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Yang J, Ruan J, Zhou B, Ye S, Gao S, Zheng X. Regulation of STAT5 phosphorylation and interaction with SHP1 by lnc-AC004893, a long non-coding RNA overexpressed in myeloproliferative neoplasms. Hematology 2024; 29:2375045. [PMID: 39012197 DOI: 10.1080/16078454.2024.2375045] [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: 12/12/2022] [Accepted: 06/25/2024] [Indexed: 07/17/2024] Open
Abstract
OBJECTIVES Constitutive activation of Janus kinase 2 (JAK2)/signal transducer and activator of transcription (STAT) signaling pathway is central to the pathogenesis of myeloproliferative neoplasms (MPNs). Long noncoding RNAs (lncRNAs) regulate diverse biological processes. However, the role of lncRNAs in MPN pathogenesis is not well studied. METHODS The expression of lnc-AC004893 in MPN patients was measured by quantitative real-time PCR (qRT-PCR). Gene-specific short hairpin RNAs (shRNAs) were designed to inhibit the expression of lnc-AC004893, and western blot was performed to explore the role of lnc-AC004893 via regulating the JAK2/STAT5 signaling pathway. Furthermore, co-IP was performed to determine the binding ability of lnc-AC004893 and STAT5 protein. Finally, the BaF3-JAK2V617F-transplanted mouse model was used to assess the biological role of lnc-ac004893 in vivo. RESULTS We report that lnc-AC004893, a poorly conserved pseudogene-209, is substantially upregulated in MPN cells compared with normal controls (NCs). Knockdown of lnc-AC004893 by specific shRNAs suppressed cell proliferation and decreased colony formation. Furthermore, the knockdown of lnc-AC004893 reduced the expression of p-STAT5 but not total STAT5 in HEL and murine IL-3-dependent Ba/F3 cells, which present constitutive and inducible activation of JAK2/STAT5 signaling. In addition, inhibition of murine lnc-ac004893 attenuated BaF3-JAK2V617F-transplanted phenotypes and extended the overall survival. Mechanistically, knockdown of lnc-AC004893 enhanced the binding ability of STAT5 and protein tyrosine phosphatase SHP1. Furthermore, knockdown of lnc-AC004893 decreased STAT5-lnc-AC004893 interaction but not SHP1-lnc-AC004893 interaction. CONCLUSION Lnc-AC004893 regulates STAT5 phosphorylation by affecting the interaction of STAT5 and SHP1. Lnc-AC004893 might be a potential therapeutic target for MPN patients.
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Affiliation(s)
- Junjun Yang
- Department of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, People's Republic of China
| | - Jichen Ruan
- Department of Hematology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, People's Republic of China
| | - Bin Zhou
- Medical Research Center, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, People's Republic of China
| | - Sisi Ye
- Medical Research Center, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, People's Republic of China
| | - Shenmeng Gao
- Medical Research Center, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, People's Republic of China
| | - Xiaoqun Zheng
- Department of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, People's Republic of China
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, People's Republic of China
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Armenta-Castro A, Núñez-Soto MT, Rodriguez-Aguillón KO, Aguayo-Acosta A, Oyervides-Muñoz MA, Snyder SA, Barceló D, Saththasivam J, Lawler J, Sosa-Hernández JE, Parra-Saldívar R. Urine biomarkers for Alzheimer's disease: A new opportunity for wastewater-based epidemiology? ENVIRONMENT INTERNATIONAL 2024; 184:108462. [PMID: 38335627 DOI: 10.1016/j.envint.2024.108462] [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: 10/08/2023] [Revised: 01/16/2024] [Accepted: 01/26/2024] [Indexed: 02/12/2024]
Abstract
While Alzheimer's disease (AD) diagnosis, management, and care have become priorities for healthcare providers and researcher's worldwide due to rapid population aging, epidemiologic surveillance efforts are currently limited by costly, invasive diagnostic procedures, particularly in low to middle income countries (LMIC). In recent years, wastewater-based epidemiology (WBE) has emerged as a promising tool for public health assessment through detection and quantification of specific biomarkers in wastewater, but applications for non-infectious diseases such as AD remain limited. This early review seeks to summarize AD-related biomarkers and urine and other peripheral biofluids and discuss their potential integration to WBE platforms to guide the first prospective efforts in the field. Promising results have been reported in clinical settings, indicating the potential of amyloid β, tau, neural thread protein, long non-coding RNAs, oxidative stress markers and other dysregulated metabolites for AD diagnosis, but questions regarding their concentration and stability in wastewater and the correlation between clinical levels and sewage circulation must be addressed in future studies before comprehensive WBE systems can be developed.
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Affiliation(s)
| | - Mónica T Núñez-Soto
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico
| | - Kassandra O Rodriguez-Aguillón
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico; Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing, Monterrey 64849, Mexico
| | - Alberto Aguayo-Acosta
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico; Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing, Monterrey 64849, Mexico
| | - Mariel Araceli Oyervides-Muñoz
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico; Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing, Monterrey 64849, Mexico
| | - Shane A Snyder
- Nanyang Environment & Water Research Institute (NEWRI), Nanyang Technological University, Singapore
| | - Damià Barceló
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research, IDAEA-CSIC, Jordi Girona, 18-26, 08034 Barcelona, Spain; Sustainability Cluster, School of Engineering at the UPES, Dehradun, Uttarakhand, India
| | - Jayaprakash Saththasivam
- Water Center, Qatar Environment & Energy Research Institute, Hamad Bin Khalifa University, Qatar Foundation, Qatar
| | - Jenny Lawler
- Water Center, Qatar Environment & Energy Research Institute, Hamad Bin Khalifa University, Qatar Foundation, Qatar
| | - Juan Eduardo Sosa-Hernández
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico; Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing, Monterrey 64849, Mexico.
| | - Roberto Parra-Saldívar
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico; Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing, Monterrey 64849, Mexico
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3
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Sabaghi F, Sadat SY, Mirsaeedi Z, Salahi A, Vazifehshenas S, Kesh NZ, Balavar M, Ghoraeian P. The Role of Long Noncoding RNAs in Progression of Leukemia: Based on Chromosomal Location. Microrna 2024; 13:14-32. [PMID: 38275047 DOI: 10.2174/0122115366265540231201065341] [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: 07/11/2023] [Revised: 08/29/2023] [Accepted: 10/12/2023] [Indexed: 01/27/2024]
Abstract
Long non-coding RNA [LncRNA] dysregulation has been seen in many human cancers, including several kinds of leukemia, which is still a fatal disease with a poor prognosis. LncRNAs have been demonstrated to function as tumor suppressors or oncogenes in leukemia. This study covers current research findings on the role of lncRNAs in the prognosis and diagnosis of leukemia. Based on recent results, several lncRNAs are emerging as biomarkers for the prognosis, diagnosis, and even treatment outcome prediction of leukemia and have been shown to play critical roles in controlling leukemia cell activities, such as proliferation, cell death, metastasis, and drug resistance. As a result, lncRNA profiles may have superior predictive and diagnostic potential in leukemia. Accordingly, this review concentrates on the significance of lncRNAs in leukemia progression based on their chromosomal position.
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Affiliation(s)
- Fatemeh Sabaghi
- Department of Molecular cell biology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Saina Yousefi Sadat
- Department of Microbiology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Zohreh Mirsaeedi
- Department of Cellular and Molecular Biology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Aref Salahi
- Department of Molecular cell biology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Sara Vazifehshenas
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Neda Zahmat Kesh
- Department of Genetics, Zanjan Branch Islamic Azad University, Zanjan, Iran
| | - Mahdieh Balavar
- Department of Genetics, Falavarjan Branch Islamic Azad University, Falavarjan, Iran
| | - Pegah Ghoraeian
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
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4
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Xiao H, Feng X, Liu M, Gong H, Zhou X. SnoRNA and lncSNHG: Advances of nucleolar small RNA host gene transcripts in anti-tumor immunity. Front Immunol 2023; 14:1143980. [PMID: 37006268 PMCID: PMC10050728 DOI: 10.3389/fimmu.2023.1143980] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 03/03/2023] [Indexed: 03/17/2023] Open
Abstract
The small nucleolar RNA host genes (SNHGs) are a group of genes that can be transcript into long non-coding RNA SNHG (lncSNHG) and further processed into small nucleolar RNAs (snoRNAs). Although lncSNHGs and snoRNAs are well established to play pivotal roles in tumorigenesis, how lncSNHGs and snoRNAs regulate the immune cell behavior and function to mediate anti-tumor immunity remains further illustrated. Certain immune cell types carry out distinct roles to participate in each step of tumorigenesis. It is particularly important to understand how lncSNHGs and snoRNAs regulate the immune cell function to manipulate anti-tumor immunity. Here, we discuss the expression, mechanism of action, and potential clinical relevance of lncSNHGs and snoRNAs in regulating different types of immune cells that are closely related to anti-tumor immunity. By uncovering the changes and roles of lncSNHGs and snoRNAs in different immune cells, we aim to provide a better understanding of how the transcripts of SNHGs participate in tumorigenesis from an immune perspective.
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Affiliation(s)
- Hao Xiao
- Department of Clinical Laboratory Medicine, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Clinical Laboratory Medicine, Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Xin Feng
- Department of Clinical Laboratory Medicine, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Clinical Laboratory Medicine, Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Mengjun Liu
- Department of Clinical Laboratory Medicine, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Clinical Laboratory Medicine, Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Hanwen Gong
- Department of Clinical Laboratory Medicine, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Clinical Laboratory Medicine, Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Xiao Zhou
- Department of Clinical Laboratory Medicine, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Clinical Laboratory Medicine, Xiangya School of Medicine, Central South University, Changsha, Hunan, China
- *Correspondence: Xiao Zhou,
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5
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Xie J, Ni J, Shi H, Wang K, Ma X, Li W, Peng B. LncRNA SNHG3 enhances BMI1 mRNA stability by binding and regulating c-MYC: Implications for the carcinogenic role of SNHG3 in bladder cancer. Cancer Med 2023; 12:5718-5735. [PMID: 36208024 PMCID: PMC10028137 DOI: 10.1002/cam4.5316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 09/13/2022] [Accepted: 09/20/2022] [Indexed: 11/06/2022] Open
Abstract
The transformation of nonmuscle-invasive bladder cancer (BLCa) to muscle-invasive type and distant metastasis are the two major threats to patients after surgery. Thus, it is important to identify the key genes of BLCa cell invasion and metastasis. Long noncoding RNA (lncRNA) is a potential clinical tool for cancer diagnosis and treatment. Herein, we verified that lncRNA SNHG3 is upregulated in human BLCa specimens and is proportional to poor clinical prognosis via a combination of bioinformatic analyses and wet bench experiments. Then, we constructed SNHG3 knockdown and overexpression cell models via lentiviral packaging and CRISPR-Cas9 technique. Fluorescence in situ hybridization assay showed that SNHG3 is distributed in both the nucleus and cytoplasm of BLCa cell lines. In vitro assays including CCK-8, EdU, colony formation, wound healing, transwell, and tube formation demonstrated that SNHG3 knockdown and overexpression potently inhibited and enhanced BLCa cell proliferation, migration, invasion, and angiogenesis. In addition, IVIS imaging revealed that SNHG3 knockdown could significantly inhibit M-NSG mice xenograft tumor growth. Next, RNA sequencing, bioinformatics analyses and western blots indicated that SNHG3 could promote c-MYC expression. RNA immunoprecipitation, actinomycin D assay and western blot assays suggested that SNHG3 could also bind c-MYC protein which subsequently facilitate the stabilization of BMI1 mRNA, thus enhancing BMI1 protein level. However, SNHG3 knockdown had a slightly weaker inhibitory effect on BMI1 expression than c-MYC knockdown. Further, in vitro assays demonstrated that BMI1 knockdown could suppress the SNHG3 activation-induced tumor promoting effect in BLCa cells. Overall, this study has provided new insights into the potential implication of lncRNA SNHG3 in the pathogenesis of BLCa. Importantly, SNHG3/c-MYC/BMI1 axis may be a novel target for regulating tumor growth and metastasis in BLCa patients.
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Affiliation(s)
- Jinbo Xie
- Department of Urology, Putuo People's Hospital, School of Medicine, Tongji University, Shanghai, China
- Department of Urology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Department of Laboratory Medicine, Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, Ontario, Canada
| | - Jinliang Ni
- Shanghai Clinical College, Anhui Medical University, Shanghai, China
| | - Huajuan Shi
- Department of Urology, Putuo People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Keyi Wang
- Department of Urology, Putuo People's Hospital, School of Medicine, Tongji University, Shanghai, China
- Department of Urology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Xiaoying Ma
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Department of Laboratory Medicine, Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, Ontario, Canada
| | - Wei Li
- Department of Urology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Bo Peng
- Department of Urology, Putuo People's Hospital, School of Medicine, Tongji University, Shanghai, China
- Department of Urology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
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6
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Zhiyu Z, Qi Z, Zhen S, Jianglei Z, Jun O. Small nucleolar RNA host gene 25 is a long non-coding RNA helps diagnose and predict outcomes in prostate cancer. Cancer Treat Res Commun 2023; 35:100687. [PMID: 36706513 DOI: 10.1016/j.ctarc.2023.100687] [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: 11/26/2022] [Revised: 01/16/2023] [Accepted: 01/17/2023] [Indexed: 01/25/2023]
Abstract
BACKGROUND The role of a long non-coding RNA called small nucleolar RNA host gene 25 (SNHG25) has been studied in some tumor types but the correlation between SNHG25 and PCA remains unknown. METHODS The relationship between clinicopathologic characteristics and SNHG25 expression was evaluated using The Cancer Genome Atlas data. The binary classifier value of SNHG25 was calculated using areas under receiver operating characteristic (ROC) curves. Outcomes were evaluated using Kaplan-Meier and Cox regression analyses. Gene set enrichment was performed to identify potential SNHG25 functions. RESULTS SNHG25 expression was significantly increased in PCA and correlated with age, primary therapy outcome, N stage, Gleason score, and residual tumor (p < 0.05). ROC curves demonstrated the effect of SNHG25 on diagnosis and outcomes (area under the curve = 0.923). Higher SNHG25 expression predicted shorter progression-free interval (PFI) (p < 0.001), and Cox regression showed that SNHG25 expression was an independent risk factor for reduced PFI (p = 0.028). SNHG25 expression was associated with mRNA and protein metabolism. CONCLUSIONS SNHG25 expression increases significantly in PCA and is negatively associated with PFI. It is a potential diagnostic and prognostic biomarker in PCA.
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Affiliation(s)
- Zhang Zhiyu
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, 215000, Jiangsu Province China
| | - Zhou Qi
- Department of Reproductive Medicine Center, the First Affiliated Hospital of Soochow University, Suzhou, 215000, Jiangsu Province China
| | - Song Zhen
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, 215000, Jiangsu Province China
| | - Zhang Jianglei
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, 215000, Jiangsu Province China
| | - Ouyang Jun
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, 215000, Jiangsu Province China.
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7
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Chang W, Wang M, Zhang Y, Yu F, Hu B, Goljanek-Whysall K, Li P. Roles of long noncoding RNAs and small extracellular vesicle-long noncoding RNAs in type 2 diabetes. Traffic 2022; 23:526-537. [PMID: 36109347 PMCID: PMC9828071 DOI: 10.1111/tra.12868] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/17/2022] [Accepted: 09/14/2022] [Indexed: 01/20/2023]
Abstract
The prevalence of a high-energy diet and a sedentary lifestyle has increased the incidence of type 2 diabetes (T2D). T2D is a chronic disease characterized by high blood glucose levels and insulin resistance in peripheral tissues. The pathological mechanism of this disease is not fully clear. Accumulated evidence has shown that noncoding RNAs have an essential regulatory role in the progression of diabetes and its complications. The roles of small noncoding RNAs, such as miRNAs, in T2D, have been extensively investigated, while the function of long noncoding RNAs (lncRNAs) in T2D has been unstudied. It has been reported that lncRNAs in T2D play roles in the regulation of pancreatic function, peripheral glucose homeostasis and vascular inflammation. In addition, lncRNAs carried by small extracellular vesicles (sEV) were shown to mediate communication between organs and participate in diabetes progression. Some sEV lncRNAs derived from stem cells are being developed as potential therapeutic agents for diabetic complications. In this review, we summarize the current knowledge relating to lncRNA biogenesis, the mechanisms of lncRNA sorting into sEV and the regulatory roles of lncRNAs and sEV lncRNAs in diabetes. Knowledge of lncRNAs and sEV lncRNAs in diabetes will aid in the development of new therapeutic drugs for T2D in the future.
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Affiliation(s)
- Wenguang Chang
- Institute for Translational Medicine, The Affiliated Hospital, College of Medicine, Qingdao University, Qingdao, China
| | - Man Wang
- Institute for Translational Medicine, The Affiliated Hospital, College of Medicine, Qingdao University, Qingdao, China
| | - Yuan Zhang
- Institute for Translational Medicine, The Affiliated Hospital, College of Medicine, Qingdao University, Qingdao, China
| | - Fei Yu
- Institute for Translational Medicine, The Affiliated Hospital, College of Medicine, Qingdao University, Qingdao, China
| | - Bin Hu
- The Institute of Medical Sciences (IMS), School of Medicine, Medical Sciences & Nutrition, University of Aberdeen, Aberdeen, UK
| | - Katarzyna Goljanek-Whysall
- Department of Physiology, Nursing and Health Sciences, College of Medicine, National University of Ireland, Galway, Ireland
| | - Peifeng Li
- Institute for Translational Medicine, The Affiliated Hospital, College of Medicine, Qingdao University, Qingdao, China
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8
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Malakoti F, Alemi F, Yeganeh SJ, Hosseini F, Shabestani N, Samemaleki S, Maleki M, Daneshvar SF, Montazer M, Yousefi B. Long noncoding RNA SNHG7-miRNA-mRNA axes crosstalk with oncogenic signaling pathways in human cancers. Chem Biol Drug Des 2022; 101:1151-1161. [PMID: 35993390 DOI: 10.1111/cbdd.14118] [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: 02/21/2022] [Revised: 06/19/2022] [Accepted: 07/08/2022] [Indexed: 11/27/2022]
Abstract
LncRNAs and miRNAs are the two most important non-coding RNAs, which have been identified to be associated with cancer progression or prevention. The dysregulation of lncRNAs conducts tumorigenesis and metastasis in different ways. One of the mechanisms is that lncRNAs interact with miRNAs to regulate distinct cellular and genomic processes and cancer progression. LncRNA SNHG7 as an oncogene sponges miRNAs and develops lncRNA-miRNA-mRNA axes, leading to the regulation of several signaling pathways such as Wnt/β-Catenin, PI3K/AKT/mTOR, SIRT1, and Snail-EMT. Therefore, in this article, after a brief overview of lncRNA SNHG7-miRNA-mRNA axes' contribution to cancer development, we will discuss the role of lncRNA SNHG7 in the genes expression and signaling pathways related to cancers development via acting as a ceRNA.
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Affiliation(s)
- Faezeh Malakoti
- Department of Biochemistry and Clinical Laboratories, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Forough Alemi
- Department of Biochemistry and Clinical Laboratories, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Shirin Jafari Yeganeh
- Department of Microbiology, Faculty of Medicine, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Foroogh Hosseini
- Department of Biochemistry and Clinical Laboratories, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Nazila Shabestani
- Department of Biochemistry and Clinical Laboratories, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Sahar Samemaleki
- Department of Immunology, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Masomeh Maleki
- Department of Biochemistry and Clinical Laboratories, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Sarvin Fathi Daneshvar
- Department of Biochemistry and Clinical Laboratories, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Majid Montazer
- Department of Thorax Surgery, Faculty of Medicine, Tuberculosis and Lung Disease Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Bahman Yousefi
- Department of Biochemistry and Clinical Laboratories, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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Jiang C, Qu S, Liu T, Hao M. Long Noncoding RNA SNHG7 Is a Diagnostic and Prognostic Marker for Colon Adenocarcinoma. Front Oncol 2022; 12:893591. [PMID: 35747807 PMCID: PMC9209656 DOI: 10.3389/fonc.2022.893591] [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: 03/10/2022] [Accepted: 05/09/2022] [Indexed: 11/13/2022] Open
Abstract
Numerous studies have shown that long noncoding RNAs (lncRNAs) play a critical role in the malignant progression of cancer. However, the potential involvement of lncRNAs in colon adenocarcinoma (COAD) remains unexplored. In this study, the expression of lncRNA SNHG7 in colon cancer tissues and its correlation with clinical characteristics were analyzed based on data from The Cancer Genome Atlas (TCGA) database. SNHG7 was found to be highly expressed in 17 types of cancer, including COAD. Next, TCGA data were further investigated to identify differentially expressed genes, and Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses were performed. In addition, the relationship between SNHG7 expression and clinical features were analyzed. SNHG7 expression was found to be a potentially valuable indicator for COAD diagnosis and prognosis. Finally, gene set enrichment analysis showed that SNHG7 may affect lupus erythematosus and reactome cellular senescence, possibly influencing the prognosis of patients with COAD. Altogether, these results suggest that SNHG7 may be associated with the occurrence and development of COAD, having potential diagnostic and prognostic value.
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Affiliation(s)
- Chengwei Jiang
- Department of Pathology, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Shanshan Qu
- Department of Pathology, China-The Second Hospital of Jilin University, Changchun, China
| | - Tie Liu
- Biobank, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Miao Hao
- Scientific Research Center, China-Japan Union Hospital of Jilin University, Changchun, China
- *Correspondence: Miao Hao,
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10
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Temporal Gene Expression Profiles Reflect the Dynamics of Lymphoid Differentiation. Int J Mol Sci 2022; 23:ijms23031115. [PMID: 35163045 PMCID: PMC8834919 DOI: 10.3390/ijms23031115] [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: 12/14/2021] [Revised: 01/10/2022] [Accepted: 01/16/2022] [Indexed: 02/01/2023] Open
Abstract
Understanding the emergence of lymphoid committed cells from multipotent progenitors (MPP) is a great challenge in hematopoiesis. To gain deeper insight into the dynamic expression changes associated with these transitions, we report the quantitative transcriptome of two MPP subsets and the common lymphoid progenitor (CLP). While the transcriptome is rather stable between MPP2 and MPP3, expression changes increase with differentiation. Among those, we found that pioneer lymphoid genes such as Rag1, Mpeg1, and Dntt are expressed continuously from MPP2. Others, such as CD93, are CLP specific, suggesting their potential use as new markers to improve purification of lymphoid populations. Notably, a six-transcription factor network orchestrates the lymphoid differentiation program. Additionally, we pinpointed 24 long intergenic-non-coding RNA (lincRNA) differentially expressed through commitment and further identified seven novel forms. Collectively, our approach provides a comprehensive landscape of coding and non-coding transcriptomes expressed during lymphoid commitment.
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11
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Najafi S, Ghafouri-Fard S, Hussen BM, Jamal HH, Taheri M, Hallajnejad M. Oncogenic Roles of Small Nucleolar RNA Host Gene 7 (SNHG7) Long Noncoding RNA in Human Cancers and Potentials. Front Cell Dev Biol 2022; 9:809345. [PMID: 35111760 PMCID: PMC8801878 DOI: 10.3389/fcell.2021.809345] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 12/10/2021] [Indexed: 12/21/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are a class of noncoding transcripts characterized with more than 200 nucleotides of length. Unlike their names, some short open reading frames are recognized for them encoding small proteins. LncRNAs are found to play regulatory roles in essential cellular processes such as cell growth and apoptosis. Therefore, an increasing number of lncRNAs are identified with dysregulation in a wide variety of human cancers. SNHG7 is an lncRNA with upregulation in cancer cells and tissues. It is frequently reported with potency of promoting malignant cell behaviors in vitro and in vivo. Like oncogenic/tumor suppressor lncRNAs, SNHG7 is found to exert its tumorigenic functions through interaction with other biological substances. These include sponging target miRNAs (various numbers are identified), regulation of several signaling pathways, transcription factors, and effector proteins. Importantly, clinical studies demonstrate association between high SNHG7 expression and clinicopathological features in cancerous patients, worse prognosis, and enhanced chemoresistance. In this review, we summarize recent studies in three eras of cell, animal, and human experiments to bold the prognostic, diagnostic, and therapeutic potentials.
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Affiliation(s)
- Sajad Najafi
- Student Research Committee, Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Bashdar Mahmud Hussen
- Department of Pharmacognosy, College of Pharmacy, Hawler Medical University, Erbil, Iraq
- Center of Research and Strategic Studies, Lebanese French University, Erbil, Iraq
| | - Hazha Hadayat Jamal
- Department of Biology, College of Education, Salahaddin University-Erbil, Erbil, Iraq
| | - Mohammad Taheri
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
| | - Mohammad Hallajnejad
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Ding J, Li C, Cheng Y, Du Z, Wang Q, Tang Z, Song C, Xia Q, Bai W, Lin L, Liu W, Xu L, Li E, Wu B. Alterations of RNA splicing patterns in esophagus squamous cell carcinoma. Cell Biosci 2021; 11:36. [PMID: 33563334 PMCID: PMC7871539 DOI: 10.1186/s13578-021-00546-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 01/29/2021] [Indexed: 02/05/2023] Open
Abstract
Alternative splicing (AS) is an important biological process for regulating the expression of various isoforms from a single gene and thus to promote proteome diversity. In this study, RNA-seq data from 15 pairs of matched esophageal squamous cell carcinoma (ESCC) and normal tissue samples as well as two cell lines were analyzed. AS events with significant differences were identified between ESCC and matched normal tissues, which were re-annotated to find protein coding genes or non-coding RNAs. A total of 45,439 AS events were found. Of these, 6019 (13.25%) significant differentially AS events were identified. Exon skipping (SE) events occupied the largest proportion of abnormal splicing events. Fifteen differential splicing events with the same trends of ΔΨ values in ESCC tissues, as well in the two cell lines were found. Four pathways and 20 biological processes related to pro-metastasis cell junction and migration were significantly enriched for the differentially spliced genes. The upregulated splicing factor SF3B4, which regulates 92 gene splicing events, could be a potential prognostic factor of ESCC. Differentially spliced genes, including HNRNPC, VCL, ZNF207, KIAA1217, TPM1 and CALD1 are shown with a sashimi plot. These results suggest that cell junction- and migration-related biological processes are influenced by AS abnormalities, and aberrant splicing events can be affected by splicing factor expression changes. The involved splicing factor SF3B4 was found to be a survival-related gene in ESCC and is presumed to regulate AS in multiple cancers. In summary, we identified significant differentially expressed AS events which may be related to the development of ESCC.
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Affiliation(s)
- Jiyu Ding
- Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, 515041, China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, 515041, China
| | - Chunquan Li
- School of Medical Informatics, Harbin Medical University, Daqing Campus, Daqing, 163319, China
| | - Yinwei Cheng
- Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, 515041, China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, 515041, China
| | - Zepeng Du
- Department of Pathology, Shantou Central Hospital, Affiliated Shantou Hospital of Sun Yat-sen University, Shantou, 515041, China
| | - Qiuyu Wang
- School of Medical Informatics, Harbin Medical University, Daqing Campus, Daqing, 163319, China
| | - Zhidong Tang
- School of Medical Informatics, Harbin Medical University, Daqing Campus, Daqing, 163319, China
| | - Chao Song
- School of Medical Informatics, Harbin Medical University, Daqing Campus, Daqing, 163319, China
| | - Qiaoxi Xia
- Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, 515041, China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, 515041, China
| | - Wenjing Bai
- Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, 515041, China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, 515041, China
| | - Ling Lin
- Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, 515041, China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, 515041, China
| | - Wei Liu
- Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, 515041, China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, 515041, China
| | - Liyan Xu
- Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, 515041, China
- Institute of Oncologic Pathology, Shantou University Medical College, Shantou, 515041, China
| | - Enmin Li
- Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, 515041, China.
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, 515041, China.
| | - Bingli Wu
- Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, 515041, China.
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, 515041, China.
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