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Montano C, Flores-Arenas C, Carpenter S. LncRNAs, nuclear architecture and the immune response. Nucleus 2024; 15:2350182. [PMID: 38738760 PMCID: PMC11093052 DOI: 10.1080/19491034.2024.2350182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 04/22/2024] [Indexed: 05/14/2024] Open
Abstract
Long noncoding RNAs (LncRNAs) are key regulators of gene expression and can mediate their effects in both the nucleus and cytoplasm. Some of the best-characterized lncRNAs are localized within the nucleus, where they modulate the nuclear architecture and influence gene expression. In this review, we discuss the role of lncRNAs in nuclear architecture in the context of their gene regulatory functions in innate immunity. Here, we discuss various approaches to functionally characterize nuclear-localized lncRNAs and the challenges faced in the field.
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Affiliation(s)
- Christy Montano
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
| | - Cristina Flores-Arenas
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
| | - Susan Carpenter
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
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2
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Tayefeh-Gholami S, Akbarzadeh S, Rajabi A, Najari P, Ghasemzadeh T, HosseinpourFeizi M, Safaralizadeh R. Investigating SNHG3 and BCYRN1 lncRnas expression in the peripheral blood cells of multiple sclerosis patients. Neurol Res 2024; 46:876-882. [PMID: 38832630 DOI: 10.1080/01616412.2024.2362585] [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: 02/07/2024] [Accepted: 05/27/2024] [Indexed: 06/05/2024]
Abstract
BACKGROUND MS (Multiple sclerosis) is a progressive neurologic disorder often appearing in the third decade of life. MS is the most frequent demyelinating disease of the central nervous system. The development of MS is influenced by environmental, genetic, and epigenetic factors. The bulk of the human transcriptome comprises lncRNAs, which play crucial regulatory roles. We aimed to assess the SNHG3 and BCYRN1 lncRNA expression in blood samples from MS patients and how these lncRNAs and disease activity are related. METHODS A total of 100 MS patients, including 8 primary progressive (PP), 82 relapsing-remitting (RR), and 10 secondary progressive (SP) MS, as well as 100 healthy controls, had their blood samples taken. Gene expression was assessed using quantitative real-time PCR. Recognizing the receiver operating characteristic (ROC) curve analysis, the diagnostic potential of lncRNA levels was evaluated. RESULTS Expressions of SNHG3 and BCYRN1 were found to have significantly increased (p < 0.0001). SNHG3 expression level showed significant differences compared to age groups and MS subtypes (p value = 0.001 and p value = 0.02).Furthermore, patients with a family history showed elevated BCYRN1 expression with a p value of 0.01. Considering the age factor, BCYRN1 exhibits altered expression levels in patient groups compared to healthy controls (p value 0.04). Additionally, the novel biomarkers SNHG3 and BCYRN1 can be used to diagnose MS (AUC = 0.97 and AUC = 0.88, respectively). DISCUSSION Increased levels of SNHG3 and BCYRN1 in the serum may serve as potential molecular biomarkers for the MS diagnosis.
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Affiliation(s)
- Samaneh Tayefeh-Gholami
- Department of Animal Biology, Faculty of Natural Science, University of Tabriz, Tabriz, Iran
| | - Sama Akbarzadeh
- Department of Biophysics, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Türkiye
- Institute of Graduate Studies in Health Sciences, Istanbul University, Istanbul, Türkiye
| | - Ali Rajabi
- Department of Animal Biology, Faculty of Natural Science, University of Tabriz, Tabriz, Iran
| | - Parisa Najari
- Department of Animal Biology, Faculty of Natural Science, University of Tabriz, Tabriz, Iran
| | - Tooraj Ghasemzadeh
- Department of Animal Biology, Faculty of Natural Science, University of Tabriz, Tabriz, Iran
| | | | - Reza Safaralizadeh
- Department of Animal Biology, Faculty of Natural Science, University of Tabriz, Tabriz, Iran
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3
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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] [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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Li S, Cui H, Lu H, Zheng S, Yuan C. Advances in noncoding RNA in children allergic rhinitis. Int Forum Allergy Rhinol 2024; 14:1350-1362. [PMID: 38946149 DOI: 10.1002/alr.23393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 06/02/2024] [Accepted: 06/08/2024] [Indexed: 07/02/2024]
Abstract
BACKGROUND A chronic condition that significantly reduces a child's quality of life is allergic rhinitis (AR). The environment and allergens that the body is regularly exposed to can cause inflammatory and immunological reactions, which can change the expression of certain genes Epigenetic changes are closely linked to the onset and severity of allergy disorders according to mounting amounts of data. Noncoding RNAs (ncRNAs) are a group of RNA molecules that cannot be converted into polypeptides. The three main categories of ncRNAs include microRNAs (miRNAs), long noncoding RNAs (lncRNAs), and circular RNAs (circRNAs). NcRNAs play a crucial role in controlling gene expression and contribute to the development of numerous human diseases. METHODS Articles are selected based on Pubmed's literature review and the author's personal knowledge. The largest and highest quality studies were included. The search selection is not standardized. RESULTS Recent findings indicate that various categories of ncRNAs play distinct yet interconnected roles and actively contribute to intricate gene regulatory networks. CONCLUSION This article demonstrates the significance and progress of ncRNAs in children's AR. The database covers three key areas: miRNAs, lncRNAs, and circRNAs. Additionally, potential avenues for future research to facilitate the practical application of ncRNAs as therapeutic targets and biomarkers will be explore.
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Affiliation(s)
- Shuman Li
- Chongqing Medical University, Chongqing, China
| | - Hongtao Cui
- Department of Pediatrics, Chongqing Hospital of Traditional Chinese Medicine, Chongqing, China
| | - Huina Lu
- Department of Pediatrics, Chongqing Hospital of Traditional Chinese Medicine, Chongqing, China
| | - Shan Zheng
- Department of Pediatrics, Chongqing Hospital of Traditional Chinese Medicine, Chongqing, China
| | - Chao Yuan
- Department of Pediatrics, Chongqing Hospital of Traditional Chinese Medicine, Chongqing, China
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Cao J, Yang Y, Duan B, Zhang H, Xu Q, Han J, Lu B. LncRNA PCED1B-AS1 mediates miR-3681-3p/MAP2K7 axis to promote metastasis, invasion and EMT in gastric cancer. Biol Direct 2024; 19:34. [PMID: 38698487 PMCID: PMC11064384 DOI: 10.1186/s13062-024-00468-z] [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: 11/28/2023] [Accepted: 03/19/2024] [Indexed: 05/05/2024] Open
Abstract
BACKGROUND LncRNA PCED1B-AS1 is abnormally expressed in multiple cancers and has been confirmed as an oncogene. Our study aimed to investigate the regulatory mechanism of lncRNA PCED1B-AS1 in gastric cancer. METHODS TCGA database was used to analyze the abnormal expression of lncRNA PCED1B-AS1 in gastric cancer. By database prediction and mass spectrometric analysis, miR-3681-3p and MAP2K7 are potential downstream target molecules of lncRNA PCED1B-AS1 and verified by dual-luciferase report assay. RT-qPCR analysis and western blot were performed to detect the expressions of PCED1B-AS1 and MAP2K7 in gastric cancer cell lines and tissues. CCK-8 kit was applied to measure the cell viability. Wound healing and Transwell experiment were used to detect the migration and invasion. Western blot and immunohistochemical staining were performed to detect the expressions of EMT-related proteins in tissues. The changes of tumor proliferation were detected by xenograft experiment in nude mice. RESULTS PCED1B-AS1 expression was higher but miR-3681-3 expression was lower in gastric cancer cell lines or tissues, compared to normal group. Function analysis verified PCED1B-AS1 promoted cell proliferation and inhibited cell apoptosis in gastric cancer cells in vitro and in vivo. LncRNA PCED1B-AS1 could bind directly to miR-3681-3p, and MAP2K7 was found to be a downstream target of miR-3681-3p. MiR-3681-3p mimics or si-MAP2K7 could partly reverse the effect of PCED1B-AS1 on gastric cancer cells. CONCLUSION PCED1B-AS1 accelerated cell proliferation and inhibited cell apoptosis through sponging miR-3681-3p to upregulate MAP2K7 expression in gastric cancer, which indicated PCED1B-AS1/miR-3681-3p/MAP2K7 axis may serve as a potential therapeutic target for gastric cancer.
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Affiliation(s)
- Jia Cao
- Endoscopy Center, Department of Gastroenterology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yicheng Yang
- Endoscopy Center, Department of Gastroenterology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Bensong Duan
- Endoscopy Center, Department of Gastroenterology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Haibin Zhang
- Endoscopy Center, Department of Gastroenterology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Qinwei Xu
- Endoscopy Center, Department of Gastroenterology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Junyi Han
- Department of Gastrointestinal Surgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China.
| | - Bing Lu
- Department of General Surgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200120, China.
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Yang B, Wang Y, Liu T, Zhang M, Luo T. The necroptosis-related signature and tumor microenvironment immune characteristics associated with clinical prognosis and drug sensitivity analysis in stomach adenocarcinoma. Aging (Albany NY) 2024; 16:6098-6117. [PMID: 38546403 PMCID: PMC11042952 DOI: 10.18632/aging.205690] [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: 08/15/2023] [Accepted: 01/30/2024] [Indexed: 04/23/2024]
Abstract
PURPOSE Necroptosis plays an important role in the tumorigenesis, development, metastasis, and drug resistance of malignant tumors. This study explored the new model for assessing stomach adenocarcinoma (STAD) prognosis and immunotherapy by combining long noncoding RNAs associated with necroptosis. METHODS Patient clinical data and STAD gene expression profiles were curated from The Cancer Genome Atlas (TCGA). Immune-related genes were sourced from a specialized molecular database. Perl software and R software were used for data processing and analysis. Necroptosis-related lncRNAs in STAD were pinpointed via R's correlation algorithms. These lncRNAs, in conjunction with clinical data, informed the construction of a prognostic lncRNA-associated risk score model using univariate and multivariate Cox regression analyses. The model's prognostic capacity was evaluated by Kaplan-Meier survival curves and validated as an independent prognostic variable. Further, a nomogram incorporating this model with clinical parameters was developed, offering refined individual survival predictions. Subsequent analyses of immune infiltration and chemosensitivity within necroptosis-related lncRNA clusters utilized an arsenal of bioinformatic tools, culminating in RT-PCR validation of lncRNA expression. RESULTS Through rigorous Cox regression, 21 lncRNAs were implicated in the risk score model. Stratification by median risk scores delineated patients into high- and low-risk cohorts, with the latter demonstrating superior prognostic outcomes. The risk model was corroborated as an independent prognostic indicator for STAD. The integrative nomogram displayed high concordance between predicted and observed survival rates, as evidenced by calibration curves. Differential immune infiltration in risk-defined groups was illuminated by the single sample GSEA (ssGSEA), indicating pronounced immune presence in higher-risk patients. Tumor microenvironment (TME) analysis showed that cluster-C3 had the highest score in the analysis of the three TMEs. Through the differential analysis of immune checkpoints, it was found that almost all immune checkpoint-related genes were expressed differently in various tumor clusters. Among them, CD44 expression was the highest. By comparing all drug sensitivities, we screened out 29 drugs with differences in drug sensitivity across different clusters. Risk score gene expression identification results showed that these lncRNAs were abnormally expressed in gastric cancer cell lines. CONCLUSIONS This investigation provides a robust methodological advance in prognosticating and personalizing immunotherapy for STAD, leveraging quantitatively derived tumor cluster risk scores. It posits the use of necroptosis-related lncRNAs as pivotal molecular beacons for guiding therapeutic strategies and enhancing clinical outcomes in STAD.
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Affiliation(s)
- Biao Yang
- Department of General Surgery, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Yingnan Wang
- Henan University of Science and Technology, Henan 471000, China
| | - Tao Liu
- Department of Emergency, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Meijing Zhang
- Department of Oncology, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Tianhang Luo
- Department of General Surgery, Changhai Hospital, Naval Medical University, Shanghai 200433, China
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Wang D, Zhao X, Li S, Guo H, Li S, Yu D. The impact of LncRNA-SOX2-OT/let-7c-3p/SKP2 Axis on head and neck squamous cell carcinoma progression: Insights from bioinformatics analysis and experimental validation. Cell Signal 2024; 115:111018. [PMID: 38110167 DOI: 10.1016/j.cellsig.2023.111018] [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: 09/27/2023] [Revised: 12/01/2023] [Accepted: 12/15/2023] [Indexed: 12/20/2023]
Abstract
BACKGROUND LncRNA SRY-box transcription factor 2 overlapping transcript (SOX2-OT) is linked to multiple cancers, but its specific role and mechanism in head and neck squamous cell carcinoma (HNSCC) remain poorly understood. METHODS We harnessed clinical data and HNSCC transcriptome profiles from UCSC Xena, TCGA, and GEO databases. Employing various algorithms, we assessed the correlation between SOX2-OT expression and the HNSCC immune microenvironment. Differential expression analysis identified immune-enriched miRNAs (DEmiRNAs) and mRNAs (DEmRNAs). Utilizing miRanda, miRWalk, and Cytoscape, we constructed a ceRNA network encompassing SOX2-OT, DEmiRNAs, and DEmRNAs. A Sankey diagram visualized pivotal SOX2-OT-miRNA-mRNA-pathways. Functional assays validated SOX2-OT silencing effects in HNSCC cells. Luciferase reporter assays verified SOX2-OT/let-7c-3p/SKP2 relationships. Additionally, a xenograft mouse model revealed SOX2-OT's impact on xenograft growth and lung metastasis. RESULTS SOX2-OT expression demonstrated a predominantly positive correlation with B lineage and VTCN1, while manifesting a negative correlation with Neutrophil and CD47 in HNSCC tissues. We discerned a ceRNA network comprising 65 DEmiRNAs and 116 DEmRNAs, while a protein-protein interaction (PPI) network revealed 97 protein nodes among DEmRNAs. Notably, the Sankey diagram spotlighted six key DEmRNAs intricately linked to the SOX2-OT-regulated DEmiRNAs immune-related pathway. Experimental assays established that SOX2-OT silencing exerted inhibitory effects on cell proliferation, migration, tumor growth, and lung metastasis within HNSCC cells, both in vitro and in vivo. We identified let-7c-3p as a target miRNA of SOX2-OT and SKP2 as a target mRNA of let-7c-3p. CONCLUSIONS Our study establishes the critical SOX2-OT/let-7c-3p/SKP2 axis as a pivotal regulator of HNSCC tumorigenesis and metastasis.
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Affiliation(s)
- Di Wang
- Department of Otolaryngology Head and Neck Surgery, The Second Hospital of Jilin University, People's Republic of China
| | - Xue Zhao
- Department of Otolaryngology Head and Neck Surgery, The Second Hospital of Jilin University, People's Republic of China
| | - Shuang Li
- Department of Otolaryngology Head and Neck Surgery, The Second Hospital of Jilin University, People's Republic of China
| | - Haixian Guo
- Department of Otolaryngology Head and Neck Surgery, The Second Hospital of Jilin University, People's Republic of China
| | - Shaonan Li
- Department of Otolaryngology Head and Neck Surgery, The Second Hospital of Jilin University, People's Republic of China
| | - Dan Yu
- Department of Otolaryngology Head and Neck Surgery, The Second Hospital of Jilin University, People's Republic of China.
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Davodabadi F, Mirinejad S, Malik S, Dhasmana A, Ulucan-Karnak F, Sargazi S, Sargazi S, Fathi-Karkan S, Rahdar A. Nanotherapeutic approaches for delivery of long non-coding RNAs: an updated review with emphasis on cancer. NANOSCALE 2024; 16:3881-3914. [PMID: 38353296 DOI: 10.1039/d3nr05656b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
The long noncoding RNAs (lncRNAs) comprise a wide range of RNA species whose length exceeds 200 nucleotides, which regulate the expression of genes and cellular functions in a wide range of organisms. Several diseases, including malignancy, have been associated with lncRNA dysregulation. Due to their functions in cancer development and progression, lncRNAs have emerged as promising biomarkers and therapeutic targets in cancer diagnosis and treatment. Several studies have investigated the anti-cancer properties of lncRNAs; however, only a few lncRNAs have been found to exhibit tumor suppressor properties. Furthermore, their length and poor stability make them difficult to synthesize. Thus, to overcome the instability of lncRNAs, poor specificity, and their off-target effects, researchers have constructed nanocarriers that encapsulate lncRNAs. Recently, translational medicine research has focused on delivering lncRNAs into tumor cells, including cancer cells, through nano-drug delivery systems in vivo. The developed nanocarriers can protect, target, and release lncRNAs under controlled conditions without appreciable adverse effects. To deliver lncRNAs to cancer cells, various nanocarriers, such as exosomes, microbubbles, polymer nanoparticles, 1,2-dioleyl-3-trimethylammoniumpropane chloride nanocarriers, and virus-like particles, have been successfully developed. Despite this, every nanocarrier has its own advantages and disadvantages when it comes to delivering nucleic acids effectively and safely. This article examines the current status of nanocarriers for lncRNA delivery in cancer therapy, focusing on their potential to enhance cancer treatment.
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Affiliation(s)
- Fatemeh Davodabadi
- Department of Biology, Faculty of Basic Science, Payame Noor University, Tehran, Iran.
| | - Shekoufeh Mirinejad
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran.
| | - Sumira Malik
- Amity Institute of Biotechnology, Amity University Jharkhand, Ranchi-834002, India.
| | - Archna Dhasmana
- Himalayan School of Biosciences, Swami Rama Himalayan University, Jolly Grant, Dehradun, Uttarakhand, 248140, India.
| | - Fulden Ulucan-Karnak
- Department of Medical Biochemistry, Institute of Health Sciences, Ege University, İzmir 35100, Turkey.
| | - Sara Sargazi
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran.
| | - Saman Sargazi
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran.
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Sonia Fathi-Karkan
- Natural Products and Medicinal Plants Research Center, North Khorasan University of Medical Sciences, Bojnurd, 94531-55166, Iran
- Department of Advanced Sciences and Technologies in Medicine, School of Medicine, North Khorasan University of Medical Sciences, Bojnurd 9414974877, Iran.
| | - Abbas Rahdar
- Department of Physics, University of Zabol, Zabol, P. O. Box. 98613-35856, Iran.
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Fitzgerald KA, Shmuel-Galia L. Lnc-ing RNA to intestinal homeostasis and inflammation. Trends Immunol 2024; 45:127-137. [PMID: 38220553 DOI: 10.1016/j.it.2023.12.005] [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: 11/28/2023] [Revised: 12/14/2023] [Accepted: 12/21/2023] [Indexed: 01/16/2024]
Abstract
Long noncoding RNAs (lncRNAs) play important roles in numerous biological processes, including the immune system. Initial research in this area focused on cell-based studies, but recent advances underscore the profound significance of lncRNAs at the organismal level, providing invaluable insights into their roles in inflammatory diseases. In this rapidly evolving field, lncRNAs have been described with pivotal roles in the intestinal tract where they regulate intestinal homeostasis and inflammation by influencing processes such as immune cell development, inflammatory signaling pathways, epithelial barrier function, and cellular metabolism. Understanding the regulation and function of lncRNAs in this tissue may position lncRNAs not only as potential disease biomarkers but also as promising targets for therapeutic intervention in inflammatory bowel disease and related diseases.
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Affiliation(s)
- Katherine A Fitzgerald
- Program in Innate Immunity, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA.
| | - Liraz Shmuel-Galia
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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Martinez-Castillo M, M. Elsayed A, López-Berestein G, Amero P, Rodríguez-Aguayo C. An Overview of the Immune Modulatory Properties of Long Non-Coding RNAs and Their Potential Use as Therapeutic Targets in Cancer. Noncoding RNA 2023; 9:70. [PMID: 37987366 PMCID: PMC10660772 DOI: 10.3390/ncrna9060070] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 10/25/2023] [Accepted: 11/08/2023] [Indexed: 11/22/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) play pivotal roles in regulating immune responses, immune cell differentiation, activation, and inflammatory processes. In cancer, they are gaining prominence as potential therapeutic targets due to their ability to regulate immune checkpoint molecules and immune-related factors, suggesting avenues for bolstering anti-tumor immune responses. Here, we explore the mechanistic insights into lncRNA-mediated immune modulation, highlighting their impact on immunity. Additionally, we discuss their potential to enhance cancer immunotherapy, augmenting the effectiveness of immune checkpoint inhibitors and adoptive T cell therapies. LncRNAs as therapeutic targets hold the promise of revolutionizing cancer treatments, inspiring further research in this field with substantial clinical implications.
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Affiliation(s)
- Moises Martinez-Castillo
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA; (M.M.-C.); (G.L.-B.); (P.A.)
- Liver, Pancreas and Motility Laboratory, Unit of Research in Experimental Medicine, School of Medicine, Universidad Nacional Autónoma de México (UNAM), Mexico City 06726, Mexico
| | - Abdelrahman M. Elsayed
- Department of Pharmacology & Toxicology, Faculty of Pharmacy, Al-Azhar University, Cairo 11754, Egypt;
- Havener Eye Institute, Department of Ophthalmology and Visual Science, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Gabriel López-Berestein
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA; (M.M.-C.); (G.L.-B.); (P.A.)
- Center for RNA Interference and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Paola Amero
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA; (M.M.-C.); (G.L.-B.); (P.A.)
| | - Cristian Rodríguez-Aguayo
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA; (M.M.-C.); (G.L.-B.); (P.A.)
- Center for RNA Interference and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
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11
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Ismail NH, Mussa A, Al-Khreisat MJ, Mohamed Yusoff S, Husin A, Al-Jamal HAN, Johan MF, Islam MA. Dysregulation of Non-Coding RNAs: Roles of miRNAs and lncRNAs in the Pathogenesis of Multiple Myeloma. Noncoding RNA 2023; 9:68. [PMID: 37987364 PMCID: PMC10660696 DOI: 10.3390/ncrna9060068] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/27/2023] [Accepted: 10/30/2023] [Indexed: 11/22/2023] Open
Abstract
The dysregulation of non-coding RNAs (ncRNAs), specifically microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), leads to the development and advancement of multiple myeloma (MM). miRNAs, in particular, are paramount in post-transcriptional gene regulation, promoting mRNA degradation and translational inhibition. As a result, miRNAs can serve as oncogenes or tumor suppressors depending on the target genes. In MM, miRNA disruption could result in abnormal gene expression responsible for cell growth, apoptosis, and other biological processes pertinent to cancer development. The dysregulated miRNAs inhibit the activity of tumor suppressor genes, contributing to disease progression. Nonetheless, several miRNAs are downregulated in MM and have been identified as gene regulators implicated in extracellular matrix remodeling and cell adhesion. miRNA depletion potentially facilitates the tumor advancement and resistance of therapeutic drugs. Additionally, lncRNAs are key regulators of numerous cellular processes, such as gene expression, chromatin remodeling, protein trafficking, and recently linked MM development. The lncRNAs are uniquely expressed and influence gene expression that supports MM growth, in addition to facilitating cellular proliferation and viability via multiple molecular pathways. miRNA and lncRNA alterations potentially result in anomalous gene expression and interfere with the regular functioning of MM. Thus, this review aims to highlight the dysregulation of these ncRNAs, which engender novel therapeutic modalities for the treatment of MM.
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Affiliation(s)
- Nor Hayati Ismail
- Department of Haematology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| | - Ali Mussa
- Department of Haematology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
- Department of Biology, Faculty of Education, Omdurman Islamic University, Omdurman 11111, Sudan
- Center for Global Health Research, Saveetha Medical College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai 600077, Tamil Nadu, India
| | - Mutaz Jamal Al-Khreisat
- Department of Haematology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| | - Shafini Mohamed Yusoff
- Department of Haematology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| | - Azlan Husin
- Department of Internal Medicine, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| | - Hamid Ali Nagi Al-Jamal
- School of Biomedicine, Faculty of Health Sciences, Universiti Sultan Zainal Abidin (UniSZA), Kuala Nerus 21300, Terengganu, Malaysia
| | - Muhammad Farid Johan
- Department of Haematology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| | - Md Asiful Islam
- WHO Collaborating Centre for Global Women’s Health, Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
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12
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Alluli A, Rijnbout St James W, Eidelman DH, Baglole CJ. Dynamic relationship between the aryl hydrocarbon receptor and long noncoding RNA balances cellular and toxicological responses. Biochem Pharmacol 2023; 216:115745. [PMID: 37597813 DOI: 10.1016/j.bcp.2023.115745] [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: 06/07/2023] [Revised: 08/10/2023] [Accepted: 08/11/2023] [Indexed: 08/21/2023]
Abstract
The aryl hydrocarbon receptor (AhR) is a cytosolic transcription factor activated by endogenous ligands and xenobiotic chemicals. Once the AhR is activated, it translocates to the nucleus, dimerizes with the AhR nuclear translator (ARNT) and binds to xenobiotic response elements (XRE) to promote gene transcription, notably the cytochrome P450 CYP1A1. The AhR not only mediates the toxic effects of environmental chemicals, but also has numerous putative physiological functions. This dichotomy in AhR biology may be related to reciprocal regulation of long non-coding RNA (lncRNA). lncRNA are defined as transcripts more than 200 nucleotides in length that do not encode a protein but are implicated in many physiological processes such as cell differentiation, cell proliferation, and apoptosis. lncRNA are also linked to disease pathogenesis, particularly the development of cancer. Recent studies have revealed that AhR activation by environmental chemicals affects the expression and function of lncRNA. In this article, we provide an overview of AhR signaling pathways activated by diverse ligands and highlight key differences in the putative biological versus toxicological response of AhR activation. We also detail the functions of lncRNA and provide current data on their regulation by the AhR. Finally, we outline how overlap in function between AhR and lncRNA may be one way in which AhR can be both a regulator of endogenous functions but also a mediator of toxicological responses to environmental chemicals. Overall, more research is still needed to fully understand the dynamic interplay between the AhR and lncRNA.
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Affiliation(s)
- Aeshah Alluli
- Meakins-Christie Laboratories, McGill University, Canada; Translational Research in Respiratory Diseases Program at the Research Institute of the McGill University Health Centre, Canada; Department of Pathology, McGill University, Canada
| | - Willem Rijnbout St James
- Meakins-Christie Laboratories, McGill University, Canada; Translational Research in Respiratory Diseases Program at the Research Institute of the McGill University Health Centre, Canada; Department of Pathology, McGill University, Canada
| | - David H Eidelman
- Meakins-Christie Laboratories, McGill University, Canada; Department of Medicine, McGill University, Canada
| | - Carolyn J Baglole
- Meakins-Christie Laboratories, McGill University, Canada; Translational Research in Respiratory Diseases Program at the Research Institute of the McGill University Health Centre, Canada; Department of Pathology, McGill University, Canada; Department of Medicine, McGill University, Canada; Department of Pharmacology and Therapeutics, McGill University, Canada.
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13
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Santus L, Sopena-Rios M, García-Pérez R, Lin AE, Adams GC, Barnes KG, Siddle KJ, Wohl S, Reverter F, Rinn JL, Bennett RS, Hensley LE, Sabeti PC, Melé M. Single-cell profiling of lncRNA expression during Ebola virus infection in rhesus macaques. Nat Commun 2023; 14:3866. [PMID: 37391481 PMCID: PMC10313701 DOI: 10.1038/s41467-023-39627-7] [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: 08/25/2022] [Accepted: 06/19/2023] [Indexed: 07/02/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are involved in numerous biological processes and are pivotal mediators of the immune response, yet little is known about their properties at the single-cell level. Here, we generate a multi-tissue bulk RNAseq dataset from Ebola virus (EBOV) infected and not-infected rhesus macaques and identified 3979 novel lncRNAs. To profile lncRNA expression dynamics in immune circulating single-cells during EBOV infection, we design a metric, Upsilon, to estimate cell-type specificity. Our analysis reveals that lncRNAs are expressed in fewer cells than protein-coding genes, but they are not expressed at lower levels nor are they more cell-type specific when expressed in the same number of cells. In addition, we observe that lncRNAs exhibit similar changes in expression patterns to those of protein-coding genes during EBOV infection, and are often co-expressed with known immune regulators. A few lncRNAs change expression specifically upon EBOV entry in the cell. This study sheds light on the differential features of lncRNAs and protein-coding genes and paves the way for future single-cell lncRNA studies.
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Affiliation(s)
- Luisa Santus
- Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Catalonia, 08034, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain
| | - Maria Sopena-Rios
- Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Catalonia, 08034, Spain
| | - Raquel García-Pérez
- Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Catalonia, 08034, Spain
| | - Aaron E Lin
- FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Harvard Program in Virology, Harvard Medical School, Boston, MA, 02115, USA
| | - Gordon C Adams
- FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Kayla G Barnes
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, 02115, USA
- Liverpool School of Tropical Medicine, Liverpool, L3 5QA, UK
| | - Katherine J Siddle
- FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Shirlee Wohl
- FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- The Scripps Research Institute, Department of Immunology and Microbiology, La Jolla, CA, USA
| | - Ferran Reverter
- Department of Genetics, Microbiology and Statistics University of Barcelona, Barcelona, Spain
| | - John L Rinn
- Department of Biochemistry, University of Colorado Boulder, Boulder, 80303, USA
| | - Richard S Bennett
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, 21702, USA
| | - Lisa E Hensley
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, 21702, USA.
| | - Pardis C Sabeti
- FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Harvard Program in Virology, Harvard Medical School, Boston, MA, 02115, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA.
| | - Marta Melé
- Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Catalonia, 08034, Spain.
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14
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Rajabi1 A, Dastmalchi1 N, Shokri N, Tayefeh-Gholami S, Yaghoubi2 SM, Safaralizadeh R. Expression Level of lncRNA CYTOR in Iranian Cervical Cancer Patients. Rep Biochem Mol Biol 2023; 12:120-126. [PMID: 37724154 PMCID: PMC10505465 DOI: 10.52547/rbmb.12.1.120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 01/22/2023] [Indexed: 09/20/2023]
Abstract
Background A critical role has been known for lncRNAs in the initiation and development of cancers. Therefore, lncRNAs have been reported as the possible biomarkers in relation to the diagnosis and therapy of malignancies. This project examined the change in CYTOR lncRNA expression in human cervical cancer samples as compared with adjacent healthy ones. Methods We provided one hundred fifteen pairs of tumorous and adjacent healthy tissue specimens of cervical cancer patients. RNAs were isolated from tissue specimens and cDNAs were synthesized. We considered quantitative Real-time PCR (qRT-PCR) to examine the expression levels of CYTOR lncRNA. In addition, the biomarker activity of CYTOR and the associations between the lncRNA and clinicopathological characteristics were evaluated. Results The significant increased expression of CYTOR was obtained in cancerous samples as compared with non-cancerous ones (P< 0.0001). A significant correlation was indicated between CYTOR expression and the squamous subtype of cervical cancer (p=0.046). The receiver operating characteristic (ROC) curve-related AUC (area under the curve), specificity, and sensitivity were calculated 0.88, 81.74%, and 80%, respectively, which may introduce CYTOR as a potential biomarker. Conclusion CYTOR may be an effective oncogene and biomarker in cervical cancer cases given its increased expression in human cervical cancer tissues.
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Affiliation(s)
- Ali Rajabi1
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran.
| | - Narges Dastmalchi1
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran.
| | - Neda Shokri
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran.
| | - Samaneh Tayefeh-Gholami
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran.
| | | | - Reza Safaralizadeh
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran.
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15
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Zhao Y, Liu Y, Zhang Q, Liu H, Xu J. The Mechanism Underlying the Regulation of Long Non-coding RNA MEG3 in Cerebral Ischemic Stroke. Cell Mol Neurobiol 2023; 43:69-78. [PMID: 34988760 DOI: 10.1007/s10571-021-01176-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 11/27/2021] [Indexed: 01/07/2023]
Abstract
Cerebral ischemic stroke is one of the leading causes of morbidity and mortality worldwide, and rapidly increasing annually with no more effective therapeutic measures. Thus, the novel diagnostic and prognostic biomarkers are urgent to be identified for prevention and therapy of ischemic stroke. Recently, long noncoding RNAs (lncRNAs), a major family of noncoding RNAs with more than 200 nucleotides, have been considered as new targets for modulating pathological process of ischemic stroke. In this review, we summarized that the lncRNA-maternally expressed gene 3 (MEG3) played a critical role in promotion of neuronal cell death and inhibition of angiogenesis in response to hypoxia or ischemia condition, and further described the challenge of overcrossing blood-brain barrier (BBB) and determination of optimal carrier for delivering lncRNA' drugs into the specific brain regions. In brief, MEG3 will be a potential diagnostic biomarker and drug target in treatment and therapy of ischemic stroke in the future.
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Affiliation(s)
- Yanfang Zhao
- Institute of Biomedical Research, Shandong Provincial Research Center for Bioinformatic Engineering and Technique, Zibo Key Laboratory of New Drug Development of Neurodegenerative Diseases, School of Life Sciences and Medicine, Shandong University of Technology, Zibo, China.
| | - Yingying Liu
- Institute of Translational Medicine, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Qili Zhang
- Institute of Biomedical Research, Shandong Provincial Research Center for Bioinformatic Engineering and Technique, Zibo Key Laboratory of New Drug Development of Neurodegenerative Diseases, School of Life Sciences and Medicine, Shandong University of Technology, Zibo, China
| | - Hongliang Liu
- Institute of Biomedical Research, Shandong Provincial Research Center for Bioinformatic Engineering and Technique, Zibo Key Laboratory of New Drug Development of Neurodegenerative Diseases, School of Life Sciences and Medicine, Shandong University of Technology, Zibo, China
| | - Jianing Xu
- Institute of Biomedical Research, Shandong Provincial Research Center for Bioinformatic Engineering and Technique, Zibo Key Laboratory of New Drug Development of Neurodegenerative Diseases, School of Life Sciences and Medicine, Shandong University of Technology, Zibo, China
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16
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Sangeeth A, Malleswarapu M, Mishra A, Gutti RK. Long Non-Coding RNAs as Cellular Metabolism and Haematopoiesis Regulators. J Pharmacol Exp Ther 2023; 384:79-91. [PMID: 35667690 DOI: 10.1124/jpet.121.001120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 05/12/2022] [Accepted: 05/13/2022] [Indexed: 12/27/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are a category of non-coding RNAs (ncRNAs) that are more than 200 bases long and play major regulatory roles in a wide range of biologic processes, including hematopoeisis and metabolism. Metabolism in cells is an immensely complex process that involves the interconnection and unification of numerous signaling pathways. A growing body of affirmation marks that lncRNAs do participate in metabolism, both directly and indirectly, via metabolic regulation of enzymes and signaling pathways, respectively. The complexities are disclosed by the latest studies demonstrating how lncRNAs could indeed alter tissue-specific metabolism. We have entered a new realm for discovery that is both intimidating and intriguing. Understanding the different functions of lncRNAs in various cellular pathways aids in the advancement of predictive and therapeutic capabilities for a wide variety of myelodysplastic and metabolic disorders. This review has tried to give an overview of the different ncRNAs and their effects on hematopoiesis and metabolism. We have focused on the pathway of action of several lncRNAs and have also delved into their prognostic value. Their use as biomarkers and possible therapeutic targets has also been discussed. SIGNIFICANCE STATEMENT: This review has tried to give an overview of the different ncRNAs and their effects on hematopoiesis and metabolism. The pathway of action of several lncRNAs and their prognostic value was discussed. Their use as biomarkers and possible therapeutic targets has also been elaborated.
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Affiliation(s)
- Anjali Sangeeth
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, (PO) Gachibowli, Hyderabad, India (A.S., M.M., R.K.G.) and Department of Bioscience & Bioengineering, Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Jodhpur, India (A.M.)
| | - Mahesh Malleswarapu
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, (PO) Gachibowli, Hyderabad, India (A.S., M.M., R.K.G.) and Department of Bioscience & Bioengineering, Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Jodhpur, India (A.M.)
| | - Amit Mishra
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, (PO) Gachibowli, Hyderabad, India (A.S., M.M., R.K.G.) and Department of Bioscience & Bioengineering, Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Jodhpur, India (A.M.)
| | - Ravi Kumar Gutti
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, (PO) Gachibowli, Hyderabad, India (A.S., M.M., R.K.G.) and Department of Bioscience & Bioengineering, Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Jodhpur, India (A.M.)
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17
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Sarkar S, Chowdhury SG, Karmakar P. Drugging non-coding RNAs-A new light of hope in senescence-related cancer therapy. Chem Biol Drug Des 2022; 101:1216-1228. [PMID: 36573649 DOI: 10.1111/cbdd.14200] [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: 09/29/2022] [Revised: 12/13/2022] [Accepted: 12/17/2022] [Indexed: 12/28/2022]
Abstract
Cancer is the most prevalent disease of concern worldwide for several decades. Diverse therapeutic aspects are in applications to control this phenomenal disease and also for decennaries. Among many causes and consequences of cancer, senescence has gained much interest in recent times. Senescence, also termed aging, is the natural process that induces cancer in neighboring cells through Senescence-Associated-Secretory Phenotypes (SASPs) production. As a cure or preventive measure of cancer progression, studies already light upon multiple proteins and their roles in associated pathways but the aspect of different non-coding RNAs (ncRNAs) is emerging recently and is under extensive research. Different approaches toward controlling senescence and inhibiting senescent cell accumulation are other aspects of cancer procurement. Thus, the role of ncRNA molecules in senescence and aging is getting much more interest as an alternate therapy for cancer treatment. In this review, at first, the roles of different ncRNAs related to several cellular processes are described. Then we tried to highlight the roles of different non-coding RNAs in senescence-induced cancer formation that extends with increasing age and emphasized non-coding RNAs as a therapeutic target solely or in combination with small molecules where drugging of small molecules targeting these non-coding RNAs can control cancer development.
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Affiliation(s)
- Swarupa Sarkar
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, India
| | | | - Parimal Karmakar
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, India
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18
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Dastmalchi N, Akbarzadeh S, Amini F, Rajabi A, Safaralizadeh R. Alterations in the expression levels of long intergenic non-coding RNA APOC1P1-3 in cervical cancer tissue samples. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2022; 42:495-505. [PMID: 36564178 DOI: 10.1080/15257770.2022.2160459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
lncRNAs play a crucial role in the carcinogenesis process. Thus, they have been recognized as the potential therapeutic and diagnostic biomarkers of cancers. This study assessed the alteration in the expression of APOC1P1-3 lncRNA in cancerous tissues compared to their adjacent non-tumorous tissues sampled from cervical cancer patients. one hundred fifteen pairs of cancerous and adjacent non-cancerous biopsy of cervical cancer specimens were collected. RNA isolation and cDNA synthesis were carried out. The qRT-PCR was used to assess the changes in the expression of APOC1P1-3 lncRNA. Moreover, the biomarker function of the lncRNA and the correlations between APOC1P1-3 and clinicopathological parameters were measured. The APOC1P1-3 expression was significantly increased in cervical cancer specimens as compared to adjacent non-tumorous specimens (p < 0.0001). A significant association was also observed between APOC1P1-3 expression and lymph node involvement (p = 0.031). Additionally, APOC1P1-3 expression demonstrated a significant association with the depth of tumor invasion (p = 0.035), and squamous type of cervical cancer (p = 0.019). The overexpression of APOC1P1-3 was significantly observed in patients younger than 50 years old as compared to another age group (p = 0.033). The results of ROC curve exhibited that APOC1P1-3 with area under the curve (AUC), specificity, and sensitivity of 0.96, 93.91%, and 78.26%, respectively can be considered as a potential biomarker. Regarding overexpression of APOC1P1-3 in human cervical cancer samples, this lncRNA may be considered as an oncogenic factor in cervical cancer patients. Besides, APOC1P1-3 may be a possible biomarker for the diagnosis and treatment of cervical cancer patients.
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Affiliation(s)
- Narges Dastmalchi
- Department of Biology, University College of Nabi Akram, Tabriz, Iran
| | - Sama Akbarzadeh
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Farnaz Amini
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Ali Rajabi
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Reza Safaralizadeh
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
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Zhao L, Luo H, Dong X, Zeng Z, Zhang J, Yi Y, Lin C. A novel necroptosis-related lncRNAs signature for survival prediction in clear cell renal cell carcinoma. Medicine (Baltimore) 2022; 101:e30621. [PMID: 36181033 PMCID: PMC9524942 DOI: 10.1097/md.0000000000030621] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is the most common kind of kidney cancer with poor prognosis. Necroptosis is a newly observed type of programmed cell death in recent years. However, the effects of necroptosis-related lncRNAs (NRlncRNAs) on ccRCC have not been widely explored. The transcription profile and clinical information were obtained from The Cancer Genome Atlas. Necroptosis-related lncRNAs were identified by utilizing a co-expression network of necroptosis-related genes and lncRNAs. Univariate Cox regression, least absolute shrinkage, and selection operator regression and multivariate Cox regression were performed to screen out ideal prognostic necroptosis-related lncRNAss and develop a multi-lncRNA signature. Finally, 6 necroptosis-related lncRNA markers were established. Patients were separated into high- and low-risk groups based on the performance value of the median risk score. Kaplan-Meier analysis identified that high-risk patients had poorer prognosis than low-risk patients. Furthermore, the area under time-dependent receiver operating characteristic curve reached 0.743 at 1 year, 0.719 at 3 years, and 0.742 at 5 years, which indicating that they can be used to predict ccRCC prognosis. In addition, the proposed signature was related to immunocyte infiltration. A nomogram model was also established to provide a more beneficial prognostic indicator for the clinic. Altogether, in the present study, the 6-lncRNA prognostic risk signature are trustworthy and effective indicators for predicting the prognosis of ccRCC.
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Affiliation(s)
- Liwen Zhao
- Department of Urology, Longyan First Affiliated Hospital of Fujian Medical University, Longyan City, China
| | - Huaijing Luo
- Department of Urology, Longyan First Affiliated Hospital of Fujian Medical University, Longyan City, China
| | - Xingmo Dong
- Department of Urology, Longyan First Affiliated Hospital of Fujian Medical University, Longyan City, China
| | - Zhihui Zeng
- Department of Urology, Longyan First Affiliated Hospital of Fujian Medical University, Longyan City, China
| | - Jianlong Zhang
- Department of Urology, Longyan First Affiliated Hospital of Fujian Medical University, Longyan City, China
| | - Yi Yi
- Department of Urology, Longyan First Affiliated Hospital of Fujian Medical University, Longyan City, China
| | - Chaolu Lin
- Department of Urology, Longyan First Affiliated Hospital of Fujian Medical University, Longyan City, China
- * Correspondence: Chaolu Lin, Department of Urology, Longyan First Affiliated Hospital of Fujian Medical University, Longyan City, Fujian Province, China (e-mail: )
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20
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Wang Y, Zhu X, Yang L, Hu X, He K, Yu C, Jiao S, Chen J, Guo R, Yang S. IDDLncLoc: Subcellular Localization of LncRNAs Based on a Framework for Imbalanced Data Distributions. Interdiscip Sci 2022; 14:409-420. [PMID: 35192174 DOI: 10.1007/s12539-021-00497-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 12/16/2021] [Accepted: 12/20/2021] [Indexed: 06/14/2023]
Abstract
Long non-coding RNAs play a crucial role in many life processes of cell, such as genetic markers, RNA splicing, signaling, and protein regulation. Considering that identifying lncRNA's localization in the cell through experimental methods is complicated, hard to reproduce, and expensive, we propose a novel method named IDDLncLoc in this paper, which adopts an ensemble model to solve the problem of the subcellular localization. In the proposal model, dinucleotide-based auto-cross covariance features, k-mer nucleotide composition features, and composition, transition, and distribution features are introduced to encode a raw RNA sequence to vector. To screen out reliable features, feature selection through binomial distribution, and recursive feature elimination is employed. Furthermore, strategies of oversampling in mini-batch, random sampling, and stacking ensemble strategies are customized to overcome the problem of data imbalance on the benchmark dataset. Finally, compared with the latest methods, IDDLncLoc achieves an accuracy of 94.96% on the benchmark dataset, which is 2.59% higher than the best method, and the results further demonstrate IDDLncLoc is excellent on the subcellular localization of lncRNA. Besides, a user-friendly web server is available at http://lncloc.club .
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Affiliation(s)
- Yan Wang
- Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, China
- School of Artificial Intelligence, Jilin University, Changchun, China
| | - Xiaopeng Zhu
- Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, China
| | - Lili Yang
- Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, China
- Department of Obstetrics, The First Hospital of Jilin University, Changchun, China
| | - Xuemei Hu
- Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, China
| | - Kai He
- Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, China
| | - Cuinan Yu
- Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, China
| | - Shaoqing Jiao
- Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, China
| | - Jiali Chen
- Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, China
| | - Rui Guo
- Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, China
| | - Sen Yang
- Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, China.
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21
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Chen F, Zhang X, Chen Y, Chai Y, Jiang X, Li H. Construction of lncRNA-miRNA-mRNA network based on ceRNA mechanism reveals the function of lncRNA in the pathogenesis of gout. J Clin Lab Anal 2022; 36:e24451. [PMID: 35524416 PMCID: PMC9169187 DOI: 10.1002/jcla.24451] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/18/2022] [Accepted: 04/12/2022] [Indexed: 11/23/2022] Open
Abstract
Objective To identify differentially expressed lncRNA, miRNA, and mRNA during the pathogenesis of gout, explore the ceRNA network regulatory mechanism of gout, and seek potential therapeutic targets. Method First, gout‐related chips were retrieved by GEO database. Then, the analysis of differentially expressed lncRNAs and mRNAs was conducted by R language and other software. Besides, miRNA and its regulated mRNA were predicted based on public databases, the intersection of differentially expressed mRNA and predicated mRNA was taken, and the lncRNA‐miRNA‐mRNA regulatory relationships were obtained to construct the ceRNA regulatory network. Subsequently, hub genes were screened by the STRING database and Cytoscape software. Then the DAVID database was used to illustrate the gene functions and related pathways of hub genes and to mine key ceRNA networks. Results Three hundred and eighty‐eight lncRNAs and 758 mRNAs were identified with significant differential expression in gout patient, which regulates hub genes in the ceRNA network, such as JUN, FOS, PTGS2, NR4A2, and TNFAIP3. In the ceRNA network, lncRNA competes with mRNA for miRNA, thus affecting the IL‐17 signaling pathway, TNF signaling pathway, Oxytocin signaling pathway, and NF‐κB signaling pathway through regulating the cell's response to chemical stress. The research indicates that five miRNAs (miR‐429, miR‐137, miR‐139‐5p, miR‐217, miR‐23b‐3p) and five lncRNAs (SNHG1, FAM182A, SPAG5‐AS1, HNF1A‐AS1, UCA1) play an important role in the formation and development of gout. Conclusion The interaction in the ceRNA network can affect the formation and development of gout by regulating the body's inflammatory response as well as proliferation, differentiation, and apoptosis of chondrocytes and osteoclasts. The identification of potential therapeutic targets and signaling pathways through ceRNA network can provide a reference for further research on the pathogenesis of gout.
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Affiliation(s)
- Feng Chen
- Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning, China
| | - Xiaoyun Zhang
- Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning, China
| | - Yueping Chen
- Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning, China
| | - Yuan Chai
- Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning, China
| | - Xiao Jiang
- The Second Hospital of Dalian Medical University, DaLian, China
| | - Huanan Li
- Affiliated Hospital of Jiangxi University of Chinese Medicine, Nanchang, China
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The Mechanisms of lncRNA-Mediated Multidrug Resistance and the Clinical Application Prospects of lncRNAs in Breast Cancer. Cancers (Basel) 2022; 14:cancers14092101. [PMID: 35565231 PMCID: PMC9103444 DOI: 10.3390/cancers14092101] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 04/05/2022] [Accepted: 04/21/2022] [Indexed: 02/01/2023] Open
Abstract
Simple Summary Multidrug resistance (MDR) is a major cause of breast cancer (BC) chemotherapy failure. Long noncoding RNAs (lncRNAs) have been shown closely related to the chemoresistance of BC. In this work, the mechanisms of lncRNA-mediated MDR in BC were elaborated from eight sections, including apoptosis, autophagy, DNA repair, cell cycle, drug efflux, epithelial-mesenchymal transition, epigenetic modification and the tumor microenvironment. Additionally, we also discuss the clinical significance of lncRNAs, which may be biomarkers for diagnosis, therapy and prognosis. Abstract Breast cancer (BC) is a highly heterogeneous disease and presents a great threat to female health worldwide. Chemotherapy is one of the predominant strategies for the treatment of BC; however, multidrug resistance (MDR) has seriously affected or hindered the effect of chemotherapy. Recently, a growing number of studies have indicated that lncRNAs play vital and varied roles in BC chemoresistance, including apoptosis, autophagy, DNA repair, cell cycle, drug efflux, epithelial-mesenchymal transition (EMT), epigenetic modification and the tumor microenvironment (TME). Although thousands of lncRNAs have been implicated in the chemoresistance of BC, a systematic review of their regulatory mechanisms remains to be performed. In this review, we systematically summarized the mechanisms of MDR and the functions of lncRNAs mediated in the chemoresistance of BC from the latest literature. These findings significantly enhance the current understanding of lncRNAs and suggest that they may be promising prognostic biomarkers for BC patients receiving chemotherapy, as well as therapeutic targets to prevent or reverse chemoresistance.
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23
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Wang Y, Xu H, Chen N, Yang J, Zhou H. LncRNA: A Potential Target for Host-Directed Therapy of Candida Infection. Pharmaceutics 2022; 14:pharmaceutics14030621. [PMID: 35335994 PMCID: PMC8954347 DOI: 10.3390/pharmaceutics14030621] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/25/2022] [Accepted: 03/09/2022] [Indexed: 02/01/2023] Open
Abstract
Despite various drugs work against Candida, candidiasis represents clinical management challenges worldwide due to the rising incidence and recurrence rate, as well as epidemics, of new drug-resistant pathogens. Recent insights into interactions between Candida and hosts contribute to exploring novel therapeutic strategies, termed host-directed therapies (HDTs). HDTs are viable adjuncts with good efficacy for the existing standard antifungal regimens. However, HDTs induce other response unintendedly, thus requiring molecular targets with highly specificity. Long noncoding RNAs (lncRNAs) with highly specific expression patterns could affect biological processes, including the immune response. Herein, this review will summarize recent advances of HDTs based on the Candida–host interaction. Especially, the findings and application strategies of lncRNAs related to the host response are emphasized. We propose it is feasible to target lncRNAs to modulate the host defense during Candida infection, which provides a new perspective in identifying options of HDTs for candidiasis.
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24
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Liu Q. The Emerging Landscape of Long Non-Coding RNAs in Wilms Tumor. Front Oncol 2022; 11:780925. [PMID: 35127486 PMCID: PMC8807488 DOI: 10.3389/fonc.2021.780925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 12/29/2021] [Indexed: 11/17/2022] Open
Abstract
Long noncoding RNAs (LncRNAs) are transcripts of nucleic acid sequences with a length of more than 200 bp, which have only partial coding capabilities. Recent studies have shown that lncRNAs located in the nucleus or cytoplasm can be used as gene expression regulatory elements due to their important regulatory effects in a variety of biological processes. Wilms tumor (WT) is a common abdominal tumor in children whose pathogenesis remains unclear. In recent years, many specifically expressed lncRNAs have been found in WT, which affect the occurrence and development of WT. At the same time, lncRNAs may have the capacity to become novel biomarkers for the diagnosis and prognosis of WT. This article reviews related research progress on the relationship between lncRNAs and WT, to provide a new direction for clinical diagnosis and treatment of WT.
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25
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Ren Z, Yu Y, Chen C, Yang D, Ding T, Zhu L, Deng J, Xu Z. The Triangle Relationship Between Long Noncoding RNA, RIG-I-like Receptor Signaling Pathway, and Glycolysis. Front Microbiol 2021; 12:807737. [PMID: 34917069 PMCID: PMC8670088 DOI: 10.3389/fmicb.2021.807737] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 11/09/2021] [Indexed: 12/11/2022] Open
Abstract
Long noncoding RNA (LncRNA), a noncoding RNA over 200nt in length, can regulate glycolysis through metabolic pathways, glucose metabolizing enzymes, and epigenetic reprogramming. Upon viral infection, increased aerobic glycolysis providzes material and energy for viral replication. Mitochondrial antiviral signaling protein (MAVS) is the only protein-specified downstream of retinoic acid-inducible gene I (RIG-I) that bridges the gap between antiviral immunity and glycolysis. MAVS binding to RIG-I inhibits MAVS binding to Hexokinase (HK2), thereby impairing glycolysis, while excess lactate production inhibits MAVS and the downstream antiviral immune response, facilitating viral replication. LncRNAs can also regulate antiviral innate immunity by interacting with RIG-I and downstream signaling pathways and by regulating the expression of interferons and interferon-stimulated genes (ISGs). Altogether, we summarize the relationship between glycolysis, antiviral immunity, and lncRNAs and propose that lncRNAs interact with glycolysis and antiviral pathways, providing a new perspective for the future treatment against virus infection, including SARS-CoV-2.
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Affiliation(s)
- Zhihua Ren
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yueru Yu
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Chaoxi Chen
- College of Life Since and Technology, Southwest Minzu University, Chengdu, China
| | - Dingyong Yang
- College of Animal Husbandry and Veterinary Medicine, Chengdu Agricultural College, Chengdu, China
| | - Ting Ding
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Ling Zhu
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Junliang Deng
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Zhiwen Xu
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
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26
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Arumugam P, Singla M, Lodha R, Rao V. Identification and characterization of novel infection associated transcripts in macrophages. RNA Biol 2021; 18:604-611. [PMID: 34747322 DOI: 10.1080/15476286.2021.1989217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
By analysis of lncRNA expression profiles of macrophages in response to Mycobacterium tuberculosis (Mtb) infection, we identified novel highly expressed transcripts, unique in encompassing a protein coding transcript- Cytidine Monophosphate Kinase 2 (CMPK2) and a previously identified lncRNA- Negative Regulator of Interferon Response (NRIR). While these transcripts (TILT1, 2,3 - TLR4 and Infection induced Long Transcript) are induced by virulent Mtb as well as lipopolysaccharide (LPS) early, lack of/delayed expression in non-viable Mtb/BCG infected cells, respectively, suggest an important role in macrophage responses. The elevated expression by 3 hr in response to fast growing bacteria further emphasizes the importance of these RNAs in the macrophage infection response. Overall, we provide evidence for the presence of multiple transcripts that form a part of the early infection response programme of macrophages.Abbreviations: IFN: Interferon; NRIR: negative regulator of interferon response; CMPK2: cytidine/ uridine monophosphate kinase; LPS: lipopolysaccharide; LAM: Lipoarabinomannan; PIMs: Phosphatidylinositol Mannosides; TILT1, 2,3: TLR4 and Infection induced Long Transcript; TLR4: Toll-like receptor 4; Mtb: Mycobacterium tuberculosis; BCG: Mycobacterium bovis BCG; MDMs: human monocyte derived macrophages.
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Affiliation(s)
- Prabhakar Arumugam
- Department of Cardio- Respiratory Disease Biology, CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi-110025, India.,Department of Biological Sciences, Academy of Scientific and Innovative Research, CSIR- HRDC campus, Sector 19, Kamla Nehru Nagar, Ghaziabad- 201002, India
| | - Mohit Singla
- Department of Pediatrics, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Rakesh Lodha
- Department of Pediatrics, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Vivek Rao
- Department of Cardio- Respiratory Disease Biology, CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi-110025, India.,Department of Biological Sciences, Academy of Scientific and Innovative Research, CSIR- HRDC campus, Sector 19, Kamla Nehru Nagar, Ghaziabad- 201002, India
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PVT1 and ZFAS1 lncRNAs expressions and their biomarker value in gastric cancer tissue sampling among Iranian population. Mol Biol Rep 2021; 48:7171-7177. [PMID: 34546507 DOI: 10.1007/s11033-021-06709-y] [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: 06/01/2021] [Accepted: 09/14/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND lncRNAs are modulatory factors with critical function in the tumorigenesis pathways, introducing them as promising therapeutic and diagnostic biomarkers for different cancers. This study is thus aimed to evaluate the differences in PVT1 and ZFAS1 gene expression in tumorous tissues as compared with adjacent healthy non-tumorous biopsies of gastric cancer cases. METHODS One hundred two pairs of tumorous and adjacent non-tumorous biopsies of GC cases were sampled. RNA isolation and cDNA production were carried out. The qRT-PCR was performed to evaluate the expression of PVT1 and ZFAS1 genes. Moreover, the associations between PVT1 or ZFAS1 and clinicopathological characteristics as well as the biomarker roles of the lncRNAs were assessed. RESULTS The PVT1 and ZFAS1 expressions showed a significant increase and decrease in GC samples as compared with non-cancerous tissues, respectively. PVT1 expression was significantly associated with and lymph-node involvement (p = 0.0007). Moreover, ZFAS1 expression demonstrated a significant association with lymph-node involvement (p = 0.0005), and tumor size >5 cm (p = 0.003). The findings of the ROC curve revealed that PVT1 and ZFAS1 may act as a possible biomarker with AUC of 0.71 and 0.79, specificity of 78.43% and 79.41%, and sensitivity of 55.88% and 64.71%. CONCLUSIONS Regarding upregulation of PVT1 and downregulation of ZFAS1 in human GC samples, these genes may respectively act as oncogenic and tumor-suppressive factors in GC cases. Furthermore, PVT1 and ZFAS1 can be considered as possible biomarkers for the detection and treatment of GC cases.
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Nociti V, Santoro M. What do we know about the role of lncRNAs in multiple sclerosis? Neural Regen Res 2021; 16:1715-1722. [PMID: 33510060 PMCID: PMC8328773 DOI: 10.4103/1673-5374.306061] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 08/21/2020] [Accepted: 11/11/2020] [Indexed: 12/24/2022] Open
Abstract
Multiple sclerosis is a chronic, inflammatory and degenerative disease of the central nervous system of unknown aetiology although well-defined evidence supports an autoimmune pathogenesis. So far, the exact mechanisms leading to autoimmune diseases are still only partially understood. We know that genetic, epigenetic, molecular, and cellular factors resulting in pathogenic inflammatory responses are certainly involved. Long non-coding RNAs (lncRNAs) are non-protein coding transcripts longer than 200 nucleotides that play an important role in both innate and acquired immunity, so there is great interest in lncRNAs involved in autoimmune diseases. The research on multiple sclerosis has been enriched with many studies on the molecular role of lncRNAs in the pathogenesis of the disease and their potential application as diagnostic and prognostic biomarkers. In particular, many multiple sclerosis fields of research are based on the identification of lncRNAs as possible biomarkers able to predict the onset of the disease, its activity degree, its progression phase and the response to disease-modifying drugs. Last but not least, studies on lncRNAs can provide a new molecular target for new therapies, missing, so far, a cure for multiple sclerosis. While our knowledge on the role of lncRNA in multiple sclerosis has recently improved, further studies are required to better understand the specific role of lncRNAs in this neurological disease. In this review, we present the most recent studies on molecular characterization of lncRNAs in multiple sclerosis disorder discussing their clinical relevance as biomarkers for diagnosis and treatments.
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Affiliation(s)
- Viviana Nociti
- Institute of Neurology, Fondazione Policlinico Universitario 'A. Gemelli' IRCCS, Università Cattolica del Sacro Cuore, Rome, Italy
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29
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Naftaly AS, Pau S, White MA. Long-read RNA sequencing reveals widespread sex-specific alternative splicing in threespine stickleback fish. Genome Res 2021; 31:1486-1497. [PMID: 34131005 PMCID: PMC8327910 DOI: 10.1101/gr.274282.120] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 06/15/2021] [Indexed: 01/07/2023]
Abstract
Alternate isoforms are important contributors to phenotypic diversity across eukaryotes. Although short-read RNA-sequencing has increased our understanding of isoform diversity, it is challenging to accurately detect full-length transcripts, preventing the identification of many alternate isoforms. Long-read sequencing technologies have made it possible to sequence full-length alternative transcripts, accurately characterizing alternative splicing events, alternate transcription start and end sites, and differences in UTR regions. Here, we use Pacific Biosciences (PacBio) long-read RNA-sequencing (Iso-Seq) to examine the transcriptomes of five organs in threespine stickleback fish (Gasterosteus aculeatus), a widely used genetic model species. The threespine stickleback fish has a refined genome assembly in which gene annotations are based on short-read RNA sequencing and predictions from coding sequence of other species. This suggests some of the existing annotations may be inaccurate or alternative transcripts may not be fully characterized. Using Iso-Seq we detected thousands of novel isoforms, indicating many isoforms are absent in the current Ensembl gene annotations. In addition, we refined many of the existing annotations within the genome. We noted many improperly positioned transcription start sites that were refined with long-read sequencing. The Iso-Seq-predicted transcription start sites were more accurate and verified through ATAC-seq. We also detected many alternative splicing events between sexes and across organs. We found a substantial number of genes in both somatic and gonadal samples that had sex-specific isoforms. Our study highlights the power of long-read sequencing to study the complexity of transcriptomes, greatly improving genomic resources for the threespine stickleback fish.
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Affiliation(s)
- Alice S Naftaly
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA
| | - Shana Pau
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA
- Department of Biology, University of Texas Arlington, Arlington, Texas 76019, USA
| | - Michael A White
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA
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30
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Varier KM, Dhandapani H, Liu W, Song J, Wang C, Hu A, Ben-David Y, Shen X, Li Y, Gajendran B. An immunotherapeutic approach to decipher the role of long non-coding RNAs in cancer progression, resistance and epigenetic regulation of immune cells. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2021; 40:242. [PMID: 34303380 PMCID: PMC8305593 DOI: 10.1186/s13046-021-01997-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 05/27/2021] [Indexed: 01/01/2023]
Abstract
Immunotherapeutic treatments are gaining attention due to their effective anti-tumor response. Particularly, the revolution of immune checkpoint inhibitors (ICIs) produces promising outcomes for various cancer types. However, the usage of immunotherapy is limited due to its low response rate, suggesting that tumor cells escape the immune surveillance. Rapid advances in transcriptomic profiling have led to recognize immune-related long non-coding RNAs (LncRNAs), as regulators of immune cell-specific gene expression that mediates immune stimulatory as well as suppression of immune response, indicating LncRNAs as targets to improve the efficacy of immunotherapy against tumours. Moreover, the immune-related LncRNAs acting as epigenetic modifiers are also under deep investigation. Thus, herein, is a summarised knowledge of LncRNAs and their regulation in the adaptive and innate immune system, considering their importance in autophagy and predicting putative immunotherapeutic responses.
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Affiliation(s)
- Krishnapriya M Varier
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550014, Guizhou Province, People's Republic of China.,The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academic of Sciences, Guiyang, 550014, Guizhou Province, People's Republic of China.,School of Pharmaceutical Sciences, Guizhou Medical University, Guiyang, 550025, Guizhou Province, People's Republic of China
| | - Hemavathi Dhandapani
- Department of Molecular Oncology, Cancer Institute (WIA), Chennai, 600020, India.,Department of Biosciences & Bioengineering, Indian Institute of Technology Bombay, Mumbai, 400076, India
| | - Wuling Liu
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550014, Guizhou Province, People's Republic of China.,The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academic of Sciences, Guiyang, 550014, Guizhou Province, People's Republic of China
| | - Jialei Song
- Guizhou University of Traditional Chinese Medicine, Guiyang, 550025, Guizhou Province, People's Republic of China
| | - Chunlin Wang
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550014, Guizhou Province, People's Republic of China.,The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academic of Sciences, Guiyang, 550014, Guizhou Province, People's Republic of China
| | - Anling Hu
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550014, Guizhou Province, People's Republic of China.,The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academic of Sciences, Guiyang, 550014, Guizhou Province, People's Republic of China
| | - Yaacov Ben-David
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550014, Guizhou Province, People's Republic of China. .,The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academic of Sciences, Guiyang, 550014, Guizhou Province, People's Republic of China.
| | - Xiangchun Shen
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550014, Guizhou Province, People's Republic of China. .,The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academic of Sciences, Guiyang, 550014, Guizhou Province, People's Republic of China. .,School of Pharmaceutical Sciences, Guizhou Medical University, Guiyang, 550025, Guizhou Province, People's Republic of China.
| | - Yanmei Li
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550014, Guizhou Province, People's Republic of China. .,The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academic of Sciences, Guiyang, 550014, Guizhou Province, People's Republic of China.
| | - Babu Gajendran
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550014, Guizhou Province, People's Republic of China. .,The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academic of Sciences, Guiyang, 550014, Guizhou Province, People's Republic of China. .,School of Pharmaceutical Sciences, Guizhou Medical University, Guiyang, 550025, Guizhou Province, People's Republic of China.
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Marete A, Ariel O, Ibeagha-Awemu E, Bissonnette N. Identification of Long Non-coding RNA Isolated From Naturally Infected Macrophages and Associated With Bovine Johne's Disease in Canadian Holstein Using a Combination of Neural Networks and Logistic Regression. Front Vet Sci 2021; 8:639053. [PMID: 33969037 PMCID: PMC8100051 DOI: 10.3389/fvets.2021.639053] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 02/15/2021] [Indexed: 01/15/2023] Open
Abstract
Mycobacterium avium ssp. paratuberculosis (MAP) causes chronic enteritis in most ruminants. The pathogen MAP causes Johne's disease (JD), a chronic, incurable, wasting disease. Weight loss, diarrhea, and a gradual drop in milk production characterize the disease's clinical phase, culminating in death. Several studies have characterized long non-coding RNA (lncRNA) in bovine tissues, and a previous study characterizes (lncRNA) in macrophages infected with MAP in vitro. In this study, we aim to characterize the lncRNA in macrophages from cows naturally infected with MAP. From 15 herds, feces and blood samples were collected for each cow older than 24 months, twice yearly over 3–5 years. Paired samples were analyzed by fecal PCR and blood ELISA. We used RNA-seq data to study lncRNA in macrophages from 33 JD(+) and 33 JD(–) dairy cows. We performed RNA-seq analysis using the “new Tuxedo” suite. We characterized lncRNA using logistic regression and multilayered neural networks and used DESeq2 for differential expression analysis and Panther and Reactome classification systems for gene ontology (GO) analysis. The study identified 13,301 lncRNA, 605 of which were novel lncRNA. We found seven genes close to differentially expressed lncRNA, including CCDC174, ERI1, FZD1, TWSG1, ZBTB38, ZNF814, and ZSCAN4. None of the genes associated with susceptibility to JD have been cited in the literature. LncRNA target genes were significantly enriched for biological process GO terms involved in immunity and nucleic acid regulation. These include the MyD88 pathway (TLR5), GO:0043312 (neutrophil degranulation), GO:0002446 (neutrophil-mediated immunity), and GO:0042119 (neutrophil activation). These results identified lncRNA with potential roles in host immunity and potential candidate genes and pathways through which lncRNA might function in response to MAP infection.
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Affiliation(s)
- Andrew Marete
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC, Canada
| | - Olivier Ariel
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC, Canada.,Faculty of Science, Sherbrooke University, Sherbrooke, QC, Canada
| | - Eveline Ibeagha-Awemu
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC, Canada
| | - Nathalie Bissonnette
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC, Canada
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Khan S, Masood M, Gaur H, Ahmad S, Syed MA. Long non-coding RNA: An immune cells perspective. Life Sci 2021; 271:119152. [PMID: 33548285 DOI: 10.1016/j.lfs.2021.119152] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 01/14/2021] [Accepted: 01/24/2021] [Indexed: 02/08/2023]
Abstract
Long non-coding RNAs (lncRNAs) were considered as accumulated genetic waste until they were found to be gene expression regulators by highly sensitive modern genomics platforms. It is a huge class of non-coding transcripts with an arbitrary length of >200 nucleotides, which has gained much attention in the past few years. Increasing evidence from several experimental studies unraveled the expression of lncRNA linked to immune response and disease progression. However, only a small number of lncRNAs have robust evidence of their function. Differential expression of lncRNAs in different immune cells is also evident. In this review, we focused on how lncRNAs expression assist in shaping immune cells (Macrophages, Dendritic cells, NK cells, T cells, B cells, eosinophils, neutrophils, and microglial cells) function and their response to the diseased conditions. Emerging evidence revealed lncRNAs may serve as key regulators in the innate and adaptive immune response system. So, the molecular mechanism insight into the function of lncRNAs in immune response may contribute to the development of potential therapeutic targets for various disease treatments. Therefore, it is imperative to explore the expression of lncRNAs and understand its relevance associated with the immune system.
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Affiliation(s)
- Salman Khan
- Department of Biotechnology, Jamia Millia Islamia, New Delhi, India
| | - Mohammad Masood
- Department of Biotechnology, Jamia Millia Islamia, New Delhi, India
| | - Harshita Gaur
- Department of Life Sciences, University of Glasgow, United Kingdom
| | - Shaniya Ahmad
- Department of Biotechnology, Jamia Millia Islamia, New Delhi, India.
| | - Mansoor Ali Syed
- Department of Biotechnology, Jamia Millia Islamia, New Delhi, India.
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33
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Duan Z, Luo Y. Targeting macrophages in cancer immunotherapy. Signal Transduct Target Ther 2021; 6:127. [PMID: 33767177 PMCID: PMC7994399 DOI: 10.1038/s41392-021-00506-6] [Citation(s) in RCA: 303] [Impact Index Per Article: 101.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 01/14/2021] [Accepted: 01/22/2021] [Indexed: 02/07/2023] Open
Abstract
Immunotherapy is regarded as the most promising treatment for cancers. Various cancer immunotherapies, including adoptive cellular immunotherapy, tumor vaccines, antibodies, immune checkpoint inhibitors, and small-molecule inhibitors, have achieved certain successes. In this review, we summarize the role of macrophages in current immunotherapies and the advantages of targeting macrophages. To better understand and make better use of this type of cell, their development and differentiation characteristics, categories, typical markers, and functions were collated at the beginning of the review. Therapeutic strategies based on or combined with macrophages have the potential to improve the treatment efficacy of cancer therapies.
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Affiliation(s)
- Zhaojun Duan
- Department of Immunology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences; School of Basic Medicine, Peking Union Medical College, Beijing, China
- Collaborative Innovation Center for Biotherapy, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences; School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Yunping Luo
- Department of Immunology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences; School of Basic Medicine, Peking Union Medical College, Beijing, China.
- Collaborative Innovation Center for Biotherapy, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences; School of Basic Medicine, Peking Union Medical College, Beijing, China.
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34
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Plasek LM, Valadkhan S. lncRNAs in T lymphocytes: RNA regulation at the heart of the immune response. Am J Physiol Cell Physiol 2021; 320:C415-C427. [PMID: 33296288 PMCID: PMC8294623 DOI: 10.1152/ajpcell.00069.2020] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Genome-wide analyses in the last decade have uncovered the presence of a large number of long non-protein-coding transcripts that show highly tissue- and state-specific expression patterns. High-throughput sequencing analyses in diverse subsets of immune cells have revealed a complex and dynamic expression pattern for these long noncoding RNAs (lncRNAs) that correlate with the functional states of immune cells. Although the vast majority of lncRNAs expressed in immune cells remain unstudied, functional studies performed on a small subset have indicated that their state-specific expressions pattern frequently has a regulatory impact on the function of immune cells. In vivo and in vitro studies have pointed to the involvement of lncRNAs in a wide variety of cellular processes, including both the innate and adaptive immune response through mechanisms ranging from epigenetic and transcriptional regulation to sequestration of functional molecules in subcellular compartments. This review will focus mainly on the role of lncRNAs in CD4+ and CD8+ T cells, which play pivotal roles in adaptive immunity. Recent studies have pointed to key physiological functions for lncRNAs during several developmental and functional stages of the life cycle of lymphocytes. Although lncRNAs play important physiological roles in lymphocytic response to antigenic stimulation, differentiation into effector cells, and secretion of cytokines, their dysregulated expression can promote or sustain pathological states such as autoimmunity, chronic inflammation, cancer, and viremia. This, together with their highly cell type-specific expression patterns, makes lncRNAs ideal therapeutic targets and underscores the need for additional studies into the role of these understudied transcripts in adaptive immune response.
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Ahmad I, Valverde A, Naqvi RA, Naqvi AR. Long Non-coding RNAs RN7SK and GAS5 Regulate Macrophage Polarization and Innate Immune Responses. Front Immunol 2020; 11:604981. [PMID: 33362791 PMCID: PMC7757381 DOI: 10.3389/fimmu.2020.604981] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 11/06/2020] [Indexed: 12/11/2022] Open
Abstract
Macrophages (Mφ) are immune cells that exhibit remarkable functional plasticity. Identification of novel endogenous factors that can regulate plasticity and innate immune functions of Mφ will unravel new strategies to curb immune-related diseases. Long non-coding RNAs (lncRNAs) are a class of endogenous, non-protein coding, regulatory RNAs that are increasingly being associated with various cellular functions and diseases. Despite their ubiquity and abundance, lncRNA-mediated epigenetic regulation of Mφ polarization and innate immune functions is poorly studied. This study elucidates the regulatory role of lncRNAs in monocyte to Mφ differentiation, M1/M2 dichotomy and innate immune responses. Expression profiling of eighty-eight lncRNAs in monocytes and in vitro differentiated M2 Mφ identified seventeen differentially expressed lncRNAs. Based on fold-change and significance, we selected four differentially expressed lncRNAs viz., RN7SK, GAS5, IPW, and ZFAS1 to evaluate their functional impact. LncRNA knockdown was performed on day 3 M2 Mφ and the impact on polarization was assessed on day 7 by surface marker analysis. Knockdown of RN7SK and GAS5 showed downregulation of M2 surface markers (CD163, CD206, or Dectin) and concomitant increase in M1 markers (MHC II or CD23). RN7SK or GAS5 knockdown showed no significant impact on CD163, CD206, or CD23 transcripts. M1/M2 markers were not impacted by IPW or ZFAS1 knockdown. Functional regulation of antigen uptake/processing and phagocytosis, two central innate immune pathways, by candidate lncRNA was assessed in M1/M2 Mφ. Compared to scramble, enhanced antigen uptake and processing were observed in both M1/M2 Mφ transfected with siRNA targeting GAS5 and RN7SK but not IPW and ZFAS1. In addition, knockdown of RN7SK significantly augmented uptake of labelled E. coli in vitro by M1/M2 Mφ, while no significant difference was in GAS5 silencing cells. Together, our results highlight the instrumental role of lncRNA (RN7SK and GAS5)-mediated epigenetic regulation of macrophage differentiation, polarization, and innate immune functions.
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Li M, Liang M, Lan T, Wu X, Xie W, Wang T, Chen Z, Shen S, Peng B. Four Immune-Related Long Non-coding RNAs for Prognosis Prediction in Patients With Hepatocellular Carcinoma. Front Mol Biosci 2020; 7:566491. [PMID: 33364253 PMCID: PMC7752774 DOI: 10.3389/fmolb.2020.566491] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 10/23/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Long non-coding RNA (LncRNA) plays an important role in the occurrence and development of hepatocellular carcinoma (HCC). This study aims to establish an immune-related LncRNA model for risk assessment and prognosis prediction in HCC patients. METHODS Hepatocellular carcinoma patient samples with complete clinical data and corresponding whole transcriptome expression were obtained from the Cancer Genome Atlas (TCGA). Immune-related genes were acquired from the Gene Set Enrichment Analysis (GSEA) website and matched with LncRNA in the TCGA to get immune-related LncRNA. Least Absolute Shrinkage and Selection Operator (LASSO) regression was used for screening the candidate LncRNAs and calculating the risk coefficient to establish the prognosis model. Patients were divided into a high-risk group and a low-risk group depending on the median risk score. The reliability of the prediction was evaluated in the validation cohort and the whole cohort. GSEA and principal component analysis were used for function evaluation. RESULTS A total of 319 samples met the screening criteria and were randomly distributed across the training cohort and the validation cohort. After comparison with the IMMUNE_RESPONSE gene set and the IMMUNE_SYSTEM_PROCESS gene set, a total of 3094 immune-related LncRNAs were screened. Ultimately, four immune-related LncRNAs were used to construct a formula using LASSO regression. According to the formula, the low-risk group showed a higher survival rate than the high-risk group in the validation cohort and the whole cohort. The receiver operating characteristic curves data demonstrated that the risk score was more specific than other traditional clinical characteristics in predicting the 5-year survival rate for HCC. CONCLUSION The four-immune-related-LncRNA model can be used for survival prediction in HCC and guide clinical therapy.
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Affiliation(s)
- Muqi Li
- Department of Liver Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Minni Liang
- Center of Surgery and Anaesthiology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Tian Lan
- Department of Pancreatobiliary Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Xiwen Wu
- Department of Liver Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Wenxuan Xie
- Department of Liver Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Tielong Wang
- Organ Transplant Center, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Organ Donation and Transplant Immunology, Guangzhou, China
- Guangdong Provincial International Cooperation Base of Science and Technology (Organ Transplantation), Guangzhou, China
| | - Zhitao Chen
- Organ Transplant Center, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Organ Donation and Transplant Immunology, Guangzhou, China
- Guangdong Provincial International Cooperation Base of Science and Technology (Organ Transplantation), Guangzhou, China
| | - Shunli Shen
- Department of Liver Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Baogang Peng
- Department of Liver Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
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Menon MP, Hua KF. The Long Non-coding RNAs: Paramount Regulators of the NLRP3 Inflammasome. Front Immunol 2020; 11:569524. [PMID: 33101288 PMCID: PMC7546312 DOI: 10.3389/fimmu.2020.569524] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 08/24/2020] [Indexed: 12/17/2022] Open
Abstract
The NOD LRR pyrin domain containing protein 3 (NLRP3) inflammasome is a cytosolic multi-proteins conglomerate with intrinsic ATPase activity. Their predominant presence in the immune cells emphasizes its significant role in immune response. The downstream effector proteins IL-1β and IL-18 are responsible for the biological functions of the NLRP3 inflammasome upon encountering the alarmins and microbial ligands. Although the NLRP3 inflammasome is essential for host defense during infections, uncontrolled activation and overproduction of IL-1β and IL-18 increase the risk of developing autoimmune and metabolic disorders. Emerging evidences suggest the action of lncRNAs in regulating the activity of NLRP3 inflammasome in various disease conditions. The long non-coding RNA (lncRNA) is an emerging field of study and evidence on their regulatory role in various diseases is grabbing attention. Recent studies emphasize the functions of lncRNAs in the fine control of the NLRP3 inflammasome at nuclear and cytoplasmic levels by interfering in chromatin architecture, gene transcription and translation. Recently, lncRNAs are also found to control the activity of various regulators of NLRP3 inflammasome. Understanding the precise role of lncRNA in controlling the activity of NLRP3 inflammasome helps us to design targeted therapies for multiple inflammatory diseases. The present review is a novel attempt to consolidate the substantial role of lncRNAs in the regulation of the NLRP3 inflammasome. A deeper insight on the NLRP3 inflammasome regulation by lncRNAs will help in developing targeted and beneficial therapeutics in the future.
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Affiliation(s)
- Mridula P. Menon
- Department of Biotechnology and Animal Science, National Ilan University, Yilan, Taiwan
| | - Kuo-Feng Hua
- Department of Biotechnology and Animal Science, National Ilan University, Yilan, Taiwan
- Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
- Department of Medical Research, China Medical University Hospital, China Medical University, Taichung, Taiwan
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Macrophage Long Non-Coding RNAs in Pathogenesis of Cardiovascular Disease. Noncoding RNA 2020; 6:ncrna6030028. [PMID: 32664594 PMCID: PMC7549353 DOI: 10.3390/ncrna6030028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/08/2020] [Accepted: 07/09/2020] [Indexed: 12/21/2022] Open
Abstract
Chronic inflammation is inextricably linked to cardiovascular disease (CVD). Macrophages themselves play important roles in atherosclerosis, as well as acute and chronic heart failure. Although the role of macrophages in CVD pathophysiology is well-recognized, little is known regarding the precise mechanisms influencing their function in these contexts. Long non-coding RNAs (lncRNAs) have emerged as significant regulators of macrophage function; as such, there is rising interest in understanding how these nucleic acids influence macrophage signaling, cell fate decisions, and activity in health and disease. In this review, we summarize current knowledge regarding lncRNAs in directing various aspects of macrophage function in CVD. These include foam cell formation, Toll-like receptor (TLR) and NF-kβ signaling, and macrophage phenotype switching. This review will provide a comprehensive understanding concerning previous, ongoing, and future studies of lncRNAs in macrophage functions and their importance in CVD.
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