1
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Meer E. Role of Noncoding RNAs in Modulating Microglial Phenotype. Glob Med Genet 2024; 11:304-311. [PMID: 39258255 PMCID: PMC11383642 DOI: 10.1055/s-0044-1790283] [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: 09/12/2024] Open
Abstract
Microglia are immunocompetent cells that are present in the retina and central nervous system, and are involved in the development maintenance and immune functions in these systems. Developing from yolk sac-primitive macrophages, they proliferate in the local tissues during the embryonic period without resorting to the production from the hematopoietic stem cells, and are critical in sustaining homeostasis and performing in disease and injury; they have morphological characteristics and distinct phenotypes according to the microenvironment. Microglia are also present in close association with resident cells in the retina where they engage in synapse formation, support normal functions, as well as immune defense. They are involved in the development of numerous neurodegenerative and ophthalmic diseases and act as diversity shields and triggers. Noncoding ribonucleic acids (ncRNAs) refer to RNA molecules synthesized from the mammalian genome, and these do not have protein-coding capacity. These ncRNAs play a role in the regulation of gene expression patterns. ncRNAs have only been recently identified as vastly significant molecules that are involved in the posttranscriptional regulation. Microglia are crucial for brain health and functions and current studies have focused on the effects caused by ncRNA on microglial types. Thus, the aim of the review was to provide an overview of the current knowledge about the regulation of microglial phenotypes by ncRNAs.
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Affiliation(s)
- Eiman Meer
- Department of Biological and Health Sciences, Pak-Austria Fachhochschule Institute of Applied Sciences and Technology, Haripur, Pakistan
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2
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Lu J, Ma H, Wang Q, Song Z, Wang J. Chemotherapy-mediated lncRNA-induced immune cell plasticity in cancer immunopathogenesis. Int Immunopharmacol 2024; 141:112967. [PMID: 39181018 DOI: 10.1016/j.intimp.2024.112967] [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: 07/02/2024] [Revised: 08/05/2024] [Accepted: 08/15/2024] [Indexed: 08/27/2024]
Abstract
Tumor cells engage with the immune system in a complex manner, utilizing evasion and adaptability mechanisms. The development of cancer and resistance to treatment relies on the ability of immune cells to adjust their phenotype and function in response to cues from the tumor microenvironment, known as immunological cell plasticity. This study delves into the role of long non-coding RNAs (lncRNAs) in enhancing immune cell flexibility in cancer, focusing on their regulatory actions in the tumor microenvironment and potential therapeutic implications. Through a comprehensive review of existing literature, the study analyzes the impact of lncRNAs on macrophages, T-cells, and MDSCs, as well as the influence of cytokines and growth factors like TNF, IL-6, HGF, and TGFβ on immunological cell plasticity and tumor immunoediting. LncRNAs exert a strong influence on immune cell plasticity through mechanisms such as transcriptional regulation, post-transcriptional modifications, and chromatin remodeling. These RNA molecules intricately modulate gene expression networks, acting as scaffolding, decoys, guides, and sponges. Moreover, both direct cell-cell interactions and soluble chemicals in the tumor microenvironment contribute to enhancing immune cell activation and survival. Understanding the influence of lncRNAs on immune cell flexibility sheds light on the biological pathways of immune evasion and cancer progression. Targeting long non-coding RNAs holds promise for amplifying anti-tumor immunity and overcoming drug resistance in cancer treatment. However, further research is necessary to determine the therapeutic potential of manipulating lncRNAs in the tumor microenvironment.
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Affiliation(s)
- Jingyuan Lu
- Tongji Medical College, Huazhong University of Science & Technology, Wuhan 430030, China.
| | - Haowei Ma
- Department of Mechanical and Aerospace Engineering, Case Western Reserve University, Cleveland, OH 44106, USA.
| | - Qian Wang
- Division of Hematology and Solid Tumor Oncology, Case Western Reserve University, Cleveland, OH 44106, USA.
| | - Zhiheng Song
- Plasma Applied Physics Lab, C&J Nyheim Plasma Institute, Drexel University, 200 Federal St, Suite 500, Camden, NJ 08103.
| | - Jinli Wang
- School of Medicine, Department of Epidemiology and Biochemistry and Molecular & Cellular Biology, Georgetown University, 3700 O ST NW, Washington, DC 20057.
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3
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Lu H, Zhang Y. Values of LncRNA SNHG14 in the Differential Diagnosis and Prognosis Evaluation of Acute Ischemic Stroke. Appl Biochem Biotechnol 2024:10.1007/s12010-024-05070-7. [PMID: 39348080 DOI: 10.1007/s12010-024-05070-7] [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] [Accepted: 09/19/2024] [Indexed: 10/01/2024]
Abstract
The long non-coding RNA (LncRNA) SNHG14 has been investigated for its potential in acute ischemic stroke (AIS) and transient ischemic attack (TIA) diagnosis. Thirty-two healthy people, 85 patients with AIS, and 40 patients with TIA had their blood tested to determine SNHG14 mRNA transcript levels using quantitative real-time polymerase chain reaction (qRT-PCR). A stroke's severity was measured using the Stroke Severity Scale developed by the National Institutes of Health (NIHSS). After 30 days, individuals with AIS were evaluated for progress using a modified Rankin Scale (mRS). There was no significant difference in SNHG14 LncRNA levels between TIA patients and controls, despite the huge rise in AIS incidence (p > 0.05) (all p < 0.001). Compared to those who did well on the AIS test, those who performed poorly had substantially greater levels of SNHG14 LncRNA (mRS 0-1 points) (mRS 0-2). LncRNA SNHG14 had an AUC of 0.714 (80%, 61.18%) when used to identify AIS in TIA patients, and a comparable finding was seen when predicting a poor 30-day prognosis of AIS (73%, 66.67%). There are also graphical representations of the findings. Improvements in NIHSS and mRS scores were associated with increases in SNHG14 LncRNA mRNA levels in individuals diagnosed with AIS. It is critical that we focus entirely on this decision (all p < 0.05). Analysis of the long non-coding RNA known as SNHG14 in the patient's blood can be used to diagnose AIS, rule out TIA, forecast the intensity of the disease, and evaluate the prognosis. You can accomplish everything on that list simultaneously.
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Affiliation(s)
- Hongxiang Lu
- Department of Laboratory, Lianyungang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Lianyungang, 222000, Jiangsu, China
| | - Yuezhan Zhang
- Department of Geriatrics, Lianyungang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Lianyungang, 222000, Jiangsu, China.
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4
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Bogle R, Patrick MT, Sreeskandarajan S, Gharaee-Kermani M, Zhang H, Li Q, Zhou R, Ma F, Kahlenberg JM, Plazyo O, Elder JT, Billi AC, Gudjonsson JE, Tsoi LC. Profiling lncRNA in psoriatic skin using scRNA-seq. J Invest Dermatol 2024:S0022-202X(24)02156-0. [PMID: 39342985 DOI: 10.1016/j.jid.2024.09.010] [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: 08/18/2023] [Revised: 08/13/2024] [Accepted: 09/12/2024] [Indexed: 10/01/2024]
Abstract
The expressions of long noncoding RNAs (lncRNAs) and their roles in epidermal differentiation have been previously defined using bulk RNA-seq. Despite their tissue-specific expression profiles, most lncRNAs are not well-annotated at the single cell level. Here, we evaluated the use of scRNA-seq to profile and characterize lncRNAs using data from 6 psoriasis patients with paired uninvolved and lesional psoriatic skin. Despite their overall lower expression, we were able to detect >7,000 skin-expressing lncRNAs and their cellular source. Differential gene expression analysis revealed 137 differentially expressed lncRNAs in lesional skin of psoriasis (PP) and identified 169 cell type-specific lncRNAs. Keratinocytes had the highest number of differentially expressed lncRNA in psoriatic skin, which we validated using spatial transcriptomic data. We further showed that expression of keratinocyte-specific lncRNA, AC020916.1, upregulated in lesional skin, is significantly correlated with expressions of genes participating in cell proliferation/epidermal differentiation, including SPRR2E and transcription factor ZFP36, particularly in the psoriatic skin. Our study highlights the potential for using scRNA-seq to profile skin-expressing lncRNA transcripts and to infer their cellular origins, providing a crucial approach that can be applied to the study of other inflammatory skin conditions.
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Affiliation(s)
- Rachael Bogle
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Matthew T Patrick
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Sutharzan Sreeskandarajan
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America; Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Mehrnaz Gharaee-Kermani
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Haihan Zhang
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America; Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Qinmengge Li
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America; Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Ruiwen Zhou
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America; Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Feiyang Ma
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - J Michelle Kahlenberg
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America; Department of Internal Medicine, Division of Rheumatology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Olesya Plazyo
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - James T Elder
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America; Ann Arbor Veterans Affairs Hospital, Ann Arbor, Michigan, United States of America
| | - Allison C Billi
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Johann E Gudjonsson
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America; Department of Internal Medicine, Division of Rheumatology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Lam C Tsoi
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America; Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, United States of America; Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America.
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5
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Guha P, Chini A, Rishi A, Mandal SS. Long noncoding RNAs in ubiquitination, protein degradation, and human diseases. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195061. [PMID: 39341591 DOI: 10.1016/j.bbagrm.2024.195061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Revised: 08/07/2024] [Accepted: 09/19/2024] [Indexed: 10/01/2024]
Abstract
Protein stability and turnover is critical in normal cellular and physiological process and their misregulation may contribute to accumulation of unwanted proteins causing cellular malfunction, neurodegeneration, mitochondrial malfunction, and disrupted metabolism. Signaling mechanism associated with protein degradation is complex and is extensively studied. Many protein and enzyme machineries have been implicated in regulation of protein degradation. Despite these insights, our understanding of protein degradation mechanisms remains limited. Emerging studies suggest that long non-coding RNAs (lncRNAs) play critical roles in various cellular and physiological processes including metabolism, cellular homeostasis, and protein turnover. LncRNAs, being large nucleic acids (>200 nt long) can interact with various proteins and other nucleic acids and modulate protein structure and function leading to regulation of cell signaling processes. LncRNAs are widely distributed across cell types and may exhibit tissue specific expression. They are detected in body fluids including blood and urine. Their expressions are also altered in various human diseases including cancer, neurological disorders, immune disorder, and others. LncRNAs are being recognized as novel biomarkers and therapeutic targets. This review article focuses on the emerging role of noncoding RNAs (ncRNAs), particularly long noncoding RNAs (lncRNAs), in the regulation of protein polyubiquitination and proteasomal degradation.
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Affiliation(s)
- Prarthana Guha
- Gene Regulation and Epigenetics Research Laboratory, Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX 76019, United States of America
| | - Avisankar Chini
- Gene Regulation and Epigenetics Research Laboratory, Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX 76019, United States of America
| | - Ashcharya Rishi
- Gene Regulation and Epigenetics Research Laboratory, Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX 76019, United States of America
| | - Subhrangsu S Mandal
- Gene Regulation and Epigenetics Research Laboratory, Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX 76019, United States of America.
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6
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Lin YS, Tsai YC, Li CJ, Wei TT, Wang JL, Lin BW, Wu YN, Wu SR, Lin SC, Lin SC. Overexpression of NUDT16L1 sustains proper function of mitochondria and leads to ferroptosis insensitivity in colorectal cancer. Redox Biol 2024; 77:103358. [PMID: 39317106 DOI: 10.1016/j.redox.2024.103358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 09/15/2024] [Accepted: 09/16/2024] [Indexed: 09/26/2024] Open
Abstract
Cancer research is continuously exploring new avenues to improve treatments, and ferroptosis induction has emerged as a promising approach. However, the lack of comprehensive analysis of the ferroptosis sensitivity in different cancer types has limited its clinical application. Moreover, identifying the key regulator that influences the ferroptosis sensitivity during cancer progression remains a major challenge. In this study, we shed light on the role of ferroptosis in colorectal cancer and identified a novel ferroptosis repressor, NUDT16L1, that contributes to the ferroptosis insensitivity in this cancer type. Mechanistically, NUDT16L1 promotes ferroptosis insensitivity in colon cancer by enhancing the expression of key ferroptosis repressor and mitochondrial genes through direct binding to NAD-capped RNAs and the indirect action of MALAT1. Our findings also reveal that NUDT16L1 localizes to the mitochondria to maintain its proper function by preventing mitochondrial DNA leakage after treatment of ferroptosis inducer in colon cancer cells. Importantly, our orthotopic injection and Nudt16l1 transgenic mouse models of colon cancer demonstrated the critical role of NUDT16L1 in promoting tumor growth. Moreover, clinical specimens revealed that NUDT16L1 was overexpressed in colorectal cancer, indicating its potential as a therapeutic target. Finally, our study shows the therapeutic potential of a NUDT16L1 inhibitor in vitro, in vivo and ex vivo. Taken together, these findings provide new insights into the crucial role of NUDT16L1 in colorectal cancer and highlight its potential as a promising therapeutic target.
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Affiliation(s)
- Yi-Syuan Lin
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Ya-Chuan Tsai
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chia-Jung Li
- Department of Obstetrics and Gynecology, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Tzu-Tang Wei
- Department and Graduate Institute of Pharmacology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Jui-Lin Wang
- National Laboratory Animal Center, National Applied Research Laboratories, Tainan, Taiwan
| | - Bo-Wen Lin
- Department of Surgery, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Ya-Na Wu
- School of Dentistry and Institute of Oral Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Shang-Rung Wu
- School of Dentistry and Institute of Oral Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Shin-Chih Lin
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Shih-Chieh Lin
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Institute of Molecular Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Department of Physiology, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
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7
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Malinowska AL, Huynh HL, Correa-Sánchez AF, Bose S. Thiol-Specific Linkers for the Synthesis of Oligonucleotide Conjugates via Metal-Free Thiol-Ene Click Reaction. Bioconjug Chem 2024. [PMID: 39264307 DOI: 10.1021/acs.bioconjchem.4c00336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2024]
Abstract
Chemical conjugation of oligonucleotides is widely used to improve their delivery and therapeutic potential. A variety of strategies are implemented to efficiently modify oligonucleotides with conjugating partners. The linkers typically used for oligonucleotide conjugation have limitations in terms of stability or ease of synthesis, which generates the need for providing new improved linkers for oligonucleotide conjugation. Herein, we report the synthesis of novel vinylpyrimidine phosphoramidite building blocks, which can be incorporated into an oligonucleotide by standard solid-phase synthesis in an automated synthesizer. These linker-bearing oligonucleotides can be easily conjugated in a biocompatible manner with thiol-functionalized molecules leading to the efficient generation of oligonucleotide conjugates.
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Affiliation(s)
- Anna L Malinowska
- Medical Research Council, Nucleic Acid Therapy Accelerator (UKRI) Research Complex at Harwell (RCaH), Rutherford Appleton Laboratory, Harwell OX11 0FA, U.K
| | - Harley L Huynh
- Medical Research Council, Nucleic Acid Therapy Accelerator (UKRI) Research Complex at Harwell (RCaH), Rutherford Appleton Laboratory, Harwell OX11 0FA, U.K
| | - Andrés F Correa-Sánchez
- Medical Research Council, Nucleic Acid Therapy Accelerator (UKRI) Research Complex at Harwell (RCaH), Rutherford Appleton Laboratory, Harwell OX11 0FA, U.K
| | - Sritama Bose
- Medical Research Council, Nucleic Acid Therapy Accelerator (UKRI) Research Complex at Harwell (RCaH), Rutherford Appleton Laboratory, Harwell OX11 0FA, U.K
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8
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Nie H, Wang X, Dong X, Wei Y, Wei J, Yip KC, Zhang Q, Li R. Down-regulation of CORO1C mediated by lncMALAT1/miR-133a-3p axis contributes to trophoblast dysfunction and preeclampsia. Placenta 2024; 156:67-76. [PMID: 39278098 DOI: 10.1016/j.placenta.2024.09.007] [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: 06/27/2024] [Revised: 09/03/2024] [Accepted: 09/09/2024] [Indexed: 09/17/2024]
Abstract
INTRODUCTION Placental trophoblast dysfunction has been proved to be closely related to the pathogenesis of preeclampsia. Coronaryxin-like actin-binding protein 1C (CORO1C) plays an important role in cell proliferation, apoptosis, invasion, and signal transduction, but its involvement in trophoblast dysfunction and preeclampsia remains uncertain. METHODS The expression of CORO1C in placental tissues of preeclampsia (PE) pregnant women and pregnant mice PE model were detected by real-time quantitative polymerase chain reaction (RT-qPCR), western blotting (WB) and immunohistochemical (IHC) staining. Next, the proliferation, invasion, migration and apoptosis were performed to explore the functions of CORO1C in HTR8/SVneo cell. Furthermore, the expression of CORO1C were detected in lncMALAT1 knockdown and overexpression HTR-8/SVneo cell. And then we investigated the possible regulatory mechanism of lncMALAT1 on CORO1C through bioinformatics analysis, FISH assays, RIP assays, RNA pull down and dual luciferase reporter assays. Finally, we further validated that lncMALAT1 regulate the function of placental trophoblast cells through CORO1C. RESULTS The expression of CORO1C was significantly decreased in the placenta of PE patients and mice model, and positively associated with neonatal birth weight. And we found that CORO1C inhibited trophoblast proliferation, migration and invasion. Furthermore, reduced expression of lncMALAT1 impaired CORO1C level, thereby resulting in trophoblast dysfunction. Mechanistically, the dysregulation of lncMALAT1 promoted the expression of miR-133a-3p, strongly enhancing its binding to the 3'UTR region of CORO1C mRNA for degradation. DISCUSSION This study demonstrated that the dysregulation of CORO1C via lncMALAT1/miR-133a-3p axis impairs trophoblast function and contributes to preeclampsia pathogenesis, providing novel insights in PE therapy through modulating CORO1C level.
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Affiliation(s)
- Hanhui Nie
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Jinan University, Guangzhou, 510630, China
| | - Xiufang Wang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Jinan University, Guangzhou, 510630, China
| | - Xiaohui Dong
- Institute of Molecular and Medical Virology, School of Medicine, Jinan University, Guangzhou, 510632, China
| | - Yiling Wei
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Jinan University, Guangzhou, 510630, China
| | - Jiachun Wei
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Jinan University, Guangzhou, 510630, China
| | - Ka Cheuk Yip
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Jinan University, Guangzhou, 510630, China
| | - Qiao Zhang
- Institute of Molecular and Medical Virology, School of Medicine, Jinan University, Guangzhou, 510632, China; Key Laboratory of Viral Pathogenesis & Infection Prevention and Control (Jinan University), Ministry of Education, Guangzhou, 510632, China.
| | - Ruiman Li
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Jinan University, Guangzhou, 510630, China.
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Yao J, Lv C, Liu P, Fan L, Zhang Z, Chen Y, Chen X, Zhang X, Zhang C, Li J, Wang X, Jiang W, Niu J, Song F, Zhang W, Sun D. LncRNA MALAT1-miR-339-5p-NIS axis is involved in the increased level of thyroid stimulating hormone (TSH) induced by combined exposure of high iodine and hyperlipidemia. J Nutr Biochem 2024; 131:109672. [PMID: 38823542 DOI: 10.1016/j.jnutbio.2024.109672] [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: 12/24/2023] [Revised: 05/12/2024] [Accepted: 05/28/2024] [Indexed: 06/03/2024]
Abstract
Hypothyroidism and subclinical hypothyroidism were both characterized by elevated levels of thyroid stimulating hormone (TSH). Previous studies had found that high iodine or hyperlipidemia alone was associated with increased TSH level. However, their combined effects on TSH have not been elucidated. In this study, combination of high iodine and hyperlipidemia was established through the combined exposure of high-water iodine and high fat diet in Wistar rats. The results showed that combined exposure of high iodine and high fat can induce higher TSH level. The mRNA and protein levels of sodium iodide transporters (NIS) and type 1 deiodinase (D1) in thyroid tissues, which were crucial genes in the synthesis of thyroid hormones, decreased remarkably in combined exposure group. Mechanistically, down-regulated long non-coding RNA (lncRNA) metastasis associated in lung denocarcinoma transcript 1 (MALAT1) may regulate the expression of NIS by increasing miR-339-5p, and regulating D1 by increasing miR-224-5p. Then, the above findings were explored in subjects exposed to high water iodine and hyperlipidemia. The results indicated that in population combined with high iodine and hyperlipidemia, TSH level increased to higher level and lncRNA MALAT1-miR-339-5p-NIS axis was obviously activated. Collectively, this study found that combined exposure of high iodine and hyperlipidemia induced a higher level of TSH, and lncRNA MALAT1-miR-339-5p-NIS axis may play important role.
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Affiliation(s)
- Jinyin Yao
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, China; Center for Endemic Disease Control, Harbin Medical University, Key Lab of Etiology and Epidemiology, Education Bureau of Heilongjiang Province & Ministry of Health (23618504), Harbin, China; Department of Public Health, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Chunpeng Lv
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, China; Center for Endemic Disease Control, Harbin Medical University, Key Lab of Etiology and Epidemiology, Education Bureau of Heilongjiang Province & Ministry of Health (23618504), Harbin, China
| | - Peng Liu
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, China; Center for Endemic Disease Control, Harbin Medical University, Key Lab of Etiology and Epidemiology, Education Bureau of Heilongjiang Province & Ministry of Health (23618504), Harbin, China
| | - Lijun Fan
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, China; Center for Endemic Disease Control, Harbin Medical University, Key Lab of Etiology and Epidemiology, Education Bureau of Heilongjiang Province & Ministry of Health (23618504), Harbin, China
| | - Zhiwei Zhang
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, China; Center for Endemic Disease Control, Harbin Medical University, Key Lab of Etiology and Epidemiology, Education Bureau of Heilongjiang Province & Ministry of Health (23618504), Harbin, China
| | - Yi Chen
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, China; Center for Endemic Disease Control, Harbin Medical University, Key Lab of Etiology and Epidemiology, Education Bureau of Heilongjiang Province & Ministry of Health (23618504), Harbin, China
| | - Xianglan Chen
- Guangdong Provincial People's Hospital Zhuhai Hospital, Zhuhai, Guangdong, China
| | - Xiaodan Zhang
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, China; Center for Endemic Disease Control, Harbin Medical University, Key Lab of Etiology and Epidemiology, Education Bureau of Heilongjiang Province & Ministry of Health (23618504), Harbin, China
| | - Chunyu Zhang
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, China; Center for Endemic Disease Control, Harbin Medical University, Key Lab of Etiology and Epidemiology, Education Bureau of Heilongjiang Province & Ministry of Health (23618504), Harbin, China; Tianjin Binhai New Area Center for Disease Control and Prevention, Tianjin, China
| | - Jinyu Li
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, China; Center for Endemic Disease Control, Harbin Medical University, Key Lab of Etiology and Epidemiology, Education Bureau of Heilongjiang Province & Ministry of Health (23618504), Harbin, China
| | - Xuesong Wang
- Shandong Institute of Prevention and Control for Endemic Disease, Jinan, Shandong, China
| | - Wen Jiang
- Shandong Institute of Prevention and Control for Endemic Disease, Jinan, Shandong, China
| | - Jianxin Niu
- Heze Center for Disease Control and Prevention, Heze, Shandong, China
| | - Feng Song
- Jining Center for Disease Control and Prevention, Jining, Shandong, China
| | - Wei Zhang
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, China; Center for Endemic Disease Control, Harbin Medical University, Key Lab of Etiology and Epidemiology, Education Bureau of Heilongjiang Province & Ministry of Health (23618504), Harbin, China.
| | - Dianjun Sun
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, China; Center for Endemic Disease Control, Harbin Medical University, Key Lab of Etiology and Epidemiology, Education Bureau of Heilongjiang Province & Ministry of Health (23618504), Harbin, China.
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10
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Wu T, Dong Y, Yang X, Mo L, You Y. Crosstalk between lncRNAs and Wnt/β-catenin signaling pathways in lung cancers: From cancer progression to therapeutic response. Noncoding RNA Res 2024; 9:667-677. [PMID: 38577016 PMCID: PMC10987302 DOI: 10.1016/j.ncrna.2024.02.013] [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: 10/24/2023] [Revised: 01/24/2024] [Accepted: 02/21/2024] [Indexed: 04/06/2024] Open
Abstract
Lung cancer (LC) is considered to have the highest mortality rate around the world. Because there are no early diagnostic signs or efficient clinical alternatives, distal metastasis and increasing numbers of recurrences are a challenge in the clinical management of LC. Long non-coding RNAs (lncRNAs) have recently been recognized as a critical regulator involved in the progression and treatment response to LC. The Wnt/β-catenin pathway has been shown to influence LC occurrence and progress. Therefore, discovering connections between Wnt signaling pathway and lncRNAs may offer new therapeutic targets for improving LC treatment and management. In this review, the purpose of this article is to present possible therapeutic approaches by reviewing particular relationships, key processes, and molecules associated to the beginning and development of LC.
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Affiliation(s)
- Ting Wu
- Research Laboratory of Translational Medicine/Laboratory of Protein Structure and Function, Hengyang Medical School, University of South China, Hengyang, 421001, China
| | - YiRan Dong
- Research Laboratory of Translational Medicine/Laboratory of Protein Structure and Function, Hengyang Medical School, University of South China, Hengyang, 421001, China
| | - XinZhi Yang
- Research Laboratory of Translational Medicine/Laboratory of Protein Structure and Function, Hengyang Medical School, University of South China, Hengyang, 421001, China
| | - Liang Mo
- Department of Thoracic Surgery, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, 421001, China
| | - Yong You
- Research Laboratory of Translational Medicine/Laboratory of Protein Structure and Function, Hengyang Medical School, University of South China, Hengyang, 421001, China
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11
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Banerjee D, Sultana S, Banerjee S. Gas5 regulates early-life stress-induced anxiety and spatial memory. J Neurochem 2024; 168:2999-3018. [PMID: 38960403 DOI: 10.1111/jnc.16167] [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: 04/01/2024] [Revised: 05/30/2024] [Accepted: 06/02/2024] [Indexed: 07/05/2024]
Abstract
Early-life stress (ES) induced by maternal separation (MS) remains a proven causality of anxiety and memory deficits at later stages of life. Emerging studies have shown that MS-induced gene expression in the hippocampus is operated at the level of transcription. However, the extent of involvement of non-coding RNAs in MS-induced behavioural deficits remains unexplored. Here, we have investigated the role of synapse-enriched long non-coding RNAs (lncRNAs) in anxiety and memory upon MS. We observed that MS led to an enhancement of expression of the lncRNA growth arrest specific 5 (Gas5) in the hippocampus; accompanied by increased levels of anxiety and deficits in spatial memory. Gas5 knockdown in early life was able to reduce anxiety and partially rescue the spatial memory deficits of maternally separated adult mice. However, the reversal of MS-induced anxiety and memory deficits is not attributed to Gas5 activity during neuronal development as Gas5 RNAi did not influence spine development. Gene Ontology analysis revealed that Gas5 exerts its function by regulating RNA metabolism and translation. Our study highlights the importance of MS-regulated lncRNA in anxiety and spatial memory.
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Affiliation(s)
| | - Sania Sultana
- National Brain Research Centre, Gurugram, Haryana, India
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12
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Dudek I, Czerkies M, Kwiatek A. Differential expression of cytokines and elevated levels of MALAT1 - Long non-coding RNA in response to non-structural proteins of human respiratory syncytial virus. Virology 2024; 597:110127. [PMID: 38850893 DOI: 10.1016/j.virol.2024.110127] [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: 01/24/2024] [Revised: 05/10/2024] [Accepted: 05/27/2024] [Indexed: 06/10/2024]
Abstract
Human Respiratory Syncytial Virus (hRSV), a prevalent respiratory pathogen affecting various age groups, can trigger prolonged and intense inflammation in humans. The severity and outcome of hRSV infection correlate with elevated levels of pro-inflammatory agents, yet the underlying reasons for this immune system overstimulation remain elusive. We focused on the impact of hRSV non-structural proteins, NS1 and NS2, on immune response within epithelial cells. Available data indicates that these proteins impair the interferon pathway. We reinforce that NS1 and NS2 induce heightened secretion of the pro-inflammatory cytokines IL-6 and CXCL8. We also indicate that hRSV non-structural proteins provoke differential gene expression of human host FosB and long non-coding RNAs (MALAT1, RP11-510N19.5). It suggests an impact of NS molecules beyond IFN pathways. Thus, new light is shed on the interplay between hRSV and host cells, uncovering unexplored avenues of viral interference, especially the NS2 role in cytokine expression and immune modulation.
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Affiliation(s)
- Inga Dudek
- Department of Molecular Virology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland.
| | - Maciej Czerkies
- Department of Biosystems and Soft Matter, Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland
| | - Agnieszka Kwiatek
- Department of Molecular Virology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland.
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13
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Aria H, Azizi M, Nazem S, Mansoori B, Darbeheshti F, Niazmand A, Daraei A, Mansoori Y. Competing endogenous RNAs regulatory crosstalk networks: The messages from the RNA world to signaling pathways directing cancer stem cell development. Heliyon 2024; 10:e35208. [PMID: 39170516 PMCID: PMC11337742 DOI: 10.1016/j.heliyon.2024.e35208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 07/08/2024] [Accepted: 07/24/2024] [Indexed: 08/23/2024] Open
Abstract
Cancer stem cells (CSCs) are one of the cell types that account for cancer heterogeneity. The cancer cells arrest in G0 and generate non-CSC progeny through self-renewal and pluripotency, resulting in tumor recurrence, metastasis, and resistance to chemotherapy. They can stimulate tumor relapse and re-grow a metastatic tumor. So, CSCs is a promising target for eradicating tumors, and developing an anti-CSCs therapy has been considered. In recent years competing endogenous RNA (ceRNA) has emerged as a significant class of post-transcriptional regulators that affect gene expression via competition for microRNA (miRNA) binding. Furthermore, aberrant ceRNA expression is associated with tumor progression. Recent findings show that ceRNA network can cause tumor progression through the effect on CSCs. To overcome therapeutic resistance due to CSCs, we need to improve our current understanding of the mechanisms by which ceRNAs are implicated in CSC-related relapse. Thus, this review was designed to discuss the role of ceRNAs in CSCs' function. Targeting ceRNAs may open the path for new cancer therapeutic targets and can be used in clinical research.
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Affiliation(s)
- Hamid Aria
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
- Department of Immunology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mahdieh Azizi
- Department of Immunology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Shima Nazem
- Department of Clinical Biochemistry, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Behnam Mansoori
- Pediatrics Department, School of Medicine, Fasa University of Medical Sciences, Fasa, Iran
| | - Farzaneh Darbeheshti
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Anoosha Niazmand
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Abdolreza Daraei
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
- Department of Medical Genetics, School of Medicine, Babol University of Medical Sciences, Babol, Iran
| | - Yaser Mansoori
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
- Department of Medical Genetics, Fasa University of Medical Sciences, Fasa, Iran
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14
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Barker SJ, Thayer MB, Kim C, Tatarakis D, Simon MJ, Dial R, Nilewski L, Wells RC, Zhou Y, Afetian M, Akkapeddi P, Chappell A, Chew KS, Chow J, Clemens A, Discenza CB, Dugas JC, Dwyer C, Earr T, Ha C, Ho YS, Huynh D, Lozano EI, Jayaraman S, Kwan W, Mahon C, Pizzo M, Robles-Colmenares Y, Roche E, Sanders L, Stergioulis A, Tong R, Tran H, Zuchero Y, Estrada AA, Gadkar K, Koth CMM, Sanchez PE, Thorne RG, Watts RJ, Sandmann T, Kane LA, Rigo F, Dennis MS, Lewcock JW, DeVos SL. Targeting the transferrin receptor to transport antisense oligonucleotides across the mammalian blood-brain barrier. Sci Transl Med 2024; 16:eadi2245. [PMID: 39141703 DOI: 10.1126/scitranslmed.adi2245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 07/24/2024] [Indexed: 08/16/2024]
Abstract
Antisense oligonucleotides (ASOs) are promising therapeutics for treating various neurological disorders. However, ASOs are unable to readily cross the mammalian blood-brain barrier (BBB) and therefore need to be delivered intrathecally to the central nervous system (CNS). Here, we engineered a human transferrin receptor 1 (TfR1) binding molecule, the oligonucleotide transport vehicle (OTV), to transport a tool ASO across the BBB in human TfR knockin (TfRmu/hu KI) mice and nonhuman primates. Intravenous injection and systemic delivery of OTV to TfRmu/hu KI mice resulted in sustained knockdown of the ASO target RNA, Malat1, across multiple mouse CNS regions and cell types, including endothelial cells, neurons, astrocytes, microglia, and oligodendrocytes. In addition, systemic delivery of OTV enabled Malat1 RNA knockdown in mouse quadriceps and cardiac muscles, which are difficult to target with oligonucleotides alone. Systemically delivered OTV enabled a more uniform ASO biodistribution profile in the CNS of TfRmu/hu KI mice and greater knockdown of Malat1 RNA compared with a bivalent, high-affinity TfR antibody. In cynomolgus macaques, an OTV directed against MALAT1 displayed robust ASO delivery to the primate CNS and enabled more uniform biodistribution and RNA target knockdown compared with intrathecal dosing of the same unconjugated ASO. Our data support systemically delivered OTV as a potential platform for delivering therapeutic ASOs across the BBB.
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Affiliation(s)
| | - Mai B Thayer
- Denali Therapeutics Inc., South San Francisco, CA, USA
| | - Chaeyoung Kim
- Denali Therapeutics Inc., South San Francisco, CA, USA
| | | | | | - Rebekah Dial
- Denali Therapeutics Inc., South San Francisco, CA, USA
| | | | | | - Yinhan Zhou
- Denali Therapeutics Inc., South San Francisco, CA, USA
| | | | | | | | - Kylie S Chew
- Denali Therapeutics Inc., South San Francisco, CA, USA
| | - Johann Chow
- Denali Therapeutics Inc., South San Francisco, CA, USA
| | | | | | - Jason C Dugas
- Denali Therapeutics Inc., South San Francisco, CA, USA
| | | | - Timothy Earr
- Denali Therapeutics Inc., South San Francisco, CA, USA
| | - Connie Ha
- Denali Therapeutics Inc., South San Francisco, CA, USA
| | - Yvonne S Ho
- Denali Therapeutics Inc., South San Francisco, CA, USA
| | - David Huynh
- Denali Therapeutics Inc., South San Francisco, CA, USA
| | | | | | - Wanda Kwan
- Denali Therapeutics Inc., South San Francisco, CA, USA
| | - Cathal Mahon
- Denali Therapeutics Inc., South San Francisco, CA, USA
| | | | | | - Elysia Roche
- Denali Therapeutics Inc., South San Francisco, CA, USA
| | - Laura Sanders
- Denali Therapeutics Inc., South San Francisco, CA, USA
| | | | - Raymond Tong
- Denali Therapeutics Inc., South San Francisco, CA, USA
| | - Hai Tran
- Denali Therapeutics Inc., South San Francisco, CA, USA
| | - Y Zuchero
- Denali Therapeutics Inc., South San Francisco, CA, USA
| | | | - Kapil Gadkar
- Denali Therapeutics Inc., South San Francisco, CA, USA
| | | | | | | | - Ryan J Watts
- Denali Therapeutics Inc., South San Francisco, CA, USA
| | | | - Lesley A Kane
- Denali Therapeutics Inc., South San Francisco, CA, USA
| | - Frank Rigo
- Ionis Pharmaceuticals, Carlsbad, CA, USA
| | - Mark S Dennis
- Denali Therapeutics Inc., South San Francisco, CA, USA
| | | | - Sarah L DeVos
- Denali Therapeutics Inc., South San Francisco, CA, USA
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15
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Aghajani Mir M. Illuminating the pathogenic role of SARS-CoV-2: Insights into competing endogenous RNAs (ceRNAs) regulatory networks. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 122:105613. [PMID: 38844190 DOI: 10.1016/j.meegid.2024.105613] [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: 03/07/2024] [Revised: 05/20/2024] [Accepted: 05/31/2024] [Indexed: 06/10/2024]
Abstract
The appearance of SARS-CoV-2 in 2019 triggered a significant economic and health crisis worldwide, with heterogeneous molecular mechanisms that contribute to its development are not yet fully understood. Although substantial progress has been made in elucidating the mechanisms behind SARS-CoV-2 infection and therapy, it continues to rank among the top three global causes of mortality due to infectious illnesses. Non-coding RNAs (ncRNAs), being integral components across nearly all biological processes, demonstrate effective importance in viral pathogenesis. Regarding viral infections, ncRNAs have demonstrated their ability to modulate host reactions, viral replication, and host-pathogen interactions. However, the complex interactions of different types of ncRNAs in the progression of COVID-19 remains understudied. In recent years, a novel mechanism of post-transcriptional gene regulation known as "competing endogenous RNA (ceRNA)" has been proposed. Long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), and viral ncRNAs function as ceRNAs, influencing the expression of associated genes by sequestering shared microRNAs. Recent research on SARS-CoV-2 has revealed that disruptions in specific ceRNA regulatory networks (ceRNETs) contribute to the abnormal expression of key infection-related genes and the establishment of distinctive infection characteristics. These findings present new opportunities to delve deeper into the underlying mechanisms of SARS-CoV-2 pathogenesis, offering potential biomarkers and therapeutic targets. This progress paves the way for a more comprehensive understanding of ceRNETs, shedding light on the intricate mechanisms involved. Further exploration of these mechanisms holds promise for enhancing our ability to prevent viral infections and develop effective antiviral treatments.
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Affiliation(s)
- Mahsa Aghajani Mir
- Deputy of Research and Technology, Babol University of Medical Sciences, Babol, Iran.
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16
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Taylor AD, Hathaway QA, Kunovac A, Pinti MV, Newman MS, Cook CC, Cramer ER, Starcovic SA, Winters MT, Westemeier-Rice ES, Fink GK, Durr AJ, Rizwan S, Shepherd DL, Robart AR, Martinez I, Hollander JM. Mitochondrial sequencing identifies long noncoding RNA features that promote binding to PNPase. Am J Physiol Cell Physiol 2024; 327:C221-C236. [PMID: 38826135 PMCID: PMC11427107 DOI: 10.1152/ajpcell.00648.2023] [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: 11/27/2023] [Revised: 05/24/2024] [Accepted: 05/24/2024] [Indexed: 06/04/2024]
Abstract
Extranuclear localization of long noncoding RNAs (lncRNAs) is poorly understood. Based on machine learning evaluations, we propose a lncRNA-mitochondrial interaction pathway where polynucleotide phosphorylase (PNPase), through domains that provide specificity for primary sequence and secondary structure, binds nuclear-encoded lncRNAs to facilitate mitochondrial import. Using FVB/NJ mouse and human cardiac tissues, RNA from isolated subcellular compartments (cytoplasmic and mitochondrial) and cross-linked immunoprecipitate (CLIP) with PNPase within the mitochondrion were sequenced on the Illumina HiSeq and MiSeq, respectively. lncRNA sequence and structure were evaluated through supervised [classification and regression trees (CART) and support vector machines (SVM)] machine learning algorithms. In HL-1 cells, quantitative PCR of PNPase CLIP knockout mutants (KH and S1) was performed. In vitro fluorescence assays assessed PNPase RNA binding capacity and verified with PNPase CLIP. One hundred twelve (mouse) and 1,548 (human) lncRNAs were identified in the mitochondrion with Malat1 being the most abundant. Most noncoding RNAs binding PNPase were lncRNAs, including Malat1. lncRNA fragments bound to PNPase compared against randomly generated sequences of similar length showed stratification with SVM and CART algorithms. The lncRNAs bound to PNPase were used to create a criterion for binding, with experimental validation revealing increased binding affinity of RNA designed to bind PNPase compared to control RNA. The binding of lncRNAs to PNPase was decreased through the knockout of RNA binding domains KH and S1. In conclusion, sequence and secondary structural features identified by machine learning enhance the likelihood of nuclear-encoded lncRNAs binding to PNPase and undergoing import into the mitochondrion.NEW & NOTEWORTHY Long noncoding RNAs (lncRNAs) are relatively novel RNAs with increasingly prominent roles in regulating genetic expression, mainly in the nucleus but more recently in regions such as the mitochondrion. This study explores how lncRNAs interact with polynucleotide phosphorylase (PNPase), a protein that regulates RNA import into the mitochondrion. Machine learning identified several RNA structural features that improved lncRNA binding to PNPase, which may be useful in targeting RNA therapeutics to the mitochondrion.
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Affiliation(s)
- Andrew D Taylor
- Division of Exercise Physiology, West Virginia University School of Medicine, Morgantown, West Virginia, United States
- Mitochondria, Metabolism, and Bioenergetics Working Group, West Virginia University School of Medicine, Morgantown, West Virginia, United States
| | - Quincy A Hathaway
- Division of Exercise Physiology, West Virginia University School of Medicine, Morgantown, West Virginia, United States
- Heart and Vascular Institute, West Virginia University, Morgantown, West Virginia, United States
- Department of Medical Education, West Virginia University School of Medicine, Morgantown, West Virginia, United States
| | - Amina Kunovac
- Division of Exercise Physiology, West Virginia University School of Medicine, Morgantown, West Virginia, United States
- Mitochondria, Metabolism, and Bioenergetics Working Group, West Virginia University School of Medicine, Morgantown, West Virginia, United States
| | - Mark V Pinti
- Mitochondria, Metabolism, and Bioenergetics Working Group, West Virginia University School of Medicine, Morgantown, West Virginia, United States
- West Virginia University School of Pharmacy, Morgantown, West Virginia, United States
| | - Mackenzie S Newman
- Department of Physiology and Pharmacology, West Virginia University School of Medicine, Morgantown, West Virginia, United States
| | - Chris C Cook
- Cardiovascular and Thoracic Surgery, West Virginia University School of Medicine, Morgantown, West Virginia, United States
| | - Evan R Cramer
- Department of Biochemistry, West Virginia University School of Medicine, Morgantown, West Virginia, United States
| | - Sarah A Starcovic
- Department of Biochemistry, West Virginia University School of Medicine, Morgantown, West Virginia, United States
| | - Michael T Winters
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University Cancer Institute, School of Medicine, Morgantown, West Virginia, United States
| | - Emily S Westemeier-Rice
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University Cancer Institute, School of Medicine, Morgantown, West Virginia, United States
| | - Garrett K Fink
- Division of Exercise Physiology, West Virginia University School of Medicine, Morgantown, West Virginia, United States
| | - Andrya J Durr
- Division of Exercise Physiology, West Virginia University School of Medicine, Morgantown, West Virginia, United States
- Mitochondria, Metabolism, and Bioenergetics Working Group, West Virginia University School of Medicine, Morgantown, West Virginia, United States
| | - Saira Rizwan
- Division of Exercise Physiology, West Virginia University School of Medicine, Morgantown, West Virginia, United States
- Mitochondria, Metabolism, and Bioenergetics Working Group, West Virginia University School of Medicine, Morgantown, West Virginia, United States
| | - Danielle L Shepherd
- Division of Exercise Physiology, West Virginia University School of Medicine, Morgantown, West Virginia, United States
- Mitochondria, Metabolism, and Bioenergetics Working Group, West Virginia University School of Medicine, Morgantown, West Virginia, United States
| | - Aaron R Robart
- Department of Biochemistry, West Virginia University School of Medicine, Morgantown, West Virginia, United States
| | - Ivan Martinez
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University Cancer Institute, School of Medicine, Morgantown, West Virginia, United States
| | - John M Hollander
- Division of Exercise Physiology, West Virginia University School of Medicine, Morgantown, West Virginia, United States
- Mitochondria, Metabolism, and Bioenergetics Working Group, West Virginia University School of Medicine, Morgantown, West Virginia, United States
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17
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Yang M, Xuan A, Liu Q, Zhu G. MALAT1 predicts the prognosis of severe community-acquired pneumonia in pediatric patients. BMC Pulm Med 2024; 24:361. [PMID: 39061025 PMCID: PMC11282807 DOI: 10.1186/s12890-024-03157-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 07/09/2024] [Indexed: 07/28/2024] Open
Abstract
BACKGROUND To evaluate the role of metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) in the prognosis of severe community-acquired pneumonia (CAP) in children. METHODS According to the median MALAT1 value of 3.2 at baseline, 93 pediatric patients with severe CAP were divided into low (n = 46, median MALAT1 level = 1.9) or high (n = 47, median MALAT1 level = 4.5) MALAT1 groups. Another 93 age-, gender-, and body mass index (BMI)-matched healthy individuals were included in the control group using the propensity-score matching (PSM) method. A multivariate Cox proportional hazards model was used to explore the association of MALAT1 level with the 28-day mortality after controlling for potential confounding factors. RESULTS The MALAT1 expressions were significantly higher in the patients with severe CAP compared with those in the healthy controls (3.2 vs. 0.9, P < 0.01). The receiver operating characteristic (ROC) analysis showed that the area under the curve (AUC) was 0.927 when the cut-off value of MALAT1 was 1.5. Moreover, the MALAT1 expressions were substantially lower in survivals than non-survivals (3.8 vs. 2.6, P < 0.01), and the multivariate Cox regression analysis indicated a positive association between MALAT1 levels and mortality risk (HR = 3.32; 95% CI: 1.05-10.47; P = 0.04). CONCLUSION MALAT1 might be a promising marker for predicting the prognosis of severe CAP in pediatric patients.
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Affiliation(s)
- Mei Yang
- Department of Pediatrics, First Affiliated Hospital of Bengbu Medical University, Anhui, China
| | - Aili Xuan
- Department of Pediatrics, First Affiliated Hospital of Bengbu Medical University, Anhui, China
| | - Qian Liu
- Department of Pediatrics, Weifang Medical College Affiliated Hospital, Shandong, China
| | - Guoji Zhu
- Department of Infectious Diseases, Children's Hospital, Soochow University, No. 92 Zhongnan Street, Jiangsu, Jiangsu Province, 215000, China.
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18
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Ruiz-Ojeda D, Guzmán-Martín CA, Bojalil R, Balderas XF, Paredes-González IS, González-Ramírez J, Torres-Rasgado E, Hernández-DíazCouder A, Springall R, Sánchez-Muñoz F. Long noncoding RNA MALAT1 in dermatologic disorders: a comprehensive review. Biomark Med 2024:1-15. [PMID: 38982732 DOI: 10.1080/17520363.2024.2369044] [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: 10/16/2023] [Accepted: 06/11/2024] [Indexed: 07/11/2024] Open
Abstract
Dermatologic disorders, affecting the integumentary system, involve diverse molecular mechanisms such as cell proliferation, apoptosis, inflammation and immune responses. Long noncoding RNAs, particularly Metastasis-Associated Lung Adenocarcinoma Transcript 1 (MALAT1), are crucial regulators of gene expression. MALAT1 influences inflammatory responses, immune cell function and signaling pathways, impacting various physiological and pathological processes, including dermatologic disorders. Dysregulation of MALAT1 is observed in skin conditions like psoriasis, atopic dermatitis and systemic lupus erythematosus. However, its precise role remains unclear. This review consolidates knowledge on MALAT1's impact on skin biology and pathology, emphasizing its potential diagnostic and therapeutic implications in dermatologic conditions.
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Affiliation(s)
- Dayanara Ruiz-Ojeda
- Posgrado en Medicina Interna, Hospital Central Sur de Alta Especialidad de Petróleos Mexicanos, Ciudad de México, C.P. 14140, México
- Departamento de Inmunología, Instituto Nacional de Cardiología Ignacio Chávez, Ciudad de México, C.P. 14080, México
| | - Carlos A Guzmán-Martín
- Doctorado en Ciencias Biológicas y de la Salud, Universidad Autónoma Metropolitana, Ciudad de México, C.P. 04960, México
- Departamento de programas de investigación, Hospital Shriners para Niños México, Ciudad de México, C.P. 04600, México
| | - Rafael Bojalil
- Departamento de Atención a la Salud, Universidad Autónoma Metropolitana-Xochimilco, Ciudad de México, C.P. 04960, México
| | - Ximena F Balderas
- Departamento de Inmunología, Instituto Nacional de Cardiología Ignacio Chávez, Ciudad de México, C.P. 14080, México
| | - Iris S Paredes-González
- Departamento de Patología Experimental, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Ciudad de México, C.P. 14080, México
| | - Javier González-Ramírez
- Laboratorio de Biología Celular, Facultad de Enfermería, Universidad Autónoma de Baja California Campus Mexicali, Mexicali, Baja California, C.P. 21376, México
| | - Enrique Torres-Rasgado
- Facultad de Medicina, Cuerpo Académico de Medicina Interna (CA-160), Benemérita Universidad Autónoma de Puebla, Puebla, C.P. 72000,México
| | - Adrián Hernández-DíazCouder
- Unidad de Investigación Médica en Bioquímica, Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, C.P. 06720, México
| | - Rashidi Springall
- Departamento de Inmunología, Instituto Nacional de Cardiología Ignacio Chávez, Ciudad de México, C.P. 14080, México
| | - Fausto Sánchez-Muñoz
- Departamento de Inmunología, Instituto Nacional de Cardiología Ignacio Chávez, Ciudad de México, C.P. 14080, México
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19
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Jang JH, Choi E, Kim T, Yeo HJ, Jeon D, Kim YS, Cho WH. Navigating the Modern Landscape of Sepsis: Advances in Diagnosis and Treatment. Int J Mol Sci 2024; 25:7396. [PMID: 39000503 PMCID: PMC11242529 DOI: 10.3390/ijms25137396] [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: 05/31/2024] [Revised: 06/27/2024] [Accepted: 07/03/2024] [Indexed: 07/16/2024] Open
Abstract
Sepsis poses a significant threat to human health due to its high morbidity and mortality rates worldwide. Traditional diagnostic methods for identifying sepsis or its causative organisms are time-consuming and contribute to a high mortality rate. Biomarkers have been developed to overcome these limitations and are currently used for sepsis diagnosis, prognosis prediction, and treatment response assessment. Over the past few decades, more than 250 biomarkers have been identified, a few of which have been used in clinical decision-making. Consistent with the limitations of diagnosing sepsis, there is currently no specific treatment for sepsis. Currently, the general treatment for sepsis is conservative and includes timely antibiotic use and hemodynamic support. When planning sepsis-specific treatment, it is important to select the most suitable patient, considering the heterogeneous nature of sepsis. This comprehensive review summarizes current and evolving biomarkers and therapeutic approaches for sepsis.
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Affiliation(s)
- Jin Ho Jang
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Internal Medicine, Transplantation Research Center, Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, Yangsan 50612, Republic of Korea; (J.H.J.); (E.C.); (T.K.); (H.J.Y.); (D.J.); (Y.S.K.)
- Department of Internal Medicine, School of Medicine, Pusan National University, Yangsan 50612, Republic of Korea
| | - Eunjeong Choi
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Internal Medicine, Transplantation Research Center, Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, Yangsan 50612, Republic of Korea; (J.H.J.); (E.C.); (T.K.); (H.J.Y.); (D.J.); (Y.S.K.)
- Department of Internal Medicine, School of Medicine, Pusan National University, Yangsan 50612, Republic of Korea
| | - Taehwa Kim
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Internal Medicine, Transplantation Research Center, Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, Yangsan 50612, Republic of Korea; (J.H.J.); (E.C.); (T.K.); (H.J.Y.); (D.J.); (Y.S.K.)
- Department of Internal Medicine, School of Medicine, Pusan National University, Yangsan 50612, Republic of Korea
| | - Hye Ju Yeo
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Internal Medicine, Transplantation Research Center, Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, Yangsan 50612, Republic of Korea; (J.H.J.); (E.C.); (T.K.); (H.J.Y.); (D.J.); (Y.S.K.)
- Department of Internal Medicine, School of Medicine, Pusan National University, Yangsan 50612, Republic of Korea
| | - Doosoo Jeon
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Internal Medicine, Transplantation Research Center, Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, Yangsan 50612, Republic of Korea; (J.H.J.); (E.C.); (T.K.); (H.J.Y.); (D.J.); (Y.S.K.)
- Department of Internal Medicine, School of Medicine, Pusan National University, Yangsan 50612, Republic of Korea
| | - Yun Seong Kim
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Internal Medicine, Transplantation Research Center, Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, Yangsan 50612, Republic of Korea; (J.H.J.); (E.C.); (T.K.); (H.J.Y.); (D.J.); (Y.S.K.)
- Department of Internal Medicine, School of Medicine, Pusan National University, Yangsan 50612, Republic of Korea
| | - Woo Hyun Cho
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Internal Medicine, Transplantation Research Center, Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, Yangsan 50612, Republic of Korea; (J.H.J.); (E.C.); (T.K.); (H.J.Y.); (D.J.); (Y.S.K.)
- Department of Internal Medicine, School of Medicine, Pusan National University, Yangsan 50612, Republic of Korea
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20
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Khoshnam SE, Moalemnia A, Anbiyaee O, Farzaneh M, Ghaderi S. LncRNA MALAT1 and Ischemic Stroke: Pathogenesis and Opportunities. Mol Neurobiol 2024; 61:4369-4380. [PMID: 38087169 DOI: 10.1007/s12035-023-03853-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 11/21/2023] [Indexed: 07/11/2024]
Abstract
Ischemic stroke (IS) stands as a prominent cause of mortality and long-term disability around the world. It arises primarily from a disruption in cerebral blood flow, inflicting severe neural injuries. Hence, there is a pressing need to comprehensively understand the intricate mechanisms underlying IS and identify novel therapeutic targets. Recently, long noncoding RNAs (lncRNAs) have emerged as a novel class of regulatory molecules with the potential to attenuate pathogenic mechanisms following IS. Among these lncRNAs, MALAT1 (metastasis-associated lung adenocarcinoma transcript 1) has been extensively studied due to its involvement in the pathophysiological processes of IS. In this review, we provide an in-depth analysis of the essential role of MALAT1 in the development and progression of both pathogenic and protective mechanisms following IS. These mechanisms include oxidative stress, neuroinflammation, cell death signaling, blood brain barrier dysfunction, and angiogenesis. Furthermore, we summarize the impact of MALAT1 on the susceptibility and severity of IS. This review highlights the potential risks associated with the therapeutic use of MALAT1 for IS, which are attributable to the stimulatory action of MALAT1 on ischemia/reperfusion injury. Ultimately, this review sheds light on the potential molecular mechanisms and associated signaling pathways underlying MALAT1 expression post-IS, with the aim of uncovering potential therapeutic targets.
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Affiliation(s)
- Seyed Esmaeil Khoshnam
- Persian Gulf Physiology Research Center, Medical Basic Sciences Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
| | - Arash Moalemnia
- Faculty of Medicine, Dezful University of Medical Sciences, Dezful, Iran
| | - Omid Anbiyaee
- School of Medicine, Cardiovascular Research Center, Namazi Hospital, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Maryam Farzaneh
- Fertility, Infertility and Perinatology Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
| | - Shahab Ghaderi
- Department of Neuroscience, School of Science and Advanced Technologies in Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
- Neurophysiology Research Center, Hamadan University of Medical Sciences, Hamadan, Iran
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21
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Mohammad T, Zolotovskaia MA, Suntsova MV, Buzdin AA. Cancer fusion transcripts with human non-coding RNAs. Front Oncol 2024; 14:1415801. [PMID: 38919532 PMCID: PMC11196610 DOI: 10.3389/fonc.2024.1415801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 05/27/2024] [Indexed: 06/27/2024] Open
Abstract
Cancer chimeric, or fusion, transcripts are thought to most frequently appear due to chromosomal aberrations that combine moieties of unrelated normal genes. When being expressed, this results in chimeric RNAs having upstream and downstream parts relatively to the breakpoint position for the 5'- and 3'-fusion components, respectively. As many other types of cancer mutations, fusion genes can be of either driver or passenger type. The driver fusions may have pivotal roles in malignisation by regulating survival, growth, and proliferation of tumor cells, whereas the passenger fusions most likely have no specific function in cancer. The majority of research on fusion gene formation events is concentrated on identifying fusion proteins through chimeric transcripts. However, contemporary studies evidence that fusion events involving non-coding RNA (ncRNA) genes may also have strong oncogenic potential. In this review we highlight most frequent classes of ncRNAs fusions and summarize current understanding of their functional roles. In many cases, cancer ncRNA fusion can result in altered concentration of the non-coding RNA itself, or it can promote protein expression from the protein-coding fusion moiety. Differential splicing, in turn, can enrich the repertoire of cancer chimeric transcripts, e.g. as observed for the fusions of circular RNAs and long non-coding RNAs. These and other ncRNA fusions are being increasingly recognized as cancer biomarkers and even potential therapeutic targets. Finally, we discuss the use of ncRNA fusion genes in the context of cancer detection and therapy.
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Affiliation(s)
- Tharaa Mohammad
- Laboratory for Translational and Genomic Bioinformatics, Moscow Center for Advanced Studies, Moscow, Russia
- Department of Molecular Genetic Technologies, Laboratory of Bioinformatics, Endocrinology Research Center, Moscow, Russia
| | - Marianna A. Zolotovskaia
- Laboratory for Translational and Genomic Bioinformatics, Moscow Center for Advanced Studies, Moscow, Russia
- Department of Molecular Genetic Technologies, Laboratory of Bioinformatics, Endocrinology Research Center, Moscow, Russia
- I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | | | - Anton A. Buzdin
- Laboratory for Translational and Genomic Bioinformatics, Moscow Center for Advanced Studies, Moscow, Russia
- Department of Molecular Genetic Technologies, Laboratory of Bioinformatics, Endocrinology Research Center, Moscow, Russia
- I.M. Sechenov First Moscow State Medical University, Moscow, Russia
- PathoBiology Group, European Organization for Research and Treatment of Cancer (EORTC), Brussels, Belgium
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
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22
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Liang X, Zhang C, Shen L, Ding L, Guo H. Role of non‑coding RNAs in UV‑induced radiation effects (Review). Exp Ther Med 2024; 27:262. [PMID: 38756908 PMCID: PMC11097301 DOI: 10.3892/etm.2024.12550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 04/04/2024] [Indexed: 05/18/2024] Open
Abstract
Ultraviolet (UV) is divided into UVA (long-wave, 320-400 nm), UVB (middle-wave, 280-320 nm) and UVC (short-wave, 100-280 nm) based on wavelength. UV radiation (UVR) from sunlight (UVA + UVB) is a major cause of skin photodamage including skin inflammation, aging and pigmentation. Accidental exposure to UVC burns the skin and induces skin cancer. In addition to the skin, UV radiation can also impair visual function. Non-coding RNAs (ncRNAs) are a class of functional RNAs that do not have coding activity but can control cellular processes at the post-transcriptional level, including microRNA (miRNA), long non-coding RNA (lncRNA) and circulatory RNA (circRNA). Through a review of the literature, it was determined that UVR can affect the expression of various ncRNAs, and that this regulation may be wavelength specific. Functionally, ncRNAs participate in the regulation of photodamage through various pathways and play pathogenic or protective regulatory roles. In addition, ncRNAs that are upregulated or downregulated by UVR can serve as biomarkers for UV-induced diseases, aiding in diagnosis and prognosis assessment. Therapeutic strategies targeting ncRNAs, including the use of natural drugs and their extracts, have shown protective effects against UV-induced photodamage. In the present review, an extensive summarization of previous studies was performed and the role and mechanism of ncRNAs in UV-induced radiation effects was reviewed to aid in the diagnosis and treatment of UV-related diseases.
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Affiliation(s)
- Xiaofei Liang
- Department of Laboratory Medicine, The First Hospital of Qiqihar, Qiqihar, Heilongjiang 161000, P.R. China
| | - Chao Zhang
- Department of Laboratory Medicine, The First Hospital of Qiqihar, Qiqihar, Heilongjiang 161000, P.R. China
| | - Lijuan Shen
- Department of Laboratory Medicine, Qiqihar MingZhu Hospital, Qiqihar, Heilongjiang 161000, P.R. China
| | - Ling Ding
- Department of Laboratory Medicine, The First Hospital of Qiqihar, Qiqihar, Heilongjiang 161000, P.R. China
| | - Haipeng Guo
- Department of Laboratory Medicine, The First Hospital of Qiqihar, Qiqihar, Heilongjiang 161000, P.R. China
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Aslanzadeh M, Stanicek L, Tarbier M, Mármol-Sánchez E, Biryukova I, Friedländer M. Malat1 affects transcription and splicing through distinct pathways in mouse embryonic stem cells. NAR Genom Bioinform 2024; 6:lqae045. [PMID: 38711862 PMCID: PMC11071118 DOI: 10.1093/nargab/lqae045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 03/14/2024] [Accepted: 04/30/2024] [Indexed: 05/08/2024] Open
Abstract
Malat1 is a long-noncoding RNA with critical roles in gene regulation and cancer metastasis, however its functional role in stem cells is largely unexplored. We here perform a nuclear knockdown of Malat1 in mouse embryonic stem cells, causing the de-regulation of 320 genes and aberrant splicing of 90 transcripts, some of which potentially affecting the translated protein sequence. We find evidence that Malat1 directly interacts with gene bodies and aberrantly spliced transcripts, and that it locates upstream of down-regulated genes at their putative enhancer regions, in agreement with functional genomics data. Consistent with this, we find these genes affected at both exon and intron levels, suggesting that they are transcriptionally regulated by Malat1. Besides, the down-regulated genes are regulated by specific transcription factors and bear both activating and repressive chromatin marks, suggesting that some of them might be regulated by bivalent promoters. We propose a model in which Malat1 facilitates the transcription of genes involved in chromatid dynamics and mitosis in one pathway, and affects the splicing of transcripts that are themselves involved in RNA processing in a distinct pathway. Lastly, we compare our findings with Malat1 perturbation studies performed in other cell systems and in vivo.
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Affiliation(s)
- Morteza Aslanzadeh
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Sweden
| | - Laura Stanicek
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Sweden
| | - Marcel Tarbier
- Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Solna, Sweden
| | - Emilio Mármol-Sánchez
- Science for Life Laboratory and Center for Palaeogenetics. Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Sweden
| | - Inna Biryukova
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Sweden
| | - Marc R Friedländer
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Sweden
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24
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Juárez-Vicuña Y, Ruiz-Ojeda D, González-Ramírez J, Flores-Balderas X, Springall R, Sánchez-Muñoz F, Guzmán-Martín CA. LncRNA MALAT1 in Keratinocyte function: A review of recent advances. Noncoding RNA Res 2024; 9:594-601. [PMID: 38532797 PMCID: PMC10963180 DOI: 10.1016/j.ncrna.2024.01.021] [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: 09/27/2023] [Revised: 01/19/2024] [Accepted: 01/30/2024] [Indexed: 03/28/2024] Open
Abstract
Keratinocytes, the principal epidermal cells, play a vital role in maintaining the structural integrity and functionality of the skin. Beyond their protective role, keratinocytes are key contributors to the process of wound healing, as they migrate to injury sites, proliferate, and generate new layers of epidermis, facilitating tissue repair and remodeling. Moreover, keratinocytes actively participate in the skin's immune responses, expressing pattern recognition receptors (PRRs) to detect microbial components and interact with immune cells to influence adaptive immunity. Keratinocytes express a diverse repertoire of signaling pathways, transcription factors, and epigenetic regulators to regulate their growth, differentiation, and response to environmental cues. Among these regulatory elements, long non-coding RNAs (lncRNAs) have emerged as essential players in keratinocyte biology. LncRNAs, including MALAT1, play diverse roles in gene regulation and cellular processes, influencing keratinocyte proliferation, differentiation, migration, and response to environmental stimuli. Dysregulation of specific lncRNAs such as MALAT1 can disrupt keratinocyte homeostasis, leading to impaired differentiation, compromised barrier integrity, and contributing to the pathogenesis of various skin disorders. Understanding the intricate interplay between lncRNAs and keratinocytes offers promising insights into the molecular underpinnings of skin health and disease, with potential implications for targeted therapies and advancements in dermatological research. Hence, our objective is to provide a comprehensive summary of the available knowledge concerning keratinocytes and their intricate relationship with MALAT1.
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Affiliation(s)
- Yaneli Juárez-Vicuña
- Departamento de Inmunología, Instituto Nacional de Cardiología Ignacio Chávez, Ciudad de México, Mexico
| | - Dayanara Ruiz-Ojeda
- Departamento de Inmunología, Instituto Nacional de Cardiología Ignacio Chávez, Ciudad de México, Mexico
- Posgrado en Medicina Interna, Hospital Central Sur de Alta Especialidad de Petróleos Mexicanos, Ciudad de México, Mexico
| | - Javier González-Ramírez
- Facultad de Enfermería, Universidad Autónoma de Baja California, Mexicali, Baja California, Mexico
- Laboratorio de Biología Celular, Unidad de Ciencias de La Salud Campus Mexicali, Universidad Autónoma de Baja California, Mexicali, Baja California, Mexico
| | - Ximena Flores-Balderas
- Departamento de Inmunología, Instituto Nacional de Cardiología Ignacio Chávez, Ciudad de México, Mexico
| | - Rashidi Springall
- Departamento de Inmunología, Instituto Nacional de Cardiología Ignacio Chávez, Ciudad de México, Mexico
| | - Fausto Sánchez-Muñoz
- Departamento de Inmunología, Instituto Nacional de Cardiología Ignacio Chávez, Ciudad de México, Mexico
| | - Carlos A. Guzmán-Martín
- Doctorado en Ciencias Biológicas y de La Salud, Universidad Autónoma Metropolitana, Ciudad de México, Mexico
- Departamento de Programas de Investigación, Hospital Shriners para Niños México, Ciudad de México, Mexico
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25
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Lv X, Yang L, Xie Y, Momeni MR. Non-coding RNAs and exosomal non-coding RNAs in lung cancer: insights into their functions. Front Cell Dev Biol 2024; 12:1397788. [PMID: 38859962 PMCID: PMC11163066 DOI: 10.3389/fcell.2024.1397788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 05/02/2024] [Indexed: 06/12/2024] Open
Abstract
Lung cancer is the second most common form of cancer worldwide Research points to the pivotal role of non-coding RNAs (ncRNAs) in controlling and managing the pathology by controlling essential pathways. ncRNAs have all been identified as being either up- or downregulated among individuals suffering from lung cancer thus hinting that they may play a role in either promoting or suppressing the spread of the disease. Several ncRNAs could be effective non-invasive biomarkers to diagnose or even serve as effective treatment options for those with lung cancer, and several molecules have emerged as potential targets of interest. Given that ncRNAs are contained in exosomes and are implicated in the development and progression of the malady. Herein, we have summarized the role of ncRNAs in lung cancer. Moreover, we highlight the role of exosomal ncRNAs in lung cancer.
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Affiliation(s)
- Xiaolong Lv
- Department of Cardiothoracic Surgery, The People’s Hospital of Changshou, Chongqing, China
| | - Lei Yang
- Department of Cardiothoracic Surgery, The People’s Hospital of Tongliang District, Chongqing, China
| | - Yunbo Xie
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
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26
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Chen R, Xie Q, Xie L, Huang J, Hu L, Lu H, Shi P, He Q, Zhang Q, Gong C, Zhang S, Wang B, Yang G, Yang Q. Thioredoxin1 Binding Metastasis-Associated Lung Adenocarcinoma Transcript 1 Attenuates Inflammation and Apoptosis after Intracerebral Hemorrhage. Aging Dis 2024; 15:1384-1397. [PMID: 37196136 PMCID: PMC11081159 DOI: 10.14336/ad.2023.0507] [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: 12/05/2022] [Accepted: 05/07/2023] [Indexed: 05/19/2023] Open
Abstract
Post-transcriptional regulation and RNA-binding proteins (RBPs) play vital roles in the occurrence of secondary injury after intracerebral hemorrhage (ICH). Therefore, we identified RBPs distinctively expressed after ICH by screening and determined thioredoxin1 (Txn1) as one of the most distinctive RBPs. We employed an ICH model and in vitro experiments to investigate the role of Txn1 in ICH. Firstly, we found that Txn1 was mainly expressed in microglia and neurons in the central nervous system, and its expression was significantly reduced in perihematomal tissue. Additionally, adeno-associated virus (AAV) carrying Txn1 was injected into the ICH rat model. Our results showed that overexpression of Txn1 reduced secondary injury and improved outcome in the ICH rat model. Moreover, to understand the therapeutic mechanism of Txn1 after ICH, we performed RNA immunoprecipitation combined with high-throughput sequencing. The results showed that Txn1 binds to inflammation- and apoptosis-related mRNAs and affects gene expression through RNA splicing and translation. Finally, RNA pull-down assays and in vitro experiments confirmed that Txn1 binds to metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), leading to reduced inflammation and apoptosis. Our study suggests that Txn1 is a potential therapeutic target for alleviating ICH-induced brain injury.
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Affiliation(s)
- Ru Chen
- Department of Neurology, Second Affiliated Hospital, Army Medical University (Third Military Medical University), Chongqing 400037, China
| | - Qi Xie
- Department of Neurology, Second Affiliated Hospital, Army Medical University (Third Military Medical University), Chongqing 400037, China
| | - Lexing Xie
- Department of Neurology, Second Affiliated Hospital, Army Medical University (Third Military Medical University), Chongqing 400037, China
| | - Jiacheng Huang
- Department of Neurology, Second Affiliated Hospital, Army Medical University (Third Military Medical University), Chongqing 400037, China
| | - Linlin Hu
- Department of Neurology, Second Affiliated Hospital, Army Medical University (Third Military Medical University), Chongqing 400037, China
| | - Hui Lu
- Department of Neurology, Second Affiliated Hospital, Army Medical University (Third Military Medical University), Chongqing 400037, China
| | - Peixia Shi
- Department of Neurology, Second Affiliated Hospital, Army Medical University (Third Military Medical University), Chongqing 400037, China
| | - Qian He
- Department of Neurology, Second Affiliated Hospital, Army Medical University (Third Military Medical University), Chongqing 400037, China
| | - Qin Zhang
- Department of Neurology, Second Affiliated Hospital, Army Medical University (Third Military Medical University), Chongqing 400037, China
| | - Changxiong Gong
- Department of Neurology, Second Affiliated Hospital, Army Medical University (Third Military Medical University), Chongqing 400037, China
| | - Shuang Zhang
- Department of Neurology, Second Affiliated Hospital, Army Medical University (Third Military Medical University), Chongqing 400037, China
| | - Bingqiao Wang
- Department of Neurology, Second Affiliated Hospital, Army Medical University (Third Military Medical University), Chongqing 400037, China
| | - Guoqiang Yang
- Department of Neurology, Second Affiliated Hospital, Army Medical University (Third Military Medical University), Chongqing 400037, China
| | - Qingwu Yang
- Department of Neurology, Second Affiliated Hospital, Army Medical University (Third Military Medical University), Chongqing 400037, China
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27
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Shadkam R, Saadat P, Azadmehr A, Chehrazi M, Daraei A. Key Non-coding Variants in Three Neuroapoptosis and Neuroinflammation-Related LncRNAs Are Protectively Associated with Susceptibility to Parkinson's Disease and Some of Its Clinical Features. Mol Neurobiol 2024; 61:2854-2865. [PMID: 37946005 DOI: 10.1007/s12035-023-03708-x] [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: 08/30/2023] [Accepted: 10/10/2023] [Indexed: 11/12/2023]
Abstract
Research findings show that genetic susceptibility to sporadic Parkinson's disease (PD), a common neurodegenerative disorder, is determined through gene variation of loci involved in its development and pathogenesis. A growing body of strong evidence has revealed that dysfunction of long non-coding RNAs (lncRNAs) plays key roles in the pathogenesis and progression of PD through impairing neuronal signaling pathways, but little is known about the relationship between their variants and PD susceptibility. In this research, we intended to study the relationship between functional SNPs rs12826786C>T, rs3200401C>T, and rs6931097G>A in the key lncRNAs stimulating neuroapoptosis and neuroinflammation in PD, including HOTAIR, MALAT1, and lincRNA-P21, respectively, with susceptibility to PD as well as its clinical symptoms.The population of this study consisted of 240 individuals, including 120 controls and 120 cases, and the sample taken from them was peripheral blood. Genotyping of the target SNPs was done using PCR-RFLP. We found that the healthy individuals carry more T allele of MALAT1-rs3200401C>T compared to the patients (P= 0.019). Furthermore, it was observed that in the dominant genetic model, subjects with genotypes carrying the T allele have a lower risk of PD (OR= 0.530; CI= 0.296-0.950; P= 0.033). Regarding the lincRNA-P21-rs6931097G>A, we observed a significant protective relationship between its GA (OR= 0.144; CI= 0.030-0.680; P= 0.014) and AA (OR= 0.195; CI= 00.047-0.799; P= 0.023) genotypes with the manifestation of tremor and bradykinesia symptoms, respectively. Furthermore, the findings indicated that the minor TT genotype of HOTAIR-rs12826786C>T was significantly associated with a reduced risk of bradykinesia symptoms (OR= 0.147; CI= 0.039-0.555; P= 0.005). Collectively, these findings suggest that MALAT1-rs3200401C>T may be an important lncRNA SNP against the development of PD, while the other two SNPs show protective effects on the clinical manifestations of PD in a way that lincRNA-P21-rs6931097G>A has a protective effect against the occurrence of tremor and bradykinesia symptoms in PD patients, and HOTAIR -rs12826786C>T indicates a protective effect against the display of bradykinesia feature. Therefore, they can have valuable potential as biomarkers for clinical evaluations of this disease.
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Affiliation(s)
- Roshanak Shadkam
- Student Research Committee, Babol University of Medical Sciences, Babol, Iran
- Department of Medical Genetics, School of Medicine, Babol University of Medical Sciences, Babol, Iran
| | - Payam Saadat
- Mobility Impairment Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Abbas Azadmehr
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Mohammad Chehrazi
- Department of Biostatistics and Epidemiology, School of Public Health, Babol University of Medical Sciences, Babol, Iran
| | - Abdolreza Daraei
- Department of Medical Genetics, School of Medicine, Babol University of Medical Sciences, Babol, Iran.
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran.
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Piórkowska K, Zygmunt K, Hunter W, Wróblewska K. MALAT1: A Long Non-Coding RNA with Multiple Functions and Its Role in Processes Associated with Fat Deposition. Genes (Basel) 2024; 15:479. [PMID: 38674413 PMCID: PMC11049917 DOI: 10.3390/genes15040479] [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: 03/13/2024] [Revised: 04/05/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
Metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) belongs to the lncRNA molecules, which are involved in transcriptional and epigenetic regulation and the control of gene expression, including the mechanism of chromatin remodeling. MALAT1 was first discovered during carcinogenesis in lung adenocarcinoma, hence its name. In humans, 66 of its isoforms have been identified, and in pigs, only 2 are predicted, for which information is available in Ensembl databases (Ensembl Release 111). MALAT1 is expressed in numerous tissues, including adipose, adrenal gland, heart, kidney, liver, ovary, pancreas, sigmoid colon, small intestine, spleen, and testis. MALAT1, as an lncRNA, shows a wide range of functions. It is involved in the regulation of the cell cycle, where it has pro-proliferative effects and high cellular levels during the G1/S and mitotic (M) phases. Moreover, it is involved in invasion, metastasis, and angiogenesis, and it has a crucial function in alternative splicing during carcinogenesis. In addition, MALAT1 plays a significant role in the processes of fat deposition and adipogenesis. The human adipose tissue stem cells, during differentiation into adipocytes, secrete MALAT1 as one the most abundant lncRNAs in the exosomes. MALAT1 expression in fat tissue is positively correlated with adipogenic FABP4 and LPL. This lncRNA is involved in the regulation of PPARγ at the transcription stage, fatty acid metabolism, and insulin signaling. The wide range of MALAT1 functions makes it an interesting target in studies searching for drugs to prevent obesity development in humans. In turn, in farm animals, it can be a source of selection markers to control the fat tissue content.
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Affiliation(s)
- Katarzyna Piórkowska
- National Research Institute of Animal Production, Animal Molecular Biology, 31-047 Cracow, Poland; (K.Z.); (K.W.)
| | - Karolina Zygmunt
- National Research Institute of Animal Production, Animal Molecular Biology, 31-047 Cracow, Poland; (K.Z.); (K.W.)
| | - Walter Hunter
- Faculty of Biotechnology and Horticulture, University of Agriculture in Cracow, 31-120 Cracow, Poland;
| | - Ksenia Wróblewska
- National Research Institute of Animal Production, Animal Molecular Biology, 31-047 Cracow, Poland; (K.Z.); (K.W.)
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Miller MJ, Gries KJ, Marcotte GR, Ryan Z, Strub MD, Kunz HE, Arendt BK, Dasari S, Ebert SM, Adams CM, Lanza IR. Human myofiber-enriched aging-induced lncRNA FRAIL1 promotes loss of skeletal muscle function. Aging Cell 2024; 23:e14097. [PMID: 38297807 PMCID: PMC11019130 DOI: 10.1111/acel.14097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 01/11/2024] [Accepted: 01/13/2024] [Indexed: 02/02/2024] Open
Abstract
The loss of skeletal muscle mass during aging is a significant health concern linked to adverse outcomes in older individuals. Understanding the molecular basis of age-related muscle loss is crucial for developing strategies to combat this debilitating condition. Long noncoding RNAs (lncRNAs) are a largely uncharacterized class of biomolecules that have been implicated in cellular homeostasis and dysfunction across a many tissues and cell types. To identify lncRNAs that might contribute to skeletal muscle aging, we screened for lncRNAs whose expression was altered in vastus lateralis muscle from older compared to young adults. We identified FRAIL1 as an aging-induced lncRNA with high abundance in human skeletal muscle. In healthy young and older adults, skeletal muscle FRAIL1 was increased with age in conjunction with lower muscle function. Forced expression of FRAIL1 in mouse tibialis anterior muscle elicits a dose-dependent reduction in skeletal muscle fiber size that is independent of changes in muscle fiber type. Furthermore, this reduction in muscle size is dependent on an intact region of FRAIL1 that is highly conserved across non-human primates. Unbiased transcriptional and proteomic profiling of the effects of FRAIL1 expression in mouse skeletal muscle revealed widespread changes in mRNA and protein abundance that recapitulate age-related changes in pathways and processes that are known to be altered in aging skeletal muscle. Taken together, these findings shed light on the intricate molecular mechanisms underlying skeletal muscle aging and implicate FRAIL1 in age-related skeletal muscle phenotypes.
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Affiliation(s)
- Matthew J. Miller
- Division of EndocrinologyMayo ClinicRochesterMinnesotaUSA
- University of IowaIowa CityIowaUSA
| | | | - George R. Marcotte
- Division of EndocrinologyMayo ClinicRochesterMinnesotaUSA
- University of IowaIowa CityIowaUSA
| | - Zachary Ryan
- Division of EndocrinologyMayo ClinicRochesterMinnesotaUSA
| | | | - Hawley E. Kunz
- Division of EndocrinologyMayo ClinicRochesterMinnesotaUSA
| | | | - Surendra Dasari
- Department of Quantitative Health SciencesMayo ClinicRochesterMinnesotaUSA
| | - Scott M. Ebert
- Division of EndocrinologyMayo ClinicRochesterMinnesotaUSA
- Emmyon, Inc.RochesterMinnesotaUSA
| | - Christopher M. Adams
- Division of EndocrinologyMayo ClinicRochesterMinnesotaUSA
- Emmyon, Inc.RochesterMinnesotaUSA
| | - Ian R. Lanza
- Division of EndocrinologyMayo ClinicRochesterMinnesotaUSA
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Shelke V, Kale A, Sankrityayan H, Anders HJ, Gaikwad AB. Long non-coding RNAs as emerging regulators of miRNAs and epigenetics in diabetes-related chronic kidney disease. Arch Physiol Biochem 2024; 130:230-241. [PMID: 34986074 DOI: 10.1080/13813455.2021.2023580] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 12/22/2021] [Indexed: 01/19/2023]
Abstract
Diabetes is one of the major cause of chronic kidney disease (CKD), including "diabetic nephropathy," and is an increasingly prevalent accelerator of the progression of non-diabetic forms of CKD. The long non-coding RNAs (lncRNAs) have come into the limelight in the past few years as one of the emerging weapons against CKD in diabetes. Available data over the past few years demonstrate the interaction of lncRNAs with miRNAs and epigenetic machinery. Interestingly, the evolving data suggest that lncRNAs play a vital role in diabetes-associated CKD by regulation of epigenetic enzymes such as DNA methyltransferase, histone deacetylases, and histone methyltransferases. LncRNAs are also engaged in the regulation of several miRNAs in diabetic nephropathy. Hence this review will elaborate on the association between lncRNAs and their interaction with epigenetic regulators involved in different aspects and thus the progression of CKD in diabetes.
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Affiliation(s)
- Vishwadeep Shelke
- Laboratory of Molecular Pharmacology, Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani, India
| | - Ajinath Kale
- Laboratory of Molecular Pharmacology, Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani, India
| | - Himanshu Sankrityayan
- Laboratory of Molecular Pharmacology, Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani, India
| | - Hans-Joachim Anders
- Division of Nephrology, Department of Internal Medicine IV, University Hospital of the Ludwig Maximilians University Munich, Munich, Germany
| | - Anil Bhanudas Gaikwad
- Laboratory of Molecular Pharmacology, Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani, India
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Shannon MJ, McNeill GL, Koksal B, Baltayeva J, Wächter J, Castellana B, Peñaherrera MS, Robinson WP, Leung PCK, Beristain AG. Single-cell assessment of primary and stem cell-derived human trophoblast organoids as placenta-modeling platforms. Dev Cell 2024; 59:776-792.e11. [PMID: 38359834 DOI: 10.1016/j.devcel.2024.01.023] [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: 11/10/2022] [Revised: 11/15/2023] [Accepted: 01/23/2024] [Indexed: 02/17/2024]
Abstract
Human trophoblast stem cells (hTSCs) and related trophoblast organoids are state-of-the-art culture systems that facilitate the study of trophoblast development and human placentation. Using single-cell transcriptomics, we evaluate how organoids derived from freshly isolated first-trimester trophoblasts or from established hTSC cell lines reproduce developmental cell trajectories and transcriptional regulatory processes defined in vivo. Although organoids from primary trophoblasts and hTSCs overall model trophoblast differentiation with accuracy, specific features related to trophoblast composition, trophoblast differentiation, and transcriptional drivers of trophoblast development show levels of misalignment. This is best illustrated by the identification of an expanded progenitor state in stem cell-derived organoids that is nearly absent in vivo and transcriptionally shares both villous cytotrophoblast and extravillous trophoblast characteristics. Together, this work provides a comprehensive resource that identifies strengths and limitations of current trophoblast organoid platforms.
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Affiliation(s)
- Matthew J Shannon
- The British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada; Department of Obstetrics & Gynecology, The University of British Columbia, Vancouver, BC, Canada
| | - Gina L McNeill
- The British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada; Department of Obstetrics & Gynecology, The University of British Columbia, Vancouver, BC, Canada
| | - Burak Koksal
- The British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada; Department of Obstetrics & Gynecology, The University of British Columbia, Vancouver, BC, Canada
| | - Jennet Baltayeva
- The British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada; Department of Obstetrics & Gynecology, The University of British Columbia, Vancouver, BC, Canada
| | - Jasmin Wächter
- Department of Obstetrics and Gynecology, Medical University of Vienna, Vienna, Austria
| | - Barbara Castellana
- The British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada; Department of Obstetrics & Gynecology, The University of British Columbia, Vancouver, BC, Canada
| | - Maria S Peñaherrera
- The British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada; Department of Medical Genetics, The University of British Columbia, Vancouver, BC, Canada
| | - Wendy P Robinson
- The British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada; Department of Medical Genetics, The University of British Columbia, Vancouver, BC, Canada
| | - Peter C K Leung
- The British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada; Department of Obstetrics & Gynecology, The University of British Columbia, Vancouver, BC, Canada
| | - Alexander G Beristain
- The British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada; Department of Obstetrics & Gynecology, The University of British Columbia, Vancouver, BC, Canada.
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Liang X, Di F, Wei H, Liu N, Chen C, Wang X, Sun M, Zhang M, Li M, Zhang J, Zhang S. Functional identification of long non-coding RNAs induced by PM 2.5 in microglia through microarray analysis. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 273:116136. [PMID: 38387142 DOI: 10.1016/j.ecoenv.2024.116136] [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: 11/21/2023] [Revised: 02/13/2024] [Accepted: 02/19/2024] [Indexed: 02/24/2024]
Abstract
As a dominating air pollutant, atmospheric fine particulate matter within 2.5 μm in diameter (PM2.5) has attracted increasing attention from the researchers all over the world, which will lead to various adverse effects on the central nervous system (CNS), yet the potential mechanism is unclear. In this study, the microglia (BV2 cell line) were exposed to different concentrations of PM2.5 (5, 10 and 20 μg/cm2) for 24 h. It was found that PM2.5 could result in adverse effects on microglia such as decreased cell viability, structural damage and even cell death. And it was reported that long non-coding RNAs (lncRNAs) could participate in multitudinous neurological diseases. Therefore, the microarray analysis was conducted in order to disclose the underlying neurotoxicity mechanism of PM2.5 by ascertaining the differentially expressed lncRNAs (DElncRNAs). The consequences indicated that the DElncRNAs were enriched in various biological pathways, including ferroptosis, IL-17 signaling pathway and NOD-like receptor signaling pathway. Moreover, the cis- and trans-regulated mRNAs by DElncRNAs as well as the corresponding transcriptional factors (TFs) were observed, such as CEBPA, MYC, MEIS1 and KLF4. In summary, our study supplies some candidate libraries and potential preventive target against PM2.5-induced toxicity through targeting lncRNAs. Furthermore, the post-transcriptional regulation will contribute to the future research on PM2.5-induced neurotoxicity.
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Affiliation(s)
- Xue Liang
- School of Public Health, Shandong First Medical University (Shandong Academy of Medical Sciences), Jinan, Shandong 250117, China; Medical Science and Technology Innovation Center, Shandong First Medical University (Shandong Academy of Medical Sciences), Jinan, Shandong 250117, China.
| | - Fanglin Di
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University (Shandong Academy of Medical Sciences), Jinan, Shandong 250117, China
| | - Haiyun Wei
- School of Public Health, Shandong First Medical University (Shandong Academy of Medical Sciences), Jinan, Shandong 250117, China
| | - Natong Liu
- School of Public Health, Shandong First Medical University (Shandong Academy of Medical Sciences), Jinan, Shandong 250117, China
| | - Chao Chen
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University (Shandong Academy of Medical Sciences), Jinan, Shandong 250117, China
| | - Xinzhi Wang
- School of Public Health, Shandong First Medical University (Shandong Academy of Medical Sciences), Jinan, Shandong 250117, China
| | - Meng Sun
- Department of Neurosurgery, The First Affiliated Hospital of Shandong First Medical University, Jinan, Shandong 250014, China
| | - Min Zhang
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University (Shandong Academy of Medical Sciences), Jinan, Shandong 250117, China
| | - Meng Li
- Department of Neurosurgery, The First Affiliated Hospital of Shandong First Medical University, Jinan, Shandong 250014, China
| | - Jie Zhang
- Medical Science and Technology Innovation Center, Shandong First Medical University (Shandong Academy of Medical Sciences), Jinan, Shandong 250117, China; Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University (Shandong Academy of Medical Sciences), Jinan, Shandong 250117, China
| | - Shuping Zhang
- Medical Science and Technology Innovation Center, Shandong First Medical University (Shandong Academy of Medical Sciences), Jinan, Shandong 250117, China; Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University (Shandong Academy of Medical Sciences), Jinan, Shandong 250117, China
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Amini A, Esmaeili F, Golpich M. Possible role of lncRNAs in amelioration of Parkinson's disease symptoms by transplantation of dopaminergic cells. NPJ Parkinsons Dis 2024; 10:56. [PMID: 38472261 PMCID: PMC10933336 DOI: 10.1038/s41531-024-00661-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 02/14/2024] [Indexed: 03/14/2024] Open
Abstract
Long non-coding RNAs (lncRNAs) are biomarkers for diagnosis and treatment of Parkinson's disease (PD). Since dopaminergic cell transplantation is a clinical method to treat PD, this study investigated the effects of dopaminergic cell therapy on the expression of some lncRNAs and genes related to PD. In this study, Twenty-eight rats were randomly assigned to four experimental groups. The control group (Sal group) received saline injections. The Par group was a PD rat model with 6-hydroxydopamine (6-OHDA) injection in right striatum (ST). PD animals were transplanted by undifferentiated P19 stem cells (Par-E group), and P19-derived dopaminergic cells (Par-N group). Cell transplant effects were evaluated using behavioral tests (cylinder, open field, and rotarod tests), and histological methods (H&E and Nissl staining, and immunohistochemistry). Moreover, the expression of lncRNAs MALAT1, MEG3, and SNHG1, alongside specific neuronal (synaptophysin) and dopaminergic (tyrosine hydroxylase) markers was evaluated by qRT-PCR. Behavioral and histopathological examinations revealed that cell transplantation partially compensated dopaminergic cell degeneration in ST and substantia nigra (SN) of PD rats. The expression of MALAT1, SNHG1, and MEG3 was decreased in the ST of the Par group, while MEG3 and SNHG1 gene expression was increased in PBMC relative to the Sal group. In PBMC of the Par-N group, all three lncRNAs showed a reduction in their expression. Conversely, MALAT1 and SNHG1 expression was increased in ST tissue, while MEG3 gene expression was decreased compared to the Sal group. In conclusion, dopaminergic cell transplantation could change the lncRNAs expression. Furthermore, it partially improves symptoms in PD rats.
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Affiliation(s)
- A Amini
- Department of Plant and Animal Biology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - F Esmaeili
- Department of Plant and Animal Biology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran.
| | - M Golpich
- Department of Plant and Animal Biology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
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Zhang X, Wu L, Jia L, Hu X, Yao Y, Liu H, Ma J, Wang W, Li L, Chen K, Liu B. The implication of integrative multiple RNA modification-based subtypes in gastric cancer immunotherapy and prognosis. iScience 2024; 27:108897. [PMID: 38318382 PMCID: PMC10839690 DOI: 10.1016/j.isci.2024.108897] [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: 07/28/2023] [Revised: 10/28/2023] [Accepted: 01/09/2024] [Indexed: 02/07/2024] Open
Abstract
Previous studies have focused on the impact of individual RNA modifications on tumor development. This study comprehensively investigated the effects of multiple RNA modifications, including m6A, alternative polyadenylation, pseudouridine, adenosine-to-inosine editing, and uridylation, on gastric cancer (GC). By analyzing 1,946 GC samples from eleven independent cohorts, we identified distinct clusters of RNA modification genes with varying survival rates and immunological characteristics. We assessed the chromatin activity of these RNA modification clusters through regulon enrichment analysis. A prognostic model was developed using Stepwise Regression and Random Survival Forest algorithms and validated in ten independent datasets. Notably, the low-risk group showed a more favorable prognosis and positive response to immune checkpoint blockade therapy. Single-cell RNA sequencing confirmed the abundant expression of signature genes in B cells and plasma cells. Overall, our findings shed light on the potential significance of multiple RNA modifications in GC prognosis, stemness development, and chemotherapy resistance.
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Affiliation(s)
- Xiangnan Zhang
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Key Laboratory of Prevention and Control of Human Major Diseases, Ministry of Education, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300060, China
| | - Liuxing Wu
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Key Laboratory of Prevention and Control of Human Major Diseases, Ministry of Education, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300060, China
- Department of Bioinformatics, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Liqing Jia
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Key Laboratory of Prevention and Control of Human Major Diseases, Ministry of Education, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300060, China
| | - Xin Hu
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Key Laboratory of Prevention and Control of Human Major Diseases, Ministry of Education, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300060, China
| | - Yanxin Yao
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Key Laboratory of Prevention and Control of Human Major Diseases, Ministry of Education, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300060, China
| | - Huahuan Liu
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Key Laboratory of Prevention and Control of Human Major Diseases, Ministry of Education, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300060, China
| | - Junfu Ma
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Key Laboratory of Prevention and Control of Human Major Diseases, Ministry of Education, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300060, China
| | - Wei Wang
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Key Laboratory of Prevention and Control of Human Major Diseases, Ministry of Education, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300060, China
| | - Lian Li
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Key Laboratory of Prevention and Control of Human Major Diseases, Ministry of Education, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300060, China
| | - Kexin Chen
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Key Laboratory of Prevention and Control of Human Major Diseases, Ministry of Education, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300060, China
| | - Ben Liu
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Key Laboratory of Prevention and Control of Human Major Diseases, Ministry of Education, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300060, China
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Sharma D, Singh A, Wilson C, Swaroop P, Kumar S, Yadav DK, Jain V, Agarwala S, Husain M, Sharawat SK. Exosomal long non-coding RNA MALAT1: a candidate of liquid biopsy in monitoring of Wilms' tumor. Pediatr Surg Int 2024; 40:57. [PMID: 38353772 DOI: 10.1007/s00383-023-05626-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/26/2023] [Indexed: 02/16/2024]
Abstract
PURPOSE Wilms' tumor (WT) is a rare kidney cancer that primarily affects children. Exosomes are extracellular vesicles that cargo nucleic acids, proteins,etc. for cellular communication. Long non-coding RNAs (lncRNAs) have utility as biomarkers for cancer diagnosis, prognosis, and disease monitoring. We hypothesize that expression of lncRNA, metastasis-associated lung adenocarcinoma transcript-1(MALAT1), is dysregulated and possibly trafficked within exosomes to influence the tissue microenvironment for metastasis and recurrence of WT. METHODS We investigated the expression of MALAT1 in thirty WT samples by qPCR. Exosomes were isolated using a precipitated and affinity-binding-based kit, and characterized using TEM, NTA, and DLS. RESULTS Mean number of exosomes was 9.01×108/mL in primary culture, 1.64×108/mL in urine, and 4.65×108/plasma:400µl. Average yield of total RNA was 1.28µg (primary-culture supernatant:1ml), 1.47µg (Urine:1ml), 1.65µg (Plasma:400 µL). We quantified MALAT1 in exosomes derived from these sources in patients of WT. Expression of MALAT1 was significantly downregulated (p=0.008) in WT samples. CONCLUSION This is the first study that demonstrated the presence of lncRNA MALAT1 in various invasive and non-invasive samples of patients with WT(primary tissue culture, urine, and plasma samples).
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Affiliation(s)
- Diwakar Sharma
- Virology and Oncology Lab, Department of Biotechnology, Jamia Millia Islamia, New Delhi, India
- Department of Medical Oncology, All India Institute of Medical Sciences, New Delhi, India
| | - Apoorv Singh
- Department of Paediatric Surgery, All India Institute of Medical Sciences, New Delhi, India
| | - Christine Wilson
- Department of Medical Oncology, All India Institute of Medical Sciences, New Delhi, India
| | - Priyanka Swaroop
- Department of Paediatric Surgery, All India Institute of Medical Sciences, New Delhi, India
| | - Sachin Kumar
- Department of Medical Oncology, All India Institute of Medical Sciences, New Delhi, India
| | - Devendra K Yadav
- Department of Paediatric Surgery, All India Institute of Medical Sciences, New Delhi, India
| | - Vishesh Jain
- Department of Paediatric Surgery, All India Institute of Medical Sciences, New Delhi, India
| | - Sandeep Agarwala
- Department of Paediatric Surgery, All India Institute of Medical Sciences, New Delhi, India
| | - Mohammad Husain
- Virology and Oncology Lab, Department of Biotechnology, Jamia Millia Islamia, New Delhi, India.
| | - Surender K Sharawat
- Department of Medical Oncology, All India Institute of Medical Sciences, New Delhi, India.
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Sun H, Cao X, Sumayya, Ma Y, Li H, Han W, Qu L. Genome-wide transcriptional profiling and functional analysis of long noncoding RNAs and mRNAs in chicken macrophages associated with the infection of avian pathogenic E. coli. BMC Vet Res 2024; 20:49. [PMID: 38326918 PMCID: PMC10848384 DOI: 10.1186/s12917-024-03890-7] [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: 08/10/2023] [Accepted: 01/18/2024] [Indexed: 02/09/2024] Open
Abstract
BACKGROUND Avian pathogenic E. coli (APEC) can cause localized or systemic infections, collectively known as avian colibacillosis, resulting in huge economic losses to poultry industry globally per year. In addition, increasing evidence indicates that long non-coding RNAs (lncRNAs) play a critical role in regulating host inflammation in response to bacterial infection. However, the role of lncRNAs in the host response to APEC infection remains unclear. RESULTS Here, we found 816 differentially expressed (DE) lncRNAs and 1,798 DE mRNAs in APEC infected chicken macrophages by RNAseq. The identified DE lncRNA-mRNAs were involved in Toll like receptor signaling pathway, VEGF signaling pathway, fatty acid metabolism, phosphatidylinositol signaling system, and other types of O-glycan biosynthesis. Furthermore, we found the novel lncRNA TCONS_00007391 as an important immune regulator in APEC infection was able to regulate the inflammatory response by directly targeting CD86. CONCLUSION These findings provided a better understanding of host response to APEC infection and also offered the potential drug targets for therapy development against APEC infection.
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Affiliation(s)
- Hongyan Sun
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China.
| | - Xinqi Cao
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Sumayya
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Yuyi Ma
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Huan Li
- School of Biological and Chemical Engineering, Yangzhou Polytechnic College, Yangzhou, 225009, China
| | - Wei Han
- The Poultry Research Institute of Chinese Academy of Agricultural Sciences, Yangzhou, 225009, China
| | - Lujiang Qu
- College of Animal Science and Technology, China Agricultural University, Beijing, 100091, China
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Weghorst F, Torres Marcén M, Faridi G, Lee YCG, Cramer KS. Deep Conservation and Unexpected Evolutionary History of Neighboring lncRNAs MALAT1 and NEAT1. J Mol Evol 2024; 92:30-41. [PMID: 38189925 PMCID: PMC10869381 DOI: 10.1007/s00239-023-10151-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 11/29/2023] [Indexed: 01/09/2024]
Abstract
Long non-coding RNAs (lncRNAs) have begun to receive overdue attention for their regulatory roles in gene expression and other cellular processes. Although most lncRNAs are lowly expressed and tissue-specific, notable exceptions include MALAT1 and its genomic neighbor NEAT1, two highly and ubiquitously expressed oncogenes with roles in transcriptional regulation and RNA splicing. Previous studies have suggested that NEAT1 is found only in mammals, while MALAT1 is present in all gnathostomes (jawed vertebrates) except birds. Here we show that these assertions are incomplete, likely due to the challenges associated with properly identifying these two lncRNAs. Using phylogenetic analysis and structure-aware annotation of publicly available genomic and RNA-seq coverage data, we show that NEAT1 is a common feature of tetrapod genomes except birds and squamates. Conversely, we identify MALAT1 in representative species of all major gnathostome clades, including birds. Our in-depth examination of MALAT1, NEAT1, and their genomic context in a wide range of vertebrate species allows us to reconstruct the series of events that led to the formation of the locus containing these genes in taxa from cartilaginous fish to mammals. This evolutionary history includes the independent loss of NEAT1 in birds and squamates, since NEAT1 is found in the closest living relatives of both clades (crocodilians and tuataras, respectively). These data clarify the origins and relationships of MALAT1 and NEAT1 and highlight an opportunity to study the change and continuity in lncRNA structure and function over deep evolutionary time.
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Affiliation(s)
- Forrest Weghorst
- Department of Neurobiology and Behavior, University of California, Irvine, USA
| | - Martí Torres Marcén
- Department of Neurobiology and Behavior, University of California, Irvine, USA
| | - Garrison Faridi
- Department of Neurobiology and Behavior, University of California, Irvine, USA
| | - Yuh Chwen G Lee
- Department of Ecology and Evolutionary Biology, University of California, Irvine, USA
| | - Karina S Cramer
- Department of Neurobiology and Behavior, University of California, Irvine, USA.
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Soni R, Mathur K, Shah J. An update on new-age potential biomarkers for Parkinson's disease. Ageing Res Rev 2024; 94:102208. [PMID: 38296162 DOI: 10.1016/j.arr.2024.102208] [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: 11/23/2023] [Revised: 01/24/2024] [Accepted: 01/24/2024] [Indexed: 02/05/2024]
Abstract
Parkinson's disease (PD) is a progressive neurodegenerative disorder that deals with dopaminergic deficiency in Substantia nigra pars compact (SNpc) region of the brain. Dopaminergic deficiency manifests into motor dysfunction. Alpha-synuclein protein aggregation is the source for inception of the pathology. Motor symptoms include rigidity, akinesia, tremor and gait dysfunction. Pre-motor symptoms are also seen in early stage of the disease; however, they are not distinguishable. Lack of early diagnosis in PD pathology poses a major challenge for development of disease modifying therapeutics. Substantial neuronal loss has already been occurred before the clinical manifestations appear and hence, it becomes impossible to halt the disease progression. Current diagnostics are majorly based on the clinical symptoms and thus fail to detect early progression of the disease. Thus, there is need for early diagnosis of PD, for detection of the disease at its inception. This will facilitate the effective use of therapies that halt the progression and will make remission possible. Many novel biomarkers are being developed that include blood-based biomarker, CSF biomarker. Other than that, there are non-invasive techniques that can detect biomarkers. We aim to discuss potential role of these new age biomarkers and their association with PD pathogenesis in this review.
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Affiliation(s)
- Ritu Soni
- Department of Pharmacology, Institute of Pharmacy, Nirma University, Ahmedabad, Gujarat 382481, India
| | - Kirti Mathur
- Department of Pharmacology, Institute of Pharmacy, Nirma University, Ahmedabad, Gujarat 382481, India
| | - Jigna Shah
- Department of Pharmacology, Institute of Pharmacy, Nirma University, Ahmedabad, Gujarat 382481, India.
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Sahayasheela VJ, Sugiyama H. RNA G-quadruplex in functional regulation of noncoding RNA: Challenges and emerging opportunities. Cell Chem Biol 2024; 31:53-70. [PMID: 37909035 DOI: 10.1016/j.chembiol.2023.08.010] [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: 04/18/2023] [Revised: 07/12/2023] [Accepted: 08/22/2023] [Indexed: 11/02/2023]
Abstract
G-quadruplexes (G4s) are stable, noncanonical structures formed in guanine (G)-rich sequences of DNA/RNA. G4 structures are reported to play a regulatory role in various cellular processes and, recently, a considerable number of studies have attributed new biological functions to these structures, especially in RNA. Noncoding RNA (ncRNA), which does not translate into a functional protein, is widely expressed and has been shown to play a key role in shaping cellular activity. There has been growing evidence of G4 formation in several ncRNA classes, and it has been identified as a key part for diverse biological functions and physio-pathological contexts in neurodegenerative diseases and cancer. This review discusses RNA G4s (rG4s) in ncRNA, focusing on the molecular mechanism underlying its function. This review also aims to highlight potential and emerging opportunities to identify and target the rG4s in ncRNA to understand its function and, ultimately, treat many diseases.
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Affiliation(s)
- Vinodh J Sahayasheela
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto 606-8502, Japan; Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Ushinomaecho, Sakyo-Ku, Kyoto 606-8501, Japan.
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Lin H, Wei X, Ye J, Chen J, Huang J, Wu T, Chen Z, Zeng Y, Peng L. Lnc-CLSTN2-1:1 Promotes Osteosarcoma Progression by Disrupting Redox Balance through PI3K/AKT Signaling Pathway. J Cancer 2024; 15:1287-1298. [PMID: 38356713 PMCID: PMC10861822 DOI: 10.7150/jca.91579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 12/27/2023] [Indexed: 02/16/2024] Open
Abstract
Objective: Most patients with osteosarcoma (OS) have an extremely poor prognosis. The primary purpose of this investigation was to explore the biological effect of Lnc-CLSTN2-1:1 on OS and the potential processes involved. Materials and procedures: We selected differentially overexpressed Lnc-CLSTN2-1:1 from our laboratory's existing RNA sequence analysis data (fibroblast osteoblast (hFOB 1.19) and three osteosarcoma cell lines (HOS, MG63, and U2OS) as the research object. Next, we detected Lnc-CLSTN2-1:1 in the osteosarcoma HOS cell line and fibroblast cells using qRT-PCR. We evaluated cell proliferation ability using EdU incorporation test, CCK-8 test, and cell clone formation; cell invasion and migration were assessed using the Transwell test, while flow cytometry examined cell cycle, apoptosis, and reactive oxygen species (ROS); Subsequently, the activity changes of selenase (GPx) glutathione peroxidase and (TrxR) thioredoxin reductase were detected. In addition, changes in related proteins were analyzed through Western blotting. Results: The expression of Lnc-CLSTN2-1:1 in osteosarcoma cells was significantly increased. The proliferation, invasion, and migration of osteosarcoma cells were significantly inhibited by knockdown of the expression of Lnc-CLSTN2-1:1, and the cell cycle-related signaling pathway PI3K/AKT/GSK-3β/cycinD1 was also inhibited. However, insulin-like growth factor-1 (igf-1) could reverse this process. In addition, we examined the activity of two selenophenases (TrxR and GPx) and the changes of ROS before and after Lnc-CLSTN2-1:1 knockdown. The results showed that both TrxR and GPx activities were reduced after Lnc-CLSTN2-1:1 knockdown, resulting in the inhibition of antioxidant stress levels, while intracellular ROS levels were high, which eventually caused killing effects on tumor cells due to the imbalance between oxidative stress and antioxidant stress. Conclusion: Our results showed that Lnc-CLSTN2-1:1 enhanced anti-oxidative stress TrxR and GPx selenoprotein activities through the PI3K/AKT signaling pathway while counteracting the loss of reactive oxygen species ROS produced by mitochondria to osteosarcoma cells, which protected osteosarcoma cells and thus promoted the proliferation and metastatic ability of OS.
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Affiliation(s)
- Hao Lin
- Department of Orthopedics, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong,534001, China
| | - Xinjian Wei
- Department of Orthopedics, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong,534001, China
| | - Junhong Ye
- Department of Orthopedics, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong,534001, China
| | - Jiaxian Chen
- Department of Orthopedics, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong,534001, China
| | - Jing Huang
- Oncology Hospital, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong,534001, China
| | - Tingrui Wu
- Department of Orthopedics, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong,534001, China
| | - Zhenju Chen
- Department of Orthopedics, Suixi Hospital of Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong,534001, China
| | - Yuming Zeng
- Department of Orthopedics, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong,534001, China
| | - Lijiao Peng
- Oncology Hospital, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong,534001, China
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Jalink EA, Schonk AW, Boon RA, Juni RP. Non-coding RNAs in the pathophysiology of heart failure with preserved ejection fraction. Front Cardiovasc Med 2024; 10:1300375. [PMID: 38259314 PMCID: PMC10800550 DOI: 10.3389/fcvm.2023.1300375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 12/11/2023] [Indexed: 01/24/2024] Open
Abstract
Heart failure with preserved ejection fraction (HFpEF) is the largest unmet clinical need in cardiovascular medicine. Despite decades of research, the treatment option for HFpEF is still limited, indicating our ongoing incomplete understanding on the underlying molecular mechanisms. Non-coding RNAs, comprising of microRNAs (miRNAs), long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs), are non-protein coding RNA transcripts, which are implicated in various cardiovascular diseases. However, their role in the pathogenesis of HFpEF is unknown. Here, we discuss the role of miRNAs, lncRNAs and circRNAs that are involved in the pathophysiology of HFpEF, namely microvascular dysfunction, inflammation, diastolic dysfunction and cardiac fibrosis. We interrogated clinical evidence and dissected the molecular mechanisms of the ncRNAs by looking at the relevant in vivo and in vitro models that mimic the co-morbidities in patients with HFpEF. Finally, we discuss the potential of ncRNAs as biomarkers and potential novel therapeutic targets for future HFpEF treatment.
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Affiliation(s)
- Elisabeth A. Jalink
- Department of Physiology, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
- Amsterdam Cardiovascular Sciences, Microcirculation, Amsterdam, Netherlands
| | - Amber W. Schonk
- Department of Physiology, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
- Amsterdam Cardiovascular Sciences, Microcirculation, Amsterdam, Netherlands
| | - Reinier A. Boon
- Department of Physiology, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
- Amsterdam Cardiovascular Sciences, Microcirculation, Amsterdam, Netherlands
- Institute for Cardiovascular Regeneration, Centre for Molecular Medicine, Goethe University Frankfurt am Main, Frankfurt am Main, Germany
- German Centre for Cardiovascular Research, Partner Site Frankfurt Rhein/Main, Frankfurt, Germany
| | - Rio P. Juni
- Department of Physiology, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
- Amsterdam Cardiovascular Sciences, Microcirculation, Amsterdam, Netherlands
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Bai S, Guo J, Zhang H. A meta-analysis of the clinicopathological significance of the lncRNA MALAT1 in human gastric cancer. Front Oncol 2024; 13:1257120. [PMID: 38239645 PMCID: PMC10794718 DOI: 10.3389/fonc.2023.1257120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 11/22/2023] [Indexed: 01/22/2024] Open
Abstract
Background Dysregulation of the long non-coding RNA metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) has been linked to some oncogenic pathways that induce cancer initiation and progression. This meta-analysis was conducted to specifically summarize the most recent research on MALAT1 function in human gastric cancer (GC). Methods The eligible studies were first identified by searching HowNet, Web of Science, PubMed, The Cochrane Library, Embase, and Nature databases for studies published as of April 1, 2023. The meta-analysis included 14 studies assessing MALAT1 expression and presenting clinical parameters and survival outcomes. Results The results illustrated that high MALAT1 expression is predictive of lymph node metastasis (pooled odds ratio [OR] = 2.99, 95% confidence interval [CI] = 1.97-4.54, P < 0.001) and distant metastasis in GC (OR = 3.11, 95% CI = 1.68-5.75, P < 0.001). In addition, MALAT1 was associated with GC tumor invasion (T3/T4 vs. T1/T2: OR = 2.90, 95% CI = 1.90- 4.41, P <0.001) and TNM stage (III/IV vs I/II: OR = 2.93, 95% CI: 1.80-4.77, P <0.001). Additionally, higher MALAT-1 expression predicted poorer overall survival in patients with GC (hazard ratio = 1.64, 95% CI = 1.20-2.09, P < 0.001). Conclusions The current findings suggest that the high MALAT1 expression is an adverse biomarker for prognostic outcomes, lymph node metastasis, TNM stage, and distant metastasis in GC and MALAT1 could be a prognostic biomarker for GC.
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Affiliation(s)
- Shaoxiong Bai
- Gastrointestinal Surgery, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
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Bhat AA, Afzal O, Afzal M, Gupta G, Thapa R, Ali H, Hassan Almalki W, Kazmi I, Alzarea SI, Saleem S, Samuel VP, Gubbiyappa SK, Subramaniyan V. MALAT1: A key regulator in lung cancer pathogenesis and therapeutic targeting. Pathol Res Pract 2024; 253:154991. [PMID: 38070223 DOI: 10.1016/j.prp.2023.154991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 11/21/2023] [Accepted: 11/27/2023] [Indexed: 01/24/2024]
Abstract
Lung cancer remains a formidable global health burden, necessitating a comprehensive understanding of the underlying molecular mechanisms driving its progression. Recently, lncRNAs have become necessary controllers of various biological functions, including cancer development. MALAT1 has garnered significant attention due to its multifaceted role in lung cancer progression. Lung cancer, among other malignancies, upregulates MALAT1. Its overexpression has been associated with aggressive tumor behavior and poor patient prognosis. MALAT1 promotes cellular proliferation, epithelial-mesenchymal transition (EMT), and angiogenesis in lung cancer, collectively facilitating tumor growth and metastasis. Additionally, MALAT1 enhances cancer cell invasion by interacting with numerous signaling pathways. Furthermore, MALAT1 has been implicated in mediating drug resistance in lung cancer, contributing to the limited efficacy of conventional therapies. Recent advancements in molecular biology and high-throughput sequencing technologies have offered fresh perspectives into the regulatory networks of MALAT1 in lung cancer. It exerts its oncogenic effects by acting as a ceRNA to sponge microRNAs, thereby relieving their inhibitory effects on target genes. Moreover, MALAT1 also influences chromatin remodeling and post-translational modifications to modulate gene expression, further expanding its regulatory capabilities. This review sheds light on the multifaceted roles of MALAT1 in lung cancer progression, underscoring its potential as an innovative therapeutic target and diagnostic biomarker. Targeting MALAT1 alone or combined with existing therapies holds promise to mitigate lung cancer progression and improve patient outcomes.
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Affiliation(s)
- Asif Ahmad Bhat
- School of Pharmacy, Suresh Gyan Vihar University, Mahal Road, Jagatpura, Jaipur 302017, India
| | - Obaid Afzal
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al Kharj 11942, Saudi Arabia
| | - Muhammad Afzal
- Department of Pharmaceutical Sciences, Pharmacy Program, Batterjee Medical College, P.O. Box 6231, Jeddah 21442, Saudi Arabia
| | - Gaurav Gupta
- Centre for Global Health Research, Saveetha Medical College, Saveetha Institute of Medical and Technical Sciences, Saveetha University, India; School of Pharmacy, Graphic Era Hill University, Dehradun 248007, India
| | - Riya Thapa
- School of Pharmacy, Suresh Gyan Vihar University, Mahal Road, Jagatpura, Jaipur 302017, India
| | - Haider Ali
- Department of Pharmacology, Kyrgyz State Medical College, Bishkek, Kyrgyzstan
| | - Waleed Hassan Almalki
- Department of Pharmacology, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Imran Kazmi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.
| | - Sami I Alzarea
- Department of Pharmacology, College of Pharmacy, Jouf University, Sakaka, Al-Jouf, Saudi Arabia
| | - Shakir Saleem
- Department of Public Health. College of Health Sciences, Saudi Electronic University, Riyadh, Saudi Arabia
| | - Vijaya Paul Samuel
- Department of Anatomy, RAK College of Medicine, RAK Medical and Health Sciences University, Ras Al Khaimah, UAE
| | | | - Vetriselvan Subramaniyan
- Pharmacology Unit, Jeffrey Cheah School of Medicine and Health Sciences, Monash University, Jalan Lagoon Selatan, Bandar Sunway, Selangor Darul Ehsan 47500, Malaysia
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Ji YL, Kang K, Lv QL, Wang DP. Roles of lncRNA-MALAT1 in the Progression and Prognosis of Gliomas. Mini Rev Med Chem 2024; 24:786-792. [PMID: 37859309 DOI: 10.2174/0113895575253875230922055711] [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: 03/30/2023] [Revised: 08/10/2023] [Accepted: 08/10/2023] [Indexed: 10/21/2023]
Abstract
Long noncoding RNAs (lncRNAs) represent a large subgroup of RNA transcripts that lack the function of coding proteins and may be essential universal genes involved in carcinogenesis and metastasis. LncRNA metastasis-associated lung adenocarcinoma transcript 1 (lncRNAMALAT1) is overexpressed in various human tumors, including gliomas. However, the biological function and molecular mechanism of action of lncRNA-MALAT1 in gliomas have not yet been systematically elucidated. Accumulating evidence suggests that the abnormal expression of lncRNA-MALAT1 in gliomas is associated with various physical properties of the glioma, such as tumor growth, metastasis, apoptosis, drug resistance, and prognosis. Furthermore, lncRNAs, as tumor progression and prognostic markers in gliomas, may affect tumorigenesis, proliferation of glioma stem cells, and drug resistance. In this review, we summarize the knowledge on the biological functions and prognostic value of lncRNA-MALAT1 in gliomas. This mini-review aims to deepen the understanding of lncRNA-MALAT1 as a novel potential therapeutic target for the individualized precision treatment of gliomas.
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Affiliation(s)
- Yu-Long Ji
- Department of Radiation Oncology, Jiangxi Key Laboratory of Translational Cancer Research, Jiangxi Cancer Hospital, Jiangxi Province, China
| | - Kai Kang
- School of Public Health, Fudan University, Shanghai, 200032, China
- Department of Research and Surveillance Evaluation, Shanghai Municipal Center for Health Promotion, Shanghai, 200040, China
| | - Qiao-Li Lv
- Department of Radiation Oncology, Jiangxi Key Laboratory of Translational Cancer Research, Jiangxi Cancer Hospital, Jiangxi Province, China
| | - Da-Peng Wang
- Department of Neurosurgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Moradi MT, Fadaei R, Sharafkhaneh A, Khazaie H, Gozal D. The role of lncRNAs in intermittent hypoxia and sleep Apnea: A review of experimental and clinical evidence. Sleep Med 2024; 113:188-197. [PMID: 38043330 DOI: 10.1016/j.sleep.2023.11.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 11/05/2023] [Accepted: 11/07/2023] [Indexed: 12/05/2023]
Abstract
In this narrative review, we present a comprehensive assessment on the putative roles of long non-coding RNAs (lncRNAs) in intermittent hypoxia (IH) and sleep apnea. Collectively, the evidence from cell culture, animal, and clinical research studies points to the functional involvement of lncRNAs in the pathogenesis, diagnosis, and potential treatment strategies for this highly prevalent disorder. Further research is clearly warranted to uncover the mechanistic pathways and to exploit the therapeutic potential of lncRNAs, thereby improving the management and outcomes of patients suffering from sleep apnea.
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Affiliation(s)
- Mohammad-Taher Moradi
- Sleep Disorders Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Reza Fadaei
- Sleep Disorders Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran; Department of Pharmacology, Vanderbilt University, Nashville, TN, USA
| | - Amir Sharafkhaneh
- Sleep Disorders and Research Center, Baylor College of Medicine, Houston, TX, USA
| | - Habibolah Khazaie
- Sleep Disorders Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran.
| | - David Gozal
- Joan C. Edwards School of Medicine, Marshall University, 1600 Medical Center Dr, Huntington, WV, 25701, USA.
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Li S, Qiu N, Ni A, Hamblin MH, Yin KJ. Role of regulatory non-coding RNAs in traumatic brain injury. Neurochem Int 2024; 172:105643. [PMID: 38007071 PMCID: PMC10872636 DOI: 10.1016/j.neuint.2023.105643] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 11/19/2023] [Indexed: 11/27/2023]
Abstract
Traumatic brain injury (TBI) is a potentially fatal health event that cannot be predicted in advance. After TBI occurs, it can have enduring consequences within both familial and social spheres. Yet, despite extensive efforts to improve medical interventions and tailor healthcare services, TBI still remains a major contributor to global disability and mortality rates. The prompt and accurate diagnosis of TBI in clinical contexts, coupled with the implementation of effective therapeutic strategies, remains an arduous challenge. However, a deeper understanding of changes in gene expression and the underlying molecular regulatory processes may alleviate this pressing issue. In recent years, the study of regulatory non-coding RNAs (ncRNAs), a diverse class of RNA molecules with regulatory functions, has been a potential game changer in TBI research. Notably, the identification of microRNAs (miRNAs), long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), and other ncRNAs has revealed their potential as novel diagnostic biomarkers and therapeutic targets for TBI, owing to their ability to regulate the expression of numerous genes. In this review, we seek to provide a comprehensive overview of the functions of regulatory ncRNAs in TBI. We also summarize regulatory ncRNAs used for treatment in animal models, as well as miRNAs, lncRNAs, and circRNAs that served as biomarkers for TBI diagnosis and prognosis. Finally, we discuss future challenges and prospects in diagnosing and treating TBI patients in the clinical settings.
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Affiliation(s)
- Shun Li
- Department of Neurology, School of Medicine, University of Pittsburgh, S514 BST, 200 Lothrop Street, Pittsburgh, PA, 15213, USA; Geriatric Research, Education and Clinical Center, Veterans Affairs Pittsburgh Healthcare System, Pittsburgh, PA, 15261, USA
| | - Na Qiu
- Department of Neurology, School of Medicine, University of Pittsburgh, S514 BST, 200 Lothrop Street, Pittsburgh, PA, 15213, USA; Geriatric Research, Education and Clinical Center, Veterans Affairs Pittsburgh Healthcare System, Pittsburgh, PA, 15261, USA
| | - Andrew Ni
- Warren Alpert Medical School, Brown University, 222 Richmond Street, Providence, RI, 02903, USA
| | - Milton H Hamblin
- Division of Biomedical Sciences, School of Medicine, University of California Riverside, 1212 Webber Hall, 900 University Avenue, Riverside, CA, 92521, USA
| | - Ke-Jie Yin
- Department of Neurology, School of Medicine, University of Pittsburgh, S514 BST, 200 Lothrop Street, Pittsburgh, PA, 15213, USA; Geriatric Research, Education and Clinical Center, Veterans Affairs Pittsburgh Healthcare System, Pittsburgh, PA, 15261, USA.
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Bhat AA, Afzal O, Agrawal N, Thapa R, Almalki WH, Kazmi I, Alzarea SI, Altamimi ASA, Kukreti N, Chakraborty A, Singh SK, Dua K, Gupta G. A comprehensive review on the emerging role of long non-coding RNAs in the regulation of NF-κB signaling in inflammatory lung diseases. Int J Biol Macromol 2023; 253:126951. [PMID: 37734525 DOI: 10.1016/j.ijbiomac.2023.126951] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/30/2023] [Accepted: 09/09/2023] [Indexed: 09/23/2023]
Abstract
Public health globally faces significant risks from conditions like acute respiratory distress syndrome (ARDS), chronic obstructive pulmonary disease (COPD), and various inflammatory lung disorders. The NF-κB signaling system partially controls lung inflammation, immunological responses, and remodeling. Non-coding RNAs (lncRNAs) are crucial in regulating gene expression. They are increasingly recognized for their involvement in NF-κB signaling and the development of inflammatory lung diseases. Disruption of lncRNA-NF-κB interactions is a potential cause and resolution factor for inflammatory respiratory conditions. This study explores the therapeutic potential of targeting lncRNAs and NF-κB signaling to alleviate inflammation and restore lung function. Understanding the intricate relationship between lncRNAs and NF-κB signaling could offer novel insights into disease mechanisms and identify therapeutic targets. Regulation of lncRNAs and NF-κB signaling holds promise as an effective approach for managing inflammatory lung disorders. This review aims to comprehensively analyze the interaction between lncRNAs and the NF-κB signaling pathway in the context of inflammatory lung diseases. It investigates the functional roles of lncRNAs in modulating NF-κB activity and the resulting inflammatory responses in lung cells, focusing on molecular mechanisms involving upstream regulators, inhibitory proteins, and downstream effectors.
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Affiliation(s)
- Asif Ahmad Bhat
- School of Pharmacy, Suresh Gyan Vihar University, Jagatpura 302017, Mahal Road, Jaipur, India
| | - Obaid Afzal
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al Kharj 11942, Saudi Arabia
| | - Neetu Agrawal
- Institute of Pharmaceutical Research, GLA University, Mathura, UP, India
| | - Riya Thapa
- School of Pharmacy, Suresh Gyan Vihar University, Jagatpura 302017, Mahal Road, Jaipur, India
| | - Waleed Hassan Almalki
- Department of Pharmacology, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Imran Kazmi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.
| | - Sami I Alzarea
- Department of Pharmacology, College of Pharmacy, Jouf University, Sakaka, Al-Jouf, Saudi Arabia
| | | | - Neelima Kukreti
- School of Pharmacy, Graphic Era Hill University, Dehradun 248007, India
| | - Amlan Chakraborty
- Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, Manchester M13 9PL, UK; Cardiovascular Disease Program, Biomedicine Discovery Institute and Department of Pharmacology, Monash University, Clayton, VIC 3800, Australia
| | - Sachin Kumar Singh
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab, 144411, India; Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney, Ultimo 2007, Australia
| | - Kamal Dua
- Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney, Ultimo 2007, Australia; Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, NSW 2007, Australia.
| | - Gaurav Gupta
- Center for Global Health research (CGHR), Saveetha Institute of Medical and Technical Science, Saveetha University, Chennai, India
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Anbiyaee O, Moalemnia A, Ghaedrahmati F, Shooshtari MK, Khoshnam SE, Kempisty B, Halili SA, Farzaneh M, Morenikeji OB. The functions of long non-coding RNA (lncRNA)-MALAT-1 in the pathogenesis of renal cell carcinoma. BMC Nephrol 2023; 24:380. [PMID: 38124072 PMCID: PMC10731893 DOI: 10.1186/s12882-023-03438-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 12/12/2023] [Indexed: 12/23/2023] Open
Abstract
Renal cell carcinoma (RCC), a prevalent form of renal malignancy, is distinguished by its proclivity for robust tumor proliferation and metastatic dissemination. Long non-coding RNAs (lncRNAs) have emerged as pivotal modulators of gene expression, exerting substantial influence over diverse biological processes, encompassing the intricate landscape of cancer development. Metastasis-associated lung adenocarcinoma transcript 1 (MALAT-1), an exemplar among lncRNAs, has been discovered to assume functional responsibilities within the context of RCC. The conspicuous expression of MALAT-1 in RCC cells has been closely linked to the advancement of tumors and an unfavorable prognosis. Experimental evidence has demonstrated the pronounced ability of MALAT-1 to stimulate RCC cell proliferation, migration, and invasion, thereby underscoring its active participation in facilitating the metastatic cascade. Furthermore, MALAT-1 has been implicated in orchestrating angiogenesis, an indispensable process for tumor expansion and metastatic dissemination, through its regulatory influence on pro-angiogenic factor expression. MALAT-1 has also been linked to the evasion of immune surveillance in RCC, as it can regulate the expression of immune checkpoint molecules and modulate the tumor microenvironment. Hence, the potential utility of MALAT-1 as a diagnostic and prognostic biomarker in RCC emerges, warranting further investigation and validation of its clinical significance. This comprehensive review provides an overview of the diverse functional roles exhibited by MALAT-1 in RCC.
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Affiliation(s)
- Omid Anbiyaee
- Cardiovascular Research Center, School of Medicine, Namazi Hospital, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Arash Moalemnia
- Faculty of Medicine, Dezful University of Medical Sciences, Dezful, Iran
| | - Farhoodeh Ghaedrahmati
- Department of Immunology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Maryam Khombi Shooshtari
- Chronic Renal Failure Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Seyed Esmaeil Khoshnam
- Persian Gulf Physiology Research Center, Medical Basic Sciences Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Bartosz Kempisty
- Department of Human Morphology and Embryology Division of Anatomy, Wrocław Medical University, Wrocław, Poland
- Department of Veterinary Surgery, Institute of Veterinary Medicine, Nicolaus Copernicus University, Torun, Poland
- Physiology Graduate Faculty North, Carolina State University, Raleigh, NC, 27695, US
- Center of Assisted Reproduction Department of Obstetrics and Gynecology, University Hospital and Masaryk University, Brno, Czech Republic
| | - Shahla Ahmadi Halili
- Department of Internal Medicine, School of Science, Chronic Renal Failure Research Center, Ahvaz Jundishapur University of Medical Science, Ahvaz, Iran
| | - Maryam Farzaneh
- Fertility, Infertility and Perinatology Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
| | - Olanrewaju B Morenikeji
- Division of Biological and Health Sciences, University of Pittsburgh at Bradford, Bradford, PA, USA.
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Ao YQ, Gao J, Jiang JH, Wang HK, Wang S, Ding JY. Comprehensive landscape and future perspective of long noncoding RNAs in non-small cell lung cancer: it takes a village. Mol Ther 2023; 31:3389-3413. [PMID: 37740493 PMCID: PMC10727995 DOI: 10.1016/j.ymthe.2023.09.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 09/01/2023] [Accepted: 09/17/2023] [Indexed: 09/24/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are a distinct subtype of RNA that lack protein-coding capacity but exert significant influence on various cellular processes. In non-small cell lung cancer (NSCLC), dysregulated lncRNAs act as either oncogenes or tumor suppressors, contributing to tumorigenesis and tumor progression. LncRNAs directly modulate gene expression, act as competitive endogenous RNAs by interacting with microRNAs or proteins, and associate with RNA binding proteins. Moreover, lncRNAs can reshape the tumor immune microenvironment and influence cellular metabolism, cancer cell stemness, and angiogenesis by engaging various signaling pathways. Notably, lncRNAs have shown great potential as diagnostic or prognostic biomarkers in liquid biopsies and therapeutic strategies for NSCLC. This comprehensive review elucidates the significant roles and diverse mechanisms of lncRNAs in NSCLC. Furthermore, we provide insights into the clinical relevance, current research progress, limitations, innovative research approaches, and future perspectives for targeting lncRNAs in NSCLC. By summarizing the existing knowledge and advancements, we aim to enhance the understanding of the pivotal roles played by lncRNAs in NSCLC and stimulate further research in this field. Ultimately, unraveling the complex network of lncRNA-mediated regulatory mechanisms in NSCLC could potentially lead to the development of novel diagnostic tools and therapeutic strategies.
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Affiliation(s)
- Yong-Qiang Ao
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China; Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jian Gao
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China; Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jia-Hao Jiang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China; Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Hai-Kun Wang
- CAS Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Shuai Wang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China; Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China.
| | - Jian-Yong Ding
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China; Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China.
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El-Sayed EH, Fathy A, Al-Deen Younes SE, Al-Shahaly MH, Omar HH. Long Non-coding RNA Genes Polymorphisms H19 (rs2251375) and MALAT1 (rs3200401) Association with Rheumatoid Arthritis and Their Correlation with Disease Activity in a Cohort of Egyptian Patients: A Pilot Study. Biochem Genet 2023; 61:2443-2456. [PMID: 37103602 DOI: 10.1007/s10528-023-10383-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 04/12/2023] [Indexed: 04/28/2023]
Abstract
Rheumatoid arthritis (RA) is a chronic, progressive, inflammatory, autoimmune disease that could be disabling throughout its course. It affects people in their most reproductive years with relatively high morbidity and mortality. Long non-coding RNAs became one of the epigenetic mechanisms to prove a link to RA pathogenesis and development, including H19 and MALAT1 genes. These two genes' expressions had proved to increase in multiple diseases, attracting attention to their polymorphisms and their possible risk role. Assess the association between H19 SNP (rs2251375) and MALAT1 SNP (rs3200401) and the susceptibility of RA and its disease activity. In this pilot study, 200 hundred subjects (100 RA patients and 100 healthy controls) were investigated for a possible link between the polymorphisms H19 SNP (rs2251375) and MALAT1 SNP (3200401) and RA susceptibility and disease activity. RA-related investigations and clinical assessment were done. Real-time PCR genotyping of both SNPs was done using TaqMan® MGB probes. There was no association between the SNPs and risk of developing RA. However, both SNPs had a significant association with high disease activity. H19 SNP (rs2251375) heterozygous genotype CA had an association with elevated levels of ESR (p = 0.04) and higher DAS28-ESR score (p = 0.03). MALAT1 (rs3200401) C allele had an association with elevated ESR (p = 0.001), DAS28-ESR (p = 0.03), and DAS28-CRP (p = 0.007), while CC genotype had an association with DAS28-CRP (p = 0.015). Linkage disequilibrium and haplotyping of the alleles of both SNPs were analyzed as both genes are present on chromosome 11, but no significant association was found between any of the combinations of the alleles (p > 0.05), denoting that (rs2251375) and (rs3200401) are not in linkage disequilibrium. There is no association between H19 SNP (rs2251375) and MALAT1 SNP (rs3200401) and the susceptibility of RA. However, there is an association between H19 SNP (rs2251375) genotype CA and MALAT1 SNP (rs3200401) genotype CC with RA high disease activity.
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Affiliation(s)
- Eman Hassan El-Sayed
- Clinical Pathology Department, Faculty of Medicine, Suez Canal University, 4.5 km Ring Road, P.O: 41111, Ismailia, Egypt
| | - Amal Fathy
- Clinical Pathology Department, Faculty of Medicine, Suez Canal University, 4.5 km Ring Road, P.O: 41111, Ismailia, Egypt
| | - Soha Ezz Al-Deen Younes
- Clinical Pathology Department, Faculty of Medicine, Suez Canal University, 4.5 km Ring Road, P.O: 41111, Ismailia, Egypt
| | - Mohsen Hassan Al-Shahaly
- Rheumatology, Physical Medicine and Rehabilitation Department, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
| | - Hanan Hassan Omar
- Clinical Pathology Department, Faculty of Medicine, Suez Canal University, 4.5 km Ring Road, P.O: 41111, Ismailia, Egypt.
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