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Park J, Peña-Tauber A, Talozzi L, Greicius MD, Guen YL. Genetic associations with human longevity are enriched for oncogenic genes. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.07.30.24311226. [PMID: 39132489 PMCID: PMC11312667 DOI: 10.1101/2024.07.30.24311226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
Human lifespan is shaped by both genetic and environmental exposures and their interaction. To enable precision health, it is essential to understand how genetic variants contribute to earlier death or prolonged survival. In this study, we tested the association of common genetic variants and the burden of rare non-synonymous variants in a survival analysis, using age-at-death (N = 35,551, median [min, max] = 72.4 [40.9, 85.2]), and last-known-age (N = 358,282, median [min, max] = 71.9 [52.6, 88.7]), in European ancestry participants of the UK Biobank. The associations we identified seemed predominantly driven by cancer, likely due to the age range of the cohort. Common variant analysis highlighted three longevity-associated loci: APOE, ZSCAN23 , and MUC5B . We identified six genes whose burden of loss-of-function variants is significantly associated with reduced lifespan: TET2 , ATM , BRCA2, CKMT1B , BRCA1 and ASXL1 . Additionally, in eight genes, the burden of pathogenic missense variants was associated with reduced lifespan: DNMT3A, SF3B1, CHL1 , TET2, PTEN, SOX21, TP53 and SRSF2 . Most of these genes have previously been linked to oncogenic-related pathways and some are linked to and are known to harbor somatic variants that predispose to clonal hematopoiesis. A direction-agnostic (SKAT-O) approach additionally identified significant associations with C1orf52, TERT, IDH2, and RLIM , highlighting a link between telomerase function and longevity as well as identifying additional oncogenic genes. Our results emphasize the importance of understanding genetic factors driving the most prevalent causes of mortality at a population level, highlighting the potential of early genetic testing to identify germline and somatic variants increasing one's susceptibility to cancer and/or early death.
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Valizadeh M, Derafsh E, Abdi Abyaneh F, Parsamatin SK, Noshabad FZR, Alinaghipour A, Yaghoobi Z, Taheri AT, Dadgostar E, Aschner M, Mirzaei H, Tamtaji OR, Nabavizadeh F. Non-Coding RNAs and Neurodegenerative Diseases: Information of their Roles in Apoptosis. Mol Neurobiol 2024; 61:4508-4537. [PMID: 38102518 DOI: 10.1007/s12035-023-03849-z] [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: 03/22/2023] [Accepted: 11/16/2023] [Indexed: 12/17/2023]
Abstract
Apoptosis can be known as a key factor in the pathogenesis of neurodegenerative disorders. In disease conditions, the rate of apoptosis expands and tissue damage may become apparent. Recently, the scientific studies of the non-coding RNAs (ncRNAs) has provided new information of the molecular mechanisms that contribute to neurodegenerative disorders. Numerous reports have documented that ncRNAs have important contributions to several biological processes associated with the increase of neurodegenerative disorders. In addition, microRNAs (miRNAs), circular RNAs (circRNAs), as well as, long ncRNAs (lncRNAs) represent ncRNAs subtypes with the usual dysregulation in neurodegenerative disorders. Dysregulating ncRNAs has been associated with inhibiting or stimulating apoptosis in neurodegenerative disorders. Therefore, this review highlighted several ncRNAs linked to apoptosis in neurodegenerative disorders. CircRNAs, lncRNAs, and miRNAs were also illustrated completely regarding the respective signaling pathways of apoptosis.
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Affiliation(s)
| | - Ehsan Derafsh
- Windsor University School of Medicine, Cayon, Canada
| | | | - Sayedeh Kiana Parsamatin
- Department of Neurology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | | | - Azam Alinaghipour
- School of Medical Sciences, Yazd Branch, Islamic Azad University, Yazd, Iran
| | - Zahra Yaghoobi
- Electrophysiology Research Center, Neuroscience Institute, Tehran University of Medical Sciences, Tehran, IR, Iran
- Department of Physiology, School of Medicine, Tehran University of Medical Sciences, Tehran, IR, Iran
| | - Abdolkarim Talebi Taheri
- Student Research Committee, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ehsan Dadgostar
- Behavioral Sciences Research Center, Isfahan University of Medical Sciences, Isfahan, IR, Iran
- Student Research Committee, Isfahan University of Medical Sciences, Isfahan, IR, Iran
| | - Michael Aschner
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Hamed Mirzaei
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Kashan University of Medical Sciences, Kashan, IR, Iran.
| | - Omid Reza Tamtaji
- Electrophysiology Research Center, Neuroscience Institute, Tehran University of Medical Sciences, Tehran, IR, Iran.
- Department of Physiology, School of Medicine, Tehran University of Medical Sciences, Tehran, IR, Iran.
| | - Fatemeh Nabavizadeh
- Electrophysiology Research Center, Neuroscience Institute, Tehran University of Medical Sciences, Tehran, IR, Iran
- Department of Physiology, School of Medicine, Tehran University of Medical Sciences, Tehran, IR, Iran
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Fu H, Zhang M, Liu X, Yang Y, Xing Y. Abnormal methylation mediated upregulation of LINC00857 boosts malignant progression of lung adenocarcinoma by modulating the miR-486-5p/NEK2 axis. THE CLINICAL RESPIRATORY JOURNAL 2024; 18:e13765. [PMID: 38721812 PMCID: PMC11079885 DOI: 10.1111/crj.13765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 11/29/2023] [Accepted: 03/12/2024] [Indexed: 05/12/2024]
Abstract
LINC00857 is frequently dysregulated in varying cancers, which in turn exerts carcinogenic effects; however, its DNA methylation status in promoter region and molecular mechanisms underlying the progression of lung adenocarcinoma (LUAD) remain rarely understood. Through bioinformatics analysis, we examined the expression state and methylation site of LINC00857 in LUAD and further investigated the properties of LINC00857 as a competitive endogenous RNA in the cancer progression. The current study revealed that the overexpression of LINC00857 in LUAD tissue and cells was mainly caused by the hypomethylation of the promoter region. LINC00857 knockdown prominently reduced cell proliferation, impeded cell migration and invasion, and restrained lymph node metastasis, with enhancing radiosensitivity. The effects of LINC00857 on tumor growth were also investigated in nude mice models. Subsequently, the downstream factors, miR-486-5p and NEK2, were screened, and the putative regulatory axis was examined. Overall, the regulatory effect of methylation-mediated LINC00857 overexpression on miR-486-5p/NEK2 axis may be a new mechanism for LUAD progression.
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Affiliation(s)
- Haoyu Fu
- Department of Radiation OncologyTangshan People's HospitalTangshanChina
| | - Mingming Zhang
- Department of Thoracic SurgeryTangshan People's HospitalTangshanChina
| | - Xiaohui Liu
- Department of Thoracic SurgeryTangshan People's HospitalTangshanChina
| | - Yiming Yang
- Department of Breast SurgeryTangshan People's HospitalTangshanChina
| | - Ying Xing
- Department of Radiation OncologyTangshan People's HospitalTangshanChina
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Yan Y, Wang J, Xu B, Ni J, Dai T, Wang L, Wang H, Hua Z, Li K, Zhou Y. Exosomal SOX21-AS1 Regulates EREG by Sponging miR-451a and Promotes the Malignancy of Pancreatic Ductal Adenocarcinoma. J Cancer 2024; 15:3321-3337. [PMID: 38817864 PMCID: PMC11134441 DOI: 10.7150/jca.95014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Accepted: 04/04/2024] [Indexed: 06/01/2024] Open
Abstract
The incidence and mortality of pancreatic ductal adenocarcinoma (PDAC) have increased. Exosomes, as a regulatory mode of intercellular communication, contain lncRNAs. SOX21-AS1 has been studied in other cancers, and its expression is elevated in PDAC, but its role in PDAC remains unclear. First, we analyzed the expression of lncRNAs in PDAC tissues and nontumor tissues through the TCGA database. Next, the results of the RT-qPCR experiment confirmed the prediction that the expression of SOX21-AS1 was elevated in PDAC tissues. In vivo and in vitro cell function assays confirmed that the degree of malignancy of PDAC was proportional to the expression of SOX21-AS1. In addition, through exosome isolation and uptake experiments, we first found that PDAC could secrete exosomal SOX21-AS1 and play an angiogenic role in HUVECs. Subsequently, the relationship between SOX21-AS1, miR-451a and epiregulin (EREG) was verified through database prediction and analysis and RIP assays. Finally, functional recovery assays in vivo and in vitro verified that SOX21-AS1 regulates the expression of EREG through combination with miR-451a and thus promotes the malignancy of PDAC. SOX21-AS1 was upregulated in PDAC. The upregulation of SOX21-AS1 can stimulate the proliferation, migration, invasion, stemness and epithelial-mesenchymal transition (EMT) progression of PDAC cells. Furthermore, PDAC cells secrete exosomal SOX21-AS1, which is absorbed by HUVECs and promotes angiogenesis. Our study first identified that SOX21-AS1 promotes the malignancy of PDAC through the SOX21-AS1/miR-451a/EREG axis, and also that exosomal SOX21-AS1 promotes angiogenesis in PDAC.
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Affiliation(s)
- Yong Yan
- Department of Hepatobiliary Surgery, The Affiliated Wuxi No. 2 People's Hospital of Nanjing Medical University, Wuxi, China
| | - Jinyi Wang
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Bin Xu
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jianming Ni
- Department of Radiology, The Affiliated Wuxi No. 2 People's Hospital of Nanjing Medical University, Wuxi, China
| | - Tu Dai
- Department of Hepatobiliary Surgery, Jiangnan University Medical Center, JUMC, Wuxi, China
| | - Liying Wang
- Department of Hepatobiliary Surgery, Jiangnan University Medical Center, JUMC, Wuxi, China
| | - Hao Wang
- Department of Hepatobiliary Surgery, Jiangnan University Medical Center, JUMC, Wuxi, China
| | - Zhiyuan Hua
- Department of Hepatobiliary Surgery, Jiangnan University Medical Center, JUMC, Wuxi, China
| | - Kuan Li
- Department of Hepatobiliary Surgery, Kunshan Hospital of Traditional Chinese Medicine, Kunshan, China
| | - Yongping Zhou
- Department of Hepatobiliary Surgery, The Affiliated Wuxi No. 2 People's Hospital of Nanjing Medical University, Wuxi, China
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Zhi Y, Du P, Li Y, Liu H, Jiang T, Zhao X, Li X. SOX21-AS1 Augmented Cervical Cancer Growth by Triggering FZD3 to Activate the Wnt/β-Catenin Signaling Pathway. Biochem Genet 2024:10.1007/s10528-024-10770-0. [PMID: 38512584 DOI: 10.1007/s10528-024-10770-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 03/01/2024] [Indexed: 03/23/2024]
Abstract
Long non-coding RNA (LncRNA) SOX21-AS1 has been reported that it plays an important role in biological processes of several cancers. However, how it functions in cervical cancer (CC) still remain unclear. This investigation seeks to explore the impact of SOX21-AS1 on CC cell proliferation, invasion and migration and its association to the FZD3 and the Wnt/β-catenin signaling pathway. SOX21-AS1 expression levels were detected using real-time quantitative PCR in 20 cases of cervical cancer together with its adjacent tissues and several cervical cancer cell lines. Transgenic technology and functional experiments were conducted to confirm the carcinogenic properties of SOX21-AS1, and western blot was utilized to analyze the regulatory network composed of SOX21-AS1, FZD3 and the Wnt/β-catenin signaling pathway in CC. Through bioinformatics analysis, we found that the expression of SOX21-AS1 in CC was the highest among 16 kinds of tumor tissues. Moreover, clinical specimens confirmed that both CC tissues and cell lines possessed elevated SOX21-AS1 expressions (P < 0.01). CC cells which stably expressed upregulated SOX21-AS1 were noted to possesses higher rates of metastasis, invasion and proliferation, lower apoptotic rates and higher expression of FZD3,β-catenin and c-myc (P < 0.01). Conversely, the use of small interfering RNA to inhibit the expression of SOX21-AS1 yielded the opposite results (P < 0.01). SOX21-AS1 functions as an oncogenic LncRNA which enhances CC cell metastasis, invasion and proliferation through FZD3 upregulation via Wnt/β-catenin-signaling pathway activation. This LncRNA may represent an important biomarker for CC patients.
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Affiliation(s)
- Yanfang Zhi
- Department of Clinical Laboratory, The Third Affiliated Hospital of Zhengzhou University, No. 7 Front Kangfu Street, Er'qi District, Zhengzhou, 450002, China
| | - Peipei Du
- Department of Laboratory, The First Affiliated Hospital of Henan University of Science and Technology, No. 636 Guanlin Road, Luolong District, Luoyang, 471032, China
| | - Ya Li
- Department of Clinical Laboratory, The Third Affiliated Hospital of Zhengzhou University, No. 7 Front Kangfu Street, Er'qi District, Zhengzhou, 450002, China
| | - Hui Liu
- Department of Clinical Laboratory, The Third Affiliated Hospital of Zhengzhou University, No. 7 Front Kangfu Street, Er'qi District, Zhengzhou, 450002, China
| | - Tao Jiang
- Department of Laboratory, The First Affiliated Hospital of Henan University of Science and Technology, No. 636 Guanlin Road, Luolong District, Luoyang, 471032, China
| | - Xin Zhao
- Department of Imaging, The Third Affiliated Hospital of Zhengzhou University, No. 7 Front Kangfu Street, Er'qi District, Zhengzhou, 450002, China.
| | - Xiaofu Li
- Department of Clinical Laboratory, The Third Affiliated Hospital of Zhengzhou University, No. 7 Front Kangfu Street, Er'qi District, Zhengzhou, 450002, China.
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Ye Y, Maroney KJ, Wiener HW, Mamaeva OA, Junkins AD, Burkholder GA, Sudenga SL, Khushman M, Al Diffalha S, Bansal A, Shrestha S. RNA-seq analysis identifies transcriptomic profiles associated with anal cancer recurrence among people living with HIV. Ann Med 2023; 55:2199366. [PMID: 37177979 PMCID: PMC10184583 DOI: 10.1080/07853890.2023.2199366] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 12/17/2022] [Accepted: 03/31/2023] [Indexed: 05/15/2023] Open
Abstract
BACKGROUND Chemoradiation therapy (CRT) is the standard of care for squamous cell carcinoma of the anus (SCCA), the most common type of anal cancer. However, approximately one fourth of patients still relapse after CRT. METHODS We used RNA-sequencing technology to characterize coding and non-coding transcripts in tumor tissues from CRT-treated SCCA patients and compare them between 9 non-recurrent and 3 recurrent cases. RNA was extracted from FFPE tissues. Library preparations for RNA-sequencing were created using SMARTer Stranded Total RNA-Seq Kit. All libraries were pooled and sequenced on a NovaSeq 6000. Function and pathway enrichment analysis was performed with Metascape and enrichment of gene ontology (GO) was performed with Gene Set Enrichment Analysis (GSEA). RESULTS There were 449 differentially expressed genes (DEGs) observed (390 mRNA, 12 miRNA, 17 lincRNA and 18 snRNA) between the two groups. We identified a core of upregulated genes (IL4, CD40LG, ICAM2, HLA-I (HLA-A, HLA-C) and HLA-II (HLA-DQA1, HLA-DRB5) in the non-recurrent SCCA tissue enriching to the gene ontology term 'allograft rejection', which suggests a CD4+ T cell driven immune response. Conversely, in the recurrent tissues, keratin (KRT1, 10, 12, 20) and hedgehog signaling pathway (PTCH2) genes involved in 'Epidermis Development,', were significantly upregulated. We identified miR-4316, that inhibit tumor proliferation and migration by repressing vascular endothelial growth factors, as being upregulated in non-recurrent SCCA. On the contrary, lncRNA-SOX21-AS1, implicated in the progression of many other cancers, was also found to be more common in our recurrent compared to non-recurrent SCCA. Our study identified key host factors which may drive the recurrence of SCCA and warrants further studies to understand the mechanism and evaluate their potential use in personalized treatment.Key MessageOur study used RNA sequencing (RNA-seq) to identify pivotal factors in coding and non-coding transcripts which differentiate between patients at risk for recurrent anal cancer after treatment. There were 449 differentially expressed genes (390 mRNA, 12 miRNA, 17 lincRNA and 18 snRNA) between 9 non-recurrent and 3 recurrent squamous cell carcinoma of anus (SCCA) tissues. The enrichment of genes related to allograft rejection was observed in the non-recurrent SCCA tissues, while the enrichment of genes related to epidermis development was positively linked with recurrent SCCA tissues.
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Affiliation(s)
- Yuanfan Ye
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, AL, USA
| | - Kevin J. Maroney
- Department of Medicine, Division of Infectious Diseases, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Howard W. Wiener
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, AL, USA
| | - Olga A. Mamaeva
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, AL, USA
| | - Anna D. Junkins
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, AL, USA
| | - Greer A. Burkholder
- Department of Medicine, Division of Infectious Diseases, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Staci L. Sudenga
- Division of Epidemiology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Mohd Khushman
- O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Sameer Al Diffalha
- Department of Pathology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Anju Bansal
- Department of Medicine, Division of Infectious Diseases, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Sadeep Shrestha
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, AL, USA
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Kalmatte A, Rekha PD, Ratnacaram CK. Emerging cell cycle related non-coding RNA biomarkers from saliva and blood for oral squamous cell carcinoma. Mol Biol Rep 2023; 50:9479-9496. [PMID: 37717257 DOI: 10.1007/s11033-023-08791-w] [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: 05/12/2023] [Accepted: 08/30/2023] [Indexed: 09/19/2023]
Abstract
The unnotified or undifferentiable early stages of oral squamous cell carcinoma (OSCC) progression are the prime reasons for late-stage detection and poor survival outcomes of oral cancer. This review summarizes the prior research and recent advancements on the influence of dysregulated non-coding RNA (ncRNA) on cell cycle and their employability as diagnostic and prognostic biomarkers of oral cancer. The literature search was performed using the following keywords: 'serum/saliva non-coding RNAs' and 'serum/saliva non-coding RNAs and cell cycle', 'serum/saliva dysregulated ncRNAs and cell cycle', 'Cdk/CKI and ncRNAs', 'tissue ncRNAs' concerning 'oral cancer''. The compiled data focuses mainly on the diagnostic and prognostic significance of MicroRNAs (miRNAs), Circular RNAs (circRNAs), and Long noncoding RNAs (lncRNAs) on oral cancer and all other cancers as well as subject-relevant articles published in languages other than English are beyond the scope of this review and excluded from the study. Moreover, articles focusing on DNA, protein, and metabolite markers are eliminated from the study. While there exist various potential biomolecules such as DNA, RNA, proteins, metabolites, and specific antigens representing predictive biomarkers in body fluids for oral cancer, this review completely focuses on non-coding RNAs restricted to saliva and blood, picking out a few of the reliable ones amongst the recent investigations based on the sophisticated techniques, cohort, and sensitivity as well as specificity, i.e., salivary miR-1307-5p, miR-3928, hsa_circ_0001874 and ENST00000412740, NR_131012, ENST00000588803, NR_038323, miR-21 in circulation. Thus, further studies are required to clinically confirm the usage of these non-invasive biomarkers in oral cancer.
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Affiliation(s)
- Asrarunissa Kalmatte
- Srinivas College Of Physiotherapy, City Campus, Pandeshwar, Mangaluru, Karnataka, 575001, India
- Yenepoya Research Centre, Yenepoya (Deemed to be University), University Road, Deralakatte, Mangaluru, Karnataka, 575018, India
| | - Punchappady Devasya Rekha
- Yenepoya Research Centre, Yenepoya (Deemed to be University), University Road, Deralakatte, Mangaluru, Karnataka, 575018, India
| | - Chandrahas Koumar Ratnacaram
- Yenepoya Research Centre, Yenepoya (Deemed to be University), University Road, Deralakatte, Mangaluru, Karnataka, 575018, India.
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Wang Z, Cui Y, Wang F, Xu L, Yan Y, Tong X, Yan H. DNA methylation-regulated LINC02587 inhibits ferroptosis and promotes the progression of glioma cells through the CoQ-FSP1 pathway. BMC Cancer 2023; 23:989. [PMID: 37848823 PMCID: PMC10580646 DOI: 10.1186/s12885-023-11502-0] [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: 01/02/2023] [Accepted: 10/09/2023] [Indexed: 10/19/2023] Open
Abstract
BACKGROUND Long noncoding RNAs (lncRNAs) are considered key players in the formation and development of tumors. Herein, Gene Expression Profiling Interactive Analysis (GEPIA) was employed as a bioinformatics technology. LINC02587 is differentially expressed in bladder urothelial cancer, glioblastoma, lung adenocarcinoma, lung SCC, melanoma, and other tumor tissue and cells. However, its impact on the emergence of glioma and its mechanism is remaining elusive. METHODS Some of the in vitro assays employed in this study were the CCK-8 / Annexin-V / Transwell assays, colony formation, and wound healing, together with Western blot (WB) evaluation. MSP / BSP assays were employed for assessing the CpG island's methylation status in the LINC02587 promoter. Through transcriptome, ferroptosis-related experiments, and WB evaluation, it was confirmed that LINC02587 is correlated with the regulation of ferroptosis in tumor cells, and CoQ-Fsp1 is one of its regulatory pathways. Moreover, the underlined in-vitro results were further validated by in-vivo studies. RESULTS The current study shows that the promoter sequence of LINC02587 is regulated by methylation. The silencing of LINC02587 can inhibit cellular proliferative, migrative, and invasive properties, and induce ferroptosis within gliomas through the CoQ-FSP1 pathway. CONCLUSIONS LINC02587 is likely to be a novel drug target in treating glioma.
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Affiliation(s)
- Zhengang Wang
- Clinical College of Neurology, Neurosurgery and Neurorehabilitation, Tianjin Medical University, Tianjin, 300350, China
- Department of Neurosurgery, Affiliated Hospital of Weifang Medical University, Weifang, Shan Dong, 261000, China
| | - Yang Cui
- Clinical College of Neurology, Neurosurgery and Neurorehabilitation, Tianjin Medical University, Tianjin, 300350, China
- Department of Neurosurgery, Hebei Yanda Hospital, Langfang, He Bei, China
| | - Fanchen Wang
- Clinical College of Neurology, Neurosurgery and Neurorehabilitation, Tianjin Medical University, Tianjin, 300350, China
- Cancer Molecular Diagnostics Core, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Lixia Xu
- Clinical College of Neurology, Neurosurgery and Neurorehabilitation, Tianjin Medical University, Tianjin, 300350, China
- Tianjin Key Laboratory of Cerebral Vascular and Neurodegenerative Diseases, Tianjin Neurosurgical Institute, Tianjin Huanhu Hospital, Tianjin, 300350, China
| | - Yan Yan
- Clinical College of Neurology, Neurosurgery and Neurorehabilitation, Tianjin Medical University, Tianjin, 300350, China.
- Clinical Laboratory, Tianjin Huanhu Hospital, Tianjin, 300350, China.
| | - Xiaoguang Tong
- Clinical College of Neurology, Neurosurgery and Neurorehabilitation, Tianjin Medical University, Tianjin, 300350, China.
- Tianjin Key Laboratory of Cerebral Vascular and Neurodegenerative Diseases, Tianjin Neurosurgical Institute, Tianjin Huanhu Hospital, Tianjin, 300350, China.
- Department of Neurosurgery, Tianjin Huanhu Hospital, Tianjin, 300350, China.
| | - Hua Yan
- Clinical College of Neurology, Neurosurgery and Neurorehabilitation, Tianjin Medical University, Tianjin, 300350, China.
- Tianjin Key Laboratory of Cerebral Vascular and Neurodegenerative Diseases, Tianjin Neurosurgical Institute, Tianjin Huanhu Hospital, Tianjin, 300350, China.
- Department of Neurosurgery, Tianjin Huanhu Hospital, Tianjin, 300350, China.
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Lei L, Peng G, Luo H, Li W. SRY-box transcription factor 21 antisense divergent transcript 1: Regulatory roles and clinical significance in neoplastic conditions and Alzheimer's Disease. J Cancer 2023; 14:3258-3274. [PMID: 37928430 PMCID: PMC10622988 DOI: 10.7150/jca.89619] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 09/24/2023] [Indexed: 11/07/2023] Open
Abstract
SRY-box transcription factor 21 antisense divergent transcript 1 (SOX21-AS1) is a multifaceted long non-coding RNA (lncRNA) that plays diverse roles in both neoplastic conditions and Alzheimer's disease. Its aberrant expression intricately regulates a wide spectrum of cellular processes, spanning from epithelial-mesenchymal transition (EMT), apoptosis, migration, metastasis, and stemness to drug resistance. SOX21-AS1 achieves these effects through its involvement in the competitive endogenous RNA (ceRNA) network, modulation of downstream genes, and regulation of critical pathways, including PI3K/AKT, Hippo, Wnt/β-catenin, and ERK signaling. Of significant clinical relevance, SOX21-AS1 expression has shown robust correlations with various clinical-pathological features. Moreover, it has demonstrated promising prognostic and diagnostic potential across a spectrum of tumors, as evidenced by existing literature and TCGA pan-cancer analyses. In Alzheimer's disease, SOX21-AS1 assumes a distinctive role. It influences neuronal viability, apoptosis, and oxidative stress by interacting with miR-107 and miR-132, and affecting the PI3K/AKT and Wnt signaling pathways. This comprehensive review sheds light on the functions of SOX21-AS1 and the regulated mechanisms underpinning its impact on neoplastic conditions and Alzheimer's disease. It underscores the clinical significance of SOX21-AS1 and positions it as a promising therapeutic target in both the oncological and neurodegenerative domains.
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Affiliation(s)
- Ling Lei
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang 330008, Jiangxi, China
- Department Prevention and Treatment Center, Jiujiang Hospital of Traditional Chinese Medicine, Jiujiang 332005, Jiangxi, China
| | - Guangxi Peng
- Wart 1 of General Surgery, Yingtan People's Hospital, Yingtan 335000, Jiangxi, China
| | - Hongliang Luo
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang 330008, Jiangxi, China
| | - Wugen Li
- Department of Radiology, The Second Affiliated Hospital of Nanchang University, Nanchang 330008, Jiangxi, China
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Stevanovic M, Kovacevic-Grujicic N, Petrovic I, Drakulic D, Milivojevic M, Mojsin M. Crosstalk between SOX Genes and Long Non-Coding RNAs in Glioblastoma. Int J Mol Sci 2023; 24:ijms24076392. [PMID: 37047365 PMCID: PMC10094781 DOI: 10.3390/ijms24076392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/17/2023] [Accepted: 03/23/2023] [Indexed: 03/31/2023] Open
Abstract
Glioblastoma (GBM) continues to be the most devastating primary brain malignancy. Despite significant advancements in understanding basic GBM biology and enormous efforts in developing new therapeutic approaches, the prognosis for most GBM patients remains poor with a median survival time of 15 months. Recently, the interplay between the SOX (SRY-related HMG-box) genes and lncRNAs (long non-coding RNAs) has become the focus of GBM research. Both classes of molecules have an aberrant expression in GBM and play essential roles in tumor initiation, progression, therapy resistance, and recurrence. In GBM, SOX and lncRNAs crosstalk through numerous functional axes, some of which are part of the complex transcriptional and epigenetic regulatory mechanisms. This review provides a systematic summary of current literature data on the complex interplay between SOX genes and lncRNAs and represents an effort to underscore the effects of SOX/lncRNA crosstalk on the malignant properties of GBM cells. Furthermore, we highlight the significance of this crosstalk in searching for new biomarkers and therapeutic approaches in GBM treatment.
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Lin CH, Li SC, Lin MH, Ho CJ, Lu YT, Lin Y, Lin PH, Tsai KW, Tsai MH. S100A6 participates in initiation of autoimmune encephalitis and is under epigenetic control. Brain Behav 2023; 13:e2897. [PMID: 36748983 PMCID: PMC10013942 DOI: 10.1002/brb3.2897] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 12/15/2022] [Accepted: 01/11/2023] [Indexed: 02/08/2023] Open
Abstract
INTRODUCTION Autoimmune encephalitis (AE) is caused by autoantibodies attacking neuronal cell surface antigens and/or synaptic antigens. We previously demonstrated that S100A6 was hypomethylated in patients with AE and that it promoted B lymphocyte infiltration through the simulated blood-brain barrier (BBB). In this study, we focused on the epigenetic regulation of S100A6, the process by which S100A6 affects B lymphocyte infiltration, and the therapeutic potential of S100A6 antibodies. METHODS We enrolled and collected serum from 10 patients with AE and 10 healthy control (HC) subjects. Promoter methylation and 5-azacytidine treatment assays were conducted to observe the methylation process of S100A6. The effect of S100A6 on B lymphocytes was analyzed using an adhesion assay and leukocyte transendothelial migration (LTEM) assay. A LTEM assay was also used to compare the effects of the serum of HCs, serum of AE patients, S100A6 recombinant protein, and S100A6 antibodies on B lymphocytes. RESULT The promoter methylation and 5-azacytidine treatment assays confirmed that S100A6 was regulated by DNA methylation. The adhesion study demonstrated that the addition of S100A6 enhanced adhesion between B lymphocytes and a BBB endothelial cell line in a concentration-dependent manner. The LTEM assay showed that the serum of AE patients, as well as S100A6, promoted B lymphocyte infiltration and that this effect could be attenuated by S100A6 antibodies. CONCLUSION We clarified that S100A6 was under epigenetic regulation in patients with AE and that it helped B lymphocytes to adhere to and infiltrate the BBB endothelial layer, which could be counteracted by S100A6 antibodies. Therefore, the methylation profile of S100A6 could be a marker of the activity of AE, and countering the effect of S100A6 may be a potential treatment target for AE.
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Affiliation(s)
- Chih-Hsiang Lin
- Department of Neurology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Sung-Chou Li
- Genomics and Proteomics Core Laboratory, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Ming-Hong Lin
- Department of Microbiology and Immunology, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Research Center for Environmental Medicine, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chen-Jui Ho
- Department of Neurology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Yan-Ting Lu
- Department of Neurology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Yuyu Lin
- Genomics and Proteomics Core Laboratory, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Pei-Hsien Lin
- Genomics and Proteomics Core Laboratory, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Kuo-Wang Tsai
- Department of Research, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei, Taiwan
| | - Meng-Han Tsai
- Department of Neurology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Genomics and Proteomics Core Laboratory, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Medical School, College of Medicine, Chang Gung University, Taoyuan, Taiwan
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12
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Stabenau KA, Samuels TL, Lam TK, Mathison AJ, Wells C, Altman KW, Battle MA, Johnston N. Pepsinogen/Proton Pump Co-Expression in Barrett's Esophageal Cells Induces Cancer-Associated Changes. Laryngoscope 2023; 133:59-69. [PMID: 35315085 DOI: 10.1002/lary.30109] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 02/27/2022] [Accepted: 03/04/2022] [Indexed: 02/02/2023]
Abstract
EDUCATIONAL OBJECTIVE At the conclusion of this presentation, participants should better understand the carcinogenic potential of pepsin and proton pump expression in Barrett's esophagus. OBJECTIVE Barrett's esophagus (BE) is a well-known risk factor for esophageal adenocarcinoma (EAC). Gastric H+ /K+ ATPase proton pump and pepsin expression has been demonstrated in some cases of BE; however, the contribution of local pepsin and proton pump expression to carcinogenesis is unknown. In this study, RNA sequencing was used to examine global transcriptomic changes in a BE cell line ectopically expressing pepsinogen and/or gastric H+ /K+ ATPase proton pumps. STUDY DESIGN In vitro translational. METHODS BAR-T, a human BE cell line devoid of expression of pepsinogen or proton pumps, was transduced by lentivirus-encoding pepsinogen (PGA5) and/or gastric proton pump subunits (ATP4A, ATP4B). Changes relative to the parental line were assessed by RNA sequencing. RESULTS Top canonical pathways associated with protein-coding genes differentially expressed in pepsinogen and/or proton pump expressing BAR-T cells included those involved in the tumor microenvironment and epithelial-mesenchymal transition. Top upstream regulators of coding transcripts included TGFB1 and ERBB2, which are associated with the pathogenesis and prognosis of BE and EAC. Top upstream regulators of noncoding transcripts included p300-CBP, I-BET-151, and CD93, which have previously described associations with EAC or carcinogenesis. The top associated disease of both coding and noncoding transcripts was cancer. CONCLUSIONS These data support the carcinogenic potential of pepsin and proton pump expression in BE and reveal molecular pathways affected by their expression. Further study is warranted to investigate the role of these pathways in carcinogenesis associated with BE. LEVEL OF EVIDENCE NA Laryngoscope, 133:59-69, 2023.
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Affiliation(s)
- Kaleigh A Stabenau
- Department of Otolaryngology and Communication Sciences, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Tina L Samuels
- Department of Otolaryngology and Communication Sciences, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Tina K Lam
- Department of Otolaryngology and Communication Sciences, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Angela J Mathison
- Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Clive Wells
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Kenneth W Altman
- Department of Otolaryngology, Geisinger Health System, Danville, California, USA
| | - Michele A Battle
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Nikki Johnston
- Department of Otolaryngology and Communication Sciences, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
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13
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Hao Y, Xie B, Fu X, Xu R, Yang Y. New Insights into lncRNAs in Aβ Cascade Hypothesis of Alzheimer's Disease. Biomolecules 2022; 12:biom12121802. [PMID: 36551230 PMCID: PMC9775548 DOI: 10.3390/biom12121802] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/24/2022] [Accepted: 11/29/2022] [Indexed: 12/04/2022] Open
Abstract
Alzheimer's disease (AD) is the most common type of dementia, but its pathogenesis is not fully understood, and effective drugs to treat or reverse the progression of the disease are lacking. Long noncoding RNAs (lncRNAs) are abnormally expressed and deregulated in AD and are closely related to the occurrence and development of AD. In addition, the high tissue specificity and spatiotemporal specificity make lncRNAs particularly attractive as diagnostic biomarkers and specific therapeutic targets. Therefore, an in-depth understanding of the regulatory mechanisms of lncRNAs in AD is essential for developing new treatment strategies. In this review, we discuss the unique regulatory functions of lncRNAs in AD, ranging from Aβ production to clearance, with a focus on their interaction with critical molecules. Additionally, we highlight the advantages and challenges of using lncRNAs as biomarkers for diagnosis or therapeutic targets in AD and present future perspectives in clinical practice.
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Affiliation(s)
- Yitong Hao
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Changchun 130021, China
| | - Bo Xie
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Changchun 130021, China
| | - Xiaoshu Fu
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Changchun 130021, China
| | - Rong Xu
- Department of Hepatobiliary and Pancreatic Surgery, The First Hospital of Jilin University, Changchun 130021, China
| | - Yu Yang
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Changchun 130021, China
- Correspondence:
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14
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Circulating Long Non-Coding RNAs Could Be the Potential Prognostic Biomarker for Liquid Biopsy for the Clinical Management of Oral Squamous Cell Carcinoma. Cancers (Basel) 2022; 14:cancers14225590. [PMID: 36428681 PMCID: PMC9688117 DOI: 10.3390/cancers14225590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/29/2022] [Accepted: 08/30/2022] [Indexed: 11/16/2022] Open
Abstract
Long non-coding RNA (lncRNA) have little or no coding potential. These transcripts are longer than 200 nucleotides. Since lncRNAs are master regulators of almost all biological processes, recent evidence proves that aberrantly expressed lncRNAs are pathogenic for oral squamous cell carcinoma (OSCC) and other diseases. LncRNAs influence chromatin modifications, transcriptional modifications, post-transcriptional modifications, genomic imprinting, cell proliferation, invasion, metastasis, and apoptosis. Consequently, they have an impact on the disease transformation, progression, and morbidity in OSCC. Therefore, circulating lncRNAs could be the potential cancer biomarker for the better clinical management (diagnosis, prognosis, and monitoring) of OSCC to provide advanced treatment strategies and clinical decisions. In this review, we report and discuss the recent understandings and perceptions of dysregulated lncRNAs with a focus on their clinical significance in OSCC-disease monitoring and treatment. Evidence clearly indicates that a specific lncRNA expression signature could act as an indicator for the early prediction of diagnosis and prognosis for the initiation, progression, recurrence, metastasis and other clinical prognostic-factors (overall survival, disease-free survival, etc.) in OSCC. The present review demonstrates the current knowledge that all potential lncRNA expression signatures are molecular biomarkers for the early prediction of prognosis in OSCC. Finally, the review provides information about the clinical significance, challenges and limitations of the clinical usage of circulating lncRNAs in a liquid biopsy method in early, pre-symptomatic, sub-clinical, accurate OSCC prognostication. More studies on lncRNA are required to unveil the biology of the inherent mechanisms involved in the process of the development of differential prognostic outcomes in OSCC.
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15
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Yu D, Zhao Z, Wang L, Qiao S, Yang Z, Wen Q, Zhu G. SOX21-AS1 activated by STAT6 promotes pancreatic cancer progression via up-regulation of SOX21. J Transl Med 2022; 20:511. [PMID: 36335356 PMCID: PMC9636668 DOI: 10.1186/s12967-022-03521-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 07/08/2022] [Indexed: 11/06/2022] Open
Abstract
Background Pancreatic cancer (PC) is a highly malignant tumor which threatens human’s health. Long non-coding RNAs (lncRNAs) are implicated in many cancers, including PC, but their mechanisms in PC have not yet been entirely clarified. We focused on revealing the potential function of lncRNA SOX21-AS1 in PC. Methods Functional assays assessed SOX21-AS1 function on PC progression. Bioinformatics analysis, along with mechanism assays were taken to unmask the regulatory mechanism SOX21-AS1 may exert in PC cells. Results SOX21-AS1 possessed a high expression level in PC cells. SOX21-AS1 absence suppressed PC cell proliferation, migration, stemness and epithelial-mesenchymal transition (EMT) while elevated cell apoptosis. SOX21-AS1 positively regulated its nearby gene SRY-box transcription factor 21 (SOX21) at post-transcriptional level. Through mechanism assays, we uncovered that SOX21-AS1 sponged SOX21-AS1 to elevate SOX21 mRNA and recruited ubiquitin-specific peptidase 10 (USP10) to deubiquitinate and stabilize SOX21 protein. Moreover, signal transducer and activator of transcription 6 (STAT6) could transcriptionally activate SOX21-AS1 and SOX21 expression. Conclusions SOX21-AS1 aggravated the malignant development of PC, which might provide the utility value for PC treatment. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-022-03521-5.
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16
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Prognostic Role of Long Noncoding RNAs in Oral Squamous Cell Carcinoma: A Meta-Analysis. DISEASE MARKERS 2022; 2021:6407528. [PMID: 34987674 PMCID: PMC8720611 DOI: 10.1155/2021/6407528] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 10/08/2021] [Accepted: 12/01/2021] [Indexed: 12/12/2022]
Abstract
Long noncoding RNAs (lncRNAs) have emerged as critical regulators of tumor progression, and lncRNA expression levels could serve as a potential molecular biomarker for the prognosis and diagnosis of some cancers. However, the prognostic value of lncRNAs in oral squamous cell carcinoma (OSCC) remains unclear. Thus, a meta-analysis was conducted to explore the potential prognostic value of lncRNAs in OSCC. We systematically searched PubMed, EBSCO, Web of Science, and Elsevier from 2005 to 2021 to identify all published studies that reported the association between lncRNAs and prognosis in OSCC. Then, we used meta-analytic methods to identify the actual effect size of lncRNAs on cancer prognosis. The hazard ratios (HRs) with 95% confidence intervals (95% CIs) were calculated to assess the strength of the association. The reliability of those results was then examined using measures of heterogeneity and testing for selective reporting biases. According to the inclusion and exclusion criteria, a total of 17 studies were eligible in our meta-analysis, involving 1384 Asian patients. The results identified a statistically significant association of high lncRNA expression with poor overall survival [adjusted pooled hazard ratio (AHR) = 1.52; 95% confidence interval (CI): [1.26–1.84], p ≤ 0.001]. The present meta-analysis demonstrated that lncRNA expression might be used as a predictive prognostic biomarker for Asian patients with OSCC.
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17
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Liu Y, Chen X, Che Y, Li H, Zhang Z, Peng W, Yang J. LncRNAs as the Regulators of Brain Function and Therapeutic Targets for Alzheimer’s Disease. Aging Dis 2022; 13:837-851. [PMID: 35656102 PMCID: PMC9116922 DOI: 10.14336/ad.2021.1119] [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: 10/14/2021] [Accepted: 11/19/2021] [Indexed: 11/13/2022] Open
Abstract
Alzheimer’s disease (AD) is the most common type of dementia and a serious threat to the health and safety of the elderly population. It has become an emerging public health problem and a major economic and social burden. However, there is currently no effective treatment for AD. Although the mechanism of AD pathogenesis has been investigated substantially, the full range of molecular factors that contribute to its development remain largely unclear. In recent years, accumulating evidence has revealed that long non-coding RNAs (lncRNAs), a type of non-coding RNA longer than 200 nucleotides, play important roles in multiple biological processes involved in AD pathogenesis. With the further exploration of genomics, the role of lncRNA in the pathogenesis of AD has been phenotypically or mechanistically studied. Herein, we systematically review the current knowledge about lncRNAs implicated in AD and elaborate on their main regulatory pathways, which may contribute to the discovery of novel therapeutic targets and drugs for AD.
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Affiliation(s)
- Yuqing Liu
- Department of Integrated Traditional Chinese & Western Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China.
- Xiangya School of Medicine, Central South University, Changsha, Hunan, China.
| | - Xin Chen
- Department of Integrated Traditional Chinese & Western Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China.
| | - Yutong Che
- Xiangya School of Medicine, Central South University, Changsha, Hunan, China.
| | - Hongli Li
- Department of Integrated Traditional Chinese & Western Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China.
| | - Zheyu Zhang
- Department of Integrated Traditional Chinese & Western Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China.
| | - Weijun Peng
- Department of Integrated Traditional Chinese & Western Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China.
- Inter-disciplinary Research Center of Language Intelligence and Cultural Heritages, Hunan University, Changsha, Hunan, China.
- Correspondence should be addressed to: Dr. Weijun Peng (E-mail: ) and Ms. Jingjing Yang (), Department of Integrated Traditional Chinese & Western Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Jingjing Yang
- Teaching and Research Section of Clinical Nursing, Xiangya Hospital, Central South University, Changsha, China.
- Xiangya Nursing School, Central South University, Changsha, China.
- Correspondence should be addressed to: Dr. Weijun Peng (E-mail: ) and Ms. Jingjing Yang (), Department of Integrated Traditional Chinese & Western Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
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18
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Yu W, Ma Y, Hou W, Wang F, Cheng W, Qiu F, Wu P, Zhang G. Identification of Immune-Related lncRNA Prognostic Signature and Molecular Subtypes for Glioblastoma. Front Immunol 2021; 12:706936. [PMID: 34899682 PMCID: PMC8657607 DOI: 10.3389/fimmu.2021.706936] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 10/25/2021] [Indexed: 12/04/2022] Open
Abstract
Background Glioblastoma multiforme (GBM) is extensively genetically and transcriptionally heterogeneous, which poses challenges for classification and management. Long noncoding RNAs (lncRNAs) play a critical role in the development and progression of GBM, especially in tumor-associated immune processes. Therefore, it is necessary to develop an immune-related lncRNAs (irlncRNAs) signature. Methods Univariate and multivariate Cox regression analyses were utilized to construct a prognostic model. GBM-specific CeRNA and PPI network was constructed to predict lncRNAs targets and evaluate the interactions of immune mRNAs translated proteins. GO and KEGG pathway analyses were used to show the biological functions and pathways of CeRNA network-related immunity genes. Consensus Cluster Plus analysis was used for GBM gene clustering. Then, we evaluated GBM subtype-specific prognostic values, clinical characteristics, genes and pathways, immune infiltration access single cell RNA-seq data, and chemotherapeutics efficacy. The hub genes were finally validated. Results A total of 17 prognostically related irlncRNAs were screened to build a prognostic model signature based on six key irlncRNAs. Based on GBM-specific CeRNAs and enrichment analysis, PLAU was predicted as a target of lncRNA-H19 and mainly enriched in the malignant related pathways. GBM subtype-A displayed the most favorable prognosis, high proportion of genes (IDH1, ATRX, and EGFR) mutation, chemoradiotherapy, and low risk and was characterized by low expression of four high-risk lncRNAs (H19, HOTAIRM1, AGAP2-AS1, and AC002456.1) and one mRNA KRT8. GSs with poor survival were mainly infiltrated by mesenchymal stem cells (MSCs) and astrocyte, and were more sensitive to gefitinib and roscovitine. Among GSs, three hub genes KRT8, NGFR, and TCEA3, were screened and validated to potentially play feasible oncogenic roles in GBM. Conclusion Construction of lncRNAs risk model and identification of GBM subtypes based on 17 irlncRNAs, which suggesting that irlncRNAs had the promising potential for clinical immunotherapy of GBM.
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Affiliation(s)
- Wanli Yu
- Department of Neurosurgery, Gaoxin Hospital of The First Affiliated Hospital of Nanchang University, Nanchang, China.,Department of Neurosurgery, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Yanan Ma
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Wenbin Hou
- Department of Urology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Fang Wang
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Wan Cheng
- The Laboratory of Artificial Intelligence and Bigdata in Ophthalmology, The Affiliated Eye Hospital of Nanjing Medical University, Nanjing, China
| | - Feng Qiu
- Oncology Department, Gaoxin Hospital of The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Pengfei Wu
- Department of Neurosurgery, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.,Anhui Provincial Stereotactic Neurosurgical Institute, Hefei, China.,Anhui Province Key Laboratory of Brain Function and Brain Disease, Hefei, China.,Anhui Provincial Clinical Research Center for Neurosurgical Disease, Hefei, China
| | - Guohua Zhang
- Central Laboratory, Gaoxin Hospital of The First Affiliated Hospital of Nanchang University, Nanchang, China
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Wang F, Gu T, Chen Y, Chen Y, Xiong D, Zhu Y. Long non-coding RNA SOX21-AS1 modulates lung cancer progress upon microRNA miR-24-3p/PIM2 axis. Bioengineered 2021; 12:6724-6737. [PMID: 34511042 PMCID: PMC8806559 DOI: 10.1080/21655979.2021.1955578] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Lung cancer is a lethal cancer that threatens human health. Several studies have demonstrated the role of long non-coding RNAs (lncRNAs) in lung cancer. SOX21-AS1 is a newly discovered oncogenic lncRNA, but its molecular mechanism in lung cancer is not known. Here, the levels of SOX21-AS1, miR-24-3p, and PIM2 were examined in lung cancer and normal tissues. The relationships between miR-24-3p and SOX21-AS1 or PIM2 were predicted using bioinformatics tools and confirmed using a luciferase reporter assays. Colony formation, MTT, flow cytometry, and transwell assays were conducted to analyze cell proliferation, apoptosis, migration, and invasion abilities, respectively. Western blotting was used to measure PIM2 expression levels in cancer tissues and cells. SOX21-AS1 expression levels were high in lung cancer tissues and cells. In contrast, the amount of miR-24-3p bound to SOX21-AS1 was relatively low in cancerous tissues and cells. The knockdown of SOX21-AS1 decreased cell proliferation, activated apoptosis, and promoted cell migration and invasion. These effects were abolished by miR-24-3p inhibition. The oncogenic function of SOX21-AS1 mediated through targeting miR-24-3p was also demonstrated in animal models. PIM2 was targeted by miR-24-3p and showed increased levels in tumor tissues and cells. Furthermore, miR-24-3p overexpression inhibited the proliferation and promoted the apoptosis of lung cancer cells. In lung cancer cells, SOX21-AS1 negatively modulated the miR-24-3p/PIM2 axis to facilitate their proliferation, migration, and invasion. These findings offer a novel idea for future research on treating lung cancer at the molecular level.
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Affiliation(s)
- Fengfeng Wang
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Soochow University, Suzhou, China.,Department of Respiration, People's Hospital of Jingjiang, Jingjiang, Jiangsu, China
| | - Tengfei Gu
- Department of Anesthesiology, People's Hospital of Lianshui County, Lianshui, Jiangsu, China
| | - Yao Chen
- Department of Respiration, People's Hospital of Jingjiang, Jingjiang, Jiangsu, China
| | - Yu Chen
- Department of Respiration, People's Hospital of Jingjiang, Jingjiang, Jiangsu, China
| | - Dan Xiong
- Department of Respiration, People's Hospital of Jingjiang, Jingjiang, Jiangsu, China
| | - Yehan Zhu
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Soochow University, Suzhou, China
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Wang J, Yang L, Li Y, Wang XB, Yang W, Liu F, Wu XB. Aberrant hypermethylation induced downregulation of antisense lncRNA STXBP5-AS1 and its sense gene STXBP5 correlate with tumorigenesis of glioma. Life Sci 2021; 278:119590. [PMID: 33965377 DOI: 10.1016/j.lfs.2021.119590] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 03/29/2021] [Accepted: 03/30/2021] [Indexed: 10/21/2022]
Abstract
AIMS The expression of antisense lncRNA STXBP5-AS1 and its sense gene STXBP5 were found to be downregulated in glioma by RNA sequencing; however, the function and mechanism of both two genes in the development of glioma have not been studied. MATERIALS AND METHODS QRT-PCR and western blot were used to determine the transcriptional and translational levels of moleculars. MSP and BSP assays were used to evaluate the methylation status of promoter CpG island. MTT, EdU, flow cytometry, and transwell assays were used to reveal biological effects. The in vivo mice model was used to validate the role of target genes in tumorigenesis. KEY FINDINGS The mRNA and protein expression of STXBP5 was significantly downregulated in glioma tissues and positively correlated with prognosis. STXBP5-AS1 was downregulated in glioma cells and tissues, and associated with tumor size and clinical stages. Both of two genes were significantly restored in cells treatment with 5-Aza. The promoter CpG island of STXBP5/STXBP5-AS1 was hypermethylated in glioma cells, but partially methylated in NHA cells. We found that promoter methylation frequency was significantly higher in glioma tissues. Functionally, overexpression of STXBP5 and STXBP5-AS1 inhibited cell proliferation, migration, and invasion and promoted apoptosis in vitro, whereas depletion of STXBP5 and STXBP5-AS1 showed opposite effects. Both the mRNA and protein expression of STXBP5 were positively regulated by STXBP5-AS1. Ectopic expression of STXBP5 and STXBP5-AS1 suppressed tumor formation in vivo. SIGNIFICANCE Our findings suggested that epigenetically silenced STXBP5-AS1 and STXBP5 might act as novel tumor suppressors of glioma.
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Affiliation(s)
- Jing Wang
- Department of Laboratory Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250000, China
| | - Lei Yang
- Department of Medical Engineering, Shandong Provincial Hospital Affiliated to Shandong First Medical University; Jinan, Shandong 250000, China
| | - Yuan Li
- Department of Laboratory Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250000, China
| | - Xing-Bang Wang
- Department of Neurology, Qilu Hospital of Shandong University, Jinan, Shandong 250000, China
| | - Wei Yang
- Department of Neurological Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250000, China
| | - Fang Liu
- Department of Laboratory Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250000, China
| | - Xiao-Ben Wu
- Department of Laboratory Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250000, China.
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Gu F, Ji D, Ni H, Chen D. SRY-Box 21 Antisense RNA 1 Knockdown Diminishes Amyloid Beta 25-35-Induced Neuronal Damage by miR-132/PI3K/AKT Pathway. Neurochem Res 2021; 46:2376-2386. [PMID: 34146195 DOI: 10.1007/s11064-021-03373-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 06/04/2021] [Accepted: 06/07/2021] [Indexed: 12/12/2022]
Abstract
Our study aimed to explore the function and mechanism of action of long noncoding RNA (lncRNA) SRY-Box 21 antisense RNA 1 (SOX21-AS1) in amyloid beta25-35 (Aβ25-35)-induced neuronal damage. To induce neuronal damage, neuronal cells and differentiated IMR-32 neuroblastoma cells were challenged by Aβ25-35. SOX21-AS1 and miR-132 quantities were detected by quantitative reverse transcription polymerase chain reaction. Cell damage was evaluated by detecting the changes of cell viability, apoptosis, and oxidative stress. Cell viability was measured using cell counting kit-8. Cell apoptosis was evaluated by flow cytometry and caspase-3 activity. The oxidative stress was analyzed by reactive oxygen species level. The expression of proteins associated with the phosphoinositide 3-kinase (PI3K)/protein kinase B (AKT) pathway was examined by western blot. SOX21-AS1 abundance was up-regulated in Aβ25-35-challenged neuronal cells. Silencing of SOX21-AS1 attenuated Aβ25-35-induced viability reduction and promotion of apoptosis and oxidative stress, suggesting that silencing of SOX21-AS1 repressed Aβ25-35-induced neuronal damage. miR-132 quantity was reduced in Aβ25-35-challenged neuronal cells, and negatively controlled by SOX21-AS1. miR-132 knockdown abolished the effect of SOX21-AS1 silencing on Aβ25-35-induced neuronal damage, indicating that SOX21-AS1 controls Aβ25-35-induced neuronal damage via regulating miR-132. The PI3K/AKT signaling was repressed in Aβ25-35-challenged cells, but this effect was counteracted upon overexpression of miR-132. In conclusion, SOX21-AS1 knockdown mitigated Aβ25-35-dependent neuronal cell damage by promoting miR-132/PI3K/AKT pathway.
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Affiliation(s)
- Fengming Gu
- Department of Intensive Care Unit, The Affiliated Huai'an Hospital of Xuzhou Medical University, The Second People's Hospital of Huai'an, Huai'an, 223002, China
| | - Daofei Ji
- Department of Neurosurgery, The Second Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221006, China
| | - Hongzao Ni
- Department of Neurosurgery, The Affiliated Huai'an Hospital of Xuzhou Medical University, The Second People's Hospital of Huai'an, Huai'an, 223002, China
| | - Depeng Chen
- Department of Intensive Care Unit, People's Hospital of Huai'an Hongze District, 102 Dongfeng Road, Huai'an, 223100, China.
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22
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Huang L, Yu X, Jiang Z, Zeng P. Novel Autophagy-Related Gene Signature Investigation for Patients With Oral Squamous Cell Carcinoma. Front Genet 2021; 12:673319. [PMID: 34220946 PMCID: PMC8248343 DOI: 10.3389/fgene.2021.673319] [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: 02/27/2021] [Accepted: 05/26/2021] [Indexed: 12/26/2022] Open
Abstract
The correlation between autophagy defects and oral squamous cell carcinoma (OSCC) has been previously studied, but only based on a limited number of autophagy-related genes in cell lines or animal models. The aim of the present study was to analyze differentially expressed autophagy-related genes through The Cancer Genome Atlas (TCGA) database to explore enriched pathways and potential biological function. Based on TCGA database, a signature composed of four autophagy-related genes (CDKN2A, NKX2-3, NRG3, and FADD) was established by using multivariate Cox regression models and two Gene Expression Omnibus datasets were applied for external validation. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed to study the function of autophagy-related genes and their pathways. The most significant GO and KEGG pathways were enriched in several key pathways that were related to the progression of autophagy and OSCC. Furthermore, a prognostic risk score was constructed based on the four genes; patients were then divided into two groups (i.e., high risk and low risk) in terms of the median of risk score. Prognosis of the two groups and results showed that patients at the low-risk group had a much better prognosis than those at the high-risk group, regardless of whether they were in the training datasets or validation datasets. Multivariate Cox regression results indicated that the risk score of the autophagy-related gene signatures could greatly predict the prognosis of patients after controlling for several clinical covariates. The findings of the present study revealed that autophagy-related gene signatures play an important role in OSCC and are potential prognostic biomarkers and therapeutic targets.
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Affiliation(s)
- Lihong Huang
- Department of Biostatistics, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xinghao Yu
- Department of Biostatistics, School of Public Health, Medical College of Soochow University, Suzhou, China
| | - Zhou Jiang
- Department of Epidemiology and Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, China
| | - Ping Zeng
- Department of Epidemiology and Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, China.,Center for Medical Statistics and Data Analysis, School of Public Health, Xuzhou Medical University, Xuzhou, China
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23
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Jiang Y, Zhang X, Rong L, Hou Y, Song J, Zhang W, He M, Xie Y, Li Y, Song F. Integrative analysis of the gastric cancer long non-coding RNA-associated competing endogenous RNA network. Oncol Lett 2021; 21:456. [PMID: 33907566 PMCID: PMC8063256 DOI: 10.3892/ol.2021.12717] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 03/10/2021] [Indexed: 12/18/2022] Open
Abstract
Gastric cancer (GC) is a common type of cancer, and identification of novel diagnostic biomarkers associated with this disease is important. The present study aimed to identify novel diagnostic biomarkers associated with the prognosis of GC, using an integrated bioinformatics approach. Differentially expressed long non-coding RNAs (lncRNAs) associated with GC were identified using Gene Expression Omnibus datasets (GSE58828, GSE72305 and GSE99416) and The Cancer Genome Atlas database. A competing endogenous RNA network that incorporated five lncRNAs [long intergenic non-protein coding RNA 501 (LINC00501), LINC00365, SOX21 antisense divergent transcript 1 (SOX21-AS1), GK intronic transcript 1 (GK-IT1) and DLEU7 antisense RNA 1 (DLEU7-AS1)], 29 microRNAs and 114 mRNAs was constructed. Gene Ontology and protein-protein interaction network analyses revealed that these lncRNAs may be involved in 'biological regulation', 'metabolic process', 'cell communication', 'developmental process', 'cell proliferation', 'reproduction' and the 'cell cycle'. The results of receiver operating characteristic curve analysis demonstrated that LINC00501 (AUC=0.819), LINC00365 (AUC=0.580), SOX21-AS1 (AUC=0.736), GK-IT1 (AUC=0.823) and DLEU7-AS1 (AUC=0.932) had the potential to become valuable diagnostic biomarkers for GC. Associations with clinicopathological characteristics demonstrated that LINC00501 expression was significantly associated with sex (P=0.015) and tumor grade (P=0.022). Furthermore, LINC00365 expression was significantly associated with lymph node metastasis (P=0.025). Gene set enrichment analysis revealed that LINC00501, LINC00365 and SOX21-AS1 were enriched in signaling pathways associated with GC. Reverse transcription-quantitative PCR analysis demonstrated that LINC00501 expression (P=0.043) was significantly upregulated in GC tissues, whereas the expression levels of LINC00365 (P=0.033) and SOX21-AS1 (P=0.037) were significantly downregulated in GC tissues. Taken together, the results of the present study suggest that LINC00501, LINC00365, SOX21-AS1, GK-IT1 and DLEU7-AS1 may be used as novel diagnostic biomarkers for GC, and may be functionally associated with GC development and progression.
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Affiliation(s)
- Yuyou Jiang
- Basic Medical College, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Xianqin Zhang
- School of Basic Medical Sciences, Chengdu Medical College, Chengdu, Sichuan 610500, P.R. China
| | - Li Rong
- Department of Infectious Disease, Chongqing Public Health Medical Center, Chongqing 400036, P.R. China
| | - Yi Hou
- Experimental Teaching and Management Center, Chongqing Medical University, Chongqing 401331, P.R. China
| | - Jing Song
- Basic Medical College, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Wanfeng Zhang
- Department of Bioinformatics, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Min He
- Basic Medical College, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Yan Xie
- Basic Medical College, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Yue Li
- Basic Medical College, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Fangzhou Song
- Basic Medical College, Chongqing Medical University, Chongqing 400016, P.R. China
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24
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Lei CS, Kung HJ, Shih JW. Long Non-Coding RNAs as Functional Codes for Oral Cancer: Translational Potential, Progress and Promises. Int J Mol Sci 2021; 22:4903. [PMID: 34063159 PMCID: PMC8124393 DOI: 10.3390/ijms22094903] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 04/30/2021] [Accepted: 05/03/2021] [Indexed: 12/24/2022] Open
Abstract
Oral cancer is one of the leading malignant tumors worldwide. Despite the advent of multidisciplinary approaches, the overall prognosis of patients with oral cancer is poor, mainly due to late diagnosis. There is an urgent need to develop valid biomarkers for early detection and effective therapies. Long non-coding RNAs (lncRNAs) are recognized as key elements of gene regulation, with pivotal roles in various physiological and pathological processes, including cancer. Over the past few years, an exponentially growing number of lncRNAs have been identified and linked to tumorigenesis and prognosis outcomes in oral cancer, illustrating their emerging roles in oral cancer progression and the associated signaling pathways. Herein, we aim to summarize the most recent advances made concerning oral cancer-associated lncRNA, and their expression, involvement, and potential clinical impact, reported to date, with a specific focus on the lncRNA-mediated molecular regulation in oncogenic signaling cascades and oral malignant progression, while exploring their potential, and challenges, for clinical applications as biomarkers or therapeutic targets for oral cancer.
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Affiliation(s)
- Cing-Syuan Lei
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan; (C.-S.L.); (H.-J.K.)
| | - Hsing-Jien Kung
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan; (C.-S.L.); (H.-J.K.)
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan, Miaoli County 35053, Taiwan
- Comprehensive Cancer Center, Department of Biochemistry and Molecular Medicine, University of California at Davis, Sacramento, CA 95817, USA
- TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei 11031, Taiwan
| | - Jing-Wen Shih
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan; (C.-S.L.); (H.-J.K.)
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
- TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei 11031, Taiwan
- Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
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25
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Cao R, Liu S, Zhang J, Ren X, Chen X, Cheng B, Xia J. Integrative Analysis of TP53INP2 in Head and Neck Squamous Cell Carcinoma. Front Genet 2021; 12:630794. [PMID: 33897760 PMCID: PMC8062980 DOI: 10.3389/fgene.2021.630794] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 03/18/2021] [Indexed: 12/28/2022] Open
Abstract
TP53INP2 plays an important role in regulating gene transcription and starvation-induced autophagy, however, its function in head and neck squamous cell carcinoma (HNSCC) remains unclear. Therefore, we assessed the expression and prognostic value of TP53INP2. In addition, RNAseq, miRNAseq, copy number variation, and mutation profiles from The Cancer Genome Atlas (TCGA) dataset were applied to evaluate the distinctive genomic patterns related to TP53INP2 expression. We found that TP53INP2 expression was lower in HNSCC compared with normal controls. Patients with higher TP53INP2 expression had longer survival time. Knockdown of TP53INP2 promoted cell viability. Functional analysis exhibited that TP53INP2 was linked to DNA replication, DNA repair, cell cycle, and multiple metabolic pathways. Moreover, TP53INP2 might affect the expression of multiple genes via enhancing the transcriptional activity of nuclear hormone receptors. A competing endogenous RNA (ceRNA) network consisting of 33 lncRNAs, eight miRNAs, and 13 mRNAs was constructed based on the expression of TP53INP2. Taken together, our study highlights the potential value of TP53INP2 in predicting the survival of HNSCC and its important role in the genesis and development of HNSCC.
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Affiliation(s)
- Ruoyan Cao
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China.,Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Suyang Liu
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China.,Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Jiayu Zhang
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China.,Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Xianyue Ren
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China.,Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Xijuan Chen
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China.,Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Bin Cheng
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China.,Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Juan Xia
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China.,Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, China
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26
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Wang Z, Ji X, Gao L, Guo X, Lian W, Deng K, Xing B. Comprehensive In Silico Analysis of a Novel Serum Exosome-Derived Competitive Endogenous RNA Network for Constructing a Prognostic Model for Glioblastoma. Front Oncol 2021; 11:553594. [PMID: 33747903 PMCID: PMC7973265 DOI: 10.3389/fonc.2021.553594] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 02/01/2021] [Indexed: 12/12/2022] Open
Abstract
Purpose Glioblastoma (GBM) is one of the most aggressive brain tumors with high mortality, and tumor-derived exosomes provide new insight into the mechanisms of GBM tumorigenesis, metastasis and therapeutic resistance. We aimed to establish an exosome-derived competitive endogenous RNA (ceRNA) network for constructing a prognostic model for GBM. Methods We obtained the expression profiles of long noncoding RNAs (lncRNAs), miRNAs, and mRNAs from the GEO and TCGA databases and identified differentially expressed RNAs in GBM to construct a ceRNA network. By performing lasso and multivariate Cox regression analyses, we identified optimal prognosis-related differentially expressed lncRNAs (DElncRNAs) and generated a risk score model termed the exosomal lncRNA (exo-lncRNA) signature. The exo-lncRNA signature was subsequently validated in the CGGA GBM cohort. Finally, a novel prognostic nomogram was constructed based on the exo-lncRNA signature and clinicopathological parameters and validated in the CGGA external cohort. Based on the ceRNA hypothesis, oncocers were identified based on highly positive correlations between lncRNAs and mRNAs mediated by the same miRNAs. Furthermore, regression analyses were performed to assess correlations between the expression abundances of lncRNAs in tumors and exosomes. Results A total of 45 DElncRNAs, six DEmiRNAs, and 38 DEmRNAs were identified, and an exosome-derived ceRNA network was built. Three optimal prognostic-related DElncRNAs, HOTAIR (HR=0.341, P<0.001), SOX21-AS1 (HR=0.30, P<0.001), and STEAP3-AS1 (HR=2.47, P<0.001), were included to construct the exo-lncRNA signature, which was further proven to be an independent prognostic factor. The novel prognostic nomogram was constructed based on the exo-lncRNA signature, patient age, pharmacotherapy, radiotherapy, IDH mutation status, and MGMT promoter status, with a concordance index of 0.878. ROC and calibration plots both suggested that the nomogram had beneficial discrimination and predictive abilities. A total of 11 pairs of prognostic oncocers were identified. Regression analysis suggested excellent consistency of the expression abundance of the three exosomal lncRNAs between exosomes and tumor tissues. Conclusions Exosomal lncRNAs may serve as promising prognostic predictors and therapeutic targets. The prognostic nomogram based on the exo-lncRNA signature might provide an intuitive method for individualized survival prediction and facilitate better treatment strategies.
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Affiliation(s)
- Zihao Wang
- Department of Neurosurgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,China Pituitary Disease Registry Center, Chinese Pituitary Adenoma Cooperative Group, Beijing, China
| | - Xin Ji
- Department of Nuclear Medicine, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, China
| | - Lu Gao
- Department of Neurosurgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,China Pituitary Disease Registry Center, Chinese Pituitary Adenoma Cooperative Group, Beijing, China
| | - Xiaopeng Guo
- Department of Neurosurgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,China Pituitary Disease Registry Center, Chinese Pituitary Adenoma Cooperative Group, Beijing, China
| | - Wei Lian
- Department of Neurosurgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,China Pituitary Disease Registry Center, Chinese Pituitary Adenoma Cooperative Group, Beijing, China
| | - Kan Deng
- Department of Neurosurgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,China Pituitary Disease Registry Center, Chinese Pituitary Adenoma Cooperative Group, Beijing, China
| | - Bing Xing
- Department of Neurosurgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,China Pituitary Disease Registry Center, Chinese Pituitary Adenoma Cooperative Group, Beijing, China
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27
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Sheng XY, Wang CH, Wang CF, Xu HY. Long-Chain Non-Coding SOX21-AS1 Promotes Proliferation and Migration of Breast Cancer Cells Through the PI3K/AKT Signaling Pathway. Cancer Manag Res 2020; 12:11005-11014. [PMID: 33173334 PMCID: PMC7648155 DOI: 10.2147/cmar.s270464] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 09/23/2020] [Indexed: 12/18/2022] Open
Abstract
Aim This study aimed to investigate the effect of long-chain non-coding SOX21-AS1 on the proliferation and migration of breast cancer (BC) cells through the PI3K/AKT signaling pathway. Methods Eighty-eight BC and adjacent tissues were collected, and BC cells and normal breast epithelial cells were purchased. LncRNA SOX21-AS1 expression in tissues and cells was detected by RT-PCR. miR-NC, si-SOX21-AS1, and Sh-SOX21-AS1 were transfected into BC cells. The PI3K/AKT signaling pathway was interfered with L740Y-P (activator of the PI3K/AKT pathway) and LY294002 (inhibitor of the PI3K/AKT pathway) in BC cells. The SOX21-AS1 expression in BC tissues and cells was tested by qRT-PCR, and the expression levels of p-PI3K, p-AKT, N-cadherin, E-cadherin, and vimentin were detected by WB. Results SOX21-AS1 was highly expressed in BC, and the p-PI3K and p-AKT levels were also high. Cell experiments showed that inhibiting SOX21-AS1 expression could inhibit the proliferation, invasion, migration, and EMT of BC cells, and up-regulating its expression could promote the proliferation, invasion, migration, and EMT of ovarian cancer cells. The tumor-forming experiment in nude mice was consistent with the results in vitro. 740Y-P intervention could reverse the inhibition effect of Si-SOX21-AS1 on BC cell proliferation, invasion, migration, and EMT, while LY294002 intervention could reverse the promotion effect of Sh-SOX21-AS1 on BC cell proliferation, invasion, migration, and EMT. Conclusion SOX21-AS1 is highly expressed in BC tissues. Silencing BC expression can inhibit the proliferation, invasion, migration, and EMT of cells by inhibiting the PI3K/AKT signaling pathway, which may be a new target for diagnosis and treatment.
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Affiliation(s)
- Xiu-Yun Sheng
- Department of Hematology and Oncology, The Second People's Hospital of Liaocheng, Liaocheng, Shandong Province, 252600, People's Republic of China
| | - Cheng-Hong Wang
- Department of Radiotherapy, The Second People's Hospital of Liaocheng, Liaocheng 252600, Shandong Province, People's Republic of China
| | - Chun-Feng Wang
- Department of Thyroid and Breast Surgery, The Second People's Hospital of Liaocheng, Liaocheng 252600, Shandong Province, People's Republic of China
| | - Hong-Yan Xu
- Department of Oncology, The Second People's Hospital of Liaocheng, Liaocheng 252600, Shandong Province, People's Republic of China
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28
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Du P, Zhi Y, Wang R, Li Y, Li H, Zhang X, Cheng G, Li X. Aberrant Methylation of the SOX21-AS1 Promoter Region Promotes Gene Expression and Its Clinical Value in Cervical Cancer. Reprod Sci 2020; 28:532-540. [PMID: 33095426 DOI: 10.1007/s43032-020-00335-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 09/28/2020] [Indexed: 12/24/2022]
Abstract
Cervical cancer is the fourth most common female cancer worldwide. Long non-coding RNAs (lncRNAs), such as SOX21-AS1, play pivotal roles in the progression and metastasis of cancer. We previously described that SOX21-AS1 was hypomethylated in cervical cancer (CC) and aimed to further explore the relationship between methylation of the SOX21-AS1 promoter and CC using clinical cervical samples. Pyrosequencing was performed to detect the methylation status of the SOX21-AS1 promoter in 33 cervical specimens. Additionally, expression levels of related genes in 43 clinical cervical specimens were measured using quantitative real-time PCR (qRT-PCR). The SOX21-AS1 promoter was significantly hypomethylated in CC (P < 0.01). SOX21-AS1 hypomethylation was also significantly associated with an advanced Federation of Gynecology and Obstetrics (FIGO) stage (P < 0.01). The expression levels of SOX21-AS1 and SOX21 were noted to be higher in cancer vs. normal cervix (all P < 0.001). Moreover, the expression of SOX21-AS1 was positively correlated with SOX21 in all samples (r = 0.891, P < 0.001). Methylation statue of the SOX21-AS1 promoter region was negatively correlated with the expression levels of SOX21-AS1 and SOX21 (SOX21-AS1, r = - 0.628; SOX21, r = - 0.648; both P < 0.001). The methylation status of SOX21-AS1 displayed promising diagnostic potential for CC, exhibiting good sensitivity (100.0%) and specificity (69.2%), with an area under the curve of 0.846. In addition, bioinformatic analyses identified a potential link between SOX21-AS1 and the Wnt signaling pathway. Furthermore, methylation status of SOX21-AS1 was negatively correlated with β-catenin/c-myc/cyclin D1 mRNA levels (rs = - 0.529, - 0.462 ,and - 0.383, respectively, P < 0.05). Our findings illuminated that lncRNA SOX21-AS1 showed hypomethylation in cervical cancer and SOX21-AS1 could serve as a novel biomarker for CC diagnosis or a potential therapeutic target.
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Affiliation(s)
- Peipei Du
- Department of Cytopathology, The Third Affiliated Hospital of Zhengzhou University, No. 7 Front Kangfu Street, Er'qi District, Zhengzhou, 450052, China.,Department of Cytopathology, Academy of Medical Sciences of Zhengzhou University, Zhengzhou, China
| | - Yanfang Zhi
- Department of Cytopathology, The Third Affiliated Hospital of Zhengzhou University, No. 7 Front Kangfu Street, Er'qi District, Zhengzhou, 450052, China
| | - Ruijie Wang
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ya Li
- Department of Cytopathology, The Third Affiliated Hospital of Zhengzhou University, No. 7 Front Kangfu Street, Er'qi District, Zhengzhou, 450052, China
| | - Huanhuan Li
- Department of Cytopathology, The Third Affiliated Hospital of Zhengzhou University, No. 7 Front Kangfu Street, Er'qi District, Zhengzhou, 450052, China
| | - Xiaoan Zhang
- Department of Imaging, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Guomei Cheng
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiaofu Li
- Department of Cytopathology, The Third Affiliated Hospital of Zhengzhou University, No. 7 Front Kangfu Street, Er'qi District, Zhengzhou, 450052, China.
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Xavier PLP, Müller S, Fukumasu H. Epigenetic Mechanisms in Canine Cancer. Front Oncol 2020; 10:591843. [PMID: 33194754 PMCID: PMC7646326 DOI: 10.3389/fonc.2020.591843] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 10/05/2020] [Indexed: 01/18/2023] Open
Abstract
A plethora of data has highlighted the role of epigenetics in the development of cancer. Initiation and progression of different cancer types are associated with a variety of changes of epigenetic mechanisms, including aberrant DNA methylation, histone modifications, and miRNA expression. At the same time, advances in the available epigenetic tools allow to investigate and reverse these epigenetic changes and form the basis for the development of anticancer drugs in human oncology. Although human and canine cancer shares several common features, only recently that studies emerged investigating the epigenetic landscape in canine cancer and applying epigenetic modulators to canine cancer. This review focuses on the existing studies involving epigenetic changes in different types of canine cancer and the use of small-molecule inhibitors in canine cancer cells.
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Affiliation(s)
- Pedro Luiz Porfirio Xavier
- Laboratory of Comparative and Translational Oncology (LOCT), Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Brazil
| | - Susanne Müller
- Structural Genomics Consortium and Institute of Pharmaceutical Chemistry, Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe University, Frankfurt am Main, Germany
| | - Heidge Fukumasu
- Laboratory of Comparative and Translational Oncology (LOCT), Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Brazil
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30
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Li SC, Tsai KW, Huang LH, Weng KP, Chien KJ, Lin Y, Tu CY, Lin PH. Serum proteins may facilitate the identification of Kawasaki disease and promote in vitro neutrophil infiltration. Sci Rep 2020; 10:15645. [PMID: 32973234 PMCID: PMC7518260 DOI: 10.1038/s41598-020-72695-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 09/04/2020] [Indexed: 12/16/2022] Open
Abstract
Kawasaki disease (KD) usually affects the children younger than 5 years of age and subsequently causes coronary artery lesions (CALs) without timely identification and treatment. Developing a robust and fast prediction method may facilitate the timely diagnosis of KD, significantly reducing the risk of CALs in KD patients. The levels of inflammatory serum proteins dramatically vary during the onsets of many immune diseases, including in KD. However, our understanding of their pathogenic roles in KD is behind satisfaction. The purpose of this study was to evaluate candidate diagnostic serum proteins and the potential mechanism in KD using iTRAQ gel-free proteomics. We enrolled subjects and conducted iTRAQ gel-free proteomics to globally screen serum proteins followed by specific validation with ELISA. Further in vitro leukocyte trans-endothelial model was also applied to investigate the pathogenesis roles of inflammatory serum proteins. We identified six KD protein biomarkers, including Protein S100-A8 (S100A8), Protein S100-A9 (S100A9), Protein S100-A12 (S100A12), Peroxiredoxin-2 (PRDX2), Neutrophil defensin 1 (DEFA1) and Alpha-1-acid glycoprotein 1 (ORM1). They enabled us to develop a high-performance KD prediction model with an auROC value of 0.94, facilitating the timely identification of KD. Further assays concluded that recombinant S100A12 protein treatment activated neutrophil surface adhesion molecules responsible for adhesion to endothelial cells. Therefore, S100A12 promoted both freshly clinically isolated neutrophils and neutrophil-like cells to infiltrate through the endothelial layer in vitro. Finally, the antibody against S100A12 may attenuate the infiltration promoted by S100A12. Our result demonstrated that evaluating S100A8, S100A9, S100A12, PRDX2, DEFA1 and ORM1 levels may be a good diagnostic tool of KD. Further in vitro study implied that S100A12 could be a potential therapeutic target for KD.
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Affiliation(s)
- Sung-Chou Li
- Genomics and Proteomics Core Laboratory, Department of Medical Research, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Kuo-Wang Tsai
- Department of Research, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei, Taiwan
| | - Lien-Hung Huang
- Department of Neurosurgery, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Ken-Pen Weng
- Congenital Structural Heart Disease Center, Department of Pediatrics, Kaohsiung Veterans General Hospital, No.386, Dazhong 1st Rd., Zuoying Dist., Kaohsiung, Taiwan. .,Department of Medicine, National Yang-Ming University, Taipei, Taiwan. .,Shu-Zen Junior College of Medicine and Management, Kaohsiung, Taiwan.
| | - Kuang-Jen Chien
- Congenital Structural Heart Disease Center, Department of Pediatrics, Kaohsiung Veterans General Hospital, No.386, Dazhong 1st Rd., Zuoying Dist., Kaohsiung, Taiwan
| | - Yuyu Lin
- Genomics and Proteomics Core Laboratory, Department of Medical Research, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Chi-Ying Tu
- Congenital Structural Heart Disease Center, Department of Pediatrics, Kaohsiung Veterans General Hospital, No.386, Dazhong 1st Rd., Zuoying Dist., Kaohsiung, Taiwan
| | - Pei-Hsien Lin
- Genomics and Proteomics Core Laboratory, Department of Medical Research, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Kaohsiung, Taiwan
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Zhang K, Qiu W, Wu B, Fang F. Long non‑coding RNAs are novel players in oral inflammatory disorders, potentially premalignant oral epithelial lesions and oral squamous cell carcinoma (Review). Int J Mol Med 2020; 46:535-545. [PMID: 32626947 PMCID: PMC7307862 DOI: 10.3892/ijmm.2020.4628] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 05/15/2020] [Indexed: 12/14/2022] Open
Abstract
In recent years, a large number of studies have shown that the abnormal expression of long non‑coding (lnc)RNAs can lead to a variety of different diseases, including inflammatory disorders, cardiovascular disease, nervous system diseases, and cancers. Recent research has demonstrated the biological characteristics of lncRNAs and the important functions of lncRNAs in oral inflammation, precancerous lesions and cancers. The present review aims to explore and discuss the potential roles of candidate lncRNAs in oral diseases by summarizing multiple lncRNA profiles in diseased and healthy oral tissues to determine the altered lncRNA signatures. In addition, to highlight the exact regulatory mechanism of lncRNAs in oral inflammatory disorders, potentially premalignant oral epithelial lesions and oral squamous cell carcinoma. The detection of lncRNAs in oral samples has the potential to be used as a diagnostic and an early detection tool for oral diseases. Furthermore, lncRNAs are promising future therapeutic targets in oral diseases, and research in this field may expand in the future.
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Affiliation(s)
- Kaiying Zhang
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Wei Qiu
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Buling Wu
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Fuchun Fang
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
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32
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Zhu Z, Li Y, Zhou J, Zhang Y, Cao RY. Acute enterovirus infections significantly alter host cellular DNA methylation status. INFECTION GENETICS AND EVOLUTION 2020; 80:104190. [DOI: 10.1016/j.meegid.2020.104190] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 12/31/2019] [Accepted: 01/09/2020] [Indexed: 01/11/2023]
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33
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Chaudhary R, Wang X, Cao B, De La Iglesia J, Masannat J, Song F, Hernandez-Prera JC, Gimbrone NT, Slebos RJC, Chung CH. Long noncoding RNA, LINC00460, as a prognostic biomarker in head and neck squamous cell carcinoma (HNSCC). Am J Transl Res 2020; 12:684-696. [PMID: 32194915 PMCID: PMC7061833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 01/17/2020] [Indexed: 06/10/2023]
Abstract
Head and neck squamous cell carcinoma (HNSCC) is an aggressive epithelial malignancy characterized by frequent mutations and metastasis. Long noncoding RNAs (lncRNAs) have been implicated in tumorigenesis and serve as novel prognostic biomarkers in different cancers. To enhance our understanding of lncRNAs that may have biological significance in HNSCC and may serve as prognostic biomarkers, we globally profiled lncRNAs in HNSCC by analyzing the RNA-seq data from The Atlas of Noncoding RNAs in Cancer (TANRIC) database. Of 3576 lncRNAs, we identified 926 (higher-688, lower-238) lncRNAs with a 2-fold abundance difference among the forty HNSCC and paired adjacent normal tissue. We investigated differential abundance of lncRNAs based on TP53 mutation and p16 status. We found 133 lncRNAs to have differential abundance by 2-fold among the mutant vs wild-type TP53 samples, whereas among p16-negative vs positive samples, we identified 710 lncRNAs with the same criteria. Meanwhile, analysis of the 15 most abundant lncRNAs in the tumor samples identified five lncRNAs whose higher abundance was associated with poor overall patient survival. Among these five, higher abundance of LINC00460 associated with poor patient survival in an independent cohort of 82 HNSCC patients. To further evaluate the potential function of LINC00460, we performed lncRNA-mRNAs co-expression analysis and found that higher abundance of LINC00460 associated with cancer-related biological pathways including EMT and other inflammatory response pathways. In summary, we report LINC00460 is more abundant in tumors compared to adjacent normal tissue and that it may serve as a potential prognostic biomarker in HNSCC.
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Affiliation(s)
- Ritu Chaudhary
- Department of Head and Neck-Endocrine Oncology, Moffitt Cancer CenterTampa, FL, USA
| | - Xuefeng Wang
- Department of Biostatistics and Bioinformatics, Moffitt Cancer CenterTampa, FL, USA
| | - Biwei Cao
- Department of Biostatistics and Bioinformatics, Moffitt Cancer CenterTampa, FL, USA
| | - Janis De La Iglesia
- Department of Head and Neck-Endocrine Oncology, Moffitt Cancer CenterTampa, FL, USA
| | - Jude Masannat
- Department of Head and Neck-Endocrine Oncology, Moffitt Cancer CenterTampa, FL, USA
| | - Feifei Song
- Department of Head and Neck-Endocrine Oncology, Moffitt Cancer CenterTampa, FL, USA
| | | | - Nicholas T Gimbrone
- Department of Head and Neck-Endocrine Oncology, Moffitt Cancer CenterTampa, FL, USA
| | - Robbert JC Slebos
- Department of Head and Neck-Endocrine Oncology, Moffitt Cancer CenterTampa, FL, USA
| | - Christine H Chung
- Department of Head and Neck-Endocrine Oncology, Moffitt Cancer CenterTampa, FL, USA
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Ghafouri-Fard S, Mohammad-Rahimi H, Jazaeri M, Taheri M. Expression and function of long non-coding RNAs in head and neck squamous cell carcinoma. Exp Mol Pathol 2020; 112:104353. [DOI: 10.1016/j.yexmp.2019.104353] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 11/25/2019] [Accepted: 12/04/2019] [Indexed: 12/31/2022]
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35
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Guardia GDA, Correa BR, Araujo PR, Qiao M, Burns S, Penalva LOF, Galante PAF. Proneural and mesenchymal glioma stem cells display major differences in splicing and lncRNA profiles. NPJ Genom Med 2020; 5:2. [PMID: 31969990 PMCID: PMC6965107 DOI: 10.1038/s41525-019-0108-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Accepted: 11/18/2019] [Indexed: 12/12/2022] Open
Abstract
Therapy resistance and recurrence in high-grade gliomas are driven by their populations of glioma stem cells (GSCs). Thus, detailed molecular characterization of GSCs is needed to develop more effective therapies. We conducted a study to identify differences in the splicing profile and expression of long non-coding RNAs in proneural and mesenchymal GSC cell lines. Genes related to cell cycle, DNA repair, cilium assembly, and splicing showed the most differences between GSC subgroups. We also identified genes distinctly associated with survival among patients of mesenchymal or proneural subgroups. We determined that multiple long non-coding RNAs with increased expression in mesenchymal GSCs are associated with poor survival of glioblastoma patients. In summary, our study established critical differences between proneural and mesenchymal GSCs in splicing profiles and expression of long non-coding RNA. These splicing isoforms and lncRNA signatures may contribute to the uniqueness of GSC subgroups, thus contributing to cancer phenotypes and explaining differences in therapeutic responses.
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Affiliation(s)
- Gabriela D A Guardia
- 1Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, São Paulo 01309-060 Brazil
| | - Bruna R Correa
- 1Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, São Paulo 01309-060 Brazil.,4Present Address: Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, 08003 Catalonia Spain
| | - Patricia Rosa Araujo
- Children's Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229 USA
| | - Mei Qiao
- Children's Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229 USA
| | - Suzanne Burns
- Children's Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229 USA
| | - Luiz O F Penalva
- Children's Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229 USA.,Department of Cell Systems and Anatomy, UT Health San Antonio, San Antonio, TX 78229 USA
| | - Pedro A F Galante
- 1Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, São Paulo 01309-060 Brazil
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36
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Xu WX, Liu Z, Deng F, Wang DD, Li XW, Tian T, Zhang J, Tang JH. MiR-145: a potential biomarker of cancer migration and invasion. Am J Transl Res 2019; 11:6739-6753. [PMID: 31814885 PMCID: PMC6895535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 10/30/2019] [Indexed: 06/10/2023]
Abstract
MircoRNAs (miRNAs) are a diverse family of highly-conserved small non-coding RNAs, which range from approximately 18 to 25 nucleotides in size. They regulate gene expression transcriptionally or post-transcriptionally via binding to the 3'-untranslated region (3'-UTR) of target message RNAs (mRNAs). MiRNAs have emerged as molecular regulators that participate in physiological and pathological processes of diverse malignancies. Among them, miRNA-145 (miR-145) played a profound role in tumorigenesis and progression of various neoplasms. In this review, we summarized the recent findings regarding miR-145, to elucidate its functional roles in cell invasion and migration of diverse human malignancies, and considered it a potential biomarker for cancer diagnosis, screening, and prognosis.
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Affiliation(s)
- Wen-Xiu Xu
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical UniversityNanjing 210029, P. R. China
- The First Clinical School of Nanjing Medical UniversityNanjing 210029, P. R. China
| | - Zhen Liu
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical UniversityNanjing 210029, P. R. China
- The First Clinical School of Nanjing Medical UniversityNanjing 210029, P. R. China
| | - Fei Deng
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical UniversityNanjing 210029, P. R. China
- The First Clinical School of Nanjing Medical UniversityNanjing 210029, P. R. China
| | - Dan-Dan Wang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical UniversityNanjing 210029, P. R. China
| | - Xing-Wang Li
- School of Clinical Medicine, Xuzhou Medical University209 Tongshan Road, Xuzhou 221004, P. R. China
| | - Tian Tian
- School of Clinical Medicine, Xuzhou Medical University209 Tongshan Road, Xuzhou 221004, P. R. China
| | - Jian Zhang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical UniversityNanjing 210029, P. R. China
| | - Jin-Hai Tang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical UniversityNanjing 210029, P. R. China
- The First Clinical School of Nanjing Medical UniversityNanjing 210029, P. R. China
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37
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Li SC, Huang LH, Chien KJ, Pan CY, Lin PH, Lin Y, Weng KP, Tsai KW. MiR-182-5p enhances in vitro neutrophil infiltration in Kawasaki disease. Mol Genet Genomic Med 2019; 7:e990. [PMID: 31605468 PMCID: PMC6900372 DOI: 10.1002/mgg3.990] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 08/19/2019] [Accepted: 09/05/2019] [Indexed: 12/18/2022] Open
Abstract
Background Kawasaki disease (KD) patients could develop coronary artery lesion (CAL) which threatens children's life. A previous study identified KD biomarker miRNAs that could discriminate KD patients from febrile non‐KD patients. We wonder whether these KD prediction biomarkers could be further applied to predict CAL formation in KD patients. Methods To examine this hypothesis, we conducted a meta‐analysis, miRNA mimic transfection, in vitro cell model and microarray assays. Results We first showed that miR‐182‐5p and miR‐183‐5p kept higher levels in the KD patients with CAL than those without CAL (p < .05). Further machine learning alignment confirmed that CAL formation could be predicted, with an auROC value of 0.86. We further treated neutrophil cells with miR‐182‐5p mimic, followed by in vitro transendotherial migration assay. As a result, miR‐182‐5p overexpression significantly (p < .05) enhanced neutrophil cells to infiltrate the endothelial layer composed of human coronary artery endothelium cells. Further microarray assay and pathway enrichment analysis showed that the genes activated with miR‐182‐5p overexpression were significantly enriched in the leukocyte transendothelial migration pathway (kegg_pathway_194, p < .05). Conclusion Therefore, our study suggested that miR‐182‐5p enhanced in vitro leukocyte infiltration by activating the leukocyte transendothelial migration pathway in CAL formation in KD.
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Affiliation(s)
- Sung-Chou Li
- Genomics and Proteomics Core Laboratory, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Lien-Hung Huang
- Genomics and Proteomics Core Laboratory, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Kuang-Jen Chien
- Department of Pediatrics, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Chao-Yu Pan
- Institute of Biomedical Science, Academia Sinica and Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan
| | - Pei-Hsien Lin
- Genomics and Proteomics Core Laboratory, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Yuyu Lin
- Genomics and Proteomics Core Laboratory, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Ken-Pen Weng
- Department of Pediatrics, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan.,Department of Medicine, National Yang-Ming University, Taipei, Taiwan.,Shu-Zen Junior College of Medicine and Management, Kaohsiung, Taiwan
| | - Kuo-Wang Tsai
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
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38
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Wang R, Li Y, Du P, Zhang X, Li X, Cheng G. Hypomethylation of the lncRNA SOX21-AS1 has clinical prognostic value in cervical cancer. Life Sci 2019; 233:116708. [DOI: 10.1016/j.lfs.2019.116708] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Revised: 07/27/2019] [Accepted: 07/28/2019] [Indexed: 12/31/2022]
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39
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Kuo HC, Pan CT, Huang YH, Huang FC, Lin YS, Li SC, Huang LH. Global Investigation of Immune Repertoire Suggests Kawasaki Disease Has Infectious Cause. Circ J 2019; 83:2070-2078. [PMID: 31378745 DOI: 10.1253/circj.cj-19-0206] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
BACKGROUND Kawasaki disease (KD) severely threatens young children's health worldwide. The pathogenic mechanism of KD has not yet been solved, so there is still debate over whether KD is an infectious disease or an autoimmune disease.Methods and Results:To solve this problem, an immune repertoire analysis of KD was conducted. We collected blood cell RNA samples and prepared them into amplicons with iRepertoire kits. The amplicons were sequenced and analyzed with the iRepertoire pipeline. We first identified KD-specific VJ and VDJ forms that had the potential to serve as biomarkers of KD. In addition, the KD-specific VDJ forms were contributed mostly by immunoglobulin G. The D50 value analysis showed that B-cell diversity in KD is decreased, suggesting unique immunoglobulins are produced in KD. Moreover, V, D and J segment usage in IgA, IgG and IgM was consistent with previous KD studies. Further comparison showed no difference in CDR3 peptide length between KD and fever controls (subjects with fever but not diagnosed as KD), indicting KD had B-cell selection phenomenon that has a non-autoimmune pattern. The comparison of amino acid usage of the CDR3 region demonstrated a preference for hydrophilic amino acids in KD. CONCLUSIONS The results of D50 value, VDJ usage and CDR3 peptide length analyses suggested the characteristics of infectious disease for KD.
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Affiliation(s)
- Ho-Chang Kuo
- Kawasaki Disease Center, Kaohsiung Chang Gung Memorial Hospital.,Department of Pediatrics, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine
| | - Cheng-Tsung Pan
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University
| | - Ying-Hsien Huang
- Kawasaki Disease Center, Kaohsiung Chang Gung Memorial Hospital.,Department of Pediatrics, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine
| | - Fu-Chen Huang
- Kawasaki Disease Center, Kaohsiung Chang Gung Memorial Hospital.,Department of Pediatrics, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine
| | - Yeong-Shin Lin
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University.,Department of Biological Science and Technology, National Chiao Tung University
| | - Sung-Chou Li
- Genomics and Proteomics Core Laboratory, Department of Medical Research, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine
| | - Lien-Hung Huang
- Genomics and Proteomics Core Laboratory, Department of Medical Research, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine
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40
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Hitte C, Le Béguec C, Cadieu E, Wucher V, Primot A, Prouteau A, Botherel N, Hédan B, Lindblad-Toh K, André C, Derrien T. Genome-Wide Analysis of Long Non-Coding RNA Profiles in Canine Oral Melanomas. Genes (Basel) 2019; 10:genes10060477. [PMID: 31234577 PMCID: PMC6628375 DOI: 10.3390/genes10060477] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 06/17/2019] [Accepted: 06/19/2019] [Indexed: 12/25/2022] Open
Abstract
Mucosal melanomas (MM) are rare aggressive cancers in humans, and one of the most common forms of oral cancers in dogs. Similar biological and histological features are shared between MM in both species, making dogs a powerful model for comparative oncology studies of melanomas. Although exome sequencing recently identified recurrent coding mutations in canine MM, little is known about changes in non-coding gene expression, and more particularly, in canine long non-coding RNAs (lncRNAs), which are commonly dysregulated in human cancers. Here, we sampled a large cohort (n = 52) of canine normal/tumor oral MM from three predisposed breeds (poodles, Labrador retrievers, and golden retrievers), and used deep transcriptome sequencing to identify more than 400 differentially expressed (DE) lncRNAs. We further prioritized candidate lncRNAs by comparative genomic analysis to pinpoint 26 dog–human conserved DE lncRNAs, including SOX21-AS, ZEB2-AS, and CASC15 lncRNAs. Using unsupervised co-expression network analysis with coding genes, we inferred the potential functions of the DE lncRNAs, suggesting associations with cancer-related genes, cell cycle, and carbohydrate metabolism Gene Ontology (GO) terms. Finally, we exploited our multi-breed design to identify DE lncRNAs within breeds. This study provides a unique transcriptomic resource for studying oral melanoma in dogs, and highlights lncRNAs that may potentially be diagnostic or therapeutic targets for human and veterinary medicine.
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Affiliation(s)
- Christophe Hitte
- University of Rennes, CNRS, IGDR-UMR 6290, F-35000 Rennes, France.
| | - Céline Le Béguec
- University of Rennes, CNRS, IGDR-UMR 6290, F-35000 Rennes, France.
| | - Edouard Cadieu
- University of Rennes, CNRS, IGDR-UMR 6290, F-35000 Rennes, France.
| | - Valentin Wucher
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain.
| | - Aline Primot
- University of Rennes, CNRS, IGDR-UMR 6290, F-35000 Rennes, France.
| | - Anaïs Prouteau
- University of Rennes, CNRS, IGDR-UMR 6290, F-35000 Rennes, France.
| | - Nadine Botherel
- University of Rennes, CNRS, IGDR-UMR 6290, F-35000 Rennes, France.
| | - Benoît Hédan
- University of Rennes, CNRS, IGDR-UMR 6290, F-35000 Rennes, France.
| | - Kerstin Lindblad-Toh
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, SE-751 24 Uppsala, Sweden.
| | - Catherine André
- University of Rennes, CNRS, IGDR-UMR 6290, F-35000 Rennes, France.
| | - Thomas Derrien
- University of Rennes, CNRS, IGDR-UMR 6290, F-35000 Rennes, France.
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41
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Zhang L, Meng X, Zhu XW, Yang DC, Chen R, Jiang Y, Xu T. Long non-coding RNAs in Oral squamous cell carcinoma: biologic function, mechanisms and clinical implications. Mol Cancer 2019; 18:102. [PMID: 31133028 PMCID: PMC6535863 DOI: 10.1186/s12943-019-1021-3] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Accepted: 04/22/2019] [Indexed: 01/17/2023] Open
Abstract
There is growing evidence that regions of the genome that cannot encode proteins play an important role in diseases. These regions are usually transcribed into long non-coding RNAs (lncRNAs). LncRNAs, little or no coding potential, are defined as capped transcripts longer than 200 nucleotides. New sequencing technologies have shown that a large number of aberrantly expressed lncRNAs are associated with multiple cancer types and indicated they have emerged as an important class of pervasive genes during the development and progression of cancer. However, the underlying mechanism in cancer is still unknown. Therefore, it is necessary to elucidate the lncRNA function. Notably, many lncRNAs dysregulation are associated with Oral squamous cell carcinoma (OSCC) and affect various aspects of cellular homeostasis, including proliferation, survival, migration or genomic stability. This review expounds the up- or down-regulation of lncRNAs in OSCC and the molecular mechanisms by which lncRNAs perform their function in the malignant cell. Finally, the potential of lncRNAs as non-invasive biomarkers for OSCC diagnosis are also described. LncRNAs hold promise as prospective novel therapeutic targets, but more research is needed to gain a better understanding of their biologic function.
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Affiliation(s)
- Lei Zhang
- College & Hospital of Stomatology, Anhui Medical University, Key Lab. of Oral Diseases Research of Anhui Province, Hefei, 230032, China.,Department of Periodontology, College and Hospital of Stomatology, Anhui Medical University, Hefei, 230032, Anhui Province, China
| | - Xiang Meng
- School of Stomatology, Anhui Medical University, Hefei, 230032, Anhui Province, China
| | - Xin-Wei Zhu
- College & Hospital of Stomatology, Anhui Medical University, Key Lab. of Oral Diseases Research of Anhui Province, Hefei, 230032, China.,Outpatient Department of Binhu District, College and Hospital of Stomatology, Anhui Medical University, Hefei, 230601, Anhui Province, China
| | - Deng-Cheng Yang
- School of Stomatology, Anhui Medical University, Hefei, 230032, Anhui Province, China
| | - Ran Chen
- School of Stomatology, Anhui Medical University, Hefei, 230032, Anhui Province, China
| | - Yong Jiang
- Department of Stomatology, The Fourth Affiliated Hospital of Anhui Medical University, 372 Tunxi Road, Hefei, 230000, Anhui Province, China.
| | - Tao Xu
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, 81 Meishan Road, Hefei, 230032, Anhui Province, China. .,Institute for Liver Diseases of Anhui Medical University, Anhui Medical University, 81 Meishan Road, Hefei, 230032, Anhui Province, China.
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42
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Liu X, Zhao X, Gou C. Identification of novel methylated DNA marker ZNF569 for head and neck squamous cell carcinoma. J Cancer 2019; 10:2250-2260. [PMID: 31258729 PMCID: PMC6584424 DOI: 10.7150/jca.31156] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 02/09/2019] [Indexed: 12/13/2022] Open
Abstract
Aberrant DNA methylation pattern plays an indispensable role in the initiation and development of head and neck squamous cell carcinoma (HNSCC). It is well recognized that lymph node metastasis is closely with unfavorable prognosis of HNSCC. Therefore, exploring the methylation events accounting for the lymph node metastasis of HNSCC is very important for improving the clinical outcome of HNSCC. Methylation data, RNA-seq data and clinical data were downloaded from The Cancer Genome Atlas (TCGA) and processed using the R package TCGA-Assembler. MethylMix was use for data analysis by integrating both methylation and gene expression data on HNSCC patients with lymph node metastasis and without lymph node metastasis. Pathway analysis was performed on significantly altered genes using ConsensusPathDB. The role of our interested gene zinc figure protein 569 (ZNF569) in HNSCC was further evaluated. Our results identified many novel hypermethylated/hypomethylated genes that might be closely associated with the lymph node metastasis of HNSCC. Pathway analysis revealed that increase in methylation of genes involved in generic transcription pathway including zinc figure proteins. ZNF569 was hypermethylated in HNSCC tissues especially those with lymph node metastasis. In addition, the expression levels of ZNF569 mRNA and protein were significantly lower in HNSCC tissues and cell lines compared to their respective controls. Moreover, overexpression of ZNF569 inhibited the proliferation, migration and invasion of HNSCC cells. HNSCC patients with lower ZNF569 expression suffered a significantly shorter overall survival than those with higher ZNF569 expression. In conclusion, we have identified many novel differentially methylated genes that might be important for the lymph node metastasis of HNSCC. In addition, ZNF569 might play a tumor suppressive role in carcinogenesis of HNSCC.
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Affiliation(s)
- Xiangzhen Liu
- First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xinyuan Zhao
- Stomatological Hospital, Southern Medical University, Guangzhou, China
| | - Chenyu Gou
- Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
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SOX21-AS1 is associated with clinical stage and regulates cell proliferation in nephroblastoma. Biosci Rep 2019; 39:BSR20190602. [PMID: 30992391 PMCID: PMC6522742 DOI: 10.1042/bsr20190602] [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] [Received: 03/12/2019] [Revised: 03/30/2019] [Accepted: 04/02/2019] [Indexed: 11/17/2022] Open
Abstract
LncRNA SOX21 antisense RNA 1 (SOX21-AS1) dysregulated in many types of human cancer, and functioned as tumor suppressor or promoter depending on tumor types. However, there was no report about the role of SOX21-AS1 in nephroblastoma. In the present study, we first found that SOX21-AS1 expression was elevated in nephroblastoma tissues and cell lines compared with adjacent normal tissues and normal human embryonic kidney cell line, respectively. Moreover, we observed nephroblastoma patients with large tumor size, advanced National Wilms Tumor Study (NWTS) stage or unfavorable histopathological type, and patients that had higher SOX21-AS1 expression levels than nephroblastoma patients with small tumor size, early NWTS stage or favorable histopathological type. The in vitro studies suggested that knockdown of SOX21-AS1 suppressed nephroblastoma cell proliferation and colony formation, and induced cell-cycle arrest through up-regulating p57 expression. In conclusion, our study suggests that SOX21-AS1 functions as oncogenic lncRNA in nephroblastoma, which may provide a novel insight for nephroblastoma carcinogenesis.
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Yang CM, Chang HS, Chen HC, You JJ, Liou HH, Ting SC, Ger LP, Li SC, Tsai KW. Low C6orf141 Expression is Significantly Associated with a Poor Prognosis in Patients with Oral Cancer. Sci Rep 2019; 9:4520. [PMID: 30872783 PMCID: PMC6418188 DOI: 10.1038/s41598-019-41194-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 02/26/2019] [Indexed: 12/21/2022] Open
Abstract
C6orf141 (Chromosome 6 open reading frame 141) is a novel gene, and its role in oral cancer progression remains unclear. C6orf141 expression in oral squamous cell carcinoma (OSCC) and adjacent normal tissues from 428 patients was examined through immunohistochemistry (IHC). Our results revealed that C6orf141 expression was significantly reduced in OSCC compared with adjacent normal tissues. Low C6orf141 expression was significantly associated with a poor American Joint Committee on Cancer pathological stage (P < 0.001), T classification (P = 0.002), and pN stage (P = 0.032). Kaplan-Meier curves revealed that low C6orf141 expression was significantly associated with shorter disease-specific survival (DSS) in patients with OSCC (log-rank P = 0.007). Multivariate analysis indicated that low C6orf141 expression was an independent prognostic biomarker for DSS (adjusted hazard ratio = 1.34; 95% confidence interval = 1.10-1.81; P = 0.05). Additionally, ectopic C6orf141 expression could significantly suppress oral cancer cell proliferation, colony formation, and migratory and invasive abilities. Xenograft tumor growth assay revealed that C6orf141 could significantly suppress oral tumor growth in vivo. Our results suggest that C6orf141 plays a novel tumor-suppressive role in oral cancer cell growth and motility. Furthermore, C6orf141 dysfunction could be a potential prognostic biomarker for OSCC and provide new therapeutic strategies in the future.
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Affiliation(s)
- Cheng-Mei Yang
- Department of Stomatology, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan.,Department of Dental Technology, Shu-Zen Junior College of Medicine and Management, Kaohsiung, Taiwan
| | - Hao-Sheng Chang
- Department of Stomatology, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan.,Department of Dental Technology, Shu-Zen Junior College of Medicine and Management, Kaohsiung, Taiwan
| | - Hung-Chih Chen
- Department of Stomatology, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan.,Department of Dental Technology, Shu-Zen Junior College of Medicine and Management, Kaohsiung, Taiwan
| | - Jyun-Jie You
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Huei-Han Liou
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Su-Chen Ting
- Planning Office of Kaohsiung Municipal United Hospital, Kaohsiung, Taiwan
| | - Luo-Ping Ger
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan.,Institute of Biomedical Sciences, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Sung-Chou Li
- Genomics & Proteomics Core Laboratory, Department of Medical Research, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.
| | - Kuo-Wang Tsai
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan. .,Institute of Biomedical Sciences, National Sun Yat-Sen University, Kaohsiung, Taiwan. .,Department of Chemical Biology, National Pingtung University of Education, Pingtung, Taiwan.
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Tan J, Xiang L, Xu G. LncRNA MEG3 suppresses migration and promotes apoptosis by sponging miR-548d-3p to modulate JAK-STAT pathway in oral squamous cell carcinoma. IUBMB Life 2019; 71:882-890. [PMID: 30809930 DOI: 10.1002/iub.2012] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 12/24/2018] [Accepted: 01/08/2019] [Indexed: 12/19/2022]
Affiliation(s)
- Jiawei Tan
- Department of Stomatology; Zhejiang Hospital; Zhejiang Hangzhou China
| | - Lixin Xiang
- Department of Stomatology; Zhejiang Hospital; Zhejiang Hangzhou China
| | - Guochao Xu
- Department of Stomatology; Zhejiang Hospital; Zhejiang Hangzhou China
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46
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Long noncoding RNAs in cancer cells. Cancer Lett 2019; 419:152-166. [PMID: 29414303 DOI: 10.1016/j.canlet.2018.01.053] [Citation(s) in RCA: 135] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 01/15/2018] [Accepted: 01/18/2018] [Indexed: 12/11/2022]
Abstract
Long noncoding RNA (lncRNA) has recently been investigated as key modulators that regulate many biological processes in human cancers via diverse mechanisms. LncRNAs can interact with macromolecules such as DNA, RNA, or protein to exert cellular effects and to act as either tumor promoters or tumor suppressors in various malignancies. Moreover, the aberrant expression of lncRNAs may be detected in multiple cancer phenotypes by employing the rapidly developing modern gene chip technology and bioinformatics analysis. Herein, we highlight the mechanisms of action of lncRNAs, their functional cellular roles and their involvement in cancer progression. Finally, we provide an overview of recent progress in the lncRNA field and future potential for lncRNAs as cancer diagnostic markers and therapeutics.
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Zhang L, Fang Y, Cheng X, Lian YJ, Xu HL. Silencing of Long Noncoding RNA SOX21-AS1 Relieves Neuronal Oxidative Stress Injury in Mice with Alzheimer's Disease by Upregulating FZD3/5 via the Wnt Signaling Pathway. Mol Neurobiol 2018; 56:3522-3537. [PMID: 30143969 DOI: 10.1007/s12035-018-1299-y] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Accepted: 08/02/2018] [Indexed: 01/08/2023]
Abstract
Alzheimer's disease (AD) represents a progressive neurodegenerative disorder characterized by distinctive neuropathological changes. Recently, long noncoding RNAs (lncRNAs) have become a key area of interest due to their potential in AD therapy. Hence, the aim of the current study was to investigate the effect of lncRNA SOX21-AS1 on neuronal oxidative stress injury in mice with AD via the Wnt signaling pathway by targeting FZD3/5. Microarray analysis was performed to screen AD-related differentially expressed genes (DEGs). Following verification of the target relationship between SOX21-AS1 and FZD3/5, the contents of OH-, malondialdehyde (MDA), superoxide dismutase (SOD), catalase (CAT), and glutathione peroxidase (GSH-Px) were determined, with the expressions of SOX21-AS1, FZD3/5, β-catenin, cyclin D1, and 4-HNE in hippocampal neuron cells subsequently detected. Cell cycle distribution and apoptosis were evaluated. Bioinformatics analysis revealed that SOX21-AS1 was upregulated in AD, while highlighting the co-expression of SOX21-AS1 and FZD3/5 genes and their involvement in the Wnt signaling pathway. AD mice exhibited diminished memory and learning ability, increased rates of MDA, OH-, SOX21-AS1, 4-HNE, and elevated levels of hippocampal neuron cell apoptosis, accompanied by decreased levels of SOD, CAT, GSH-Px, FZD3/5, β-catenin, and cyclin D1. Silencing of SOX21-AS1 resulted in decreased OH-, MDA contents, SOX21-AS1, and 4-HNE, and increased SOD, CAT, GSH-Px, FZD3/5, β-catenin, and cyclin D1, as well as reduced apoptosis of hippocampal neuron cells. Taken together, the key findings of the present study demonstrated that silencing of lncRNA SOX21-AS1 could act to alleviate neuronal oxidative stress and suppress neuronal apoptosis in AD mice through the upregulation of FZD3/5 and subsequent activation of the Wnt signaling pathway.
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Affiliation(s)
- Lu Zhang
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, No. 1, Jianshe East Road, Erqi District, Zhengzhou, 450052, Henan Province, People's Republic of China.
| | - Yu Fang
- ICU, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, People's Republic of China
| | - Xuan Cheng
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, No. 1, Jianshe East Road, Erqi District, Zhengzhou, 450052, Henan Province, People's Republic of China
| | - Ya-Jun Lian
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, No. 1, Jianshe East Road, Erqi District, Zhengzhou, 450052, Henan Province, People's Republic of China
| | - Hong-Liang Xu
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, No. 1, Jianshe East Road, Erqi District, Zhengzhou, 450052, Henan Province, People's Republic of China
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48
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Yao J, Li Z, Yang Z, Xue H, Chang H, Zhang X, Li T, Guo K. Long noncoding RNA TOB1-AS1, an epigenetically silenced gene, functioned as a novel tumor suppressor by sponging miR-27b in cervical cancer. Am J Cancer Res 2018; 8:1483-1498. [PMID: 30210918 PMCID: PMC6129502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Accepted: 07/09/2018] [Indexed: 06/08/2023] Open
Abstract
Cervical cancer is one of the most common cancers in females, accounting for a majority of cancer-related deaths in worldwide. Long non-coding RNAs (lncRNAs) have been identified as critical regulators in many tumor-related biological processes. Thus, investigation into the function and mechanism of lncRNAs in the development of cervical cancer is very necessary. In this study, we found that the expression of TOB1-AS1 was significantly decreased in cervical cancer tissues compared with the adjacent normal tissues. The methylation status of TOB1-AS1-related CpG island was analyzed using methylation specific PCR and bisulfite sequencing analysis, revealing that the aberrant hypermethylation of TOB1-AS1-related CpG island was frequently observed in primary tumors and cervical cancer cells. The expression of TOB1-AS1 in cervical cancer cells could be reversed by demethylation agent treatment. Functionally, overexpression of TOB1-AS1 significantly inhibited cell proliferation, cell cycle progression, invasion and induced apoptosis, while knockdown of TOB1-AS1 exhibited the opposite effect. Furthermore, it was determined that TOB1-AS1 was able to bind and degrade the expression of miR-27b. Upregulation of miR-27b promoted cell growth, cell cycle transition from G1 phase to S phase, and invasion and reduced apoptosis, phenomenon could be reversed by TOB1-AS1. Inhibition of miR-27b attenuated the promotive effect of si-TOB1-AS1 on cellular processes. Upregulation of TOB1-AS1 also suppressed tumor growth in vivo. Clinically, methylation of TOB1-AS1 and low expression of TOB1-AS1 was significantly correlated with tumor stage and tumor size, respectively. Univariate and multivariate analyses confirmed that low level of TOB1-AS1 was an independent risk factor for death. In conclusion, we suggested that the epigenetically silenced TOB1-AS1 was unable to restrain miR-27b, which contributed to cervical cancer progression.
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Affiliation(s)
- Jihang Yao
- Department of Gynecology, The First Hospital of China Medical UniversityShenyang 110001, Liaoning, China
| | - Zhenghong Li
- Department of Gynecology, The First Hospital of China Medical UniversityShenyang 110001, Liaoning, China
| | - Ziwei Yang
- Department of Clinical Laboratory, The First Hospital of China Medical UniversityShenyang 110001, Liaoning, China
| | - Hui Xue
- Department of Gynecology, The First Hospital of China Medical UniversityShenyang 110001, Liaoning, China
| | - Hua Chang
- Department of Gynecology, The First Hospital of China Medical UniversityShenyang 110001, Liaoning, China
| | - Xue Zhang
- Department of Gynecology, The First Hospital of China Medical UniversityShenyang 110001, Liaoning, China
| | - Tianren Li
- Department of Gynecology, The First Hospital of China Medical UniversityShenyang 110001, Liaoning, China
| | - Kejun Guo
- Department of Gynecology, The First Hospital of China Medical UniversityShenyang 110001, Liaoning, China
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Peng L, Yuan XQ, Zhang CY, Peng JY, Zhang YQ, Pan X, Li GC. The emergence of long non-coding RNAs in hepatocellular carcinoma: an update. J Cancer 2018; 9:2549-2558. [PMID: 30026854 PMCID: PMC6036883 DOI: 10.7150/jca.24560] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Accepted: 03/31/2018] [Indexed: 12/11/2022] Open
Abstract
Hepatocellular carcinoma (HCC) accounting for roughly 90% of all primary liver neoplasms is the sixth most frequent neoplasm and the second prominent reason of tumor fatality worldwide. As regulators of diverse biological processes, long non-coding RNAs (lncRNAs) are involved in onset and development of neoplasms. With the continuous booming of well-featured lncRNAs in HCC from 2016 to now, we reviewed the newly-presented comprehension about the relationship between lncRNAs and HCC in this study. To be specific, we summarized the overview function and study tools of lncRNAs, elaborated the roles of lncRNAs in HCC, and sketched the molecule mechanisms of lncRNAs in HCC. In addition, the application of lncRNAs serving as biomarkers in early diagnosis and outcome prediction of HCC patients was highlighted.
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Affiliation(s)
- Li Peng
- Key Laboratory of Carcinogenesis of the Chinese Ministry of Health and the Key Laboratory of Carcinogenesis and Cancer Invasion of Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha 410078, P.R. China; Cancer Research Institute, Central South University, Changsha 410078, P.R. China
- Guangdong Province Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Research Center of Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, P.R. China
| | - Xiao-Qing Yuan
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
- Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong 510120, China
| | - Chao-Yang Zhang
- Key Laboratory of Carcinogenesis of the Chinese Ministry of Health and the Key Laboratory of Carcinogenesis and Cancer Invasion of Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha 410078, P.R. China; Cancer Research Institute, Central South University, Changsha 410078, P.R. China
| | - Jiang-Yun Peng
- Guangdong Province Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Research Center of Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, P.R. China
| | - Ya-Qin Zhang
- Key Laboratory of Carcinogenesis of the Chinese Ministry of Health and the Key Laboratory of Carcinogenesis and Cancer Invasion of Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha 410078, P.R. China; Cancer Research Institute, Central South University, Changsha 410078, P.R. China
| | - Xi Pan
- Department of Oncology, the third Xiangya Hospital, Central South University, Changsha 410013, P.R. China
| | - Guan-Cheng Li
- Key Laboratory of Carcinogenesis of the Chinese Ministry of Health and the Key Laboratory of Carcinogenesis and Cancer Invasion of Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha 410078, P.R. China; Cancer Research Institute, Central South University, Changsha 410078, P.R. China
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50
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Wei C, Wang H, Xu F, Liu Z, Jiang R. LncRNA SOX21-AS1 is associated with progression of hepatocellular carcinoma and predicts prognosis through epigenetically silencing p21. Biomed Pharmacother 2018; 104:137-144. [PMID: 29772433 DOI: 10.1016/j.biopha.2018.05.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 04/24/2018] [Accepted: 05/07/2018] [Indexed: 12/16/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) have been widely reported in various cancers due to their special molecular mechanisms. LncRNA SOX21-AS1 has been discovered to be a tumor facilitator in several types of human cancers. However, the expression pattern, clinical value and biological effects in hepatocellular carcinoma (HCC) are still unknown. In this study, we detected the high expression level of SOX21-AS1 in tumor tissues and cell lines through performing qRT-PCR analysis. The prognostic value of SOX21-AS1 was identified. Moreover, the biological effects of SOX21-AS1 on HCC cell activities were evaluated by functional assays, such as MTT, colony formation assay and transwell assay. As a result, silenced SOX21-AS1 suppressed cell proliferation and metastasis, resulted in cell cycle arrest, and induced apoptosis in hepatocellular carcinoma. Mechanically, RIP was conducted to prove that SOX21-AS1 could bind with EZH2. ChIp assay was carried out and manifested that SOX21-AS1 epigenetically silenced p21 via recruiting EZH2 to the promoter of p21. Finally, rescue assays were designed and carefully conducted to investigate whether SOX21-AS1 can interact with p21 to affect hepatocellular carcinoma progression. Generally, our results suggested that SOX21-AS1 could be a potential prognostic biomarker or a therapeutic target for hepatocellular carcinoma.
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Affiliation(s)
- Congxin Wei
- Department of Radiology, Qilu Hospital, Shandong University, Jinan, 250012, China
| | - Hong Wang
- Department of Anesthesiology, Yidu Central Hospital, Weifang Medical University, Qingzhou, 262500, China
| | - Fei Xu
- Department of Anesthesiology, Yidu Central Hospital, Weifang Medical University, Qingzhou, 262500, China
| | - Zeng Liu
- Department of General Surgery, Qilu Hospital, Shandong University, Jinan, 250012, China
| | - Runde Jiang
- Department of General Surgery, Qilu Hospital, Shandong University, Jinan, 250012, China.
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