X, Zhang M, Guo L, Qi T, Wang H, Tang H, Qiao X, Shahzad K, Xing C, Wu J. Transcriptome Analysis Implicates Involvement of Long Noncoding RNAs in Cytoplasmic Male Sterility and Fertility Restoration in Cotton. Int J Mol Sci 2019; 20:ijms20225530. [PMID: 31698756 PMCID: PMC6888562 DOI: 10.3390/ijms20225530] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 10/31/2019] [Accepted: 11/04/2019] [Indexed: 12/20/2022] Open
Abstract
The cytoplasmic male sterility (CMS)/restorer-of-fertility system is an important tool to exploit heterosis during commercially hybrid seed production. The importance of long noncoding RNAs (lncRNAs) in plant development is recognized, but few analyses of lncRNAs during anther development of three-line hybrid cotton (CMS-D2 line A, maintainer line B, restorer-of-fertility line R) have been reported. Here, we performed transcriptome sequencing during anther development in three-line hybrid cotton. A total of 80,695 lncRNAs were identified, in which 43,347 and 44,739 lncRNAs were differentially expressed in A–B and A–R comparisons, respectively. These lncRNAs represent functional candidates involved in CMS and fertility restoration. GO analysis indicated that cellular hormone metabolic processes and oxidation–reduction reaction processes might be involved in CMS, and cellular component morphogenesis and small molecular biosynthetic processes might participate in fertility restoration. Additionally, 63 lncRNAs were identified as putative precursors of 35 miRNAs, and quantitative reverse transcription polymerase chain reaction (qRT-PCR) showed a similar expression pattern to RNA-seq data. Furthermore, construction of lncRNA regulatory networks indicated that several miRNA–lncRNA–mRNA networks might be involved in CMS and fertility restoration. Our findings provide systematic identification of lncRNAs during anther development and lays a solid foundation for the regulatory mechanisms and utilization in hybrid cotton breeding.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Chaozhu Xing
- Correspondence: (C.X.); (J.W.); Tel.: +86-372-256-2371 (C.X.); +86-372-256-2288 (J.W.)
| | - Jianyong Wu
- Correspondence: (C.X.); (J.W.); Tel.: +86-372-256-2371 (C.X.); +86-372-256-2288 (J.W.)
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40
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Li J, Fang H, Jiang F, Ning Y. External validation of a panel of plasma microRNA biomarkers for lung cancer. Biomark Med 2019; 13:1557-1564. [PMID: 31674214 DOI: 10.2217/bmm-2019-0213] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Aim: We externally validate plasma miRNAs biomarkers for lung cancer in a large and retrospective sample set collected from a geographically distant population. Methods: Plasma samples are tested blindly to the clinical annotations by using PCR for quantitation of the four miRNAs in cohort 1 consisting of 232 lung cancer cases and 243 controls and cohort 2 comprising 239 cases and 246 controls. Results: Combined use of the four plasma miRNAs has 91% sensitivity and 95% specificity for diagnosis of lung cancer, and 85% sensitivity for early-stage lung cancer, while maintaining a specificity of 95%. Conclusion: The diagnostic values of the biomarkers are reproducibly confirmed in the independent and large sample sets, providing an assay for lung cancer detection.
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Affiliation(s)
- Jin Li
- Department of Medicine, Fuyang Hospital, 100 Qinghe Road, Fuyang, Anhui, 236037, PR China
| | - HongBin Fang
- Department of Biostatistics, Bioinformatics & Biomathematics, Georgetown University Medical Center, 4000 Reservoir Road, NW, Washington DC 20057, USA
| | - Fang Jiang
- Cancer Center, University of Maryland Baltimore, N9E17 22 S. Greene Street, Baltimore, 21201 MD, USA
| | - Yang Ning
- Department of Medicine, Fuyang Hospital, 100 Qinghe Road, Fuyang, Anhui, 236037, PR China
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41
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Genome-wide discovery and characterization of long noncoding RNAs in patients with multiple myeloma. BMC Med Genomics 2019; 12:135. [PMID: 31619233 PMCID: PMC6794882 DOI: 10.1186/s12920-019-0577-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 08/30/2019] [Indexed: 12/12/2022] Open
Abstract
Background Long noncoding RNAs (lncRNAs) are involved in a wide range of biological processes in tumorigenesis. However, the role of lncRNA expression in the biology, prognosis, and molecular classification of human multiple myeloma (MM) remains unclear, especially the biological functions of the vast majority of lncRNAs. Recently, lncRNAs have been identified in neoplastic hematologic disorders. Evidence has accumulated on the molecular mechanisms of action of lncRNAs, providing insight into their functional roles in tumorigenesis. This study aimed to characterize potential lncRNAs in patients with MM. Methods In this study, the whole-transcriptome strand-specific RNA sequencing of samples from three newly diagnosed patients with MM was performed. The whole transcriptome, including lncRNAs, microRNAs, and mRNAs, was analyzed. Using these data, MM lncRNAs were systematically analyzed, and the lncRNAs involved in the occurrence of MM were identified. Results The results revealed that MM lncRNAs had distinctive characteristics different from those of other malignant tumors. Further, the functions of a set of lncRNAs preferentially expressed in MM were verified, and several lncRNAs were identified as competing endogenous RNAs. More importantly, the aberrant expression of certain lncRNAs, including maternally expressed gene3, colon cancer–associated transcript1, and coiled-coil domain-containing 26, as well as some novel lncRNAs involved in the occurrence of MM was established. Further, lncRNAs were related to some microRNAs, regulated each other, and participated in MM development. Conclusions Genome-wide screening and functional analysis enabled the identification of a set of lncRNAs involved in the occurrence of MM. The interaction exists among microRNAs and lncRNAs.
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42
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Zheng GZ, Li W, Liu ZY. Alternative role of noncoding RNAs: coding and noncoding properties. J Zhejiang Univ Sci B 2019; 20:920-927. [PMID: 31595728 DOI: 10.1631/jzus.b1900336] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Noncoding RNAs (ncRNAs) have played a critical role in cellular biological functions. Recently, some peptides or proteins originating from annotated ncRNAs were identified in organism development and various diseases. Here, we briefly review several novel peptides translated by annotated ncRNAs and related key functions. In addition, we summarize the potential mechanism of bifunctional ncRNAs and propose a specific "switch" triggering the transformation from the noncoding to the coding state under certain stimuli or cellular stress. The coding properties of ncRNAs and their peptide products may provide a novel horizon in proteomic research and can be regarded as a potential therapeutic target for the treatment of various diseases.
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Affiliation(s)
- Gui-Zhen Zheng
- Department of Emergency Internal Medicine, Shanghai East Hospital, Tongji University, Shanghai 200120, China
| | - Wei Li
- Department of General Surgery, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China
| | - Zhi-Yong Liu
- Department of Laboratory Diagnostics, Changhai Hospital, Second Military Medical University, Shanghai 200433, China.,Kunming General Hospital of Chengdu Military Command, Kunming 650032, China
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Xiong Y, Liu Z, Li Z, Wang S, Shen N, Xin Y, Huang T. Long non‑coding RNA nuclear paraspeckle assembly transcript 1 interacts with microRNA‑107 to modulate breast cancer growth and metastasis by targeting carnitine palmitoyltransferase‑1. Int J Oncol 2019; 55:1125-1136. [PMID: 31485672 DOI: 10.3892/ijo.2019.4869] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 02/28/2019] [Indexed: 11/06/2022] Open
Abstract
Previous studies revealed that the long non‑coding RNA nuclear paraspeckle assembly transcript 1 (NEAT1) exhibits abnormal expression in numerous cancer types, including breast cancer (BC); however, the regulatory mechanism of NEAT1 in BC remains unclear. In the present study, the effect of NEAT1 on the progression of BC and its regulation mechanism was investigated. The expression levels of NEAT1 and microRNA‑107 (miR‑107) in BC cells were analyzed using the reverse transcription‑quantitative polymerase chain reaction (RT‑qPCR). NEAT1 was knocked down in BC cells, and mimics‑miR‑107 or inhibitor‑miR‑107 were transfected into BC cells. Subsequently, cell proliferation, invasion and migration, apoptosis and cell cycle distribution were determined. The regulatory mechanism of NEAT1, miR‑107 and carnitine palmitoyltransferase‑1 (CPT1A) was analyzed using a luciferase reporter assay system, western blotting and RT‑qPCR. NEAT1 expression was increased in BC cells, whereas miR‑107 expression was decreased, compared with normal mammary gland cells. NEAT1 promoted the progression of BC cells through inhibiting apoptosis‑associated genes and promoting cell cycle‑ and invasion‑associated gene expression, whereas miR‑107 served the opposite function. Furthermore, NEAT1 promoted the expression of CPT1A, which was mediated by miR‑107. The results of the present study indicate that NEAT1 promotes the expression of CPT1A by inhibiting miR‑107 to improve the progression of BC cells; therefore, NEAT1 is a potential therapeutic target of BC.
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Affiliation(s)
- Yiquan Xiong
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Zeming Liu
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Zhi Li
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Shuntao Wang
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Na Shen
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Yue Xin
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Tao Huang
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
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LncRNA LUCAT1 facilitates tumorigenesis and metastasis of triple-negative breast cancer through modulating miR-5702. Biosci Rep 2019; 39:BSR20190489. [PMID: 31399501 PMCID: PMC6722493 DOI: 10.1042/bsr20190489] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 06/28/2019] [Accepted: 07/16/2019] [Indexed: 12/16/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is a subtype of aggressive breast cancer with high recurrence and poor survival. Emerging evidence has indicated that long non-coding RNAs (lncRNAs) play pivotal roles in the development and progression of multiple cancers. Although there are substantial studies revealing that lung cancer-associated transcript 1 (LUCAT1) functions as a tumor promotor in various human cancers, the molecular mechanism of LUCAT1 in TNBC remains largely to be explored. In our study, we identified that LUCAT1 expression was dramatically enhanced in TNBC samples and cells. High LUCAT1 expression was strongly associated with advanced stages and poor prognosis of TNBC. LUCAT1 contributed to TNBC development through accelerating cell proliferation, cell cycle progression and metastasis as well as attenuating cell apoptosis. Moreover, miR-5702 was proved to directly bind to LUCAT1 and be negatively modulated by LUCAT1. Knockdown of miR-5702 reversed the suppressing influences of LUCAT1 depletion on TNBC progression. In conclusion, it was the first investigation to shed light on the significant function and underlying regulatory mechanism of LUCAT1 in TNBC tumorigenesis. We validated that LUCAT1 induced tumorigenesis and metastasis of TNBC via miR-5702, which provided clues for improving the treatment of TNBC.
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Xu Y, Chen L, Liu M, Lu Y, Yue Y, Liu Y, Chen H, Xie F, Zhang C. High-throughput transcriptome sequencing reveals extremely high doses of ionizing radiation-response genes in Caenorhabditis elegans. Toxicol Res (Camb) 2019; 8:754-766. [PMID: 31588352 PMCID: PMC6762013 DOI: 10.1039/c9tx00101h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 08/06/2019] [Indexed: 12/27/2022] Open
Abstract
This study sought novel ionizing radiation-response (IR-response) genes in Caenorhabditis elegans (C. elegans). C. elegans was divided into three groups and exposed to different high doses of IR: 0 gray (Gy), 200 Gy, and 400 Gy. Total RNA was extracted from each group and sequenced. When the transcriptomes were compared among these groups, many genes were shown to be differentially expressed, and these genes were significantly enriched in IR-related biological processes and pathways, including gene ontology (GO) terms related to cellular behaviours, cellular growth and purine metabolism and kyoto encyclopedia of genes and genomes (KEGG) pathways related to ATP binding, GTPase regulator activity, and RNA degradation. Quantitative reverse-transcription PCR (qRT-PCR) confirmed that these genes displayed differential expression across the treatments. Further gene network analysis showed a cluster of novel gene families, such as the guanylate cyclase (GCY), Sm-like protein (LSM), diacylglycerol kinase (DGK), skp1-related protein (SKR), and glutathione S-transferase (GST) gene families which were upregulated. Thus, these genes likely play important roles in IR response. Meanwhile, some important genes that are well known to be involved in key signalling pathways, such as phosphoinositide-specific phospholipase C-3 (PLC-3), phosphatidylinositol 3-kinase age-1 (AGE-1), Raf homolog serine/threonine-protein kinase (LIN-45) and protein cbp-1 (CBP-1), also showed differential expression during IR response, suggesting that IR response might perturb these key signalling pathways. Our study revealed a series of novel IR-response genes in Caenorhabditis elegans that might act as regulators of IR response and represent promising markers of IR exposure.
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Affiliation(s)
- Youqin Xu
- Department of Biochemistry and Molecular Biology , School of Basic Medical Science , Southern Medical University and Guangdong Provincial Key Laboratory of Single Cell Technology and Application , Guangzhou , Guangdong Province , China . ; Tel: +86-13824447151
- Department of Medical Oncology , Taishan People's Hospital , Guangdong Province , China
| | - Lina Chen
- Basic Medical College , Xiangnan University , Chenzhou , China
| | - Mengyi Liu
- Department of Biochemistry and Molecular Biology , School of Basic Medical Science , Southern Medical University and Guangdong Provincial Key Laboratory of Single Cell Technology and Application , Guangzhou , Guangdong Province , China . ; Tel: +86-13824447151
| | - Yanfang Lu
- Department of Biochemistry and Molecular Biology , School of Basic Medical Science , Southern Medical University and Guangdong Provincial Key Laboratory of Single Cell Technology and Application , Guangzhou , Guangdong Province , China . ; Tel: +86-13824447151
| | - Yanwei Yue
- Blood Transfusion Department , The First Affiliated Hospital of Xi'an Jiaotong University , Xi'an , China
| | - Yue Liu
- Department of Biochemistry and Molecular Biology , School of Basic Medical Science , Southern Medical University and Guangdong Provincial Key Laboratory of Single Cell Technology and Application , Guangzhou , Guangdong Province , China . ; Tel: +86-13824447151
| | - Honghao Chen
- Department of Biochemistry and Molecular Biology , School of Basic Medical Science , Southern Medical University and Guangdong Provincial Key Laboratory of Single Cell Technology and Application , Guangzhou , Guangdong Province , China . ; Tel: +86-13824447151
| | - Fuliang Xie
- Department of Biochemistry and Molecular Biology , School of Basic Medical Science , Southern Medical University and Guangdong Provincial Key Laboratory of Single Cell Technology and Application , Guangzhou , Guangdong Province , China . ; Tel: +86-13824447151
- Department of Biology , East Carolina University , Greenville , NC , USA
| | - Chao Zhang
- Department of Biochemistry and Molecular Biology , School of Basic Medical Science , Southern Medical University and Guangdong Provincial Key Laboratory of Single Cell Technology and Application , Guangzhou , Guangdong Province , China . ; Tel: +86-13824447151
- Department of Medical Oncology , Taishan People's Hospital , Guangdong Province , China
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Long non-coding RNA: Classification, biogenesis and functions in blood cells. Mol Immunol 2019; 112:82-92. [DOI: 10.1016/j.molimm.2019.04.011] [Citation(s) in RCA: 199] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 04/16/2019] [Accepted: 04/23/2019] [Indexed: 12/20/2022]
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Xiao Y, Su M, Ou W, Wang H, Tian B, Ma J, Tang J, Wu J, Wu Z, Wang W, Zhou Y. Involvement of noncoding RNAs in epigenetic modifications of esophageal cancer. Biomed Pharmacother 2019; 117:109192. [PMID: 31387188 DOI: 10.1016/j.biopha.2019.109192] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 06/19/2019] [Accepted: 06/28/2019] [Indexed: 12/16/2022] Open
Abstract
Esophageal cancer (EC) is a serious digestive malignancy and is a leading cause of cancer-related mortality. Apart from genetic mutations, many epigenetic alterations including DNA methylation and histone modifications associated with chromatin remodeling have been identified in the regulation of gene expression in EC. Recently, noncoding RNAs, and mainly lncRNAs and miRNAs, have been revealed to be involved in the epigenetic regulation of EC. In this review, we focus on describing new insights on epigenetic processes associated with noncoding RNAs, which have been characterized to be responsible for the development and progression of EC.
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Affiliation(s)
- Yuhang Xiao
- Department of Pharmacy, Xiangya Hospital of Xiangya School of Medicine, Central South University, Changsha, PR China
| | - Min Su
- Department of the 2nd Thoracic Surgery, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, PR China; Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, PR China
| | - Wei Ou
- Department of Pharmacy, The First People's Hospital of Yue Yang, Yue Yang, PR China
| | - Hui Wang
- Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, PR China
| | - Bo Tian
- Department of the 2nd Thoracic Surgery, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, PR China
| | - Junliang Ma
- Department of the 2nd Thoracic Surgery, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, PR China
| | - Jinming Tang
- Department of the 2nd Thoracic Surgery, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, PR China
| | - Jie Wu
- Department of the 2nd Thoracic Surgery, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, PR China
| | - Zhining Wu
- Department of the 2nd Thoracic Surgery, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, PR China
| | - Wenxiang Wang
- Department of the 2nd Thoracic Surgery, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, PR China; Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, PR China.
| | - Yong Zhou
- Department of the 2nd Thoracic Surgery, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, PR China.
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Has2 natural antisense RNA and Hmga2 promote Has2 expression during TGFβ-induced EMT in breast cancer. Matrix Biol 2019; 80:29-45. [DOI: 10.1016/j.matbio.2018.09.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 09/04/2018] [Accepted: 09/04/2018] [Indexed: 12/16/2022]
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Gao Z, Zhou H, Wang Y, Chen J, Ou Y. Regulatory effects of lncRNA ATB targeting miR-200c on proliferation and apoptosis of colorectal cancer cells. J Cell Biochem 2019; 121:332-343. [PMID: 31222825 DOI: 10.1002/jcb.29180] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 05/22/2019] [Accepted: 05/23/2019] [Indexed: 01/17/2023]
Abstract
This investigation was intended to elucidate whether long noncoding RNA (lncRNA)-activated by transforming growth factor-β (ATB) interacting with miR-200c could mediate colorectal cancer (CRC) progression, offering potential strategies for diagnosing and treating CRC. Here totally 315 patients with CRC were recruited, and their CRC tissues and adjacent normal tissues were gathered. Concurrently, four colon cancer cell lines (ie, SW620, Lovo, HCT116, and SW480) and the human colon mucosal epithelial cell line (NCM460) were also purchased. Moreover, si-ATB, si-NC, miR-200c mimic, miR-200c inhibitor, and miR-NC were prepared for transfection into the CRC cells, and their effects on CRC cell lines were evaluated based on the conduction of 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay, colony formation assay, and flow cytometry assay. Eventually, the Luciferase reporter gene assay was carried out to judge if there existed a targeted relationship between ATB and miR-200c. The results of Cox regression analyses suggested that overexpressed lncRNA ATB, underexpressed miR-200c, poor tumor differentiation, lymph-vascular invasion, and perineural invasion were symbolic of shortened survival of the patients with CRC (all P < .05). Besides, transfection of pcDNA3.1-ATB and miR-200c inhibitor could boost the viability and proliferation of Lovo and SW620 cell lines (all P < .05). Meanwhile, the expressions of p53 and p21 were also reduced under treatments of pcDNA3.1-ATB and miR-200c inhibitor (P < .05). In addition, CDK2 seemed to reverse the contribution of miR-200c to intensifying viability and proliferation of Lovo and SW420 cell lines (P < .05). Furthermore, ATB might downregulate miR-200c expression by targeting it (P < .05), and CDK2 was subjected to dual regulation of both ATB and miR-200c (P < .05). In conclusion, the lncRNA ATB/miR-200c/CDK2 signaling was responsible for intensified proliferation and prohibited apoptosis of CRC cells, which might provide effective approaches for diagnosing and treating CRC.
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Affiliation(s)
- Zhenyuan Gao
- Department of Medical Oncology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, China
| | - Hairong Zhou
- Department of Medical Oncology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, China
| | - Yaping Wang
- Department of Medical Oncology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, China
| | - Juan Chen
- Department of Medical Oncology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, China
| | - Yimei Ou
- Department of Medical Oncology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, China
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50
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Sallam T, Sandhu J, Tontonoz P. Long Noncoding RNA Discovery in Cardiovascular Disease: Decoding Form to Function. Circ Res 2019; 122:155-166. [PMID: 29301847 DOI: 10.1161/circresaha.117.311802] [Citation(s) in RCA: 191] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Despite significant improvements during the past 3 decades, cardiovascular disease remains a leading worldwide health epidemic. The recent identification of a fascinating group of mediators known as long noncoding RNAs (lncRNAs) has provided a wealth of new biology to explore for cardiovascular risk mitigation. lncRNAs are expressed in a highly context-specific fashion, and multiple lines of evidence implicated them in diverse biological processes. Indeed, abnormalities of lncRNAs have been directly linked with human ailments, including cardiovascular biology and disease. Of particular interest to the cardiovascular research community, dysregulation in lncRNA regulatory circuits have been associated with cardiac pathological hypertrophy, vascular disease, cell fate programming and development, atherosclerosis, dyslipidemia, and metabolic syndrome. Although techniques in interrogating noncoding RNAs are rapidly evolving, a major challenge in studying lncRNAs remains navigating through multiple technical constraints. In this review, we provide a road map for lncRNA discovery and interrogation in biological systems relevant to cardiovascular disease and highlight approaches to decipher their modes of action.
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Affiliation(s)
- Tamer Sallam
- From the Division of Cardiology, Department of Medicine (T.S.) and Department of Pathology and Laboratory Medicine, Howard Hughes Medical Institute (J.S., P.T.), University of California, Los Angeles.
| | - Jaspreet Sandhu
- From the Division of Cardiology, Department of Medicine (T.S.) and Department of Pathology and Laboratory Medicine, Howard Hughes Medical Institute (J.S., P.T.), University of California, Los Angeles
| | - Peter Tontonoz
- From the Division of Cardiology, Department of Medicine (T.S.) and Department of Pathology and Laboratory Medicine, Howard Hughes Medical Institute (J.S., P.T.), University of California, Los Angeles
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