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Wang L, Li B, Cheng D. Influence of Long Non-Coding RNAs on Human Oocyte Development. Pharmgenomics Pers Med 2024; 17:337-345. [PMID: 38979513 PMCID: PMC11229482 DOI: 10.2147/pgpm.s449101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 06/12/2024] [Indexed: 07/10/2024] Open
Abstract
Recent research findings have highlighted the pivotal roles played by lncRNAs in both normal human development and disease pathogenesis. LncRNAs are expressed in oocytes and early embryos, and their expression levels change dynamically once the embryonic genome is activated during early human embryonic development. Abnormal expression of lncRNAs was found in follicular fluid, granulosa cells and oocytes of patients, and these lncRNAs were related to cell proliferation and apoptosis, nuclear maturation and follicle development. The expression levels of some lncRNAs in cumulus cells demonstrate correlations with the quality of oocytes and early embryos. This paper aims to present a comprehensive overview of the influence of LncRNAs on the developmental process of human oocytes as well as their involvement in certain infertility-related diseases.
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Affiliation(s)
- Leitong Wang
- Embryo Laboratory, Jinghua Hospital of Shenyang, Shenyang, Liaoning Province, 110000, People’s Republic of China
| | - Baoshan Li
- Embryo Laboratory, Jinghua Hospital of Shenyang, Shenyang, Liaoning Province, 110000, People’s Republic of China
| | - Dongkai Cheng
- Embryo Laboratory, Jinghua Hospital of Shenyang, Shenyang, Liaoning Province, 110000, People’s Republic of China
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2
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Rahimipour Anaraki S, Farzami P, Hosseini Nasab SS, Kousari A, Fazlollahpour Naghibi A, Shariat Zadeh M, Barati R, Taha SR, Karimian A, Nabi-Afjadi M, Yousefi B. Natural products and the balancing act of autophagy-dependent/independent ferroptosis in cancer therapy. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2024; 397:2531-2549. [PMID: 37878043 DOI: 10.1007/s00210-023-02782-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 10/11/2023] [Indexed: 10/26/2023]
Abstract
The control of biological cell death is essential for the body's appropriate growth. The resistance of cells to the apoptotic process presents a new difficulty in the treatment of cancer. To combat cancer cells, researchers are working to find new apoptotic pathways and components to activate. One of the processes of regulated cell death (RCD) is referred to as ferroptosis marked by a decline in the activity of lipid glutathione peroxidase 4 (GPX4) after the buildup of reactive oxygen species (ROS). Since lipid peroxidation is a crucial component of ferroptosis and is required for its start, numerous medicines have been studied, particularly for the treatment of cancer. In this context, autophagy is an additional form of RCD that can govern ferroptosis through shared signaling pathways/factors involved in both mechanisms. In this review, we will explore the molecular mechanisms underlying ferroptosis and its association with autophagy, to gain fresh insights into their interplay in cancer advancement, and the potential of natural products for its treatment.
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Affiliation(s)
| | - Payam Farzami
- Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Ali Kousari
- Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran
| | - Andarz Fazlollahpour Naghibi
- Infectious Diseases and Tropical Medicine Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | | | - Reza Barati
- Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Seyed Reza Taha
- Oncopathology Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Ansar Karimian
- Faculty of Medicine, Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohsen Nabi-Afjadi
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
| | - Bahman Yousefi
- Faculty of Medicine, Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
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3
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Alrefai AA, Abouelenin MAH, Salman MMA, Tawfeek GAE, Abbas MA. Expression profile of long-noncoding RNAs MIR31HG, NKILA, and PACER in systemic lupus erythematosus patients. Clin Biochem 2024; 126:110734. [PMID: 38395324 DOI: 10.1016/j.clinbiochem.2024.110734] [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: 04/13/2023] [Revised: 01/09/2024] [Accepted: 02/20/2024] [Indexed: 02/25/2024]
Abstract
OBJECTIVES Growing evidence suggests that systemic lupus erythematosus (SLE), an organ-damaging systemic autoimmune illness, may be influenced by long-noncoding RNAs (lncRNAs). This study aimed to assess the relative expression of lncRNAs (MIR31HG, NKILA, and PACER) in patients with SLE to evaluate their role in the disease. DESIGN AND METHODS This study involved 70 patients with SLE and 70 apparently healthy control subjects. The expression levels of lnc-MIR31HG, NKILA, and PACER were quantified using real-time PCR. RESULTS Lnc-MIR31HG, NKILA, and PACER were significantly upregulated in SLE cases compared to controls (P < 0.001). ROC curve analysis revealed a 91.43 % sensitivity of PACER for the diagnosis of SLE at a cutoff point of > 1.46, followed by NKILA with 90 % sensitivity at a cutoff point of > 1.16, and MIR31HG with 85.71 % sensitivity at a cutoff point of > 1.43. MIR31HG had the highest sensitivity for the diagnosis of lupus nephritis (86.67 %) at a cutoff point of > 7.19, then NKILA with 80 % sensitivity at a cutoff point of > 8.12, and finally PACER expression with 73.33 % sensitivity at a cutoff point of > 18.19. Moreover, MIR31HG and NKILA revealed a significant correlation with albumin/creatinine ratio, estimated glomerular filtration rate, and the SLEDAI score. Regression analysis revealed the potential roles of MIR31HG, NKILA, and PACER expression as predictors for SLE. CONCLUSION An upregulated lncRNA panel (MIR31HG, NKILA, and PACER) could play a role in the pathogenesis and, hence, the predispositiontoSLE. MIR31HG and NKILA can serve as prognostic markers significantly linked with disease activity.
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Affiliation(s)
- Abeer A Alrefai
- Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Menoufia University, Menoufia, Egypt; Department of Biochemistry- Faculty of Medicine, Umm-Al Qura University, Saudi Arabia.
| | - Mai A H Abouelenin
- Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Menoufia University, Menoufia, Egypt.
| | - Maha M A Salman
- Department of Physical Medicine, Rheumatology and Rehabilitation, Faculty of Medicine, Menoufia University, Menoufia, Egypt.
| | - Gehan A E Tawfeek
- Department of Clinical Pathology, Faculty of Medicine, Menoufia University, Menoufia, Egypt
| | - Mona A Abbas
- Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Menoufia University, Menoufia, Egypt.
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4
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Yarahmadi G, Tavakoli Ataabadi S, Dashti Z, Dehghanian M. A review on expression and regulatory mechanisms of miR-337-3p in cancer. J Biomol Struct Dyn 2024:1-10. [PMID: 38500239 DOI: 10.1080/07391102.2024.2329294] [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: 09/04/2023] [Accepted: 03/06/2024] [Indexed: 03/20/2024]
Abstract
A group of diseases generally referred to as cancer represents a serious threat to people's health all over the world and has a significant negative influence on every aspect of the lives of patients. The development of cancer is influenced by several environmental, genetic, and epigenetic factors. MicroRNAs (miRNAs), a class of non-coding RNAs, can alter the expression of genes involved in cell proliferation, migration, metastasis, and apoptosis, lead to the pathogenesis of cancer. Additionally, several effectors modify miRNAs directly, including methylation, circular RNAs, and long non-coding RNAs (lncRNAs). In this review, we have explained the role of mir-337-3p in the pathways related to the pathogenesis of different cancers. Studying the functional role of miR-337-3p is necessary for detecting novel molecules as tumor markers and discovering novel targets for cancer treatment.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ghafour Yarahmadi
- Department of Medical Genetics, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Sadegh Tavakoli Ataabadi
- Department of Medical Genetics School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Zahra Dashti
- Department of Medical Genetics, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
- Department of Genetics, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences Campus, Yazd, Iran
| | - Mehran Dehghanian
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
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5
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Teixeira LCR, Mamede I, Luizon MR, Gomes KB. Role of long non-coding RNAs in the pathophysiology of Alzheimer's disease and other dementias. Mol Biol Rep 2024; 51:270. [PMID: 38302810 DOI: 10.1007/s11033-023-09178-7] [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: 11/04/2023] [Accepted: 12/18/2023] [Indexed: 02/03/2024]
Abstract
Dementia is the term used to describe a group of cognitive disorders characterized by a decline in memory, thinking, and reasoning abilities that interfere with daily life activities. Examples of dementia include Alzheimer's Disease (AD), Frontotemporal dementia (FTD), Amyotrophic lateral sclerosis (ALS), Vascular dementia (VaD) and Progressive supranuclear palsy (PSP). AD is the most common form of dementia. The hallmark pathology of AD includes formation of β-amyloid (Aβ) oligomers and tau hyperphosphorylation in the brain, which induces neuroinflammation, oxidative stress, synaptic dysfunction, and neuronal apoptosis. Emerging studies have associated long non-coding RNAs (lncRNAs) with the pathogenesis and progression of the neurodegenerative diseases. LncRNAs are defined as RNAs longer than 200 nucleotides that lack the ability to encode functional proteins. LncRNAs play crucial roles in numerous biological functions for their ability to interact with different molecules, such as proteins and microRNAs, and subsequently regulate the expression of their target genes at transcriptional and post-transcriptional levels. In this narrative review, we report the function and mechanisms of action of lncRNAs found to be deregulated in different types of dementia, with the focus on AD. Finally, we discuss the emerging role of lncRNAs as biomarkers of dementias.
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Affiliation(s)
- Lívia Cristina Ribeiro Teixeira
- Department of Clinical and Toxicological Analysis, Faculty of Pharmacy, Federal University of Minas Gerais, Antônio Carlos Avenue, 6627, Pampulha, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Izabela Mamede
- Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Marcelo Rizzatti Luizon
- Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Karina Braga Gomes
- Department of Clinical and Toxicological Analysis, Faculty of Pharmacy, Federal University of Minas Gerais, Antônio Carlos Avenue, 6627, Pampulha, Belo Horizonte, Minas Gerais, 31270-901, Brazil.
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6
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Zhang Y, Wang Q, Xue H, Guo Y, Wei S, Li F, Gong L, Pan W, Jiang P. Epigenetic Regulation of Autophagy in Bone Metabolism. FUNCTION 2024; 5:zqae004. [PMID: 38486976 PMCID: PMC10935486 DOI: 10.1093/function/zqae004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 01/18/2024] [Accepted: 01/24/2024] [Indexed: 03/17/2024] Open
Abstract
The skeletal system is crucial for supporting bodily functions, protecting vital organs, facilitating hematopoiesis, and storing essential minerals. Skeletal homeostasis, which includes aspects such as bone density, structural integrity, and regenerative processes, is essential for normal skeletal function. Autophagy, an intricate intracellular mechanism for degrading and recycling cellular components, plays a multifaceted role in bone metabolism. It involves sequestering cellular waste, damaged proteins, and organelles within autophagosomes, which are then degraded and recycled. Autophagy's impact on bone health varies depending on factors such as regulation, cell type, environmental cues, and physiological context. Despite being traditionally considered a cytoplasmic process, autophagy is subject to transcriptional and epigenetic regulation within the nucleus. However, the precise influence of epigenetic regulation, including DNA methylation, histone modifications, and non-coding RNA expression, on cellular fate remains incompletely understood. The interplay between autophagy and epigenetic modifications adds complexity to bone cell regulation. This article provides an in-depth exploration of the intricate interplay between these two regulatory paradigms, with a focus on the epigenetic control of autophagy in bone metabolism. Such an understanding enhances our knowledge of bone metabolism-related disorders and offers insights for the development of targeted therapeutic strategies.
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Affiliation(s)
- Yazhou Zhang
- Department of Foot and Ankle Surgery, Tengzhou Central People’s Hospital, Tengzhou 277500, China
| | - Qianqian Wang
- Department of Pediatric Intensive Care Unit, Tengzhou Central People’s Hospital, Tengzhou 277500, China
| | - Hongjia Xue
- Department of Computer Science, University College London, London, WC1E 6BT, UK
| | - Yujin Guo
- Institute of Clinical Pharmacy & Pharmacology, Jining First People’s Hospital, Jining 272000, China
| | - Shanshan Wei
- Department of Pharmacy, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250000, China
- Department of Graduate, Shandong Academy of Medical Sciences, Shandong First Medical University, Jinan 250000, China
| | - Fengfeng Li
- Department of Neurosurgery, Tengzhou Central People’s Hospital, Tengzhou 277500, China
| | - Linqiang Gong
- Department of Gastroenterology, Tengzhou Central People's Hospital, Tengzhou 277500, China
| | - Weiliang Pan
- Department of Foot and Ankle Surgery, Tengzhou Central People’s Hospital, Tengzhou 277500, China
| | - Pei Jiang
- Translational Pharmaceutical Laboratory, Jining First People’s Hospital, Shandong First Medical University, Jining 272000, China
- Institute of Translational Pharmacy, Jining Medical Research Academy, Jining 272000, China
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Adiga D, Eswaran S, Sriharikrishnaa S, Khan NG, Prasada Kabekkodu S, Kumar D. Epigenetics of Alzheimer’s Disease: Past, Present and Future. ENZYMATIC TARGETS FOR DRUG DISCOVERY AGAINST ALZHEIMER'S DISEASE 2023:27-72. [DOI: 10.2174/9789815136142123010005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/02/2024]
Abstract
Alzheimer’s disease (AD) exemplifies a looming epidemic lacking effective
treatment and manifests with the accumulation of neurofibrillary tangles, amyloid-β
plaques, neuroinflammation, behavioral changes, and acute cognitive impairments. It is
a complex, multifactorial disorder that arises from the intricate interaction between
environment and genetic factors, restrained via epigenetic machinery. Though the
research progress has improved the understanding of clinical manifestations and
disease advancement, the causal mechanism of detrimental consequences remains
undefined. Despite the substantial improvement in recent diagnostic modalities, it is
challenging to distinguish AD from other forms of dementia. Accurate diagnosis is a
major glitch in AD as it banks on the symptoms and clinical criteria. Several studies are
underway in exploring novel and reliable biomarkers for AD. In this direction,
epigenetic alterations have transpired as key modulators in AD pathogenesis with the
impeding inferences for the management of this neurological disorder. The present
chapter aims to discuss the significance of epigenetic modifications reported in the
pathophysiology of AD such as DNA methylation, hydroxy-methylation, methylation
of mtDNA, histone modifications, and noncoding RNAs. Additionally, the chapter also
describes the possible therapeutic avenues that target epigenetic modifications in AD.
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Affiliation(s)
- Divya Adiga
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy
of Higher Education (MAHE), Manipal – 576104, Karnataka, India
| | - Sangavi Eswaran
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy
of Higher Education (MAHE), Manipal – 576104, Karnataka, India
| | - S. Sriharikrishnaa
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy
of Higher Education (MAHE), Manipal – 576104, Karnataka, India
| | - Nadeem G. Khan
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy
of Higher Education (MAHE), Manipal – 576104, Karnataka, India
| | - Shama Prasada Kabekkodu
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy
of Higher Education (MAHE), Manipal – 576104, Karnataka, India
| | - Dileep Kumar
- Department of Pharmaceutical Chemistry, Poona College of Pharmacy, Bharati Vidyapeeth
(Deemed to be University), Erandwane, Pune – 411038, Maharashtra, India
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8
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Hu J, Liu J, Zhou S, Luo H. A review on the role of gamma-butyrobetaine hydroxylase 1 antisense RNA 1 in the carcinogenesis and tumor progression. Cancer Cell Int 2023; 23:263. [PMID: 37925403 PMCID: PMC10625699 DOI: 10.1186/s12935-023-03113-3] [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: 08/02/2023] [Accepted: 10/27/2023] [Indexed: 11/06/2023] Open
Abstract
Gamma-butyrobetaine hydroxylase 1 antisense RNA 1 (BBOX1-AS1), located on human chromosome 11 p14, emerges as a critical player in tumorigenesis with diverse oncogenic effects. Aberrant expression of BBOX1-AS1 intricately regulates various cellular processes, including cell growth, epithelial-mesenchymal transition, migration, invasion, metastasis, cell death, and stemness. Notably, the expression of BBOX1-AS1 was significantly correlated with clinical-pathological characteristics and tumor prognoses, and it could also be used for the diagnosis of lung and esophageal cancers. Through its involvement in the ceRNA network, BBOX1-AS1 competitively binds to eight miRNAs in ten different cancer types. Additionally, BBOX1-AS1 can directly modulate downstream protein-coding genes or act as an mRNA stabilizer. The implications of BBOX1-AS1 extend to critical signaling pathways, including Hedgehog, Wnt/β-catenin, and MELK/FAK pathways. Moreover, it influences drug resistance in hepatocellular carcinoma. The present study provides a systematic review of the clinical significance of BBOX1-AS1's aberrant expression in diverse tumor types. It sheds light on the intricate molecular mechanisms through which BBOX1-AS1 influences cancer initiation and progression and outlines potential avenues for future research in this field.
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Affiliation(s)
- Juan Hu
- Medical Service Division, The Second Affiliated Hospital of Nanchang University, Nanchang, 330000, Jiangxi, China
| | - Jipeng Liu
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Nanchang University, 1 Minde Road, Nanchang, 330000, Jiangxi, People's Republic of China
| | - Siwei Zhou
- Second School of Clinical Medicine, Nanchang University, Nanchang, 330038, Jiangxi, China
| | - Hongliang Luo
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Nanchang University, 1 Minde Road, Nanchang, 330000, Jiangxi, People's Republic of China.
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9
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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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10
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Zhu XZ, Qiu Z, Lei SQ, Leng Y, Li WY, Xia ZY. The Role of P53 in Myocardial Ischemia-Reperfusion Injury. Cardiovasc Drugs Ther 2023:10.1007/s10557-023-07480-x. [PMID: 37389674 DOI: 10.1007/s10557-023-07480-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/09/2023] [Indexed: 07/01/2023]
Abstract
PURPOSE P53 is one of the key tumor suppressors. In normal cells, p53 is maintained at low levels by the ubiquitination of the ubiquitinated ligase MDM2. In contrast, under stress conditions such as DNA damage and ischemia, the interaction between p53 and MDM2 is blocked and activated by phosphorylation and acetylation, thereby mediating the trans-activation of p53 through its target genes to regulate a variety of cellular responses. Previous studies have shown that the expression of p53 is negligible in normal myocardium, tends to increase in myocardial ischemia and is maximally induced in ischemia-reperfused myocardium, demonstrating a possible key role of p53 in the development of MIRI. In this review, we detail and summarize recent studies on the mechanism of action of p53 in MIRI and describe the therapeutic agents targeting the relevant targets to provide new strategies for the prevention and treatment of MIRI. METHODS We collected 161 relevant papers mainly from Pubmed and Web of Science (search terms "p53" and "myocardial ischemia-reperfusion injury"). After that, we selected pathway studies related to p53 and classified them according to their contents. We eventually analyzed and summarized them. RESULTS AND CONCLUSION In this review, we detail and summarize recent studies on the mechanism of action of p53 in MIRI and validate its status as an important intermediate affecting MIRI. On the one hand, p53 is regulated and modified by multiple factors, especially non-coding RNAs; on the other hand, p53 regulates apoptosis, programmed necrosis, autophagy, iron death and oxidative stress in MIRI through multiple pathways. More importantly, several studies have reported medications targeting p53-related therapeutic targets. These medications are expected to be effective options for the alleviation of MIRI, but further safety and clinical studies are needed to convert them into clinical applications.
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Affiliation(s)
- Xi-Zi Zhu
- Department of Anesthesiology, Renmin Hospital of Wuhan University, 99 Zhang Zhidong Road, Wuhan, Hubei, 430060, People's Republic of China
| | - Zhen Qiu
- Department of Anesthesiology, Renmin Hospital of Wuhan University, 99 Zhang Zhidong Road, Wuhan, Hubei, 430060, People's Republic of China
| | - Shao-Qing Lei
- Department of Anesthesiology, Renmin Hospital of Wuhan University, 99 Zhang Zhidong Road, Wuhan, Hubei, 430060, People's Republic of China
| | - Yan Leng
- Department of Anesthesiology, Renmin Hospital of Wuhan University, 99 Zhang Zhidong Road, Wuhan, Hubei, 430060, People's Republic of China
| | - Wen-Yuan Li
- Department of Anesthesiology, Renmin Hospital of Wuhan University, 99 Zhang Zhidong Road, Wuhan, Hubei, 430060, People's Republic of China
| | - Zhong-Yuan Xia
- Department of Anesthesiology, Renmin Hospital of Wuhan University, 99 Zhang Zhidong Road, Wuhan, Hubei, 430060, People's Republic of China.
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11
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Kumar S, Agrawal A, Vindal V. BCLncRDB: a comprehensive database of LncRNAs associated with breast cancer. Funct Integr Genomics 2023; 23:178. [PMID: 37227514 DOI: 10.1007/s10142-023-01112-1] [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: 03/28/2023] [Revised: 05/11/2023] [Accepted: 05/17/2023] [Indexed: 05/26/2023]
Abstract
Breast cancer, the most common cancer in women, is characterized by high morbidity and mortality worldwide. Recent evidence has shown that long non-coding RNAs (lncRNAs) play a crucial role in the development and progression of breast cancer. However, despite increasing data and evidence indicating the implication of lncRNAs in breast cancer, no web resource or database exists primarily for lncRNAs associated with only breast cancer. Therefore, we developed a manually curated, comprehensive database, "BCLncRDB," for lncRNAs associated with breast cancer. For this, we collected, processed, and analyzed available data on breast cancer-associated lncRNAs from different sources, including previously published research articles, the Gene Expression Omnibus (GEO) Database of the National Centre for Biotechnology Information (NCBI), The Cancer Genome Atlas (TCGA), and the Ensembl database; subsequently, these data were hosted at BCLncRDB for public access. Currently, the database contains 5324 unique breast cancer-lncRNA associations and has the following features: (i) a user-friendly, easy-to-use web interface for searching and browsing about lncRNAs of the user's interest, (ii) differentially expressed and methylated lncRNAs, (iii) stage- and subtype-specific lncRNAs, and (iv) drugs, subcellular localization, sequence, and chromosome information of these lncRNAs. Thus, the BCLncRDB provides a one-stop dedicated platform for exploring breast cancer-related lncRNAs to advance and support the ongoing research on this disease. The BCLncRDB is publicly available for use at http://sls.uohyd.ac.in/new/bclncrdb_v1 .
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Affiliation(s)
- Swapnil Kumar
- Department of Biotechnology & Bioinformatics, School of Life Sciences, South Campus, University of Hyderabad, Prof. C. R. Rao Road, Gachibowli, Hyderabad, 500046, India
| | - Avantika Agrawal
- Department of Biotechnology & Bioinformatics, School of Life Sciences, South Campus, University of Hyderabad, Prof. C. R. Rao Road, Gachibowli, Hyderabad, 500046, India
| | - Vaibhav Vindal
- Department of Biotechnology & Bioinformatics, School of Life Sciences, South Campus, University of Hyderabad, Prof. C. R. Rao Road, Gachibowli, Hyderabad, 500046, India.
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12
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Han Y, Zhu Y, Dutta S, Almuntashiri S, Wang X, Zhang D. A proinflammatory long noncoding RNA Lncenc1 regulates inflammasome activation in macrophage. Am J Physiol Lung Cell Mol Physiol 2023; 324:L584-L595. [PMID: 36880658 PMCID: PMC10085550 DOI: 10.1152/ajplung.00056.2022] [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: 02/15/2022] [Revised: 02/13/2023] [Accepted: 02/28/2023] [Indexed: 03/08/2023] Open
Abstract
Mammalian genomes encode thousands of long noncoding RNAs (lncRNAs). LncRNAs are extensively expressed in various immune cells. The lncRNAs have been reported to be involved in diverse biological processes, including the regulation of gene expression, dosage compensation, and genomic imprinting. However, very little research has been conducted to explore how they alter innate immune responses during host-pathogen interactions. In this study, we found that a lncRNA, named long noncoding RNA, embryonic stem cells expressed 1 (Lncenc1), was strikingly increased in mouse lungs after gram-negative (G-) bacterial infection or exposure to lipopolysaccharides (LPS). Interestingly, our data indicated that Lncenc1 was upregulated in macrophages but not in primary epithelial cells (PECs) or polymorphonuclear leukocytes (PMN). The upregulation was also observed in human THP-1 and U937 macrophages. Besides, Lncenc1 was highly induced during ATP-induced inflammasome activation. Functionally, Lncenc1 showed proinflammatory effects in macrophages as demonstrated by increased expressions of cytokine and chemokines, as well as enhanced NF-κB promoter activity. Overexpression of Lncenc1 promoted the releases of IL-1β and IL-18, and Caspase-1 activity in macrophages, suggesting a role in inflammasome activation. Consistently, knockdown of Lncenc1 inhibited inflammasome activation in LPS-treated macrophages. Moreover, knockdown of Lncenc1 using antisense oligo (ASO)-loaded exosomes (EXO) attenuated LPS-induced lung inflammation in mice. Similarly, Lncenc1 deficiency protects mice from bacteria-induced lung injury and inflammasome activation. Taken together, our work identified Lncenc1 as a modulator of inflammasome activation in macrophages during bacterial infection. Our study suggested that Lncenc1 could serve as a therapeutic target for lung inflammation and injury.
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Affiliation(s)
- Yohan Han
- Clinical and Experimental Therapeutics, College of Pharmacy, University of Georgia, Augusta, Georgia, United States
- Charlie Norwood Department of Veterans Affairs Medical Center, Augusta, Georgia, United States
| | - Yin Zhu
- Clinical and Experimental Therapeutics, College of Pharmacy, University of Georgia, Augusta, Georgia, United States
- Charlie Norwood Department of Veterans Affairs Medical Center, Augusta, Georgia, United States
| | - Saugata Dutta
- Clinical and Experimental Therapeutics, College of Pharmacy, University of Georgia, Augusta, Georgia, United States
- Charlie Norwood Department of Veterans Affairs Medical Center, Augusta, Georgia, United States
| | - Sultan Almuntashiri
- Clinical and Experimental Therapeutics, College of Pharmacy, University of Georgia, Augusta, Georgia, United States
- Charlie Norwood Department of Veterans Affairs Medical Center, Augusta, Georgia, United States
- Department of Clinical Pharmacy, College of Pharmacy, University of Hail, Hail, Saudi Arabia
| | - Xiaoyun Wang
- Clinical and Experimental Therapeutics, College of Pharmacy, University of Georgia, Augusta, Georgia, United States
- Charlie Norwood Department of Veterans Affairs Medical Center, Augusta, Georgia, United States
| | - Duo Zhang
- Clinical and Experimental Therapeutics, College of Pharmacy, University of Georgia, Augusta, Georgia, United States
- Charlie Norwood Department of Veterans Affairs Medical Center, Augusta, Georgia, United States
- Department of Medicine, Medical College of Georgia, Augusta University, Augusta, Georgia, United States
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Wu M, Li T, Li G, Niu B, Wu T, Yan L, Wang S, He S, Huang C, Tong W, Li N, Jiang J. LncRNA DANCR deficiency promotes high glucose-induced endothelial to mesenchymal transition in cardiac microvascular cells via the FoxO1/DDAH1/ADMA signaling pathway. Eur J Pharmacol 2023; 950:175732. [PMID: 37116560 DOI: 10.1016/j.ejphar.2023.175732] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 03/31/2023] [Accepted: 04/17/2023] [Indexed: 04/30/2023]
Abstract
Cardiac fibrosis is the main pathological basis of diabetic cardiomyopathy (DCM), and endothelial-to-meschenymal transition (EndMT) is a key driver to cardiac fibrosis and plays an important role in the pathogenesis of DCM. Asymmetric dimethylarginine (ADMA), a crucial pathologic factor in diabetes mellitus, is involved in organ fibrosis. This study aims to evaluate underlying mechanisms of ADMA in DCM especially for EndMT under diabetic conditions. A diabetic rat model was induced by streptozotocin (STZ) injection, and human cardiac microvascular endothelial cells (HCMECs) were stimulated with high glucose to induce EndMT. Subsequently, the role of ADMA in EndMT was detected either by exogenous ADMA or by over-expressing dimethylarginine dimethylaminohydrolase 1 (DDAH1, degradation enzyme for ADMA) before high glucose stimulation. Furthermore, the relationships among forkhead box protein O1 (FoxO1), DDAH1 and ADMA were evaluated by FoxO1 over-expression or FoxO1 siRNA. Finally, we examined the roles of LncRNA DANCR in FoxO1/DDAH1/ADMA pathway and EndMT of HCMECs. Here, we found that EndMT in HCMECs was induced by high glucose, as evidenced by down-regulated expression of CD31 and up-regulated expression of FSP-1 and collagen Ⅰ. Importantly, ADMA induced EndMT in HCMECs, and over-expressing DDAH1 protected from developing EndMT by high glucose. Furthermore, we demonstrated that over-expression of FoxO1-ADA with mutant phosphorylation sites of T24A, S256D, and S316A induced EndMT of HCMECs by down-regulating of DDAH1 and elevating ADMA, and that EndMT of HCMECs induced by high glucose was reversed by FoxO1 siRNA. We also found that LncRNA DANCR siRNA induced EndMT of HCMECs, activated FoxO1, and inhibited DDAH1 expression. Moreover, over-expression of LncRNA DANCR could markedly attenuated high glucose-mediated EndMT of HCMECs by inhibiting the activation of FoxO1 and increasing the expression of DDAH1. Collectively, our results indicate that LncRNA DANCR deficiency promotes high glucose-induced EndMT in HCMECs by regulating FoxO1/DDAH1/ADMA pathway.
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Affiliation(s)
- Meiting Wu
- Department of Pharmacology, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410078, China; Department of Nephrology, Institute of Nephrology, 2nd Affiliated Hospital of Hainan Medical University, Haikou, 570100, China
| | - Ting Li
- Department of Pharmacology, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410078, China
| | - Ge Li
- Department of Pharmacology, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410078, China; Department of Basic Medicine, Zhaoqing Medical College, Zhaoqing, 526020, China
| | - Bingxuan Niu
- Department of Pharmacology, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410078, China; Collage of Pharmacy, Xinxiang Medical University, Xinxiang, 453002, China
| | - Tian Wu
- Department of Pharmacology, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410078, China
| | - Li Yan
- Department of Pharmacology, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410078, China
| | - Shiming Wang
- Department of Pharmacology, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410078, China
| | - Shuangyi He
- Department of Pharmacology, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410078, China
| | - Chuyi Huang
- Department of Pharmacology, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410078, China
| | - Weiqiang Tong
- Department of Pharmacology, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410078, China
| | - Niansheng Li
- Department of Pharmacology, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410078, China
| | - Junlin Jiang
- Department of Pharmacology, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410078, China; Provincial Key Laboratory of Cardiovascular Research, Central South University, Changsha, 410078, China.
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14
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Lu S, Lu P. Comprehensive LncRNA and Potential Molecular Mechanism Analysis in Noninfectious Uveitis. Transl Vis Sci Technol 2023; 12:2. [PMID: 36857067 PMCID: PMC9987169 DOI: 10.1167/tvst.12.3.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023] Open
Abstract
Purpose Long noncoding RNA (lncRNA) is noncoding RNA and have played a key role or be treated as a biomarker in a variety of diseases such as tumors. However, extensive lncRNA analysis for uveitis has not been explored completely. In this study, we analyzed the lncRNAs with altered expression in peripheral blood comprehensively for three major autoimmune diseases (ankylosing spondylitis [AS], Behҫet's disease [BD], and sarcoidosis) to search potential hub gene and molecular mechanism for noninfectious uveitis. Methods In total, we included 18 patients with AS and 12 patients with sarcoidosis versus 25 controls for GSE18781; we also included 15 patients with BD versus 14 controls for GSE17114 in this study. The lncRNA and messenger RNA (mRNA) expression levels were determined by microarray using serum samples from patients and healthy controls. Results Twenty-one lncRNAs and 1073 mRNAs were detected in patients with AS, 4 lncRNAs and 62 mRNAs in patients with BD, and 196 lncRNAs and 5376 mRNAs in patients with sarcoidosis. Thus, we suspected lncRNA XIST and MIAT, mRNA FCGBP, CD247, CTSW, AES, NCR3, TIGIT, CASP5, DUSP2, and TBX21 may be the most possible hub genes for AS, BD, and sarcoidosis. These RNAs were involved in the mitogen-activated protein kinase signaling pathway and inflammatory cytokine pathways. Conclusions In this study, comprehensive bioinformatics analysis identified lncRNAs with altered expression in three major autoimmune diseases that may combine with noninfectious uveitis. This study provides novel insights into the molecular pathogenetic mechanisms and key information toward developing new diagnostic biomarkers and special therapeutic targets for noninfectious uveitis in AS, BD, and sarcoidosis. Translational Relevance LncRNAs and their potential mechanisms provide new strategies for prevention and treatment for noninfectious uveitis in patients with AS, BD, and sarcoidosis.
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Affiliation(s)
- Shiheng Lu
- Department of Ophthalmology, The First Affiliated Hospital of Soochow University, Suzhou, China.,Department of Ophthalmology, Shanghai Eye Disease Prevention and Treatment Center, Shanghai Eye Hospital, Shanghai, China
| | - Peirong Lu
- Department of Ophthalmology, The First Affiliated Hospital of Soochow University, Suzhou, China
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15
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Ghafouri-Fard S, Safarzadeh A, Hussen BM, Taheri M, Mokhtari M. Contribution of CRNDE lncRNA in the development of cancer and the underlying mechanisms. Pathol Res Pract 2023; 244:154387. [PMID: 36893710 DOI: 10.1016/j.prp.2023.154387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 02/19/2023] [Accepted: 02/23/2023] [Indexed: 03/09/2023]
Abstract
Colorectal Neoplasia Differentially Expressed (CRNDE) is an lncRNA with crucial roles in cancer development. It is located on chromosome 16 on the opposite strand to the adjacent IRX5 gene, implying the presence of a shared bidirectional promoter for these two genes. Expression of CRNDE has been assessed in a diverse array of hematological malignancies and solid tumors, representing its potential as a therapeutic target in these conditions. This lncRNA has a regulatory effect on activity of several pathways and axes that are involved in the regulation of cell apoptosis, immune responses and tumorigenesis. The current review is an updated review about the role of CRNDE in the development of cancers.
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Affiliation(s)
- Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Arash Safarzadeh
- Phytochemistry Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Bashdar Mahmud Hussen
- Department of Pharmacognosy, College of Pharmacy, Hawler Medical University, Erbil, Kurdistan Region, Iraq
| | - Mohammad Taheri
- Institute of Human Genetics, Jena University Hospital, Jena, Germany; Urology and Nephrology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Majid Mokhtari
- Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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16
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lncRNA-disease association prediction based on the weight matrix and projection score. PLoS One 2023; 18:e0278817. [PMID: 36595551 PMCID: PMC9810171 DOI: 10.1371/journal.pone.0278817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 11/25/2022] [Indexed: 01/04/2023] Open
Abstract
With the development of medical science, long noncoding RNA (lncRNA), originally considered as a noise gene, has been found to participate in a variety of biological activities. Several recent studies have shown the involvement of lncRNA in various human diseases, such as gastric cancer, prostate cancer, lung cancer, and so forth. However, obtaining lncRNA-disease relationship only through biological experiments not only costs manpower and material resources but also gains little. Therefore, developing effective computational models for predicting lncRNA-disease association relationship is extremely important. This study aimed to propose an lncRNA-disease association prediction model based on the weight matrix and projection score (LDAP-WMPS). The model used the relatively perfect lncRNA-miRNA relationship data and miRNA-disease relationship data to predict the lncRNA-disease relationship. The integrated lncRNA similarity matrix and the integrated disease similarity matrix were established by fusing various methods to calculate the similarity between lncRNA and disease. This study improved the existing weight algorithm, applied it to the lncRNA-miRNA-disease triple network, and thus proposed a new lncRNA-disease weight matrix calculation method. Combined with the improved projection algorithm, the lncRNA-miRNA relationship and miRNA-disease relationship were used to predict the lncRNA-disease relationship. The simulation results showed that under the Leave-One-Out-Cross-Validation framework, the area under the receiver operating characteristic curve of LDAP-WMPS could reach 0.8822, which was better than the latest result. Taking adenocarcinoma and colorectal cancer as examples, the LDAP-WMPS model was found to effectively infer the lncRNA-disease relationship. The simulation results showed good prediction performance of the LDAP-WMPS model, which was an important supplement to the research of lncRNA-disease association prediction without lncRNA-disease relationship data.
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17
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Bravo-Vázquez LA, Frías-Reid N, Ramos-Delgado AG, Osorio-Pérez SM, Zlotnik-Chávez HR, Pathak S, Banerjee A, Bandyopadhyay A, Duttaroy AK, Paul S. MicroRNAs and long non-coding RNAs in pancreatic cancer: From epigenetics to potential clinical applications. Transl Oncol 2023; 27:101579. [PMID: 36332600 PMCID: PMC9637816 DOI: 10.1016/j.tranon.2022.101579] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 10/05/2022] [Accepted: 10/18/2022] [Indexed: 11/08/2022] Open
Abstract
MicroRNAs (miRNAs) and long non-coding RNAs (lncRNAs) are two relevant classes of non-coding RNAs (ncRNAs) that play a pivotal role in a number of molecular processes through different epigenetic regulatory mechanisms of gene expression. As a matter of fact, the altered expression of these types of RNAs leads to the development and progression of a varied range of multifactorial human diseases. Several recent reports elucidated that miRNA and lncRNAs have been implicated in pancreatic cancer (PC). For instance, dysregulation of such ncRNAs has been found to be associated with chemoresistance, apoptosis, autophagy, cell differentiation, tumor suppression, tumor growth, cancer cell proliferation, migration, and invasion in PC. Moreover, several aberrantly expressed miRNAs and lncRNAs have the potential to be used as biomarkers for accurate PC diagnosis. Additionally, miRNAs and lncRNAs are considered as promising clinical targets for PC. Therefore, in this review, we discuss recent experimental evidence regarding the clinical implications of miRNAs and lncRNAs in the pathophysiology of PC, their future potential, as well as the challenges that have arisen in this field of study in order to drive forward the design of ncRNA-based diagnostics and therapeutics for PC.
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Affiliation(s)
- Luis Alberto Bravo-Vázquez
- School of Engineering and Sciences, Tecnologico de Monterrey, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc. San Pablo, Queretaro 76130, Mexico
| | - Natalia Frías-Reid
- School of Engineering and Sciences, Tecnologico de Monterrey, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc. San Pablo, Queretaro 76130, Mexico
| | - Ana Gabriela Ramos-Delgado
- School of Engineering and Sciences, Tecnologico de Monterrey, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc. San Pablo, Queretaro 76130, Mexico
| | - Sofía Madeline Osorio-Pérez
- School of Engineering and Sciences, Tecnologico de Monterrey, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc. San Pablo, Queretaro 76130, Mexico
| | - Hania Ruth Zlotnik-Chávez
- School of Engineering and Sciences, Tecnologico de Monterrey, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc. San Pablo, Queretaro 76130, Mexico
| | - Surajit Pathak
- Department of Medical Biotechnology, Faculty of Allied Health Sciences, Chettinad Academy of Research and Education (CARE), Chettinad Hospital and Research Institute (CHRI), Chennai, India
| | - Antara Banerjee
- Department of Medical Biotechnology, Faculty of Allied Health Sciences, Chettinad Academy of Research and Education (CARE), Chettinad Hospital and Research Institute (CHRI), Chennai, India
| | - Anindya Bandyopadhyay
- International Rice Research Institute, Manila 4031, Philippines; Reliance Industries Ltd., Navi Mumbai 400701, India
| | - Asim K Duttaroy
- Department of Nutrition, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, POB 1046, Blindern, Oslo, Norway.
| | - Sujay Paul
- School of Engineering and Sciences, Tecnologico de Monterrey, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc. San Pablo, Queretaro 76130, Mexico.
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Imai K, Ishimoto T, Doke T, Tsuboi T, Watanabe Y, Katsushima K, Suzuki M, Oishi H, Furuhashi K, Ito Y, Kondo Y, Maruyama S. Long non-coding RNA lnc-CHAF1B-3 promotes renal interstitial fibrosis by regulating EMT-related genes in renal proximal tubular cells. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 31:139-150. [PMID: 36700051 PMCID: PMC9841231 DOI: 10.1016/j.omtn.2022.12.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022]
Abstract
Renal interstitial fibrosis (RIF) is a common pathological manifestation of chronic kidney diseases. Epithelial-mesenchymal transition (EMT) of tubular epithelial cells is considered a major cause of RIF. Although long non-coding RNAs (lncRNAs) are reportedly involved in various pathophysiological processes, the roles and underlying molecular mechanisms of lncRNAs in the progression of RIF are poorly understood. In this study, we investigated the function of lncRNAs in RIF. Microarray assays showed that expression of the lncRNA lnc-CHAF1B-3 (also called claudin 14 antisense RNA 1) was significantly upregulated in human renal proximal tubular cells by both transforming growth factor-β1 (TGF-β1) and hypoxic stimulation, accompanied with increased expression of EMT-related genes. Knockdown of lnc-CHAF1B-3 significantly suppressed TGF-β1-induced upregulated expression of collagen type I alpha 1, cadherin-2, plasminogen activator inhibitor-1, snail family transcriptional repressor I (SNAI1) and SNAI2. Quantitative reverse transcriptase PCR analyses of paraffin-embedded kidney biopsy samples from IgA nephropathy patients revealed lnc-CHAF1B-3 expression was correlated positively with urinary protein levels and correlated negatively with estimated glomerular filtration rate. In situ hybridization demonstrated that lnc-CHAF1B-3 is expressed only in proximal tubules. These findings suggest lnc-CHAF1B-3 affects the progression of RIF by regulating EMT-related signaling. Thus, lnc-CHAF1B-3 is a potential target in the treatment of RIF.
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Affiliation(s)
- Kentaro Imai
- Department of Nephrology, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan
| | - Takuji Ishimoto
- Department of Nephrology, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan,Department of Nephrology and Rheumatology, Aichi Medical University, Nagakute, Aichi, 480-1195, Japan,Corresponding author: Takuji Ishimoto, Department of Nephrology and Rheumatology, Aichi Medical University, Nagakute, Aichi, 480-1195, Japan.
| | - Tomohito Doke
- Department of Nephrology, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan
| | - Toshiki Tsuboi
- Department of Nephrology, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan
| | - Yu Watanabe
- Department of Nephrology, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan
| | - Keisuke Katsushima
- Department of Cancer Biology, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan
| | - Miho Suzuki
- Department of Cancer Biology, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan
| | - Hideto Oishi
- Department of Nephrology, Komaki City Hospital, Komaki, Aichi, 485-8520, Japan
| | - Kazuhiro Furuhashi
- Department of Nephrology, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan
| | - Yasuhiko Ito
- Department of Nephrology and Rheumatology, Aichi Medical University, Nagakute, Aichi, 480-1195, Japan
| | - Yutaka Kondo
- Department of Cancer Biology, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan
| | - Shoichi Maruyama
- Department of Nephrology, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan
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A Cuproptosis-Related lncRNAs Signature Could Accurately Predict Prognosis in Patients with Clear Cell Renal Cell Carcinoma. Anal Cell Pathol (Amst) 2022; 2022:4673514. [PMID: 36588797 PMCID: PMC9800904 DOI: 10.1155/2022/4673514] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 11/28/2022] [Accepted: 12/03/2022] [Indexed: 12/24/2022] Open
Abstract
Background Clear cell renal cell carcinoma (ccRCC) is the most common subtype of kidney cancers. As cuproptosis, a new cell death mechanism proposed recently, differs from all other known mechanisms regulating cell death, we aimed to create prognostic markers using cuproptosis-related long non-coding ribonucleic acids (RNAs; lncRNAs) and elucidate the molecular mechanism. Methods Data from transcriptome RNA sequencing of ccRCC samples and the relevant clinical data were downloaded from The Cancer Genome Atlas, and Pearson's correlation analysis was implemented to obtain the cuproptosis-related lncRNAs. Then, univariate Cox, multivariate Cox, and Least Absolute Shrinkage and Selection Operator Cox analyses were performed to construct the risk signatures. The cuproptosis-related lncRNAs predictive signature was evaluated with receiver operating characteristic curves and subgroup analysis. Finally, Gene Set Enrichment Analysis (GSEA), single-sample GSEA (ssGSEA), tumor immune microenvironment (TIME), and immune checkpoints were performed to explore the relationship between immunity and patient prognosis. Results Five cuproptosis-related lncRNAs, including FOXD2-AS1, LINC00460, AC091212.1, AC007365.1, and AC026401.3, were used to construct the signature. In the training and test sets, low-risk groups (as identified by a risk score lower than the median) demonstrated a better prognosis with an area under the curve for 1-, 3-, and 5-year survival being 0.793, 0.716, and 0.719, respectively. GSEA analysis suggested significant enrichment of the tricarboxylic acid cycle and metabolism-related pathways in the low-risk group. Besides, both ssGSEA and TIME suggested that the high-risk group exhibited more active immune infiltration. Conclusion We proposed a cuproptosis-related lncRNAs signature, which had the potential for prognoses and prediction. Our findings might contribute to elucidating potential genomic biomarkers and targets for future therapies in the cuproptosis-related signaling pathways.
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Meszaros A, Ahmed J, Russo G, Tompa P, Lazar T. The evolution and polymorphism of mono-amino acid repeats in androgen receptor and their regulatory role in health and disease. Front Med (Lausanne) 2022; 9:1019803. [PMID: 36388907 PMCID: PMC9642029 DOI: 10.3389/fmed.2022.1019803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 09/30/2022] [Indexed: 12/24/2022] Open
Abstract
Androgen receptor (AR) is a key member of nuclear hormone receptors with the longest intrinsically disordered N-terminal domain (NTD) in its protein family. There are four mono-amino acid repeats (polyQ1, polyQ2, polyG, and polyP) located within its NTD, of which two are polymorphic (polyQ1 and polyG). The length of both polymorphic repeats shows clinically important correlations with disease, especially with cancer and neurodegenerative diseases, as shorter and longer alleles exhibit significant differences in expression, activity and solubility. Importantly, AR has also been shown to undergo condensation in the nucleus by liquid-liquid phase separation, a process highly sensitive to protein solubility and concentration. Nonetheless, in prostate cancer cells, AR variants also partition into transcriptional condensates, which have been shown to alter the expression of target gene products. In this review, we summarize current knowledge on the link between AR repeat polymorphisms and cancer types, including mechanistic explanations and models comprising the relationship between condensate formation, polyQ1 length and transcriptional activity. Moreover, we outline the evolutionary paths of these recently evolved amino acid repeats across mammalian species, and discuss new research directions with potential breakthroughs and controversies in the literature.
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Affiliation(s)
- Attila Meszaros
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie (VIB), Brussels, Belgium
- Structural Biology Brussels (SBB), Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Junaid Ahmed
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie (VIB), Brussels, Belgium
- Structural Biology Brussels (SBB), Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Giorgio Russo
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie (VIB), Brussels, Belgium
- Structural Biology Brussels (SBB), Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Peter Tompa
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie (VIB), Brussels, Belgium
- Structural Biology Brussels (SBB), Vrije Universiteit Brussel (VUB), Brussels, Belgium
- Research Centre for Natural Sciences (RCNS), ELKH, Budapest, Hungary
| | - Tamas Lazar
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie (VIB), Brussels, Belgium
- Structural Biology Brussels (SBB), Vrije Universiteit Brussel (VUB), Brussels, Belgium
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21
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Sohrabifar N, Ghaderian SMH, Alipour Parsa S, Ghaedi H, Jafari H. Variation in the expression level of MALAT1, MIAT and XIST lncRNAs in coronary artery disease patients with and without type 2 diabetes mellitus. Arch Physiol Biochem 2022; 128:1308-1315. [PMID: 32447981 DOI: 10.1080/13813455.2020.1768410] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Background: The MALAT1, MIAT, and XIST long noncoding RNAs (lncRNAs) participate in the pathogenesis of complex diseases and also serve as diagnostic markers. The study aimed to assess their expressions in CAD patients with or without T2DM against diabetic and non-diabetic controls.Methods: The expression levels of three lncRNAs in 50 CAD patients (with or without diabetes) and 50 non-CAD subjects (with or without diabetes) were evaluated by using the TaqMan Assay method.Results: MALAT1 and MIAT were upregulated in CAD patients (p Value= .0008 and .0078, respectively). The expression level of XIST was significantly elevated diabetic compared to non-diabetic CAD patients (p Value= .0003). MALAT1 gene had the highest diagnostic power for discrimination of CAD patients from controls (AUC= 0.682, p Value=.001).Conclusions: The current study supports the participation of lncRNAs in the pathogenesis of CAD and T2DM and highlights their potential as diagnostic biomarkers.
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Affiliation(s)
- Nasim Sohrabifar
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sayyed Mohammad Hossein Ghaderian
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Urogenital Stem Cell Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Saeed Alipour Parsa
- Department of Cardiology, Cardiovascular Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamid Ghaedi
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hossein Jafari
- Faculty of Medicine, Abadan University of Medical Sciences, Abadan, Iran
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22
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Wang Y, Tang Z, Guo W. XIST sponges miR-320d to promote chordoma progression by regulating ARF6. J Bone Oncol 2022; 35:100447. [PMID: 35899235 PMCID: PMC9309415 DOI: 10.1016/j.jbo.2022.100447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 07/06/2022] [Accepted: 07/13/2022] [Indexed: 11/30/2022] Open
Abstract
XIST was highly expressed in chordoma tissues. XIST knockdown inhibited chordoma progression by downregulating ARF6. MiR-320d inhibited the malignant behaviors of chordoma cells. XIST positively upregulated ARF6 expression via sponging miR-320d in chordoma cells.
Background Long non-coding RNAs (lncRNAs) have been demonstrated to play important roles in various tumors, including chordoma. The purpose of this study was to investigate the role and mechanism of lncRNA X-inactive specific transcript (XIST) in chordoma. Methods RNA levels and protein levels were measured by real-time quantitative polymerase chain reaction (RT‑qPCR) and western blot assay, respectively. Cell proliferation was assessed by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay, 5-ethynyl-2′-deoxyuridine (EdU) assay and colony formation assay. Tanswell assay was used to examine cell migration and invasion. Cellular glycolysis was examined via the measurement of extracellular acidification rate (ECAR) and lactate production. The interaction between microRNA-320d (miR-320d) and XIST or ADP-ribosylation factor 6 (ARF6) was predicted by bioinformatics analysis and verified by a dual-luciferase reporter and RNA-pull down assays. The xenograft tumor model was used to explore the biological function of XIST in vivo. Results XIST was overexpressed in chordoma tissues. XIST knockdown suppressed chordoma cell proliferation, migration, invasion, and glycolysis. XIST acted as a sponge of miR-320d. Moreover, miR-320d overexpression inhibited the proliferation, migration, invasion, and glycolysis of chordoma cells. ARF6 was a direct target of miR-320d, and XIST upregulated ARF6 expression via sponging miR-320d. Furthermore, overexpression of ARF6 reversed the inhibitory effects of XIST knockdown on chordoma cell proliferation, migration, invasion, and glycolysis. Importantly, XIST silencing blocked xenograft tumor growth in vivo. Conclusion XIST knockdown inhibited chordoma progression via regulating the miR-320d/ARF6 axis, providing a novel insight into chordoma pathogenesis.
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Affiliation(s)
- Yonggang Wang
- Department of Orthopedics, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei Province, China
| | - Zhouzhou Tang
- Department of Orthopedics, Jingzhou Central Hospital, Jingzhou 434020, Hubei Province, China
| | - Weichun Guo
- Department of Orthopedics, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei Province, China
- Corresponding author at: Department of Orthopedics, Renmin Hospital of Wuhan University, No. 238, Jiefang Road, Wuchang District, Wuhan City, Hubei Province, China.
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Xu W, Wu L, Lu H, Xiang X, Wang F, Li S. LncRNA PCGEM1 promotes colorectal cancer cell proliferation and migration in positive feedback loop through PCGEM1/miR-433-3p/CTCF axis. Pathol Res Pract 2022; 237:154017. [PMID: 35872368 DOI: 10.1016/j.prp.2022.154017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 06/23/2022] [Accepted: 07/10/2022] [Indexed: 11/16/2022]
Abstract
BACKGROUND AND OBJECTIVES Prostate cancer gene expression marker 1 (PCGEM1) has been identified as an oncogenic long non-coding RNA (lncRNA) in diverse cancers, but it has never been linked with colorectal cancer (CRC). Former studies have shown the mutual regulation between lncRNAs and transcription factors (TFs) in cancer. CCCTC binding factor (CTCF) has been reported to transcriptionally activate lncRNAs in cancers. We predicted the binding of CTCF on PCGEM1 promoter through UCSC (https://genome.ucsc.edu/), but their relation has not been studied. We aimed to investigate whether and how PCGEM1 functioned in CRC cells and the interaction between PCGEM1 and CTCF. METHODS AND RESULTS The impacts of PCGEM1 and CTCF inhibition on CRC cells were verified through loss-of-function experiments. Mechanism experiments were used to prove the binding between CTCF and PCGEM1 in CRC progression. PCGEM1 possessed a high expression level in CRC cells as well as tumors. CTCF transcriptionally activated PCGEM1 expression. Knockdown of PCGEM1 or CTCF impeded proliferation and migration and drove apoptosis of CRC cells. Moreover, PCGEM1 bound miR-433-3p to prevent miR-433-3p from targeting CTCF. CONCLUSION We first revealed PCGEM1/miR-433-3p/CTCF positive feedback loop as an oncogenic axis in CRC cells, which potentially provides new clues for the advancement of CRC treatment.
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Affiliation(s)
- Weijun Xu
- Department of Gastroenterology, Jinling Hospital, the Affiliated Hospital of Nanjing Medical University, Nanjing 210002, Jiangsu, China
| | - Lin Wu
- Department of Gastroenterology, Jinling Hospital, the Affiliated Hospital of Nanjing Medical University, Nanjing 210002, Jiangsu, China
| | - Heng Lu
- Department of Gastroenterology, Jinling Hospital, the Affiliated Hospital of Nanjing Medical University, Nanjing 210002, Jiangsu, China
| | - Xiaosong Xiang
- Department of Gastroenterology, Jinling Hospital, the Affiliated Hospital of Nanjing Medical University, Nanjing 210002, Jiangsu, China
| | - Fangyu Wang
- Department of Gastroenterology, Jinling Hospital, the Affiliated Hospital of Nanjing Medical University, Nanjing 210002, Jiangsu, China
| | - Sheng Li
- Department of Oncology, Jiangsu Institute of Cancer Research, the Affiliated Cancer Hospital of Nanjing Medical University, Nanjing 210009, Jiangsu, China.
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24
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Ji Y, Yang Y, Yin Z. Polymorphisms in lncRNA CCAT1 on the susceptibility of lung cancer in a Chinese northeast population: A case-control study. Cancer Med 2022; 12:500-512. [PMID: 35650713 PMCID: PMC9844612 DOI: 10.1002/cam4.4902] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 05/04/2022] [Accepted: 05/15/2022] [Indexed: 02/06/2023] Open
Abstract
OBJECT To explore the association of rs1948915, rs7013433 in long noncoding RNA (lncRNA) CCAT1 and rs6983267 in MYC enhancer region with the risk of lung cancer in a Chinese northeast population, a case-control study was conducted. METHODS The hospital-based case-control study contained 669 lung cancer patients and 697 healthy controls. Taqman® Probe allele resolution was used for genotyping. The differences between the case-control groups were analyzed using Student t-test and chi-square test. Logistic regression analysis was used to assess the relationship between the genotypes and the risk of lung cancer. Cross-generation analysis was used to explore the relationship between gene-environment interaction and lung cancer. RESULTS There was no association between the three selected single-nucleotide polymorphisms (SNPs) and the susceptibility of lung cancer. Rs1948915 CT was correlated with lung adenocarcinoma. In female stratification, rs1948915 CT/CC was associated with a decreased susceptibility of lung cancer significantly. Additionally, the additive and multiplicative interaction models showed that there was no interaction between the three selected SNPs and smoking status in lung cancer. CONCLUSIONS There may be an association between lung adenocarcinoma and rs1948915 polymorphism in the Chinese northeast population, while rs7013433 and rs6983267 might have no association. There was no interaction between the three selected SNPs and smoking status.
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Affiliation(s)
- Yangtao Ji
- Department of Laboratory Medicine, National Clinical Research Center for Laboratory MedicineThe First Affiliated Hospital of China Medical UniversityShenyangLiaoningPeople's Republic of China
| | - Yue Yang
- Department of Laboratory MedicineThe First Affiliated Hospital of China Medical UniversityShenyangLiaoningPeople's Republic of China
| | - Zhihua Yin
- Department of EpidemiologySchool of Public Health, China Medical UniversityShenyangLiaoningPeople's Republic of China
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25
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Zhan LF, Zhang Q, Zhao L, Dong X, Pei XY, Peng LL, Zhang XW, Meng B, Shang WD, Pan ZW, Xu CQ, Lu YJ, Zhang MY. LncRNA-6395 promotes myocardial ischemia-reperfusion injury in mice through increasing p53 pathway. Acta Pharmacol Sin 2022; 43:1383-1394. [PMID: 34493812 PMCID: PMC9160051 DOI: 10.1038/s41401-021-00767-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 08/15/2021] [Indexed: 02/07/2023] Open
Abstract
Myocardial ischemia-reperfusion (I/R) injury is a pathological process characterized by cardiomyocyte apoptosis, which leads to cardiac dysfunction. Increasing evidence shows that abnormal expression of long noncoding RNAs (lncRNAs) plays a crucial role in cardiovascular diseases. In this study we investigated the role of lncRNAs in myocardial I/R injury. Myocardial I/R injury was induced in mice by ligating left anterior descending coronary artery for 45 min followed by reperfusion for 24 h. We showed that lncRNA KnowTID_00006395, termed lncRNA-6395 was significantly upregulated in the infarct area of mouse hearts following I/R injury as well as in H2O2-treated neonatal mouse ventricular cardiomyocytes (NMVCs). Overexpression of lncRNA-6395 led to cell apoptosis and the expression change of apoptosis-related proteins in NMVCs, whereas knockdown of lncRNA-6395 attenuated H2O2-induced cell apoptosis. LncRNA-6395 knockout mice (lncRNA-6395+/-) displayed improved cardiac function, decreased plasma LDH activity and infarct size following I/R injury. We demonstrated that lncRNA-6395 directly bound to p53, and increased the abundance of p53 protein through inhibiting ubiquitination-mediated p53 degradation and thereby facilitated p53 translocation to the nucleus. More importantly, overexpression of p53 canceled the inhibitory effects of lncRNA-6395 knockdown on cardiomyocyte apoptosis, whereas knockdown of p53 counteracted the apoptotic effects of lncRNA-6395 in cardiomyocytes. Taken together, lncRNA-6395 as an endogenous pro-apoptotic factor, regulates cardiomyocyte apoptosis and myocardial I/R injury by inhibiting degradation and promoting sub-cellular translocation of p53.
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Affiliation(s)
- Lin-feng Zhan
- grid.410736.70000 0001 2204 9268Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Medicine Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081 China
| | - Qi Zhang
- grid.410736.70000 0001 2204 9268Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Medicine Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081 China
| | - Lu Zhao
- grid.410736.70000 0001 2204 9268Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Medicine Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081 China
| | - Xue Dong
- grid.410736.70000 0001 2204 9268Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Medicine Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081 China
| | - Xin-yu Pei
- grid.410736.70000 0001 2204 9268Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Medicine Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081 China
| | - Li-li Peng
- grid.410736.70000 0001 2204 9268Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Medicine Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081 China
| | - Xiao-wen Zhang
- grid.410736.70000 0001 2204 9268Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Medicine Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081 China
| | - Bo Meng
- grid.410736.70000 0001 2204 9268Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Medicine Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081 China
| | - Wen-di Shang
- grid.410736.70000 0001 2204 9268Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Medicine Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081 China
| | - Zhen-wei Pan
- grid.410736.70000 0001 2204 9268Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Medicine Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081 China
| | - Chao-qian Xu
- grid.410736.70000 0001 2204 9268Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Medicine Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081 China
| | - Yan-jie Lu
- grid.410736.70000 0001 2204 9268Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Medicine Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081 China ,grid.410736.70000 0001 2204 9268China Northern Translational Medicine Research and Cooperation Center, Heilongjiang Academy of Medical Sciences, Harbin Medical University, Harbin, 150081 China
| | - Ming-yu Zhang
- grid.410736.70000 0001 2204 9268Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Medicine Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081 China
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The lncRNA Punisher Regulates Apoptosis and Mitochondrial Homeostasis of Vascular Smooth Muscle Cells via Targeting miR-664a-5p and OPA1. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:5477024. [PMID: 35663194 PMCID: PMC9159832 DOI: 10.1155/2022/5477024] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 03/19/2022] [Accepted: 04/15/2022] [Indexed: 12/14/2022]
Abstract
Long noncoding RNAs (lncRNAs) are important regulators of various cellular functions. Recent studies have shown that a novel lncRNA termed Punisher is highly expressed in cardiovascular progenitors and has potential role in cardiovascular diseases. However, its role, especially in molecular mechanism, is unclear. In our present study, we observed that Punisher was obviously downregulated in atherosclerotic plaques. Further research proved that it can suppress the apoptosis of VSMCs potentially contributing to the progression of atherosclerosis. Intriguingly, Punisher revealed to regulate mitochondria fission as well as mitochondrial functions induced by hydrogen peroxide (H2O2) in VSMCs. Mechanistically, Punisher was further proved to serve as a ceRNA which directly binds to miR-664a-5p and consequently regulates its target OPA1, and finally contributes to the biological function of VSMCs. Particularly, Punisher overexpression distinctly suppressed neointima formation and VSMC apoptosis in vivo. Encouragingly, these results were in accordance with findings obtained with the clinical evaluation of patients with atherosclerosis. Our data provides the significant relationship among OPA1, mitochondrial homeostasis, VSMC apoptosis, and atherosclerosis. And lncRNA Punisher and miR-664a-5p could serve as the novel and potential targets in the diagnosis and treatment of cardiovascular diseases.
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27
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GCEN: An Easy-to-Use Toolkit for Gene Co-Expression Network Analysis and lncRNAs Annotation. Curr Issues Mol Biol 2022; 44:1479-1487. [PMID: 35723358 PMCID: PMC9164028 DOI: 10.3390/cimb44040100] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 03/13/2022] [Accepted: 03/23/2022] [Indexed: 02/07/2023] Open
Abstract
Gene co-expression network analysis has been widely used in gene function annotation, especially for long noncoding RNAs (lncRNAs). However, there is a lack of effective cross-platform analysis tools. For biologists to easily build a gene co-expression network and to predict gene function, we developed GCEN, a cross-platform command-line toolkit developed with C++. It is an efficient and easy-to-use solution that will allow everyone to perform gene co-expression network analysis without the requirement of sophisticated programming skills, especially in cases of RNA-Seq research and lncRNAs function annotation. Because of its modular design, GCEN can be easily integrated into other pipelines.
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Long Non-Coding RNAs at the Chromosomal Risk Loci Identified by Prostate and Breast Cancer GWAS. Genes (Basel) 2021; 12:genes12122028. [PMID: 34946977 PMCID: PMC8701176 DOI: 10.3390/genes12122028] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/16/2021] [Accepted: 12/17/2021] [Indexed: 12/20/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are emerging as key players in a variety of cellular processes. Deregulation of the lncRNAs has been implicated in prostate and breast cancers. Recently, germline genetic variations associated with cancer risk have been correlated with lncRNA expression and/or function. In addition, single nucleotide polymorphisms (SNPs) at well-characterized cancer-associated lncRNAs have been analyzed for their association with cancer risk. These SNPs may occur within the lncRNA transcripts or spanning regions that may alter the structure, function, and expression of these lncRNA molecules and contribute to cancer progression and may have potential as therapeutic targets for cancer treatment. Additionally, some of these lncRNA have a tissue-specific expression profile, suggesting them as biomarkers for specific cancers. In this review, we highlight some of the cancer risk-associated SNPs that modulated lncRNAs with a potential role in prostate and breast cancers and speculate on how these lncRNAs may contribute to cancer development.
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29
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Liu S, Chong W. Roles of LncRNAs in Regulating Mitochondrial Dysfunction in Septic Cardiomyopathy. Front Immunol 2021; 12:802085. [PMID: 34899764 PMCID: PMC8652231 DOI: 10.3389/fimmu.2021.802085] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 11/10/2021] [Indexed: 01/20/2023] Open
Abstract
Sepsis is an abnormal systemic inflammatory response of the host immune system to infection and can lead to fatal multiorgan dysfunction syndrome. Epidemiological studies have shown that approximately 10-70% of sepsis cases can lead to septic cardiomyopathy. Since the pathogenesis of septic cardiomyopathy is not clear, it is difficult for medical doctors to treat the disease. Therefore, finding effective interventions to prevent and reduce myocardial damage in septic cardiomyopathy is clinically significant. Epigenetics is the study of stable genetic phenotype inheritance that does not involve changing gene sequences. Epigenetic inheritance is affected by both gene and environmental regulation. Epigenetic studies focus on the modification and influence of chromatin structure, mainly including chromatin remodelling, DNA methylation, histone modification and noncoding RNA (ncRNA)-related mechanisms. Recently, long ncRNA (lncRNA)-related mechanisms have been the focus of epigenetic studies. LncRNAs are expected to become important targets to prevent, diagnose and treat human diseases. As the energy metabolism centre of cells, mitochondria are important targets in septic cardiomyopathy. Intervention measures to prevent and treat mitochondrial damage are of great significance for improving the prognosis of septic cardiomyopathy. LncRNAs play important roles in life activities. Recently, studies have focused on the involvement of lncRNAs in regulating mitochondrial dysfunction. However, few studies have revealed the involvement of lncRNAs in regulating mitochondrial dysfunction in septic cardiomyopathy. In this article, we briefly review recent research in this area.
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Affiliation(s)
- Shuang Liu
- Department of Emergency, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Wei Chong
- Department of Emergency, The First Affiliated Hospital of China Medical University, Shenyang, China
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30
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Xin M, Guo Q, Lu Q, Lu J, Wang PS, Dong Y, Li T, Chen Y, Gerhard GS, Yang XF, Autieri M, Yang L. Identification of Gm15441, a Txnip antisense lncRNA, as a critical regulator in liver metabolic homeostasis. Cell Biosci 2021; 11:208. [PMID: 34906243 PMCID: PMC8670210 DOI: 10.1186/s13578-021-00722-1] [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: 07/26/2021] [Accepted: 11/30/2021] [Indexed: 12/12/2022] Open
Abstract
Background The majority of mammalian genome is composed of non-coding regions, where numerous long non-coding RNAs (lncRNAs) are transcribed. Although lncRNAs have been identified to regulate fundamental biological processes, most of their functions remain unknown, especially in metabolic homeostasis. Analysis of our recent genome-wide screen reveals that Gm15441, a thioredoxin-interacting protein (Txnip) antisense lncRNA, is the most robustly induced lncRNA in the fasting mouse liver. Antisense lncRNAs are known to regulate their sense gene expression. Given that Txnip is a critical metabolic regulator of the liver, we aimed to investigate the role of Gm15441 in the regulation of Txnip and liver metabolism. Methods We examined the response of Gm15441 and Txnip under in vivo metabolic signals such as fasting and refeeding, and in vitro signals such as insulin and key metabolic transcription factors. We investigated the regulation of Txnip expression by Gm15441 and the underlying mechanism in mouse hepatocytes. Using adenovirus-mediated liver-specific overexpression, we determined whether Gm15441 regulates Txnip in the mouse liver and modulates key aspects of liver metabolism. Results We found that the expression levels of Gm15441 and Txnip showed a similar response pattern to metabolic signals in vivo and in vitro, but that their functions were predicted to be opposite. Furthermore, we found that Gm15441 robustly reduced Txnip protein expression in vitro through sequence-specific regulation and translational inhibition. Lastly, we confirmed the Txnip inhibition by Gm15441 in vivo (mice) and found that Gm15441 liver-specific overexpression lowered plasma triglyceride and blood glucose levels and elevated plasma ketone body levels. Conclusions Our data demonstrate that Gm15441 is a potent Txnip inhibitor and a critical metabolic regulator in the liver. This study reveals the therapeutic potential of Gm15441 in treating metabolic diseases. Supplementary Information The online version contains supplementary material available at 10.1186/s13578-021-00722-1.
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Affiliation(s)
- Mingyang Xin
- Department of Medical Genetics and Molecular Biochemistry, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
| | - Qian Guo
- Department of Medical Genetics and Molecular Biochemistry, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
| | - Qingchun Lu
- Department of Medical Genetics and Molecular Biochemistry, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
| | - Juan Lu
- Department of Medical Genetics and Molecular Biochemistry, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA.,Department of Intensive Care Unit, The First Hospital of Jilin University, Changchun, 130021, China
| | - Po-Shun Wang
- Department of Medical Genetics and Molecular Biochemistry, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
| | - Yun Dong
- Department of Medical Genetics and Molecular Biochemistry, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA.,Department of Endocrinology, Nanxishan Hospital of Guangxi Zhuang Autonomous Region, Guilin, 541001, China
| | - Tao Li
- Department of Medical Genetics and Molecular Biochemistry, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA.,Department of Infectious diseases, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, China
| | - Ye Chen
- Department of Mathematics and Statistics, Northern Arizona University, Flagsta, AZ, 86011, USA
| | - Glenn S Gerhard
- Department of Medical Genetics and Molecular Biochemistry, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
| | - Xiao-Feng Yang
- Center for Metabolic Disease Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
| | - Michael Autieri
- Cardiovascular Research Center, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
| | - Ling Yang
- Department of Medical Genetics and Molecular Biochemistry, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA.
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Xuan P, Zhan L, Cui H, Zhang T, Nakaguchi T, Zhang W. Graph Triple-Attention Network for Disease-related LncRNA Prediction. IEEE J Biomed Health Inform 2021; 26:2839-2849. [PMID: 34813484 DOI: 10.1109/jbhi.2021.3130110] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Abnormal expressions of long non-coding RNAs (lncRNAs) are associated with various human diseases. Identifying disease-related lncRNAs can help clarify complex disease pathogeneses. The latest methods for lncRNA-disease association prediction rely on diverse data about lncRNAs and diseases. These methods, however, cannot adequately integrate the neighbour topological information of lncRNA and disease nodes. Moreover, more intrinsic features of lncRNA-disease node pairs can be explored to better predict the latent associations between lncRNAs and diseases. We developed a novel method, named GTAN, to predict the association propensities between lncRNAs and diseases. GTAN integrates various information about lncRNAs and diseases, including similarities, associations and interactions among lncRNAs, diseases and miRNAs, and exploits neighbour topology and attribute representations of a pair of lncRNA-disease nodes. We adopted in GTAN a graph neural network architecture with three attention mechanisms and multi-layer convolutional neural networks. First, a neighbour-level self-attention mechanism is constructed to learn the importance of each neighbour for an interested lncRNA or disease node. Second, topology-level attention is proposed to enhance contextual dependencies among multiple local topology representations of the lncRNA or disease node. An attention-enhanced graph neural network framework is then established to learn a topology representation of top-ranked neighbours for a pair of lncRNA-disease nodes. GTAN also has attribute-level attention to distinguish various contributions of attributes of the lncRNA-disease pair. Finally, attribute representation is learned by multi-layer CNN to integrate detailed features and representative features of the pair. Extensive experimental results demonstrated that GTAN outperformed state-of-the-art methods. The improved recall rates also showed GTANs capacity for retrieving more actual lncRNA-disease associations in the top-ranked candidates. The ablation studies confirmed the important contributions of three attention mechanisms. Case studies on lung cancer, prostate cancer and colon cancer further showed GTANs ability in discovering potential lncRNA candidates related to diseases.
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Emerging role of long non-coding RNAs in endothelial dysfunction and their molecular mechanisms. Biomed Pharmacother 2021; 145:112421. [PMID: 34798473 DOI: 10.1016/j.biopha.2021.112421] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/10/2021] [Accepted: 11/10/2021] [Indexed: 02/06/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are the novel class of transcripts involved in transcriptional, post-transcriptional, translational, and post-translational regulation of physiology and the pathology of diseases. Studies have evidenced that the impairment of endothelium is a critical event in the pathogenesis of atherosclerosis and its complications. Endothelial dysfunction is characterized by an imbalance in vasodilation and vasoconstriction, oxidative stress, proinflammatory factors, and nitric oxide bioavailability. Disruption of the endothelial barrier permeability, the first step in developing atherosclerotic lesions is a consequence of endothelial dysfunction. Though several factors interfere with the normal functioning of the endothelium, intrinsic epigenetic mechanisms governing endothelial function are regulated by lncRNAs and perturbations contribute to the pathogenesis of the disease. This review comprehensively addresses the biogenesis of lncRNA and molecular mechanisms underlying and regulation in endothelial function. An insight correlating lncRNAs and endothelial dysfunction-associated diseases can positively impact the development of novel biomarkers and therapeutic targets in endothelial dysfunction-associated diseases and treatment strategies.
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Wang X, Chen J. Long non-coding RNA TUG1 promotes proliferation and migration in PDGF-BB-stimulated HASMCs by regulating miR-216a-3p/SMURF2 axis. BMC Mol Cell Biol 2021; 22:56. [PMID: 34749662 PMCID: PMC8573901 DOI: 10.1186/s12860-021-00396-0] [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: 01/11/2021] [Accepted: 10/15/2021] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Abnormal proliferation and migration of human airway smooth muscle cells (HASMCs) play an important role in the development of childhood asthma. Long non-coding RNAs (lncRNAs) have been demonstrated to participate in HASMC proliferation and migration. We aimed to explore more effects and molecular mechanism of taurine upregulated gene 1 (TUG1) in childhood asthma. RESULTS TUG1 and SMURF2 were overexpressed and miR-216a-3p was downregulated in childhood asthma patients and PDGF-BB-stimulated HASMCs. TUG1 knockdown attenuated PDGF-BB-triggered proliferation and migration of HASMCs. MiR-216a-3p was targeted by TUG1, and miR-216a-3p suppression counteracted the repressive effects of TUG1 interference on proliferation and migration in PDGF-BB-treated HASMCs. SMURF2 was a downstream target of miR-216a-3p, and SMURF2 upregulation abated the inhibiting effects of miR-216a-3p on migration and proliferation in PDGF-BB-exposed HASMCs. TUG1 sponged miR-216a-3p to positively regulate SMURF2 expression. CONCLUSION TUG1 downregulation inhibited PDGF-BB-induced HASMC proliferation and migration by regulating miR-216a-3p/SMURF2 axis, offering novel insight into the potential application of TUG1 for childhood asthma treatment.
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Affiliation(s)
- Xinfang Wang
- Department of Pediatrics, Hangzhou First People's Hospital Affiliated to Zhejiang University, Zhejiang, Hangzhou, China
| | - Junsong Chen
- Respiratory Department, Hangzhou Children's Hospital, 195 Wenhui Road, Zhejiang, 310003, Hangzhou, China.
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Lee PW, Wu BS, Yang CY, Lee OKS. Molecular Mechanisms of Mesenchymal Stem Cell-Based Therapy in Acute Kidney Injury. Int J Mol Sci 2021; 22:11406. [PMID: 34768837 PMCID: PMC8583897 DOI: 10.3390/ijms222111406] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/18/2021] [Accepted: 10/20/2021] [Indexed: 12/12/2022] Open
Abstract
Acute kidney injury (AKI) causes a lot of harm to human health but is treated by only supportive therapy in most cases. Recent evidence shows that mesenchymal stem cells (MSCs) benefit kidney regeneration through releasing paracrine factors and extracellular vesicles (EVs) to the recipient kidney cells and are considered to be promising cellular therapy for AKI. To develop more efficient, precise therapies for AKI, we review the therapeutic mechanism of MSCs and MSC-derived EVs in AKI and look for a better understanding of molecular signaling and cellular communication between donor MSCs and recipient kidney cells. We also review recent clinical trials of MSC-EVs in AKI. This review summarizes the molecular mechanisms of MSCs' therapeutic effects on kidney regeneration, expecting to comprehensively facilitate future clinical application for treating AKI.
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Grants
- Yin Yen-Liang Foundation Development and Construction Plan (107F-M01-0504) National Yang-Ming University
- MOST 108-2923-B-010-002-MY3, MOST 109-2314-B-010-053-MY3, MOST 109-2811-B-010-532, MOST 109-2926-I-010-502, MOST 109-2823-8-010-003-CV, MOST 109-2622-B-010-006, MOST 109-2321-B-010-006, MOST 110-2923-B-A49A-501-MY3, and MOST 110-2321-B-A49-003 Ministry of Science and Technology, Taiwan
- V106D25-003-MY3, VGHUST107-G5-3-3, VGHUST109-V5-1-2, and V110C-194 Taipei Veterans General Hospital
- Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B) Ministry of Education
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Affiliation(s)
- Pei-Wen Lee
- Institute of Clinical Medicine, School of Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan; (P.-W.L.); (B.-S.W.)
- Hong Deh Clinic, Taipei 11251, Taiwan
| | - Bo-Sheng Wu
- Institute of Clinical Medicine, School of Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan; (P.-W.L.); (B.-S.W.)
- Faculty of Medicine, School of Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
| | - Chih-Yu Yang
- Institute of Clinical Medicine, School of Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan; (P.-W.L.); (B.-S.W.)
- Faculty of Medicine, School of Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
- Department of Medicine, Division of Nephrology, Taipei Veterans General Hospital, Taipei 11217, Taiwan
- Center for Intelligent Drug Systems and Smart Bio-Devices (IDS2B), National Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan
- Stem Cell Research Center, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
| | - Oscar Kuang-Sheng Lee
- Institute of Clinical Medicine, School of Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan; (P.-W.L.); (B.-S.W.)
- Faculty of Medicine, School of Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
- Stem Cell Research Center, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
- Department of Orthopedics, China Medical University Hospital, Taichung 40447, Taiwan
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Zhao L, Chen H, Wu L, Li Z, Zhang R, Zeng Y, Yang T, Ruan H. LncRNA KCNQ1OT1 promotes the development of diabetic nephropathy by regulating miR-93-5p/ROCK2 axis. Diabetol Metab Syndr 2021; 13:108. [PMID: 34654473 PMCID: PMC8518197 DOI: 10.1186/s13098-021-00726-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 09/28/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) have been reported to play vital roles in diabetic nephropathy (DN). The aim of this study was to explore the function of mechanism of lncRNA KCNQ1 opposite strand/antisense transcript 1 (KCNQ1OT1) in DN. METHODS DN cell models were established using high glucose (HG) treatment in human glomerular mesangial cells (HGMC) and human renal glomerular endothelial cells (HRGEC). The expression levels of KCNQ1OT1, microRNA-93-5p (miR-93-5p), and Rho associated coiled-coil containing protein kinase 2 (ROCK2) mRNA was detected by quantitative real-time polymerase chain reaction (qRT-PCR). Cell Counting Kit-8 (CCK-8) assay and flow cytometry were used to detect cell proliferation and apoptosis, respectively. ROCK2 and apoptosis/fibrosis-related protein levels were examined by western blot. The predicted interaction between miR-93-5p and KCNQ1OT1 or ROCK2 was verified by dual-luciferase reporter assay and RNA immunoprecipitation (RIP) assay. RESULTS KCNQ1OT1 was upregulated in DN patients and DN cell models. KCNQ1OT1 knockdown inhibited cell proliferation and fibrosis and induced apoptosis in DN cell models. MiR-93-5p was a direct target of KCNQ1OT1, and miR-93-5p inhibition restored the KCNQ1OT1 knockdown-mediated effects on cell proliferation, fibrosis and apoptosis in DN cell models. In addition, ROCK2 was identified as a target of miR-93-5p, and miR-93-5p overexpression suppressed cell proliferation and fibrosis and accelerated apoptosis by targeting ROCK2 in DN cell models. Moreover, KCNQ1OT1 regulated ROCK2 expression by binding to miR-93-5p. CONCLUSION KCNQ1OT1 knockdown inhibited cell proliferation and fibrosis and induced apoptosis in DN by regulating miR-93-5p/ROCK2 axis, providing potential value for the treatment of DN.
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Affiliation(s)
- Li Zhao
- Department of Nephrology, Affiliated Dongfeng Hospital, Hubei University of Medicine, Shiyan, Hubei, People's Republic of China
| | - Huaqian Chen
- Department of Nephrology, Affiliated Dongfeng Hospital, Hubei University of Medicine, Shiyan, Hubei, People's Republic of China
| | - Lin Wu
- Department of Nephrology, Sinopharm Hanjiang Hospital, Hubei University of Medicine, Shiyan, Hubei, People's Republic of China
| | - Zhengdong Li
- Department of Nephrology, Affiliated Dongfeng Hospital, Hubei University of Medicine, Shiyan, Hubei, People's Republic of China
| | - Ren Zhang
- Department of Nephrology, Affiliated Dongfeng Hospital, Hubei University of Medicine, Shiyan, Hubei, People's Republic of China
| | - Yan Zeng
- Department of Nephrology, Affiliated Dongfeng Hospital, Hubei University of Medicine, Shiyan, Hubei, People's Republic of China
| | - Tao Yang
- Department of Nephrology, Affiliated Dongfeng Hospital, Hubei University of Medicine, Shiyan, Hubei, People's Republic of China
| | - Hualing Ruan
- Department of Endocrinology, Zhangwan District, Affiliated Dongfeng Hospital, Hubei University of Medicine, No. 16 Daling Road, Shiyan, Hubei, China.
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Bahreini F, Jabbari P, Gossing W, Aziziyan F, Frohme M, Rezaei N. The role of noncoding RNAs in pituitary adenoma. Epigenomics 2021; 13:1421-1437. [PMID: 34558980 DOI: 10.2217/epi-2021-0165] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Pituitary adenomas (PAs) are common cranial tumors that affect the quality of life in patients. Early detection of PA is beneficial for avoiding clinical complications of this disease and increasing the quality of life. Noncoding RNAs, including long noncoding RNA, miRNA and circRNA, regulate protein expression, mostly by inhibiting the translation process. Studies have shown that dysregulation of noncoding RNAs is associated with PA. Hence understanding the expression pattern of noncoding RNAs can be considered a promising method for developing biomarkers. This article reviews data on the expression pattern of dysregulated noncoding RNAs involved in PA. Possible molecular mechanisms by which the dysregulated noncoding RNA could possibly induce PA are also described.
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Affiliation(s)
- Farbod Bahreini
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.,Network of Immunity in Infection, Malignancy & Autoimmunity (NIIMA), Universal Scientific Education & Research Network (USERN), Tehran, Iran
| | - Parnian Jabbari
- Network of Immunity in Infection, Malignancy & Autoimmunity (NIIMA), Universal Scientific Education & Research Network (USERN), Tehran, Iran.,Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran.,Department of Genetics, Genomics & Bioinformatics, University of California, Riverside, CA, USA
| | - Wilhelm Gossing
- Division Molecular Biotechnology & Functional Genomics, Technical University of Applied Sciences Wildau, Hochschulring 1, 15745, Wildau, Germany
| | - Fatemeh Aziziyan
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Marcus Frohme
- Division Molecular Biotechnology & Functional Genomics, Technical University of Applied Sciences Wildau, Hochschulring 1, 15745, Wildau, Germany
| | - Nima Rezaei
- Network of Immunity in Infection, Malignancy & Autoimmunity (NIIMA), Universal Scientific Education & Research Network (USERN), Tehran, Iran.,Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran.,Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
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Berberine Attenuates MPP +-Induced Neuronal Injury by Regulating LINC00943/miR-142-5p/KPNA4/NF-κB Pathway in SK-N-SH Cells. Neurochem Res 2021; 46:3286-3300. [PMID: 34427876 DOI: 10.1007/s11064-021-03431-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 08/16/2021] [Accepted: 08/18/2021] [Indexed: 12/14/2022]
Abstract
Berberine plays a neuro-protective role in neurodegenerative diseases, including Parkinson's disease (PD). Long non-coding RNAs (lncRNAs) play critical roles in PD pathogenesis. The purpose of this study was to investigate whether LINC00943 was involved in the role of berberine in PD. 1-methyl-4-phenyl-1, 2, 3, 6-tetrahydropyridine (MPTP) or 1-methyl-4-phenyl pyridine (MPP+) were used to construct PD mouse and cell models, respectively. Cell proliferation was evaluated by Cell Counting Kit-8 (CCK-8) and 5-Ethynyl-2'-deoxyuridine (Edu) assays. Inflammation and cell apoptosis were assessed by enzyme-linked immunosorbent assay (ELISA) and flow cytometry, respectively. Quantitative real-time PCR (qRT-PCR) was employed to test the expression of LINC00943, microRNA (miR)-142-5p, and karyopherin subunit alpha 4 (KPNA4) mRNA. The protein levels of NF-κB pathway-related markers and KPNA4 were measured by western blot. Oxidative stress level was assessed by corresponding kits. The interaction between miR-142-5p and LINC00943 or KPNA4 was determined via dual-luciferase reporter and RNA immunoprecipitation (RIP) assays. Berberine inhibited MPP+-induced injury in SK-N-SH cells by promoting cell proliferation and suppressing inflammation, apoptosis, and oxidative injury. LINC00943 and KPNA4 were upregulated and miR-142-5p was downregulated in PD mouse and cell models. LINC00943 (or KPNA4) overexpression or miR-142-5p inhibition abated the neuro-protective role of berberine in PD cell model. Moreover, miR-142-5p was a target of LINC00943, and KPNA4 could specially bind to miR-142-5p. Additionally, berberine inhibited NF-κB pathway by regulating LINC00943/miR-142-5p/KPNA4 axis. Berberine protected SK-N-SH cell from MPP+-induced neuronal damage via regulating LINC00943/miR-142-5p/KPNA4/NF-κB pathway, highlighting novel evidence for the neuro-protective role of berberine in PD.
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Zhai X, Wu Y, Wang Z, Zhao D, Li H, Chong T, Zhao J. Long Noncoding RNA LINC01133 Promotes the Malignant Behaviors of Renal Cell Carcinoma by Regulating the miR-30b-5p/Rab3D Axis. Cell Transplant 2021; 29:963689720964413. [PMID: 33054325 PMCID: PMC7784578 DOI: 10.1177/0963689720964413] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Renal cell carcinoma (RCC) is the most common type of kidney cancer with rising incidence. Long noncoding RNA (lncRNA) LINC01133 is a novel lncRNA that is involved in the development of several types of cancers. However, the role of LINC01133 in RCC has not been reported. Thus, in this study, we investigated the functions of LINC01133 in RCC. The qualitative real-time polymerase chain reaction analysis was performed to examine the levels of LINC01133 in RCC tissues and adjacent tissues, as well as RCC cell lines. The results showed that LINC01133 was highly expressed in RCC tissue specimens and cell lines. Downregulation of LINC01133 significantly inhibited the proliferation, migration, and invasion of RCC cells. Further mechanistic investigations proved that LINC01133 directly interacted with microRNA (miR)-30b-5p and regulated the miR-30b-5p expression in RCC cell lines. Moreover, miR-30b-5p exhibited tumor-suppressive activity in RCC cell lines, which was mediated by targeting Ras-related protein Rab-3D (Rab3D). In vivo study showed that LINC01133 knockdown suppressed tumor growth in the nude mice. Taken together, these findings indicated that LINC01133 might be an oncogene in RCC through regulation of the miR-30b-5p/Rab3D axis. Thus, LINC01133 might serve as a potential therapeutic target for the treatment of RCC.
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Affiliation(s)
- Xiaoqiang Zhai
- Department of Urology, The Second Affiliated Hospital of Medical School, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Yan Wu
- Department of Obstetrics and Gynecology, Xijing Hospital, Air Force Military Medical University, Xi'an, Shaanxi, China
| | - Zhenlong Wang
- Department of Urology, The Second Affiliated Hospital of Medical School, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Dawei Zhao
- Department of Urology, 3201 Hospital of Xi'an Jiaotong University Health Science Center, Hanzhong, Shaanxi, China
| | - Hecheng Li
- Department of Urology, The Second Affiliated Hospital of Medical School, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Tie Chong
- Department of Urology, The Second Affiliated Hospital of Medical School, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Jun Zhao
- Department of Urology, The Second Affiliated Hospital of Medical School, Xi'an Jiaotong University, Xi'an, Shaanxi, China
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Liu Y, Zhuang Y, Fu X, Li C. LncRNA POU3F3 promotes melanoma cell proliferation by downregulating lncRNA MEG3. Discov Oncol 2021; 12:21. [PMID: 35201451 PMCID: PMC8777492 DOI: 10.1007/s12672-021-00414-9] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 05/17/2021] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND LncRNA POU3F3 (POU3F3) is overexpressed and plays oncogenic roles in esophageal squamous-cell carcinomas. LncRNA MEG3 (MEG3) has been characterized as a tumor suppressive lncRNA in different types of cancer. Our preliminary deep sequencing analysis revealed the inverse correlation between POU3F3 and MEG2 across melanoma tissues, indicating the interaction between them in melanoma. Therefore, this study was performed to investigate the crosstalk between POU3F3 and MEG3 in melanoma. METHODS Tumor and adjacent healthy tissues collected from 60 melanoma patients were subjected to RNA extractions and RT-qPCRs to analyze the differential expression of POU3F3 and MEG2 in melanoma. In melanoma cells, POU3F3 and MEG2 were overexpressed to study the interactions between them. CCK-8 assays were performed to analyze the roles of POU3F3 and MEG2 in regulating melanoma cell proliferation. RESULTS We found that POU3F3 was upregulated, while lncRNA MEG3 was downregulated in melanoma. Expression levels of POU3F3 and MEG3 were inversely correlated across tumor tissues. In vitro experiments showed that POU3F3 overexpression decreased MEG3 expression in melanoma cells, while MEG3 overexpression failed to affect POU3F3. POU3F3 overexpression increased melanoma cell proliferation, while MEG3 overexpression decreased melanoma cell proliferation. In addition, rescue experiments showed that MEG3 overexpression attenuated the enhancing effects of POU3F3 overexpression. CONCLUSION POU3F3 may promote melanoma cell proliferation by downregulating MEG3.
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Affiliation(s)
- Yingnan Liu
- Department of Hand and Microvascular Surgery, Shenzhen People's Hospital, The Second Clinical Medical College, Jinan University, Shenzhen, 518000, Guangdong, China
- Department of Hand and Microvascular Surgery, Shenzhen People's Hospital, The First Affiliated Hospital,Southern University of Science and Technology, Shenzhen, 518000, Guangdong, China
| | - Yongqing Zhuang
- Department of Hand and Microvascular Surgery, Shenzhen People's Hospital, The Second Clinical Medical College, Jinan University, Shenzhen, 518000, Guangdong, China
- Department of Hand and Microvascular Surgery, Shenzhen People's Hospital, The First Affiliated Hospital,Southern University of Science and Technology, Shenzhen, 518000, Guangdong, China
| | - Xiaokuan Fu
- Department of Hand and Microvascular Surgery, Shenzhen People's Hospital, The Second Clinical Medical College, Jinan University, Shenzhen, 518000, Guangdong, China
- Department of Hand and Microvascular Surgery, Shenzhen People's Hospital, The First Affiliated Hospital,Southern University of Science and Technology, Shenzhen, 518000, Guangdong, China
| | - Chaofei Li
- Department of General Surgery, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, 12th floor, Building 9, No. 197, Ruijin 2nd Road, Huangpu District, Shanghai, 200025, China.
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Zhang R, Chen L, Huang F, Wang X, Li C. Long non-coding RNA NEAT1 promotes lipopolysaccharide-induced acute lung injury by regulating miR-424-5p/MAPK14 axis. Genes Genomics 2021; 43:815-827. [PMID: 33904112 DOI: 10.1007/s13258-021-01103-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 04/12/2021] [Indexed: 12/21/2022]
Abstract
BACKGROUND Many long non-coding RNAs (lncRNAs) have been suggested to play critical roles in acute lung injury (ALI) pathogenesis, including lncRNA nuclear enriched abundant transcript 1 (NEAT1). OBJECTIVE We aimed to further elucidate the functions and molecular mechanism of NEAT1 in ALI. METHODS Human pulmonary alveolar epithelial cells (HPAEpiCs) stimulated by lipopolysaccharide (LPS) were served as a cellular model of ALI. Cell viability and cell apoptosis were determined by cell counting kit-8 (CCK-8) assay and flow cytometry, respectively. The expression of NEAT1, microRNA-424-5p (miR-424-5p), and mitogen-activated protein kinase 14 (MAPK14) was measured by quantitative real-time polymerase chain reaction (qRT-PCR) or western blot analysis. Caspase activity was determined by caspase activity kit. The inflammatory responses were evaluated using enzyme-linked immunosorbent assay (ELISA). The oxidative stress factors were analyzed by corresponding kits. RESULTS NEAT1 was upregulated in LPS-stimulated HPAEpiCs. NEAT1 knockdown weakened LPS-induced injury by inhibiting apoptosis, inflammation and oxidative stress in HPAEpiCs. Moreover, miR-424-5p was a direct target of NEAT1, and its knockdown reversed the effects caused by NEAT1 knockdown in LPS-induced HPAEpiCs. Furthermore, MAPK14 was a downstream target of miR-424-5p, and its overexpression attenuated the effects of miR-424-5p on reduction of LPS-induced injury in HPAEpiCs. Besides, NEAT1 acted as a sponge of miR-424-5p to regulate MAPK14 expression. CONCLUSION NEAT1 knockdown alleviated LPS-induced injury of HPAEpiCs by regulating miR-424-5p/MAPK14 axis, which provided a potential therapeutic target for the treatment of ALI.
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Affiliation(s)
- Rui Zhang
- Department of Paediatrics, Suizhou Hospital, Hubei University of Medicine, Long Men Street 60th, Zeng Du District, Suizhou, 441300, Hubei, China
| | - Lina Chen
- Department of Paediatrics, Suizhou Hospital, Hubei University of Medicine, Long Men Street 60th, Zeng Du District, Suizhou, 441300, Hubei, China
| | - Fei Huang
- Department of Paediatrics, Suizhou Hospital, Hubei University of Medicine, Long Men Street 60th, Zeng Du District, Suizhou, 441300, Hubei, China
| | - Xiaorong Wang
- Department of Paediatrics, Suizhou Hospital, Hubei University of Medicine, Long Men Street 60th, Zeng Du District, Suizhou, 441300, Hubei, China
| | - Cuihong Li
- Department of Paediatrics, Suizhou Hospital, Hubei University of Medicine, Long Men Street 60th, Zeng Du District, Suizhou, 441300, Hubei, China.
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Xia H, Niu Q, Ding Y, Zhang Z, Yuan J, Jin W. Long noncoding HOXA11-AS knockdown suppresses the progression of non-small cell lung cancer by regulating miR-3619-5p/SALL4 axis. J Mol Histol 2021; 52:729-740. [PMID: 34050851 DOI: 10.1007/s10735-021-09981-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 05/19/2021] [Indexed: 10/21/2022]
Abstract
Accumulating evidence suggested that many long noncoding RNAs (lncRNAs) were widely involved in the development and progression of non-small cell lung cancer (NSCLC). However, the roles of lncRNA homeobox A11 antisense (HOXA11-AS) and its underlying mechanism in NSCLC remains largely unknown. The expression levels of HOXA11-AS, miR-3619-5p and sal-like protein 4 (SALL4) were detected by quantitative real-time polymerase chain reaction (qRT-PCR). Western blot analysis was used to measure the protein levels of hexokinase II (HK2) and SALL4. Cell proliferation, apoptosis, migration and invasion were determined by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay, flow cytometry and transwell assay, respectively. The glucose consumption and lactate production were measured using glucose assay kit and lactate assay kit, respectively. The potential binding sites between miR-3619-5p and HOXA11-AS or SALL4 were predicted by online software and verified by luciferase report assay. A xenograft tumor model was established to confirm the function of HOXA11-AS in NSCLC in vivo. HOXA11-AS and SALL4 were upregulated while miR-3619-5p was downregulated in NSCLC tissues and cells. HOXA11-AS knockdown suppressed cell proliferation, migration, invasion, and glycolysis but promoted apoptosis in NSCLC cells. Moreover, miR-3619-5p could directly bind to HOXA11-AS and its inhibition attenuated the inhibitory effect of HOXA11-AS knockdown on progression of NSCLC cells. Furthermore, SALL4 was a direct target of miR-3619-5p and its overexpression reversed the anti-tumor role of miR-3619-5p in NSCLC cells. Besides, HOXA11-AS modulated SALL4 expression via sponging miR-3619-5p. Additionally, silencing HOXA11-AS inhibited tumor growth though upregulating miR-3619-5p and downregulating SALL4. Collectively, HOXA11-AS knockdown inhibited the progression of NSCLC by regulating miR-3619-5p/SALL4 axis, which might offer a novel avenue for interpreting the mechanism of NSCLC development.
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Affiliation(s)
- Hongwei Xia
- Department of Thoracic Surgery, Qingpu Branch of Zhongshan Hospital Affiliated To Fudan University, No.1158, Gongyuan East Road, Qingpu District, Shanghai, 210700, China
| | - Qingling Niu
- Department of Pediatrics, Qingpu Branch, Zhongshan Hospital Affiliated To Fudan University, Shanghai, China
| | - Yanguang Ding
- Department of Thoracic Surgery, Qingpu Branch of Zhongshan Hospital Affiliated To Fudan University, No.1158, Gongyuan East Road, Qingpu District, Shanghai, 210700, China
| | - Zhiqiang Zhang
- Department of Thoracic Surgery, Qingpu Branch of Zhongshan Hospital Affiliated To Fudan University, No.1158, Gongyuan East Road, Qingpu District, Shanghai, 210700, China
| | - Jun Yuan
- Department of Thoracic Surgery, Qingpu Branch of Zhongshan Hospital Affiliated To Fudan University, No.1158, Gongyuan East Road, Qingpu District, Shanghai, 210700, China
| | - Wei Jin
- Department of Thoracic Surgery, Qingpu Branch of Zhongshan Hospital Affiliated To Fudan University, No.1158, Gongyuan East Road, Qingpu District, Shanghai, 210700, China.
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Daulatabad SV, Srivastava R, Janga SC. Lantern: an integrative repository of functional annotations for lncRNAs in the human genome. BMC Bioinformatics 2021; 22:279. [PMID: 34039271 PMCID: PMC8157669 DOI: 10.1186/s12859-021-04207-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 05/18/2021] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND With advancements in omics technologies, the range of biological processes where long non-coding RNAs (lncRNAs) are involved, is expanding extensively, thereby generating the need to develop lncRNA annotation resources. Although, there are a plethora of resources for annotating genes, despite the extensive corpus of lncRNA literature, the available resources with lncRNA ontology annotations are rare. RESULTS We present a lncRNA annotation extractor and repository (Lantern), developed using PubMed's abstract retrieval engine and NCBO's recommender annotation system. Lantern's annotations were benchmarked against lncRNAdb's manually curated free text. Benchmarking analysis suggested that Lantern has a recall of 0.62 against lncRNAdb for 182 lncRNAs and precision of 0.8. Additionally, we also annotated lncRNAs with multiple omics annotations, including predicted cis-regulatory TFs, interactions with RBPs, tissue-specific expression profiles, protein co-expression networks, coding potential, sub-cellular localization, and SNPs for ~ 11,000 lncRNAs in the human genome, providing a one-stop dynamic visualization platform. CONCLUSIONS Lantern integrates a novel, accurate semi-automatic ontology annotation engine derived annotations combined with a variety of multi-omics annotations for lncRNAs, to provide a central web resource for dissecting the functional dynamics of long non-coding RNAs and to facilitate future hypothesis-driven experiments. The annotation pipeline and a web resource with current annotations for human lncRNAs are freely available on sysbio.lab.iupui.edu/lantern.
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Affiliation(s)
- Swapna Vidhur Daulatabad
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University, Informatics and Communications Technology Complex, 535 W Michigan St., IT 475H, Indianapolis, IN, 46202, USA
| | - Rajneesh Srivastava
- Department of Surgery, Indiana Center for Regenerative Medicine and Engineering (ICRME), Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Sarath Chandra Janga
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University, Informatics and Communications Technology Complex, 535 W Michigan St., IT 475H, Indianapolis, IN, 46202, USA.
- Department of Medical and Molecular Genetics, Medical Research and Library Building, Indiana University School of Medicine, 975 West Walnut Street, Indianapolis, IN, 46202, USA.
- Centre for Computational Biology and Bioinformatics, Indiana University School of Medicine, 5021 Health Information and Translational Sciences (HITS), 410 West 10th Street, Indianapolis, IN, 46202, USA.
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Long non-coding RNA NEAT1 promotes lipopolysaccharide-induced injury in human tubule epithelial cells by regulating miR-93-5p/TXNIP axis. Med Microbiol Immunol 2021; 210:121-132. [PMID: 33885954 DOI: 10.1007/s00430-021-00705-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 04/03/2021] [Indexed: 12/17/2022]
Abstract
Many long non-coding RNAs (lncRNAs) have been found to play crucial roles in sepsis-induced acute kidney injury (AKI), including lncRNA nuclear-enriched abundant transcript 1 (NEAT1). We aimed to further elucidate the functions and molecular mechanism of NEAT1 in sepsis-induced AKI. Sepsis-induced AKI cell model was established by treatment with lipopolysaccharide (LPS) in human tubule epithelial (HK2) cells. Cell viability and apoptosis were determined by Cell Counting Kit-8 (CCK-8) assay and flow cytometry, respectively. Western blot assay was performed to measure all protein levels. The concentrations of inflammatory factors were evaluated using enzyme-linked immunosorbent assay (ELISA). The expression levels of inflammatory factors, NEAT1, microRNA-93-5p (miR-93-5p), and thioredoxin-interacting protein (TXNIP) were measured by quantitative real-time polymerase chain reaction (qRT-PCR). The oxidative stress factors were detected using corresponding kits. The interaction between miR-93-5p and NEAT1 or TXNIP was predicted by bioinformatics analysis and verified by dual-luciferase reporter and RNA Immunoprecipitation (RIP) assays. NEAT1 was upregulated in serum of sepsis patients and LPS-induced HK2 cells. NEAT1 silence alleviated LPS-induced HK2 cell injury by inhibiting apoptosis, inflammation and oxidative stress. Moreover, miR-93-5p was a direct target of NEAT1, and suppression of NEAT1 weakened LPS-induced injury by upregulating miR-93-5p in HK2 cells. Furthermore, TXNIP was a downstream target of miR-93-5p, and miR-93-5p attenuated LPS-induced HK2 cell injury by downregulating TXNIP. In addition, NEAT1 regulated TXNIP expression by acting as a sponge of miR-93-5p. NEAT1 might aggravate LPS-induced injury in HK2 cells by regulating miR-93-5p/TXNIP axis, providing a potential therapeutic strategy for sepsis-associated AKI.
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44
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Hao C, Chen S. Knockdown of lncRNA TTTY15 alleviates ischemia/reperfusion-induced inflammation and apoptosis of PC12 cells by targeting miR-766-5p. Exp Ther Med 2021; 21:511. [PMID: 33791020 PMCID: PMC8005683 DOI: 10.3892/etm.2021.9942] [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] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 02/22/2021] [Indexed: 12/26/2022] Open
Abstract
The pathogenesis of ischemic stroke is extremely complex and has a significant impact on the quality of life of the patients. Accumulating studies have reported that long non-coding RNAs (lncRNAs) may be associated with the progression of ischemic stroke. However, the role and underlying mechanism of action of the lncRNA testis-specific transcript Y-linked 15 (TTTY15) in ischemic stroke remains unknown. The present study analyzed the expression levels of TTTY15 in PC12 cells injured by oxygen-glucose deprivation/reperfusion (OGD/R). The effects of the knockdown of TTTY15 expression on the levels of the inflammatory cytokines TNF-α, IL-1β, IL-18 and IL-10, cell apoptosis and the expression levels of the apoptosis-associated proteins Bcl-2, Bax, cleaved caspase-3, caspase-3, cleaved caspase-9 and caspase-9, were subsequently analyzed in OGD/R-treated PC12 cells using ELISA, flow cytometry and western blotting, respectively. In addition, the downstream target gene of TTTY15 was verified using a dual luciferase reporter assay. The effects of TTTY15 on the inflammation and apoptosis of PC12 cells treated with OGD/R were determined by targeting miR-766-5p. The results of the present study revealed that TTTY15 expression was upregulated in OGD/R-treated PC12 cells. The knockdown of TTTY15 significantly decreased the concentrations of the proinflammatory factors TNF-α, IL-1β and IL-18, while it increased the concentration of the anti-inflammatory cytokine IL-10 in OGD/R-treated PC12 cells. Apoptosis was also suppressed following gene silencing of TTTY15. Subsequently, miR-766-5p was identified as a target gene of TTTY15 using a dual luciferase reporter assay and the expression levels of TTTY15 and miR-766-5p were found to be negatively correlated. The overexpression of miR-766-5p alleviated the stimulatory effect of TTTY15 overexpression on the inflammation and apoptosis of PC12 cells treated with OGD/R. Therefore, the present study revealed that TTTY15 knockdown improved the OGD/R-induced injury of PC12 cells by upregulating miR-766-5p expression.
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Affiliation(s)
- Chenguang Hao
- Department of Neurology, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang 830054, P.R. China
| | - Shibao Chen
- Department of Neurology, Bayingolin Mongolian Autonomous Prefecture People's Hospital, Korla, Xinjiang 841000, P.R. China
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45
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Zhang M, Cheng K. Long non-coding RNA KCNQ1OT1 promotes hydrogen peroxide-induced lens epithelial cell apoptosis and oxidative stress by regulating miR-223-3p/BCL2L2 axis. Exp Eye Res 2021; 206:108543. [PMID: 33744257 DOI: 10.1016/j.exer.2021.108543] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 03/02/2021] [Accepted: 03/10/2021] [Indexed: 12/24/2022]
Abstract
Many long non-coding RNAs (lncRNAs) can exert crucial roles in the pathogenesis of cataract, including lncRNA KCNQ1 opposite strand/antisense transcript 1 (KCNQ1OT1). We aimed to further elucidate the biological role and regulatory molecular mechanism of KCNQ1OT1 in cataract. The expression of KCNQ1OT1 and miR-223-3p and BCL2 like 2 (BCL2L2) was examined by qRT-PCR. Cataract cell model was constructed by treatment with hydrogen peroxide (H2O2) in lens epithelial cells (SRA01/04). SRA01/04 cell viability and cell apoptosis were tested using CCK-8 assay and flow cytometry, respectively. Western blot (WB) was performed to measure the levels of apoptosis-related proteins and BCL2L2 protein. The oxidative stress factors were analyzed by corresponding kits. The interaction between miR-223-3p and KCNQ1OT1 or BCL2L2 was validated by dual-luciferase reporter and RNA Immunoprecipitation (RIP) assays. We found that KCNQ1OT1 was upregulated in cataract anterior lens capsule samples and H2O2-induced SRA01/04 cells. Knockdown of KCNQ1OT1 suppressed H2O2-induced SRA01/04 cell apoptosis and oxidative stress. KCNQ1OT1 acted as a sponge of miR-223-3p. Inhibition of miR-223-3p could abate the function of KCNQ1OT1 silence in H2O2-treated SRA01/04 cells. Additionally, BCL2L2 was a direct target of miR-223-3p, and miR-223-3p weakened H2O2-induced SRA01/04 cell apoptosis and oxidative stress by targeting BCL2L2. Collectively, the data suggest a role for the KCNQ1OT1/miR-223-3p/BCL2L2 axis in cataract formation but the data was generated using an epithelial cell line.
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Affiliation(s)
- Min Zhang
- Department of Ophthalmology, Jinan Maternal and Child Health Hospital, Jinan, 250001, Shandong, China
| | - Kai Cheng
- Department of Ophthalmology, Jinan Maternal and Child Health Hospital, Jinan, 250001, Shandong, China.
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46
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Rong R, Wang M, You M, Li H, Xia X, Ji D. Pathogenesis and prospects for therapeutic clinical application of noncoding RNAs in glaucoma: Systematic perspectives. J Cell Physiol 2021; 236:7097-7116. [PMID: 33634475 PMCID: PMC8451868 DOI: 10.1002/jcp.30347] [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: 11/11/2020] [Revised: 01/24/2021] [Accepted: 02/16/2021] [Indexed: 12/18/2022]
Abstract
Noncoding ribonucleic acids (ncRNAs) are an increasingly studied class of RNA molecules with extensive biological activities, including important roles in human development, health, and disease. Glaucoma is a neurodegenerative disease of the retina, and one of the leading causes of blindness worldwide. However, the specific roles of ncRNAs in the development and progression of glaucoma are unclear, and related reports are fragmented. An in‐depth understanding of ncRNAs participating in the pathogenesis and progression of glaucoma would be helpful for opening up new avenues to facilitate the early diagnosis and clinical treatment. Therefore, in this review, we aimed to discuss the current research progress, the potentialfuture clinical applications and the research limitations of three critical classes of ncRNAs in glaucoma, namely microRNAs, long noncoding RNAs, and circular RNAs.
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Affiliation(s)
- Rong Rong
- Eye Center of Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, China
| | - Mengxiao Wang
- Eye Center of Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, China
| | - Mengling You
- Eye Center of Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, China
| | - Haibo Li
- Eye Center of Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, China
| | - Xiaobo Xia
- Eye Center of Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, China
| | - Dan Ji
- Eye Center of Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, China
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47
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Yin D, Xu F, Lu M, Li X. Long non-coding RNA RMST promotes oxygen-glucose deprivation-induced injury in brain microvascular endothelial cells by regulating miR-204-5p/VCAM1 axis. Life Sci 2021; 284:119244. [PMID: 33607153 DOI: 10.1016/j.lfs.2021.119244] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 02/08/2021] [Accepted: 02/09/2021] [Indexed: 02/06/2023]
Abstract
AIMS Many long non-coding RNAs (lncRNAs) have been suggested to play critical roles in the pathogenesis of ischemic stroke, including lncRNA rhabdomyosarcoma 2-associated transcript (RMST). We aimed to elucidate the role and molecular mechanism of RMST in ischemic stroke. MATERIALS AND METHODS The in vitro ischemic stroke model was established by treating brain microvascular endothelial cells with oxygen-glucose deprivation (OGD). The expression of RMST, miR-204-5p and vascular cell adhesion molecule 1 (VCAM1) were determined by quantitative real-time polymerase chain reaction (qRT-PCR). The interaction between miR-204-5p and RMST or VCAM1 was confirmed using dual-luciferase reporter and RNA immunoprecipitation (RIP) assays. Cell viability, migration and apoptosis were assessed by Cell Counting Kit-8 (CCK-8), wound healing assay and flow cytometry, respectively. Lactic dehydrogenase (LDH) leakage rate was determined by LDH activity assay kit. The protein level of VCAM1 was analyzed by western blot (WB) assay. KEY FINDINGS RMST was upregulated in OGD-treated HBMEC and bEnd.3 cells. MiR-204-5p was a direct target of RMST, and miR-204-5p inhibition abated the inhibitory effect of RMST knockdown on OGD-induced injury via inhibiting cell viability and migration and promoting apoptosis in HBMEC and bEnd.3 cells. Moreover, VCAM1 was identified as a direct target of miR-204-5p, and VCAM1 alleviated the effect of miR-204-5p on reduction of OGD-induced injury in HBMEC and bEnd.3 cells. In addition, RMST regulated VCAM1 expression via sponging miR-204-5p. SIGNIFICANCE RMST knockdown attenuated OGD-induced injury of HBMEC and bEnd.3 cells via regulating miR-204-5p/VCAM1 axis, indicating a possible therapeutic strategy for future ischemic stroke therapy.
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Affiliation(s)
- Dongliang Yin
- Department of Neurology, The Third Hospital of Jinan, Jinan 250000, China
| | - Furong Xu
- Department of Neurology, Chengdu Seventh People's Hospital, Chengdu 610000, China
| | - Ming Lu
- Department of Neurology, The Third Hospital of Jinan, Jinan 250000, China
| | - Xuewen Li
- Department of Neurosurgery, Dingxi People's Hospital, Dingxi 743000, China.
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Jiang J, Cheng L, Yan L, Ge M, Yang L, Ying H, Kong Q. Decoding the role of long noncoding RNAs in the healthy aging of centenarians. Brief Bioinform 2021; 22:6124916. [PMID: 33517370 DOI: 10.1093/bib/bbaa439] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 11/23/2020] [Accepted: 12/29/2020] [Indexed: 12/20/2022] Open
Abstract
Aging is the largest risk factor of major human diseases. Long noncoding RNAs (lncRNAs) as the key regulatory elements have shown a strong impact on multiple biological processes as well as human disease mechanisms. However, the roles of lncRNAs in aging/healthy aging processes remain largely unknown. Centenarians are good models for healthy aging studies due to avoiding major chronic diseases and disabilities. To illustrate their ubiquitous nature in the genome and the 'secrets' of healthy aging regulation from the perspective of lncRNAs, peripheral blood samples from two regions consisting 76 centenarians (CENs), 54 centenarian-children (F1) and 41 spouses of centenarian-children (F1SP) were collected for deep RNA-seq. We identified 11 CEN-specific lncRNAs that is particularly expressed in longevous individuals. By kmers clustering, hundreds of human lncRNAs show similarities with CEN-specific lncRNAs, especially with ENST00000521663 and ENST00000444998. Using F1SP as normal elder controls (age: 59.9 ± 6.6 years), eight lncRNAs that are differentially expressed in longevous elders (CEN group, age: 102.2 ± 2.4 years) were identified as candidate aging/health aging-related lncRNAs (car-lncs). We found that the expression of eight car-lncs in human diploid fibroblasts displayed dynamic changes during cell passage and/or H2O2/rapamycin treatment; of which, overexpression either of THBS1-IT1 and THBS1-AS1, two lncRNAs that highly expressed in CENs, can remarkably decrease p16, p21 and the activity of senescent related β-galactosidase, suggesting that THBS1-IT1 and THBS1-AS1 can inhibit cellular senescence. We provided the first comprehensive analysis of lncRNA expression in longevous populations, and our results hinted that dysregulated lncRNAs in CENs are potential protective factors in healthy aging process.
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Affiliation(s)
- Jianjun Jiang
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Department of Molecular & Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.,Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lehua Cheng
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Kunming Key Laboratory of Healthy Aging Study, Chinese Academy of Sciences, Kunming, 650223, China
| | - Liang Yan
- Department of Molecular & Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Mingxia Ge
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Kunming Key Laboratory of Healthy Aging Study, Chinese Academy of Sciences, Kunming, 650223, China.,KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Liqin Yang
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Kunming Key Laboratory of Healthy Aging Study, Chinese Academy of Sciences, Kunming, 650223, China.,KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, 650223, China
| | - Haoqiang Ying
- Department of Molecular & Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Qingpeng Kong
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.,Kunming Key Laboratory of Healthy Aging Study, Chinese Academy of Sciences, Kunming, 650223, China.,KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China
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Liu W, Sheng L, Nie L, Wen X, Mo X. Functional interaction between long non-coding RNA and microRNA in rheumatoid arthritis. J Clin Lab Anal 2020; 34:e23489. [PMID: 33319382 PMCID: PMC7755821 DOI: 10.1002/jcla.23489] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 06/22/2020] [Accepted: 07/01/2020] [Indexed: 01/07/2023] Open
Abstract
MicroRNA (miRNA) has received widespread attention for its role in several key cellular processes such as cell differentiation, cell proliferation, apoptosis, and autoimmune diseases. Although we now have a good understanding of miRNA expression and function, our knowledge regarding the molecular mechanism of long non‐coding RNA (lncRNA) is still in its infancy. In this review, we will briefly introduce the definition and function of lncRNA and summarize the interactions between lncRNA and miRNA and their research progress in rheumatoid arthritis (RA). The expression of miR‐16, miR‐146a, miR‐155, and miR‐223 and the interactions between HOTAIR and miR138, ZFAS1 and miR‐27a, and GAPLINC and miR‐575 are representative examples that may augment the understanding of the pathogenesis of RA and help in the development of new biomarkers and target therapies.
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Affiliation(s)
- Weiwei Liu
- Medical College of Northwest Minzu University, Lanzhou, China
| | - Li Sheng
- Medical College of Northwest Minzu University, Lanzhou, China
| | - Lei Nie
- Medical College of Northwest Minzu University, Lanzhou, China
| | - Xiaoyun Wen
- Medical College of Northwest Minzu University, Lanzhou, China
| | - Xiaodan Mo
- Medical College of Northwest Minzu University, Lanzhou, China
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50
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Xiao Y, Xiao Z, Feng X, Chen Z, Kuang L, Wang L. A novel computational model for predicting potential LncRNA-disease associations based on both direct and indirect features of LncRNA-disease pairs. BMC Bioinformatics 2020; 21:555. [PMID: 33267800 PMCID: PMC7709313 DOI: 10.1186/s12859-020-03906-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 11/25/2020] [Indexed: 12/25/2022] Open
Abstract
Background Accumulating evidence has demonstrated that long non-coding RNAs (lncRNAs) are closely associated with human diseases, and it is useful for the diagnosis and treatment of diseases to get the relationships between lncRNAs and diseases. Due to the high costs and time complexity of traditional bio-experiments, in recent years, more and more computational methods have been proposed by researchers to infer potential lncRNA-disease associations. However, there exist all kinds of limitations in these state-of-the-art prediction methods as well. Results In this manuscript, a novel computational model named FVTLDA is proposed to infer potential lncRNA-disease associations. In FVTLDA, its major novelty lies in the integration of direct and indirect features related to lncRNA-disease associations such as the feature vectors of lncRNA-disease pairs and their corresponding association probability fractions, which guarantees that FVTLDA can be utilized to predict diseases without known related-lncRNAs and lncRNAs without known related-diseases. Moreover, FVTLDA neither relies solely on known lncRNA-disease nor requires any negative samples, which guarantee that it can infer potential lncRNA-disease associations more equitably and effectively than traditional state-of-the-art prediction methods. Additionally, to avoid the limitations of single model prediction techniques, we combine FVTLDA with the Multiple Linear Regression (MLR) and the Artificial Neural Network (ANN) for data analysis respectively. Simulation experiment results show that FVTLDA with MLR can achieve reliable AUCs of 0.8909, 0.8936 and 0.8970 in 5-Fold Cross Validation (fivefold CV), 10-Fold Cross Validation (tenfold CV) and Leave-One-Out Cross Validation (LOOCV), separately, while FVTLDA with ANN can achieve reliable AUCs of 0.8766, 0.8830 and 0.8807 in fivefold CV, tenfold CV, and LOOCV respectively. Furthermore, in case studies of gastric cancer, leukemia and lung cancer, experiment results show that there are 8, 8 and 8 out of top 10 candidate lncRNAs predicted by FVTLDA with MLR, and 8, 7 and 8 out of top 10 candidate lncRNAs predicted by FVTLDA with ANN, having been verified by recent literature. Comparing with the representative prediction model of KATZLDA, comparison results illustrate that FVTLDA with MLR and FVTLDA with ANN can achieve the average case study contrast scores of 0.8429 and 0.8515 respectively, which are both notably higher than the average case study contrast score of 0.6375 achieved by KATZLDA. Conclusion The simulation results show that FVTLDA has good prediction performance, which is a good supplement to future bioinformatics research.
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Affiliation(s)
- Yubin Xiao
- College of Computer Engineering and Applied Mathematics, Changsha University, Changsha, 410001, People's Republic of China.,Key Laboratory of Hunan Province for Internet of Things and Information Security, Xiangtan University, Xiangtan, 411105, People's Republic of China
| | - Zheng Xiao
- Hunan Province Key Laboratory of Tumor Cellular and Molecular Pathology, Cancer Research Institute, University of South China, Hengyang, 421001, Hunan, People's Republic of China
| | - Xiang Feng
- College of Computer Engineering and Applied Mathematics, Changsha University, Changsha, 410001, People's Republic of China
| | - Zhiping Chen
- College of Computer Engineering and Applied Mathematics, Changsha University, Changsha, 410001, People's Republic of China
| | - Linai Kuang
- Key Laboratory of Hunan Province for Internet of Things and Information Security, Xiangtan University, Xiangtan, 411105, People's Republic of China
| | - Lei Wang
- College of Computer Engineering and Applied Mathematics, Changsha University, Changsha, 410001, People's Republic of China. .,Key Laboratory of Hunan Province for Internet of Things and Information Security, Xiangtan University, Xiangtan, 411105, People's Republic of China.
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