1
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Kumar M, Patel K, Chinnapparaj S, Sharma T, Aggarwal A, Singla N, Karthigeyan M, Singh A, Sahoo SK, Tripathi M, Takkar A, Gupta T, Pal A, Attri SV, Bansal YS, Ratho RK, Gupta SK, Khullar M, Vashishta RK, Mukherjee KK, Grover VK, Prasad R, Chatterjee A, Gowda H, Bhagat H. Dysregulated Genes and Signaling Pathways in the Formation and Rupture of Intracranial Aneurysm. Transl Stroke Res 2023:10.1007/s12975-023-01178-w. [PMID: 37644376 DOI: 10.1007/s12975-023-01178-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 03/21/2023] [Accepted: 07/10/2023] [Indexed: 08/31/2023]
Abstract
Intracranial aneurysm (IA) has the potential to rupture. Despite scientific advances, we are still not in a position to screen patients for IA and identify those at risk of rupture. It is critical to comprehend the molecular basis of disease to facilitate the development of novel diagnostic strategies. We used transcriptomics to identify the dysregulated genes and understand their role in the disease biology. In particular, RNA-Seq was performed in tissue samples of controls, unruptured IA, and ruptured IA. Dysregulated genes (DGs) were identified and analyzed to understand the functional aspects of molecules. Subsequently, candidate genes were validated at both transcript and protein level. There were 314 DGs in patients with unruptured IA when compared to control samples. Out of these, SPARC and OSM were validated as candidate molecules in unruptured IA. PI3K-AKT signaling pathway was found to be an important pathway for the formation of IA. Similarly, 301 DGs were identified in the samples of ruptured IA when compared with unruptured IAs. CTSL was found to be a key candidate molecule which along with Hippo signaling pathway may be involved in the rupture of IA. We conclude that activation of PI3K-AKT signaling pathway by OSM along with up-regulation of SPARC is important for the formation of IA. Further, regulation of Hippo pathway through PI3K-AKT signaling results in the down-regulation of YAP1 gene. This along with up-regulation of CTSL leads to further weakening of aneurysm wall and its subsequent rupture.
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Affiliation(s)
- Munish Kumar
- Division of Neuro-anesthesia, Department of Anesthesia and Intensive Care, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Krishna Patel
- Institute of Bioinformatics, International Tech Park, Bangalore, India
| | - Shobia Chinnapparaj
- Division of Neuro-anesthesia, Department of Anesthesia and Intensive Care, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Tanavi Sharma
- Division of Neuro-anesthesia, Department of Anesthesia and Intensive Care, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Ashish Aggarwal
- Department of Neurosurgery, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Navneet Singla
- Department of Neurosurgery, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Madhivanan Karthigeyan
- Department of Neurosurgery, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Apinderpreet Singh
- Department of Neurosurgery, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Sushanta Kumar Sahoo
- Department of Neurosurgery, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Manjul Tripathi
- Department of Neurosurgery, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Aastha Takkar
- Department of Neurology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Tulika Gupta
- Department of Anatomy, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Arnab Pal
- Department of Biochemistry, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Savita Verma Attri
- Pediatric Biochemistry, Department of Pediatrics, Advanced Pediatrics Centre, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Yogender Singh Bansal
- Department of Forensic Medicine, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Radha Kanta Ratho
- Department of Virology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Sunil K Gupta
- Department of Neurosurgery, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Madhu Khullar
- Department of Experimental Medicine and Biotechnology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Rakesh Kumar Vashishta
- Department of Histopathology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Kanchan Kumar Mukherjee
- Department of Neurosurgery, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Vinod Kumar Grover
- Division of Neuro-anesthesia, Department of Anesthesia and Intensive Care, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Rajendra Prasad
- Department of Biochemistry, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Aditi Chatterjee
- Institute of Bioinformatics, International Tech Park, Bangalore, India
| | - Harsha Gowda
- Institute of Bioinformatics, International Tech Park, Bangalore, India
| | - Hemant Bhagat
- Division of Neuro-anesthesia, Department of Anesthesia and Intensive Care, Postgraduate Institute of Medical Education and Research, Chandigarh, India.
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Zhang J, Ryu JY, Tirado SR, Dickinson LD, Abosch A, Aziz-Sultan MA, Boulos AS, Barrow DL, Batjer HH, Binyamin TR, Blackburn SL, Chang EF, Chen PR, Colby GP, Cosgrove GR, David CA, Day AL, Folkerth RD, Frerichs KU, Howard BM, Jahromi BR, Niemela M, Ojemann SG, Patel NJ, Richardson RM, Shi X, Valle-Giler EP, Wang AC, Welch BG, Williams Z, Zusman EE, Weiss ST, Du R. A Transcriptomic Comparative Study of Cranial Vasculature. Transl Stroke Res 2023:10.1007/s12975-023-01186-w. [PMID: 37612482 DOI: 10.1007/s12975-023-01186-w] [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: 07/06/2023] [Revised: 07/06/2023] [Accepted: 08/07/2023] [Indexed: 08/25/2023]
Abstract
In genetic studies of cerebrovascular diseases, the optimal vessels to use as controls remain unclear. Our goal is to compare the transcriptomic profiles among 3 different types of control vessels: superficial temporal artery (STA), middle cerebral arteries (MCA), and arteries from the circle of Willis obtained from autopsies (AU). We examined the transcriptomic profiles of STA, MCA, and AU using RNAseq. We also investigated the effects of using these control groups on the results of the comparisons between aneurysms and the control arteries. Our study showed that when comparing pathological cerebral arteries to control groups, all control groups presented similar responses in the activation of immunological processes, the regulation of intracellular signaling pathways, and extracellular matrix productions, despite their intrinsic biological differences. When compared to STA, AU exhibited upregulation of stress and apoptosis genes, whereas MCA showed upregulation of genes associated with tRNA/rRNA processing. Moreover, our results suggest that the matched case-control study design, which involves control STA samples collected from the same subjects of matched aneurysm samples in our study, can improve the identification of non-inherited disease-associated genes. Given the challenges associated with obtaining fresh intracranial arteries from healthy individuals, our study suggests that using MCA, AU, or paired STA samples as controls are feasible strategies for future large-scale studies investigating cerebral vasculopathies. However, the intrinsic differences of each type of control should be taken into consideration when interpreting the results. With the limitations of each control type, it may be most optimal to use multiple tissues as controls.
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Affiliation(s)
- Jianing Zhang
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | - Jee-Yeon Ryu
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | - Selena-Rae Tirado
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | | | - Aviva Abosch
- Department of Neurosurgery, University of Nebraska Medical Center, Omaha, NE, USA
| | - M Ali Aziz-Sultan
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | - Alan S Boulos
- Department of Neurosurgery, Albany Medical Center, Albany, NY, USA
| | - Daniel L Barrow
- Department of Neurosurgery, Emory University, Atlanta, GA, USA
| | - H Hunt Batjer
- Department of Neurosurgery, University of Texas Southwestern, Dallas, TX, USA
| | | | - Spiros L Blackburn
- Department of Neurosurgery, University of Texas Health Science Center, Houston, TX, USA
| | - Edward F Chang
- Department of Neurosurgery, University of California San Francisco, San Francisco, CA, USA
- Department of Neurosurgery, University of California Los Angeles, Los Angeles, CA, USA
| | - P Roc Chen
- Department of Neurosurgery, University of Texas Health Science Center, Houston, TX, USA
| | - Geoffrey P Colby
- Department of Neurosurgery, University of California Los Angeles, Los Angeles, CA, USA
| | - G Rees Cosgrove
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | - Carlos A David
- Department of Neurosurgery, University of North Carolina Chapel Hill, Chapel Hill, NC, USA
| | - Arthur L Day
- Department of Neurosurgery, University of Texas Health Science Center, Houston, TX, USA
| | - Rebecca D Folkerth
- Department of Forensic Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Kai U Frerichs
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | - Brian M Howard
- Department of Neurosurgery, Emory University, Atlanta, GA, USA
| | - Behnam R Jahromi
- Department of Neurosurgery, Helsinki University and Helsinki University Hospital, Helsinki, Finland
| | - Mika Niemela
- Department of Neurosurgery, Helsinki University and Helsinki University Hospital, Helsinki, Finland
| | - Steven G Ojemann
- Department of Neurosurgery, University of Colorado, Denver, CO, USA
| | - Nirav J Patel
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | - R Mark Richardson
- Department of Neurosurgery, Massachusetts General Hospital, Boston, MA, USA
| | - Xiangen Shi
- Department of Neurosurgery, Affiliated Fuxing Hospital, Capital Medical University, Beijing, China
| | | | - Anthony C Wang
- Department of Neurosurgery, University of California Los Angeles, Los Angeles, CA, USA
| | - Babu G Welch
- Department of Neurosurgery, University of Texas Southwestern, Dallas, TX, USA
| | - Ziv Williams
- Department of Neurosurgery, Massachusetts General Hospital, Boston, MA, USA
| | | | - Scott T Weiss
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Rose Du
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA.
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Transcriptomic Studies on Intracranial Aneurysms. Genes (Basel) 2023; 14:genes14030613. [PMID: 36980884 PMCID: PMC10048068 DOI: 10.3390/genes14030613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 02/25/2023] [Accepted: 02/26/2023] [Indexed: 03/05/2023] Open
Abstract
Intracranial aneurysm (IA) is a relatively common vascular malformation of an intracranial artery. In most cases, its presence is asymptomatic, but IA rupture causing subarachnoid hemorrhage is a life-threating condition with very high mortality and disability rates. Despite intensive studies, molecular mechanisms underlying the pathophysiology of IA formation, growth, and rupture remain poorly understood. There are no specific biomarkers of IA presence or rupture. Analysis of expression of mRNA and other RNA types offers a deeper insight into IA pathobiology. Here, we present results of published human studies on IA-focused transcriptomics.
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Ling C, Yang Y, Hu X, Cai M, Wang H, Chen C. Phoenixin-14 alleviates inflammatory smooth muscle cell-induced endothelial cell dysfunction in vitro. Cytokine 2022; 157:155973. [PMID: 35907364 DOI: 10.1016/j.cyto.2022.155973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 06/30/2022] [Accepted: 07/19/2022] [Indexed: 11/15/2022]
Abstract
BACKGROUND Intracranial aneurysm (IA) is cerebrovascular disorder which refers to local vessel wall damage to intracranial arteries, forming abnormal bulge. Both endothelial cells (ECs) and vascular smooth muscle cells (VSMCs) are closely associated with IA formation and rupture. Inflammatory SMCs (iSMCs) were reported to induce EC dysfunction and result in IA progression. Phoenixin-14 (PNX-14) is a recently discovered brain peptide with pleiotropic roles, which participates in reproduction, cardio protection, lipid deposition and blood glucose metabolism. PNX-14 was previously reported to protect brain endothelial cells against oxygen-glucose deprivation/reoxygenation (OGD/R)-induced cell injury. Therefore, our study was designed to investigate the influence of PNX-14 on iSMCs-induced endothelial dysfunction. METHODS Inflammation in SMCs was induced by cyclic mechanical stretch. Human umbilical vein endothelial cells (HUVECs) were exposed to SMC- or iSMC-conditioned medium and then treated with 100 nM PNX-14 for 24 h. The levels of proinflammatory cytokines (IL-1β, IL-6 and TNF-α) in cell supernatants were analyzed by ELISA. Cell viability, apoptosis, angiogenesis and migration were subjected to CCK-8 assay, flow cytometry analysis, tube formation assay and Transwell migration assay. The protein levels of proinflammatory cytokines and apoptosis markers (Bcl-2 and Bax) were evaluated by western blotting. RESULTS Cyclic mechanical stretch upregulated IL-1β, IL-6 and TNF-α levels in SMCs. Treatment with SMC- or iSMC-conditioned medium HUVECs inhibited cell viability, angiogenesis and migration and induced apoptosis in HUVECs. iSMC-conditioned medium has more significant effects on cell functions. However, the influence of SMC- or iSMC-conditioned medium treatment on HUVEC biological functions were reversed by PNX-14 treatment. PNX-14 exerts no significant influence on the biological functions of HUVECs treated with SMC medium. CONCLUSION PNX-14 alleviates iSMCs-induced endothelial cell dysfunction in vitro.
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Affiliation(s)
- Cong Ling
- Department of Neurosurgery, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Yang Yang
- Department of Radiology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Xiling Hu
- Department of Internal Medicine, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Meiqin Cai
- Department of Neurosurgery, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Hui Wang
- Department of Neurosurgery, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, China.
| | - Chuan Chen
- Department of Neurosurgery, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, China.
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Characterization of Long Non-coding RNA Signatures of Intracranial Aneurysm in Circulating Whole Blood. Mol Diagn Ther 2021; 24:723-736. [PMID: 32939739 DOI: 10.1007/s40291-020-00494-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND AND OBJECTIVE Long non-coding RNAs (lncRNAs) may serve as biomarkers for complex disease states, such as intracranial aneurysms. In this study, we investigated lncRNA expression differences in the whole blood of patients with unruptured aneurysms. METHODS Whole blood RNA from 67 subjects (34 with aneurysm, 33 without) was used for next-generation RNA sequencing. Differential expression analysis was used to define a signature of intracranial aneurysm-associated lncRNAs. To estimate the signature's ability to classify aneurysms and to identify the most predictive lncRNAs, we implemented a nested cross-validation pipeline to train classifiers using linear discriminant analysis. Ingenuity pathway analysis was used to study potential biological roles of differentially expressed lncRNAs, and lncRNA ontology was used to investigate ontologies enriched in signature lncRNAs. Co-expression correlation analysis was performed to investigate associated differential protein-coding messenger RNA expression. RESULTS Of 4639 detected lncRNAs, 263 were significantly different (p < 0.05) between the two groups, and 84 of those had an absolute fold-change ≥ 1.5. An eight-lncRNA signature (q < 0.35, fold-change ≥ 1.5) was able to separate patients with and without aneurysms on principal component analysis, and had an estimated accuracy of 70.9% in nested cross-validation. Bioinformatics analyses showed that networks of differentially expressed lncRNAs (p < 0.05) were enriched for cell death and survival, connective tissue disorders, carbohydrate metabolism, and cardiovascular disease. Signature lncRNAs shared ontologies that reflected regulation of gene expression, signaling, ubiquitin processing, and p53 signaling. Co-expression analysis showed correlations with messenger RNAs related to inflammatory responses. CONCLUSIONS Differential expression in whole blood lncRNAs is detectable in patients harboring aneurysms, and reflects expression/signaling regulation, and ubiquitin and p53 pathways. Following validation in larger cohorts, these lncRNAs may be potential diagnostic targets for aneurysm detection by blood testing.
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Hu Y, Chen W, Li C, Wang X, Luo J, Cheng B. LncRNA ANRIL Facilitates Vascular Smooth Muscle Cell Proliferation and Suppresses Apoptosis via Modulation of miR-7/FGF2 Pathway in Intracranial Aneurysms. Neurocrit Care 2021; 36:106-115. [PMID: 34286462 DOI: 10.1007/s12028-021-01262-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 04/20/2021] [Indexed: 11/26/2022]
Abstract
BACKGROUND Proliferation and apoptosis of vascular smooth muscle cells (VSMCs) are linked to intracranial aneurysm (IA) formation and progression. Long antisense noncoding RNA in the INK4 locus (ANRIL) has been reported to regulate VSMC functions in several cardiovascular diseases. However, little is known about how ANRIL influences VSMC proliferation and apoptosis during IA pathogenesis. METHODS The expression level of ANRIL in the plasma and arterial wall tissues of patients with IA was detected by real-time quantitative polymerase chain reaction. The functional role of ANRIL in the regulation of VSMC proliferation and apoptosis and its downstream regulatory mechanism were determined using Cell Counting Kit 8, immunofluorescence, terminal-deoxynucleotidyl transferase-mediated UTP nick end labeling, western blotting, luciferase reporter assay, and RNA immunoprecipitation assay. RESULTS ANRIL was downregulated in the plasma and arterial wall tissues of patients with IA, when compared with control groups. Overexpression of ANRIL significantly promoted VSMC proliferation and blocked cell apoptosis. Mechanistic studies demonstrated that ANRIL directly bound to microRNA-7 (miR-7) and that overexpression of miR-7 overturned the increased cell proliferation and decreased cell apoptosis, which was induced by ANRIL restoration. Besides, further study showed that ANRIL positively regulated fibroblast growth factor 2 (FGF2) expression via targeting miR-7. CONCLUSIONS These results suggested that ANRIL affects VSMC proliferation and apoptosis via regulation of the miR-7/FGF2 pathway in IA, which provided a potential novel strategy for the treatment of IA.
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Affiliation(s)
- Yangchun Hu
- Department of Neurosurgery, First Affiliated Hospital of Anhui Medical University, Hefei City, Anhui Province, China.
| | - Weiwei Chen
- Department of Neurosurgery, First Affiliated Hospital of Anhui Medical University, Hefei City, Anhui Province, China
| | - Chao Li
- Department of Neurosurgery, First Affiliated Hospital of Anhui Medical University, Hefei City, Anhui Province, China
| | - Xiaojian Wang
- Department of Neurosurgery, First Affiliated Hospital of Anhui Medical University, Hefei City, Anhui Province, China
| | - Jing Luo
- Department of Neurosurgery, First Affiliated Hospital of Anhui Medical University, Hefei City, Anhui Province, China
| | - Baochun Cheng
- Department of Neurosurgery, First Affiliated Hospital of Anhui Medical University, Hefei City, Anhui Province, China
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Long non-coding RNA H19: Physiological functions and involvements in central nervous system disorders. Neurochem Int 2021; 148:105072. [PMID: 34058282 DOI: 10.1016/j.neuint.2021.105072] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 05/08/2021] [Accepted: 05/16/2021] [Indexed: 12/26/2022]
Abstract
Central nervous system (CNS) disorders are some of the most complex and challenging diseases because of the intricate structure and functions of the CNS. Long non-coding RNA (LncRNA) H19, which had been mistaken for "transcription noise" previously, has now been found to be closely related to the development and homeostasis of the CNS. Several recent studies indicate that it plays an important role in the pathogenesis, treatment, and even prognosis of CNS disorders. LncRNA H19 is correlated with susceptibility to various CNS disorders such as intracranial aneurysms, ischemic stroke, glioma, and neuroblastoma. Moreover, it participates in the pathogenesis of CNS disorders by regulating transcription, translation, and signaling pathways, suggesting that it is a promising biomarker and therapeutic target for these disorders. This article reviews the functions and mechanisms of lncRNA H19 in various CNS disorders, including cerebral ischemia, cerebral hemorrhage, glioma, pituitary adenoma, neuroblastoma, Parkinson's disease, Alzheimer's disease, traumatic spinal cord injury, neuropathic pain, and temporal lobe epilepsy, to provide a theoretical basis for further research on the role of lncRNA H19 in CNS disorders.
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Wan J, Guo C, Fang H, Xu Z, Hu Y, Luo Y. Autophagy-Related Long Non-coding RNA Is a Prognostic Indicator for Bladder Cancer. Front Oncol 2021; 11:647236. [PMID: 33869042 PMCID: PMC8049181 DOI: 10.3389/fonc.2021.647236] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 02/12/2021] [Indexed: 12/15/2022] Open
Abstract
Bladder cancer (BC) is one of the most common malignant urinary system tumors, and its prognosis is poor. In recent years, autophagy has been closely linked to the development of BC. Therefore, we investigated the potential prognostic role of autophagy-related long non-coding RNA (lncRNA) in patients with BC. We obtained the lncRNA information and autophagy genes, respectively, from The Cancer Genome Atlas (TCGA) data set and the human autophagy database (HADb) and performed a co-expression analysis to identify autophagy gene-associated lncRNAs. Then, we divided the data into training group and testing group. In the training group, 15 autophagy-related lncRNAs were found to have a prognostic value (AC026369.3, USP30-as1, AC007991.2, AC104785.1, AC010503.4, AC037198.1, AC010331.1, AF131215.6, AC084357.2, THUMPD3-AS1, U62317.4, MAN1B1-DTt, AC024060.1, AL662844.4, and AC005229.4). The patients were divided into low-risk group and high-risk group based on the prognostic lncRNAs. The overall survival (OS) time for the high-risk group was shorter than that for the low-risk group [risk ratio (hazard ratio, HR) = 1.08, 95% CI: 1.06-1.10; p < 0.0001]. Using our model, the defined risk value can predict the prognosis of a patient. Next, the model was assessed in the TCGA testing group to further validate these results. A total of 203 patients with BC were recruited to verify the lncRNA characteristics. We divided these patients into high-risk group and low-risk group. The results of testing data set show that the survival time of high-risk patients is shorter than that of low-risk patients. In the training group, the area under the curve (AUC) was more than 0.7, indicating a high level of accuracy. The AUC for a risk model was greater than that for each clinical feature alone, indicating that the risk value of a model was the best indicator for predicting the prognosis. Further training data analysis showed that the gene set was significantly enriched in cancer-related pathways, including actin cytoskeleton regulation and gap junctions. In conclusion, our 15 autophagy-related lncRNAs have a prognostic potential for BC, and may play key roles in the biology of BC.
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Affiliation(s)
- Jiaming Wan
- Department of Urology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Cheng Guo
- Department of Otorhinolaryngology Head and Neck Surgery, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Hongpeng Fang
- Department of Urology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Zhongye Xu
- Department of Urology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yongwei Hu
- Department of Urology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yun Luo
- Department of Urology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
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Cao H, Chen J, Lai X, Liu T, Qiu P, Que S, Huang Y. Circular RNA expression profile in human primary multiple intracranial aneurysm. Exp Ther Med 2021; 21:239. [PMID: 33603847 PMCID: PMC7851595 DOI: 10.3892/etm.2021.9670] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 12/08/2020] [Indexed: 12/17/2022] Open
Abstract
Primary multiple intracranial aneurysm (MIA) is a vascular disease that frequently leads to fatal vascular rupture and subarachnoid hemorrhage. However, the epigenetic regulation associated with MIA has remained largely elusive. Circular RNAs (circRNAs) serve important roles in cardiovascular diseases; however, their association with MIA has remained to be investigated. The present study initially aimed to explore novel mechanisms of MIA through examining circRNA expression profiles. Comprehensive circRNA expression profiles were detected by RNA sequencing (RNA-Seq) in human peripheral blood mononuclear cells. The RNA-Seq results were validated by reverse transcription-quantitative PCR. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses suggested the functions of these circRNAs. A competing endogenous RNA network was constructed to reveal the circRNA-microRNA-mRNA relationship. Among the 3,328 differentially expressed circRNAs between the MIA and matched control groups, 60 exhibited significant expression changes (|log2 fold change|≥2; P<0.05). Among these 60 circRNAs, 20 were upregulated, while the other 40 were downregulated. A number of downregulated circRNAs were involved in inflammation. The most significant KEGG pathway was ‘leukocyte transendothelial migration’. The circRNAs Homo sapiens (hsa)_circ_0135895, hsa_circ_0000682 and hsa_circ_0000690, which were also associated with the above-mentioned pathway, were indicated to be able to regulate protein tyrosine kinase 2, protein kinase Cβ and integrin subunit αL, respectively. To the best of our knowledge, the present study was the first to perform a circRNA sequencing analysis of MIA. The results specifically predicted the regulatory role of circRNAs in the pathogenesis of MIA. ‘Leukocyte transendothelial migration’ may be critical for the pathogenesis of MIA.
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Affiliation(s)
- Huimin Cao
- Central Laboratory, Longyan First Hospital Affiliated to Fujian Medical University, Longyan, Fujian 364000, P.R. China
| | - Jia Chen
- Central Laboratory, Longyan First Hospital Affiliated to Fujian Medical University, Longyan, Fujian 364000, P.R. China
| | - Xiaoyan Lai
- Department of Neurosurgery, Longyan First Hospital Affiliated to Fujian Medical University, Longyan, Fujian 364000, P.R. China
| | - Tianqin Liu
- Department of Neurosurgery, Longyan First Hospital Affiliated to Fujian Medical University, Longyan, Fujian 364000, P.R. China
| | - Ping Qiu
- Department of Neurosurgery, Longyan First Hospital Affiliated to Fujian Medical University, Longyan, Fujian 364000, P.R. China
| | - Shuanglin Que
- Department of Neurosurgery, Longyan First Hospital Affiliated to Fujian Medical University, Longyan, Fujian 364000, P.R. China
| | - Yanming Huang
- Department of Neurosurgery, Longyan First Hospital Affiliated to Fujian Medical University, Longyan, Fujian 364000, P.R. China
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Pan W, Gao Y, Wan W, Xiao W, You C. LncRNA SAMMSON Overexpression Suppresses Vascular Smooth Muscle Cell Proliferation via Inhibiting miR-130a Maturation to Participate in Intracranial Aneurysm. Neuropsychiatr Dis Treat 2021; 17:1793-1799. [PMID: 34113109 PMCID: PMC8187098 DOI: 10.2147/ndt.s311499] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 05/21/2021] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND MiR-130a is a recently identified critical player in vascular smooth muscle cell (VSMC) proliferation, which participates in intracranial aneurysm (IA). However, the involvement of miR-130a in IA and its upstream regulator are unknown. Our preliminary sequencing analysis revealed a close correlation between miR-130a and lncRNA SAMMSON across IA samples. Therefore, we further studied the crosstalk between SAMMSON and miR-130a in IA. METHODS SAMMSON and miR-130a expression were measured using RT-qPCR. SAMMSON subcellular location was analyzed with nuclear fractionation assay. Their direct interaction was explored with RNA pull-down assay. The role of SAMMSON in miR-130a maturation was studied with overexpression analysis. VSMC cell proliferation was analyzed with BrdU assay. RESULTS SAMMSON and premature miR-130a were deregulated in IA, while mature miR-130a was upregulated in IA. SAMMSON is localized in both the nucleus and cytoplasm, and direct interaction between SAMMSON and miR-130a was observed. SAMMSON overexpression suppressed miR-130a maturation in VSMCs and reduced the enhancing effects of miR-130a on VSMC cell proliferation. CONCLUSION SAMMSON is overexpressed in IA and suppresses VSMC proliferation via inhibiting miR-130a maturation.
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Affiliation(s)
- Wen Pan
- Brain Center, Shougang Shuigang General Hospital, Liupanshui City, Guizhou Province, 553000, People's Republic of China
| | - Yuan Gao
- Department of Neurosurgery, Liupanshui People's Hospital, Liupanshui City, Guizhou Province, 553001, People's Republic of China
| | - Weifeng Wan
- Department of Neurosurgery, Affiliated Hospital of Southwest Medical University, Luzhou City, Sichuan Province, 646000, People's Republic of China
| | - Wenfeng Xiao
- Department of Neurosurgery, Sichuan Mianyang 404 Hospital, Mianyang City, Sichuan Province, 510700, People's Republic of China
| | - Chao You
- Department of Neurosurgery West China Hospital, Sichuan University, Chengdu Province, 610041, People's Republic of China
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Sun Y, Wen Y, Ruan Q, Yang L, Huang S, Xu X, Cai Y, Li H, Wu S. Exploring the association of long noncoding RNA expression profiles with intracranial aneurysms, based on sequencing and related bioinformatics analysis. BMC Med Genomics 2020; 13:147. [PMID: 33023605 PMCID: PMC7542138 DOI: 10.1186/s12920-020-00805-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 09/29/2020] [Indexed: 12/23/2022] Open
Abstract
Background The present study aims to investigate the complete long non-coding RNA (lncRNA) and messenger RNA (mRNA) expression profiles in Intracranial aneurysm (IA) patients and controls by RNA sequencing, which reveals the lncRNA with predictive value for IA risk. Methods The comprehensive lncRNA and mRNA expression profiles were detected by RNA-Seq in human IA walls and superficial temporal arteries (STAs), followed by bioinformatics analyses, such as GO analysis, KEGG pathway analysis, and CNC network construction. Subsequently, qRT-PCR was used to profile the expression levels of selected lncRNA (lncRNA ENST000000576153, lncRNA ENST00000607042, lncRNA ENST00000471220, lncRNA ENST00000478738, lncRNA MALAT1, lncRNA ENST00000508090 and lncRNA ENST00000579688) in 30 (small) or 130 (large) peripheral blood leukocytes, respectively. Multivariate logistic regression was utilized to analyze the effects of lncRNA on IA. Receiver operating characteristic (ROC) curve was further drawn to explore the value of lncRNA in predicting IA. Results Totally 900 up-regulated and 293 down-regulated lncRNAs, as well as 1297 up-regulated and 831 down-regulated mRNAs were discovered in sequencing. Enrichment analyses revealed that they were actively involved in immune/inflammatory response and cell adhesion/extracellular matrix. Co-expression analysis and further enrichment analyses showed that five candidate lncRNAs might participate in IA’s inflammatory response. Besides, after controlling other conventional risk factors, multivariate logistic regression analysis disclosed that low expression of lncRNA ENST00000607042, lncRNA ENST00000471220, lncRNA ENST00000478738, lncRNA MALAT1 in peripheral blood leukocytes were independent risk factors for IA. LncRNA ENST00000607042 has superior diagnostic value for IA. Conclusions This study reveals the complete lncRNAs expression profiles in IA. The inflammatory response was closely related to IA. Besides, lncRNA ENST00000607042 might be a novel biomarker for IA risk.
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Affiliation(s)
- Yi Sun
- Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Minhou County, Fuzhou, 350122, China
| | - Yeying Wen
- Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Minhou County, Fuzhou, 350122, China
| | - Qishuang Ruan
- Department of Orthopedics, Fujian Medical University Union Hospital, Fuzhou, 350001, China
| | - Le Yang
- Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Minhou County, Fuzhou, 350122, China
| | - Shuna Huang
- Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Minhou County, Fuzhou, 350122, China
| | - Xingyan Xu
- Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Minhou County, Fuzhou, 350122, China
| | - Yingying Cai
- Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Minhou County, Fuzhou, 350122, China
| | - Huangyuan Li
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Minhou County, Fuzhou, 350122, China.
| | - Siying Wu
- Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Minhou County, Fuzhou, 350122, China.
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Jia Q, Yan S, Huang J, Xu S. Restored microRNA-133a-3p or Depleted PSAT1 Restrains Endothelial Cell Damage-Induced Intracranial Aneurysm Via Suppressing the GSK3β/β-Catenin Pathway. NANOSCALE RESEARCH LETTERS 2020; 15:177. [PMID: 32902711 PMCID: PMC7479668 DOI: 10.1186/s11671-020-03396-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 08/03/2020] [Indexed: 06/11/2023]
Abstract
It is unclear about the functional role of microRNA-133a-3p (miR-133a-3p) in intracranial aneurysm (IA). Hence, the aim of the present study was to investigate the regulatory role of miR-133a-3p on the regulation of vascular endothelial injury-induced IA through phosphoserine aminotransferase 1 (PSAT1)/glycogen synthase kinase 3β (GSK3β)/β-catenin signaling pathway. Normal intracranial arteriole tissues and IA tissues were gathered from patients with brain trauma and IA. The expression of miR-133a-3p, PSAT1, GSK3β, and β-catenin in tissues was determined by RT-qPCR and western blot analysis. The endothelial cells (ECs) of the human IA were cultured and treated with miR-133a-3p mimic and si-PSAT1 to determine their functions in endothelial cell migration, apoptosis, and proliferation. The expression of miR-133a-3p, PSAT1, GSK3β, β-catenin, Ki-67, CyclinD1, Bax, and Bcl-2 in ECs were tested by RT-qPCR or western blot analysis. Moreover, IA rat model was established to detect the pathological changes and the expression of miR-133a-3p, PSAT1, GSK3β, β-catenin, VEGF, and MMP-9 in IA tissues in vivo. Expression of miR-133a-3p was related to the number and size of IA. MiR-133a-3p expression was deceased and the PSAT1, GSK3β, and β-catenin expression was raised in IA. Restored miR-133a-3p and depleted PSAT1 alleviated the pathological change; reduced PSAT1, GSK3β, and β-catenin expression in IA; suppressed apoptosis and advanced proliferation and migration of IA ECs, as well as reduced VEGF and MMP-9 expression in IA tissues in vivo. Our study suggests that overexpression of miR-133a-3p or downregulation of PSAT1 restrains endothelial cell damage and advances endothelial cell proliferation via inhibiting the GSK3β/β-catenin pathway in IA. MiR-133a-3p might be a potential candidate marker and therapeutic target for IA.
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Affiliation(s)
- Qiang Jia
- Department of Neurosurgery, Tianjin Huanhu Hospital, Tianjin, 300050, Tianjin, China
| | - Shixin Yan
- Department of Radiology, Tianjin Huanhu Hospital, Tianjin, 300050, Tianjin, China
| | - Jie Huang
- Department of Neurology, Cangzhou People's Hospital, 20 North Street, Cangzhou, 061000, Hebei, China.
| | - Shixin Xu
- Clinical Laboratory, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, 314 An shan xin Road, Nan Kai District, Tianjin, 300000, Tianjin, China.
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13
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Gao G, Zhang Y, Yu J, Chen Y, Gu D, Niu C, Fu X, Wei J. Long Non-coding RNA MALAT1/microRNA-143/VEGFA Signal Axis Modulates Vascular Endothelial Injury-Induced Intracranial Aneurysm. NANOSCALE RESEARCH LETTERS 2020; 15:139. [PMID: 32602008 PMCID: PMC7324453 DOI: 10.1186/s11671-020-03357-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 05/20/2020] [Indexed: 05/10/2023]
Abstract
The roles of some long non-coding RNAs (lncRNAs) in intracranial aneurysm (IA) have been investigated in many studies. The aim of this study is to elucidate the mechanism of lncRNA metastasis-associated lung adenocarcinoma transcript 1 (MALAT1)/microRNA-143 (miR-143)/vascular endothelial growth factor-A (VEGFA) signal axis in vascular endothelial injury-induced IA. MALAT1, miR-143, and VEGFA expression in IA tissues and normal arterial tissues were detected. Matrix metalloproteinase 9 (MMP-9) in tissues, von Willebrand factor (vWF) in serum and tissues, and endothelin-1 (ET-1) in serum were detected. The modeled IA rats were injected with silenced or overexpressed MALAT1 for detecting vascular endothelial injury. Vascular endothelial cells from patients with IA were abstracted and transfected with silenced or overexpressed MALAT1 to verify the impacts of MALAT1 on cell viability and apoptosis. The connections among MALAT1, miR-143, and VEGFA were verified by online prediction, luciferase activity, and RNA-pull down assays. Overexpression of MALAT1 and VEGFA and poor expression of miR-143 were found in IA tissues. Downregulation of MALAT1 inhibited blood pressure, the expression of ET-1, vWF, and MMP-9, as well as the apoptotic index of vascular endothelial cells of rats with IA. Downregulated MALAT1 inhibited apoptosis and promoted viability of vascular endothelial cells in IA. MALAT1 bound to miR-143 and miR-143 targeted VEGFA. This study suggests that MALAT1 elevates VEGFA expression through competitive binding to miR-143, thereby boosting apoptosis and attenuating viability of vascular endothelial cells in IA.
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Affiliation(s)
- Ge Gao
- Department of Neurosurgery, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, 17 Lu' jiang Road, Hefei, 230001, Anhui, People's Republic of China.
- Department of Neurosurgery, Anhui Provincial Hospital Affiliated to Anhui Medical University, Hefei, Anhui, People's Republic of China.
| | - Yang Zhang
- Department of Neurosurgery, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, 17 Lu' jiang Road, Hefei, 230001, Anhui, People's Republic of China
- Department of Neurosurgery, Anhui Provincial Hospital Affiliated to Anhui Medical University, Hefei, Anhui, People's Republic of China
| | - Jian Yu
- Department of Neurosurgery, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, 17 Lu' jiang Road, Hefei, 230001, Anhui, People's Republic of China
- Department of Neurosurgery, Anhui Provincial Hospital Affiliated to Anhui Medical University, Hefei, Anhui, People's Republic of China
| | - Yu Chen
- Department of Neurosurgery, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, 17 Lu' jiang Road, Hefei, 230001, Anhui, People's Republic of China
- Department of Neurosurgery, Anhui Provincial Hospital Affiliated to Anhui Medical University, Hefei, Anhui, People's Republic of China
| | - Daqun Gu
- Department of Neurosurgery, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, 17 Lu' jiang Road, Hefei, 230001, Anhui, People's Republic of China
- Department of Neurosurgery, Anhui Provincial Hospital Affiliated to Anhui Medical University, Hefei, Anhui, People's Republic of China
| | - Chaoshi Niu
- Department of Neurosurgery, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, 17 Lu' jiang Road, Hefei, 230001, Anhui, People's Republic of China
- Department of Neurosurgery, Anhui Provincial Hospital Affiliated to Anhui Medical University, Hefei, Anhui, People's Republic of China
| | - Xianming Fu
- Department of Neurosurgery, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, 17 Lu' jiang Road, Hefei, 230001, Anhui, People's Republic of China
- Department of Neurosurgery, Anhui Provincial Hospital Affiliated to Anhui Medical University, Hefei, Anhui, People's Republic of China
| | - Jianjun Wei
- Department of Neurosurgery, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, 17 Lu' jiang Road, Hefei, 230001, Anhui, People's Republic of China
- Department of Neurosurgery, Anhui Provincial Hospital Affiliated to Anhui Medical University, Hefei, Anhui, People's Republic of China
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Transcriptome-wide Profiling of Cerebral Cavernous Malformations Patients Reveal Important Long noncoding RNA molecular signatures. Sci Rep 2019; 9:18203. [PMID: 31796831 PMCID: PMC6890746 DOI: 10.1038/s41598-019-54845-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 11/20/2019] [Indexed: 12/13/2022] Open
Abstract
Cerebral cavernous malformations (CCMs) are low-flow vascular malformations in the brain associated with recurrent hemorrhage and seizures. The current treatment of CCMs relies solely on surgical intervention. Henceforth, alternative non-invasive therapies are urgently needed to help prevent subsequent hemorrhagic episodes. Long non-coding RNAs (lncRNAs) belong to the class of non-coding RNAs and are known to regulate gene transcription and involved in chromatin remodeling via various mechanism. Despite accumulating evidence demonstrating the role of lncRNAs in cerebrovascular disorders, their identification in CCMs pathology remains unknown. The objective of the current study was to identify lncRNAs associated with CCMs pathogenesis using patient cohorts having 10 CCM patients and 4 controls from brain. Executing next generation sequencing, we performed whole transcriptome sequencing (RNA-seq) analysis and identified 1,967 lncRNAs and 4,928 protein coding genes (PCGs) to be differentially expressed in CCMs patients. Among these, we selected top 6 differentially expressed lncRNAs each having significant correlative expression with more than 100 differentially expressed PCGs. The differential expression status of the top lncRNAs, SMIM25 and LBX2-AS1 in CCMs was further confirmed by qRT-PCR analysis. Additionally, gene set enrichment analysis of correlated PCGs revealed critical pathways related to vascular signaling and important biological processes relevant to CCMs pathophysiology. Here, by transcriptome-wide approach we demonstrate that lncRNAs are prevalent in CCMs disease and are likely to play critical roles in regulating important signaling pathways involved in the disease progression. We believe, that detailed future investigations on this set of identified lncRNAs can provide useful insights into the biology and, ultimately, contribute in preventing this debilitating disease.
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Xie G, Meng T, Luo Y, Liu Z. SKF-LDA: Similarity Kernel Fusion for Predicting lncRNA-Disease Association. MOLECULAR THERAPY. NUCLEIC ACIDS 2019; 18:45-55. [PMID: 31514111 PMCID: PMC6742806 DOI: 10.1016/j.omtn.2019.07.022] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 07/13/2019] [Accepted: 07/24/2019] [Indexed: 01/24/2023]
Abstract
Recently, prediction of lncRNA-disease associations has attracted more and more attentions. Various computational models have been proposed; however, there is still room to improve the prediction accuracy. In this paper, we propose a kernel fusion method with different types of similarities for the lncRNAs and diseases. The expression similarity and cosine similarity are used for lncRNAs, and the semantic similarity and cosine similarity are used for the diseases. To eliminate the noise effect, a neighbor constraint is enforced to refine all the similarity matrices before fusion. Experimental results show that the proposed similarity kernel fusion (SKF)-LDA method has the superiority performance in terms of AUC values and other measurements. In the schemes of LOOCV and 5-fold CV, AUC values of SKF-LDA achieve 0.9049 and 0.8743±0.0050 respectively. In addition, the conducted case studies of three diseases (hepatocellular carcinoma, lung cancer, and prostate cancer) show that SKF-LDA can predict related lncRNAs accurately.
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Affiliation(s)
- Guobo Xie
- School of Computer Science, Guangdong University of Technology, Guangzhou, China
| | - Tengfei Meng
- School of Computer Science, Guangdong University of Technology, Guangzhou, China
| | - Yu Luo
- School of Computer Science, Guangdong University of Technology, Guangzhou, China.
| | - Zhenguo Liu
- Department of Thoracic Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China.
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16
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Huang Q, Huang QY, Sun Y, Wu S. High-Throughput Data Reveals Novel Circular RNAs via Competitive Endogenous RNA Networks Associated with Human Intracranial Aneurysms. Med Sci Monit 2019; 25:4819-4830. [PMID: 31254341 PMCID: PMC6615076 DOI: 10.12659/msm.917081] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Background Little is known about epigenetic regulation of intracranial aneurysms (IAs). Circular non-coding RNAs (circRNAs) play crucial roles in cardiovascular diseases, but they have received scant research attention regarding their relationship with IAs. This study aimed to explore new pathological mechanisms of IA through circRNA expression profiles and to provide novel therapeutic strategies. Material/Methods The comprehensive circRNA and mRNA expression profiles were detected by RNA-Seq in human IA walls and superficial temporal arteries (STAs). The RNA-Seq findings were validated by qRT-PCR. GO and KEGG analyses indicated the functions of these circRNAs. A competing endogenous RNA (ceRNA) network was constructed to reveal the circRNA-miRNA-mRNA relationship. Two newly discovered circRNAs were further detected in peripheral blood of IA patients and healthy people to clarify their expression patterns in the periphery. Results Many differentially expressed circRNAs are closely involved in immune/inflammatory response and cell adhesion/adherens junction. The novel circRNAs (hsa_circ_0072309 and hsa_circ_0008433) regulate DDR2 and MMP2, respectively, which are associated with SMC dysfunction and vascular injury through ceRNA. Moreover, we found differential expression of these 2 circRNAs in the peripheral blood of IA patients, and the expression pattern of hsa_circ_0072309 had central and peripheral consistency. Conclusions To the best of our knowledge, this is the first study to perform circRNA sequencing analysis of IAs. hsa_circ_0072309 and hsa_circ_0008433 are novel and pivotal circRNAs related to IAs. This study provides new insights into therapeutic targets and biomarkers for IA patients.
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Affiliation(s)
- Qing Huang
- The School of Public Health, Fujian Medical University, Fuzhou, Fujian, China (mainland).,The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian, China (mainland)
| | - Qiu-Yu Huang
- The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian, China (mainland)
| | - Yi Sun
- The School of Public Health, Fujian Medical University, Fuzhou, Fujian, China (mainland)
| | - Siying Wu
- The School of Public Health, Fujian Medical University, Fuzhou, Fujian, China (mainland)
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17
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Replication of GWAS Loci Revealed an Increased Risk of BET1L and H19 Polymorphisms with Intracranial Aneurysm. DISEASE MARKERS 2019; 2019:9490639. [PMID: 31275455 PMCID: PMC6589239 DOI: 10.1155/2019/9490639] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 04/25/2019] [Accepted: 05/05/2019] [Indexed: 02/05/2023]
Abstract
A genome-wide association study (GWAS) identified that BET1L rs2280543 at chromosome 11p15.5 was a susceptibility loci of intracranial aneurysm (IA). Long noncoding RNA H19, located in this region, was reported to play a crucial role in the formation of IA. In this study, we aimed to examine whether BET1L rs2280543 and potentially functional polymorphisms in H19 influence the risk of IA. A hospital-based case-control study was performed involving 542 IA patients and 588 age- and gender-matched controls. The BET1L rs2280543 and H19 polymorphisms were genotyped using the TaqMan assay. The BET1L rs2280543 CT, CT/TT genotypes, and T allele were associated with an increased risk of IA (CT vs. CC, adjusted OR = 1.43, 95% CI: 1.08-1.90, P = 0.01; CT/TT vs. CC, adjusted OR = 1.48, 95% CI: 1.12-1.94, P = 0.005; and T vs. C, adjusted OR = 1.44, 95% CI: 1.13-1.83, P = 0.003). Similarly, the H19 rs217727 TT genotype and T allele were associated with an increased risk of IA (TT vs. CC, adjusted OR = 1.90, 95% CI: 1.35-2.67, P < 0.001; T vs. C, adjusted OR = 1.38, 95% CI: 1.16-1.64, P < 0.001). Combined analyses revealed that the rs2280543 CC-rs217727 CT/TT, rs2280543 CT/TT-rs2735971 GG, and rs217727 CT/TT-rs2735971 GG genotypes were related to the risk of IA. Interaction analysis showed that the 3-loci model of rs2280543-rs217727-rs2839698 contributed to an increased risk of IA. These findings suggest that the GWAS-discovered risk loci BET1L rs2280543 may increase IA susceptibility by interacting with lncRNA H19.
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Zhang Y, Tao Y, Liao Q. Long noncoding RNA: a crosslink in biological regulatory network. Brief Bioinform 2019; 19:930-945. [PMID: 28449042 DOI: 10.1093/bib/bbx042] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Indexed: 01/17/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) had been defined as a novel class of functional RNAs longer than 200 nucleotides around a decade ago. It is widely acknowledged that lncRNAs play a significant role in regulation of gene expression, but the biological and molecular mechanisms are diverse and complex, and remain to be determined. Especially, the regulatory network of lncRNAs associated with other biological molecules is still a controversial matter, thus becoming a new frontier of the studies on transcriptome. Recent advance in high-throughput sequencing technologies and bioinformatics approaches may be an accelerator to lift the mysterious veil. In this review, we will outline well-known associations between lncRNAs and other biological molecules, demonstrate the diverse bioinformatics approaches applied in prediction and analysis of lncRNA interaction and perform a case study for lncRNA linc00460 to concretely decipher the lncRNA regulatory network.
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Affiliation(s)
- Yuwei Zhang
- Department of Preventative Medicine, Zhejiang Provincial Key Laboratory of Pathological and Physiological Technology, Medicine School of Ningbo University, Ningbo, Zhejiang, China
| | - Yang Tao
- Department of Preventative Medicine, Zhejiang Provincial Key Laboratory of Pathological and Physiological Technology, Medicine School of Ningbo University, Ningbo, Zhejiang, China
| | - Qi Liao
- Department of Preventative Medicine, Zhejiang Provincial Key Laboratory of Pathological and Physiological Technology, Medicine School of Ningbo University, Ningbo, Zhejiang, China
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Luan F, Chen W, Chen M, Yan J, Chen H, Yu H, Liu T, Mo L. An autophagy-related long non-coding RNA signature for glioma. FEBS Open Bio 2019; 9:653-667. [PMID: 30984540 PMCID: PMC6443865 DOI: 10.1002/2211-5463.12601] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 11/30/2018] [Accepted: 01/21/2019] [Indexed: 12/28/2022] Open
Abstract
Glioma is one of the most common types of malignant primary central nervous system tumor, and prognosis for this disease is poor. As autophagic drugs have been reported to induce glioma cell death, we investigated the potential prognostic role of autophagy-associated long non-coding RNA (lncRNA) in glioma patients. In this study, we obtained 879 lncRNAs and 216 autophagy genes from the Chinese Glioma Genome Atlas microarray, and found that 402 lncRNAs are correlated with the autophagy genes. Subsequently, 10 autophagy-associated lncRNAs with prognostic value (PCBP1-AS1, TP53TG1, DHRS4-AS1, ZNF674-AS1, GABPB1-AS1, DDX11-AS1, SBF2-AS1, MIR4453HG, MAPKAPK5-AS1 and COX10-AS1) were identified in glioma patients using multivariate Cox regression analyses. A prognostic signature was then established based on these prognostic lncRNAs, dividing patients into low-risk and high-risk groups. The overall survival time was shorter in the high-risk group than that in the low-risk group [hazard ratio (HR) = 5.307, 95% CI: 4.195-8.305; P < 0.0001]. Gene set enrichment analysis revealed that the gene sets were significantly enriched in cancer-related pathways, including interleukin (IL) 6/Janus kinase/signal transducer and activator of transcription (STAT) 3 signaling, tumor necrosis factor α signaling via nuclear factor κB, IL2/STAT5 signaling, the p53 pathway and the KRAS signaling pathway. The Cancer Genome Atlas dataset was used to validate that high-risk patients have worse survival outcomes than low-risk patients (HR = 1.544, 95% CI: 1.110-2.231; P = 0.031). In summary, our signature of 10 autophagy-related lncRNAs has prognostic potential for glioma, and these autophagy-related lncRNAs may play a key role in glioma biology.
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Affiliation(s)
- Fangkun Luan
- Department of Neurosurgery Affiliated Tumor Hospital of Guangxi Medical University Nanning China
| | - Wenjie Chen
- Department of Ultrasound Affiliated Tumor Hospital of Guangxi Medical University Nanning China
| | - Miao Chen
- Department of Neurosurgery Affiliated Tumor Hospital of Guangxi Medical University Nanning China
| | - Jun Yan
- Department of Neurosurgery Affiliated Tumor Hospital of Guangxi Medical University Nanning China
| | - Hao Chen
- Department of Neurosurgery Affiliated Tumor Hospital of Guangxi Medical University Nanning China
| | - Haiyue Yu
- Department of Neurosurgery Affiliated Tumor Hospital of Guangxi Medical University Nanning China
| | - Tieqi Liu
- Department of Neurosurgery Affiliated Tumor Hospital of Guangxi Medical University Nanning China
| | - Ligen Mo
- Department of Neurosurgery Affiliated Tumor Hospital of Guangxi Medical University Nanning China
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20
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Ji T, Wang Y, Zhu Y, Gao C, Li X, Li J, Bai F, Bai S. Long noncoding RNA Gm6135 functions as a competitive endogenous RNA to regulate toll‐like receptor 4 expression by sponging miR‐203‐3p in diabetic nephropathy. J Cell Physiol 2018; 234:6633-6641. [PMID: 30295314 DOI: 10.1002/jcp.27412] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Accepted: 08/20/2018] [Indexed: 12/19/2022]
Affiliation(s)
- Ting‐Ting Ji
- Department of Nephrology Qingpu Branch of Zhongshan Hospital Affiliated to Fudan University Shanghai China
| | - Ya‐Kun Wang
- Department of Nephrology Qingpu Branch of Zhongshan Hospital Affiliated to Fudan University Shanghai China
| | - Ying‐Chun Zhu
- Department of Nephrology Qingpu Branch of Zhongshan Hospital Affiliated to Fudan University Shanghai China
| | - Cong‐Pu Gao
- Department of Nephrology Qingpu Branch of Zhongshan Hospital Affiliated to Fudan University Shanghai China
| | - Xiao‐Ying Li
- Department of Nephrology Qingpu Branch of Zhongshan Hospital Affiliated to Fudan University Shanghai China
| | - Ji Li
- Department of Nephrology Qingpu Branch of Zhongshan Hospital Affiliated to Fudan University Shanghai China
| | - Feng Bai
- Department of Endocrinology and Metabolism Huai’an Hospital Affiliated to Xuzhou Medical University and Huai’an Second People’s Hospital Huai’an China
| | - Shou‐Jun Bai
- Department of Nephrology Qingpu Branch of Zhongshan Hospital Affiliated to Fudan University Shanghai China
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Zeng HF, Qiu HY, Feng FB. Long Noncoding RNA LINC01133 Functions as an miR-422a Sponge to Aggravate the Tumorigenesis of Human Osteosarcoma. Oncol Res 2018; 26:335-343. [PMID: 28390115 PMCID: PMC7844760 DOI: 10.3727/096504017x14907375885605] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) have been verified to participate in various types of malignant tumors, including osteosarcoma (OS), which is the most common primary bone tumor with outstanding morbidity. Although an increasing number of lncRNAs have been reported to mediate the occurrence of OS, the potential mechanisms are still unclear. This study intends to uncover the mechanism by which lncRNA LINC01133 functions as an miRNA sponge to mediate OS tumorigenicity. In this study, we found that the expression level of LINC01133 was statistically upregulated in OS tumor tissue and cell lines compared to noncancerous tissues and a normal human osteoplastic cell line. LINC01133 silencing could also observably suppress the proliferation, migration, and invasion of OS cells (HOS and U2-OS). Bioinformatics analysis predicted that LINC01133 specifically targeted miR-422a, which was validated by dual-luciferase reporter assay. Furthermore, functional experiments revealed that miR-422a played a tumor-suppressive role in OS progression and could effectively reverse the function of LINC01133. In summary, our study discovered that lncRNA LINC01133 aggravates the proliferation, migration, and invasion of OS by sponging miR-422a, which provides a novel insight in the tumorigenesis of OS.
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Affiliation(s)
- Hai-Feng Zeng
- *Department of Plastic Surgery, Zhejiang Provincial People’s Hospital, People’s Hospital of Hangzhou Medical College, Hangzhou, P.R. China
| | - Hai-Yan Qiu
- †Department of Endocrinology, Hangzhou First People’s Hospital, Nanjing Medical University, Nanjing, P.R. China
| | - Fa-Bo Feng
- ‡Department of Orthopedics, Zhejiang Provincial People’s Hospital, People’s Hospital of Hangzhou Medical College, Hangzhou, P.R. China
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22
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Aberrant expression of lncRNAs and mRNAs in patients with intracranial aneurysm. Oncotarget 2018; 8:2477-2484. [PMID: 27965470 PMCID: PMC5356817 DOI: 10.18632/oncotarget.13908] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 12/01/2016] [Indexed: 01/14/2023] Open
Abstract
Intracranial aneurysm (IA) is pathological dilatations of the cerebral artery and rupture of IAs can cause subarachnoid hemorrhage, which has a high ratio of fatality and morbidity. However, the pathogenesis of IAs remains unknown. We performed long noncoding RNA (lncRNA) and messenger RNA (mRNA) expression profiles in IA tissues and superficial temporal arteries (STAs). A total of 4129 differentially expressed lncRNAs and 2926 differentially expressed mRNAs were obtained from the microarrays (P < 0.05). Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses showed that up-regulated mRNAs were enriched in immune response, inflammatory response, regulation of immune response and lysosome, et al; while the down-regulated mRNAs were enriched in muscle contraction, smooth muscle contraction, cGMP-PKG signaling pathway and vascular smooth muscle contraction, et al. The lncRNA-mRNA co-expression networks were represented in immune response, inflammatory response, muscle contraction and vascular smooth muscle contraction. These findings may gain insight in the pathogenesis of IAs and provide clues to find key roles for IA patients.
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23
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Wang W, Zhao Z, Yang F, Wang H, Wu F, Liang T, Yan X, Li J, Lan Q, Wang J, Zhao J. An immune-related lncRNA signature for patients with anaplastic gliomas. J Neurooncol 2017; 136:263-271. [PMID: 29170907 DOI: 10.1007/s11060-017-2667-6] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 11/11/2017] [Indexed: 12/26/2022]
Abstract
We investigated immune-related long non-coding RNAs (lncRNAs) that may be exploited as potential therapeutic targets in anaplastic gliomas. We obtained 572 lncRNAs and 317 immune genes from the Chinese Glioma Genome Atlas microarray and constructed immune-related lncRNAs co-expression networks to identify immune-related lncRNAs. Two additional datasets (GSE16011, REMBRANDT) were used for validation. Gene set enrichment analysis and principal component analysis were used for functional annotation. Immune-lncRNAs co-expression networks were constructed. Nine immune-related lncRNAs (SNHG8, PGM5-AS1, ST20-AS1, LINC00937, AGAP2-AS1, MIR155HG, TUG1, MAPKAPK5-AS1, and HCG18) signature was identified in patients with anaplastic gliomas. Patients in the low-risk group showed longer overall survival (OS) and progression-free survival than those in the high-risk group (P < 0.0001; P < 0.0001). Additionally, patients in the high-risk group displayed no-deletion of chromosomal arms 1p and/or 19q, isocitrate dehydrogenase wild-type, classical and mesenchymal TCGA subtype, G3 CGGA subtype, and lower Karnofsky performance score (KPS). Moreover, the signature was an independent factor and was significantly associated with the OS (P = 0.000, hazard ratio (HR) = 1.434). These findings were further validated in two additional datasets (GSE16011, REMBRANDT). Low-risk and high-risk groups displayed different immune status based on principal components analysis. Our results showed that the nine immune-related lncRNAs signature has prognostic value for anaplastic gliomas.
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Affiliation(s)
- Wen Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, No. 6 Tiantan Xili, Dongcheng District, Beijing, 100050, China.,Department of Neurosurgery, The Second Affiliated Hospital of Soochow University, Suzhou, 215123, China.,Chinese Glioma Cooperative Group (CGCG), Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Zheng Zhao
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, 100050, China.,Chinese Glioma Cooperative Group (CGCG), Beijing, China
| | - Fan Yang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, No. 6 Tiantan Xili, Dongcheng District, Beijing, 100050, China.,Beijing Neurosurgical Institute, Capital Medical University, Beijing, 100050, China.,Chinese Glioma Cooperative Group (CGCG), Beijing, China
| | - Haoyuan Wang
- Department of Neurosurgery, The First Affiliated Hospital of Anhui Medical University, Hefei, 230032, China.,Chinese Glioma Cooperative Group (CGCG), Beijing, China
| | - Fan Wu
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, 100050, China.,Chinese Glioma Cooperative Group (CGCG), Beijing, China
| | - Tingyu Liang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, No. 6 Tiantan Xili, Dongcheng District, Beijing, 100050, China.,Beijing Neurosurgical Institute, Capital Medical University, Beijing, 100050, China.,Chinese Glioma Cooperative Group (CGCG), Beijing, China
| | - Xiaoyan Yan
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, 100050, China.,Chinese Glioma Cooperative Group (CGCG), Beijing, China
| | - Jiye Li
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, 100050, China
| | - Qing Lan
- Department of Neurosurgery, The Second Affiliated Hospital of Soochow University, Suzhou, 215123, China
| | - Jiangfei Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, No. 6 Tiantan Xili, Dongcheng District, Beijing, 100050, China. .,Chinese Glioma Cooperative Group (CGCG), Beijing, China. .,China National Clinical Research Center for Neurological Diseases, Beijing, China.
| | - Jizong Zhao
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, No. 6 Tiantan Xili, Dongcheng District, Beijing, 100050, China. .,Department of Neurosurgery, The Second Affiliated Hospital of Soochow University, Suzhou, 215123, China. .,China National Clinical Research Center for Neurological Diseases, Beijing, China.
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Meng YB, He X, Huang YF, Wu QN, Zhou YC, Hao DJ. Long Noncoding RNA CRNDE Promotes Multiple Myeloma Cell Growth by Suppressing miR-451. Oncol Res 2017; 25:1207-1214. [PMID: 28276319 PMCID: PMC7841033 DOI: 10.3727/096504017x14886679715637] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
It has been determined that long noncoding RNAs (lncRNAs) are identified as a potential regulatory factor in multiple tumors as well as multiple myeloma (MM). However, the role of colorectal neoplasia differentially expressed (CRNDE) in the pathogenesis of MM remains unclear. In this study, we found that the CRNDE expression level, in MM samples and cell lines, is higher than that in the control detected by real-time qPCR, which is also closely related to tumor progression and poor survival in MM patients. Knockdown of CRNDE significantly inhibits the proliferative vitality of MM cells (U266 and RPMI-8226), induces cell cycle arrest in the G0/G1 phase, and promotes apoptosis. After being transfected with siRNA, miR-451 expression observably increases. Bioinformatics analysis and luciferase assay reveal the interaction by complementary bonding between CRNDE and miR-451. Pearson’s correlation shows that CRNDE is negatively correlated to miR-451 expression in human MM samples. Subsequently, miR-451 inhibitor rescues the inhibited tumorigenesis induced by CRNDE knockdown. Our study illustrates that lncRNA CRNDE induces the proliferation and antiapoptosis capability of MM by acting as a ceRNA or molecular sponge via negatively targeting miR-451, which could act as a novel diagnostic marker and therapeutic target for MM.
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