1
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Li W, Zhang H, You Z, Guo B. LncRNAs in Immune and Stromal Cells Remodel Phenotype of Cancer Cell and Tumor Microenvironment. J Inflamm Res 2024; 17:3173-3185. [PMID: 38774447 PMCID: PMC11108079 DOI: 10.2147/jir.s460730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 05/07/2024] [Indexed: 05/24/2024] Open
Abstract
Emerging studies suggest that long non-coding RNAs (lncRNAs) participate in the mutual regulation of cells in tumor microenvironment, thereby affecting the anti-tumor immune activity of immune cells. Additionally, the intracellular pathways mediated by lncRNAs can affect the expression of immune checkpoints or change the cell functions, including cytokines secretion, of immune and stromal cells in tumor microenvironment, which further influences cancer patients' prognosis and treatment response. With the in-depth research, lncRNAs have shown great potency as a new immunotherapy target and predict immunotherapy response. The research on lncRNAs provides us with a new insight into developing new immunotherapy drugs and predicting the outcome of immunotherapy. With development of RNA sequencing technology, amounts of lncRNAs were found to be dysregulated in immune and stromal cells rather than tumor cells. These lncRNAs function through ceRNA network or regulating transcript factor activity, thus leading abnormal differentiation and activation of immune and stromal cells. Here, we review the function of lncRNAs in the immune microenvironment and focus on the alteration of lncRNAs in immune and stromal cells, and discuss how these alterations affect tumor growth, metastasis and treatment response.
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Affiliation(s)
- Wenbin Li
- Department of Clinical Oncology, Qianjiang Hospital Affiliated to Renmin Hospital of Wuhan University, Qianjiang, Hubei, People’s Republic of China
- Department of Clinical Oncology, Qianjiang Central Hospital of Hubei Province, Qianjiang, Hubei, People’s Republic of China
| | - Haohan Zhang
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, Hubei, People’s Republic of China
| | - Zuo You
- Department of Traditional Chinese Medicine, Xianfeng County People’s Hospital, Enshi, Hubei, People’s Republic of China
| | - Baozhu Guo
- Department of Pain, Renmin Hospital of Wuhan University, Wuhan, Hubei, People’s Republic of China
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2
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Pastva O, Klein K. Long Non-Coding RNAs in Sjögren's Disease. Int J Mol Sci 2024; 25:5162. [PMID: 38791207 PMCID: PMC11121283 DOI: 10.3390/ijms25105162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 04/25/2024] [Accepted: 04/28/2024] [Indexed: 05/26/2024] Open
Abstract
Sjögren's disease (SjD) is a heterogeneous autoimmune disease characterized by severe dryness of mucosal surfaces, particularly the mouth and eyes; fatigue; and chronic pain. Chronic inflammation of the salivary and lacrimal glands, auto-antibody formation, and extra-glandular manifestations occur in subsets of patients with SjD. An aberrant expression of long, non-coding RNAs (lncRNAs) has been described in many autoimmune diseases, including SjD. Here, we review the current literature on lncRNAs in SjD and their role in regulating X chromosome inactivation, immune modulatory functions, and their potential as biomarkers.
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Affiliation(s)
- Ondřej Pastva
- Department of Rheumatology and Immunology, Inselspital, Bern University Hospital, University of Bern, 3008 Bern, Switzerland
- Department for BioMedical Research (DBMR), University of Bern, 3008 Bern, Switzerland
| | - Kerstin Klein
- Department of Rheumatology and Immunology, Inselspital, Bern University Hospital, University of Bern, 3008 Bern, Switzerland
- Department for BioMedical Research (DBMR), University of Bern, 3008 Bern, Switzerland
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3
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Hao S, Zuo F, Zhang H, Wang Y, Huang L, Ma F, Song T, Zhang T, Ren X, Wang N. LncRNA RP11-301G19.1 is required for the maintenance of vascular smooth muscle cell contractile phenotype via sponging miR-17-5P/ATOH8 axis. IUBMB Life 2024. [PMID: 38651683 DOI: 10.1002/iub.2824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 03/22/2024] [Indexed: 04/25/2024]
Abstract
Long noncoding RNAs (LncRNAs) play essential roles in regulating gene expression in various biological processes. However, the function of lncRNAs in vascular smooth muscle cell (VSMC) transformation remains to be explained. In this work, we discover that a new bone marrow protein (BMP) signaling target, lncRNA RP11-301G19.1, is significantly induced in BMP7-treated VSMCs through lncRNA microarray analysis. Addition of BMP signaling inhibitor LDN-193189 attenuates the expression of ACTA2 and SM-22α, as well as the mRNA level of RP11-301G19.1. Furthermore, lncRNA RP11-301G19.1 is critical to the VSMC differentiation and is directly activated by SMAD1/9. Mechanistically, knocking down of RP11-301G19.1 leads to the decrease of ATOH8, another BMP target, while the forced expression of RP11-301G19.1 reactivates ATOH8. In addition, miR-17-5p, a miRNA negatively regulated by BMP-7, contains predicted binding sites for lncRNA RP11-301G19.1 and ATOH8 3'UTR. Accordingly, overexpression of miR-17-5p decreases the levels of them. Together, our results revealed the role of lncRNA RP11-301G19.1 as a miRNA sponge to upregulate ATOH8 in VSMC phenotype transformation.
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Affiliation(s)
- Shuning Hao
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education and Tianjin, Tianjin, China
| | - Feifei Zuo
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education and Tianjin, Tianjin, China
| | - Hongmin Zhang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education and Tianjin, Tianjin, China
| | - Ying Wang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education and Tianjin, Tianjin, China
| | - Liwen Huang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education and Tianjin, Tianjin, China
| | - Fenghui Ma
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education and Tianjin, Tianjin, China
| | - Tiefeng Song
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education and Tianjin, Tianjin, China
| | - Tongcun Zhang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education and Tianjin, Tianjin, China
| | - Xuejun Ren
- Department of Cardiology, Beijing Anzhen Hospital Affiliated to Capital Medical University, Beijing, China
| | - Nan Wang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education and Tianjin, Tianjin, China
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4
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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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5
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Doghish AS, Ali MA, Elrebehy MA, Mohamed HH, Mansour R, Ghanem A, Hassan A, Elballal MS, Elazazy O, Elesawy AE, Abdel Mageed SS, Nassar YA, Mohammed OA, Abulsoud AI. The interplay between toxoplasmosis and host miRNAs: Mechanisms and consequences. Pathol Res Pract 2023; 250:154790. [PMID: 37683390 DOI: 10.1016/j.prp.2023.154790] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 08/24/2023] [Accepted: 09/01/2023] [Indexed: 09/10/2023]
Abstract
Toxoplasmosis is one of the highly prevalent zoonotic diseases worldwide caused by the parasite Toxoplasma gondii (T. gondii). The infection with T. gondii could pass unidentified in immunocompetent individuals; however, latent cysts remain dormant in their digestive tract, but they could be shed and excreted with feces infesting the environment. However, active toxoplasmosis can create serious consequences, particularly in newborns and infected persons with compromised immunity. These complications include ocular toxoplasmosis, in which most cases cannot be treated. Additionally, it caused many stillbirths and miscarriages. Circulating miRNAs are important regulatory molecules ensuring that the normal physiological role of various organs is harmonious. Upon infection with T. gondii, the tightly regulated miRNA profile is disrupted to favor the parasite's survival and further participate in the disease pathogenesis. Interestingly, this dysregulated profile could be useful in acute and chronic disease discrimination and in providing insights into the pathomechanisms of the disease. Thus, this review sheds light on the various roles of miRNAs in signaling pathways regulation involved in the pathogenesis of T. gondii and provides insights into the application of miRNAs clinically for its diagnosis and prognosis.
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Affiliation(s)
- Ahmed S Doghish
- Department of Biochemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt; Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City, Cairo 11231, Egypt.
| | - Mohamed A Ali
- School of Biotechnology, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt
| | - Mahmoud A Elrebehy
- Department of Biochemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt.
| | - Hend H Mohamed
- School of Biotechnology, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt; Biochemistry Department, Faculty of Science, Cairo University, Giza 12613, Egypt
| | - Reda Mansour
- Zoology and Entomology Department, Faculty of Science, Helwan University, Helwan 11795, Egypt; Biology Department, School of Biotechnology, Badr University in Cairo, Badr City, Cairo 11829, Egypt
| | - Aml Ghanem
- School of Biotechnology, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt
| | - Ahmed Hassan
- School of Biotechnology, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt; Botany and Microbiology Department, Faculty of Science, Helwan University, Helwan 11795, Egypt
| | - Mohammed S Elballal
- Department of Biochemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt
| | - Ola Elazazy
- Department of Biochemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt
| | - Ahmed E Elesawy
- Department of Biochemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt
| | - Sherif S Abdel Mageed
- Pharmacology and Toxicology Department, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt
| | - Yara A Nassar
- Biology Department, School of Biotechnology, Badr University in Cairo, Badr City, Cairo 11829, Egypt
| | - Osama A Mohammed
- Department of Clinical Pharmacology, College of Medicine, University of Bisha, Bisha 61922, Saudi Arabia
| | - Ahmed I Abulsoud
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City, Cairo 11231, Egypt; Biochemistry Department, Faculty of Pharmacy, Heliopolis University, Cairo 11785, Egypt
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6
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Baghdadi H, Heidari R, Zavvar M, Ahmadi N, Shakouri Khomartash M, Vahidi M, Mohammadimehr M, Bashash D, Ghorbani M. Long Non-Coding RNA Signatures in Lymphopoiesis and Lymphoid Malignancies. Noncoding RNA 2023; 9:44. [PMID: 37624036 PMCID: PMC10458434 DOI: 10.3390/ncrna9040044] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 07/09/2023] [Accepted: 07/27/2023] [Indexed: 08/26/2023] Open
Abstract
Lymphoid cells play a critical role in the immune system, which includes three subgroups of T, B, and NK cells. Recognition of the complexity of the human genetics transcriptome in lymphopoiesis has revolutionized our understanding of the regulatory potential of RNA in normal lymphopoiesis and lymphoid malignancies. Long non-coding RNAs (lncRNAs) are a class of RNA molecules greater than 200 nucleotides in length. LncRNAs have recently attracted much attention due to their critical roles in various biological processes, including gene regulation, chromatin organization, and cell cycle control. LncRNAs can also be used for cell differentiation and cell fate, as their expression patterns are often specific to particular cell types or developmental stages. Additionally, lncRNAs have been implicated in lymphoid differentiation, such as regulating T-cell and B-cell development, and their expression has been linked to immune-associated diseases such as leukemia and lymphoma. In addition, lncRNAs have been investigated as potential biomarkers for diagnosis, prognosis, and therapeutic response to disease management. In this review, we provide an overview of the current knowledge about the regulatory role of lncRNAs in physiopathology processes during normal lymphopoiesis and lymphoid leukemia.
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Affiliation(s)
- Hamed Baghdadi
- Department of Medical Laboratory Sciences, School of Allied Medical Sciences, AJA University of Medical Sciences, Tehran 1411718541, Iran; (H.B.); (M.V.); (M.M.)
| | - Reza Heidari
- Research Center for Cancer Screening and Epidemiology, AJA University of Medical Sciences, Tehran 1411718541, Iran;
- Medical Biotechnology Research Center, AJA University of Medical Sciences, Tehran 1411718541, Iran;
| | - Mahdi Zavvar
- Department of Medical Laboratory Sciences, School of Allied Medical Sciences, Tehran University of Medical Sciences, Tehran 443614177, Iran;
| | - Nazanin Ahmadi
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran 1985717443, Iran;
| | | | - Mahmoud Vahidi
- Department of Medical Laboratory Sciences, School of Allied Medical Sciences, AJA University of Medical Sciences, Tehran 1411718541, Iran; (H.B.); (M.V.); (M.M.)
- Medical Biotechnology Research Center, AJA University of Medical Sciences, Tehran 1411718541, Iran;
| | - Mojgan Mohammadimehr
- Department of Medical Laboratory Sciences, School of Allied Medical Sciences, AJA University of Medical Sciences, Tehran 1411718541, Iran; (H.B.); (M.V.); (M.M.)
- Medical Biotechnology Research Center, AJA University of Medical Sciences, Tehran 1411718541, Iran;
| | - Davood Bashash
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran 1985717443, Iran;
| | - Mahdi Ghorbani
- Department of Medical Laboratory Sciences, School of Allied Medical Sciences, AJA University of Medical Sciences, Tehran 1411718541, Iran; (H.B.); (M.V.); (M.M.)
- Medical Biotechnology Research Center, AJA University of Medical Sciences, Tehran 1411718541, Iran;
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7
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He X, He H, Zhang Y, Wu T, Chen Y, Tang C, Xia T, Zhang X, Xie C. Role of ceRNA network in inflammatory cells of rheumatoid arthritis. ZHONG NAN DA XUE XUE BAO. YI XUE BAN = JOURNAL OF CENTRAL SOUTH UNIVERSITY. MEDICAL SCIENCES 2023; 48:750-759. [PMID: 37539578 PMCID: PMC10930406 DOI: 10.11817/j.issn.1672-7347.2023.220621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Indexed: 08/05/2023]
Abstract
Rheumatoid arthritis (RA) is a chronic inflammatory autoimmune disease caused by inflammatory cells. Various inflammatory cells involved in RA include fibroblast-like synoviocytes, macrophages, CD4+T-lymphocytes, B lymphocytes, osteoclasts and chondrocytes. The close interaction between various inflammatory cells leads to imbalance of immune response and disorder of the expression of mRNA in inflammatory cells. It helps to drive production of pro-inflammatory cytokines and stimulate specific antigen-specific T- and B-lymphocytes to produce autoantibodies which is an important pathogenic factor for RA. Competing endogenous RNA (ceRNA) can regulate the expression of mRNA by competitively binding to miRNA. The related ceRNA network is a new regulatory mechanism for RNA interaction. It has been found to be involved in the regulation of abnormal biological processes such as proliferation, apoptosis, invasion and release of inflammatory factors of RA inflammatory cells. Understanding the ceRNA network in 6 kinds of RA common inflammatory cells provides a new idea for further elucidating the pathogenesis of RA, and provides a theoretical basis for the discovery of new biomarkers and effective therapeutic targets.
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Affiliation(s)
- Xiaoyu He
- Department of Rheumatology and Immunology, First Affiliated Hospital of Bengbu Medical College, Bengbu Anhui 233004.
| | - Haohua He
- Department of Rheumatology and Immunology, First Affiliated Hospital of Bengbu Medical College, Bengbu Anhui 233004
| | - Yan Zhang
- Department of Clinical Medicine, Bengbu Medical College, Bengbu Anhui 233030
| | - Tianyu Wu
- School of Public Health, Bengbu Medical College, Bengbu Anhui 233030
| | - Yongjie Chen
- School of Public Health, Bengbu Medical College, Bengbu Anhui 233030
| | - Chengzhi Tang
- School of Public Health, Bengbu Medical College, Bengbu Anhui 233030
| | - Tian Xia
- Department of Clinical Medicine, Bengbu Medical College, Bengbu Anhui 233030
| | - Xiaonan Zhang
- Key Laboratory of Cardiovascular and Cerebrovascular Diseases, Bengbu Medical College, Bengbu Anhui 233030.
| | - Changhao Xie
- Department of Rheumatology and Immunology, First Affiliated Hospital of Bengbu Medical College, Bengbu Anhui 233004.
- Anhui Province Key Laboratory of Immunology in Chronic Diseases, Bengbu Medical College, Bengbu Anhui 233030, China.
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8
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Duns G, Winkle M, Chong L, Ennishi D, Morin RD, Diepstra A, Scott DW, Kluiver JL, Steidl C, van den Berg A. Long non-coding RNAs associated with transcriptomic signatures and treatment outcome in diffuse large B-cell lymphoma. Br J Haematol 2023. [PMID: 37190862 DOI: 10.1111/bjh.18870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/29/2023] [Accepted: 05/06/2023] [Indexed: 05/17/2023]
Affiliation(s)
- Gerben Duns
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
- Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Melanie Winkle
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, The Netherlands
| | - Lauren Chong
- Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Daisuke Ennishi
- Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Ryan D Morin
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Arjan Diepstra
- Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - David W Scott
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Joost L Kluiver
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, The Netherlands
| | - Christian Steidl
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Anke van den Berg
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, The Netherlands
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9
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Kumar D, Sahoo SS, Chauss D, Kazemian M, Afzali B. Non-coding RNAs in immunoregulation and autoimmunity: Technological advances and critical limitations. J Autoimmun 2023; 134:102982. [PMID: 36592512 PMCID: PMC9908861 DOI: 10.1016/j.jaut.2022.102982] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/11/2022] [Accepted: 12/15/2022] [Indexed: 01/02/2023]
Abstract
Immune cell function is critically dependent on precise control over transcriptional output from the genome. In this respect, integration of environmental signals that regulate gene expression, specifically by transcription factors, enhancer DNA elements, genome topography and non-coding RNAs (ncRNAs), are key components. The first three have been extensively investigated. Even though non-coding RNAs represent the vast majority of cellular RNA species, this class of RNA remains historically understudied. This is partly because of a lag in technological and bioinformatic innovations specifically capable of identifying and accurately measuring their expression. Nevertheless, recent progress in this domain has enabled a profusion of publications identifying novel sub-types of ncRNAs and studies directly addressing the function of ncRNAs in human health and disease. Many ncRNAs, including circular and enhancer RNAs, have now been demonstrated to play key functions in the regulation of immune cells and to show associations with immune-mediated diseases. Some ncRNAs may function as biomarkers of disease, aiding in diagnostics and in estimating response to treatment, while others may play a direct role in the pathogenesis of disease. Importantly, some are relatively stable and are amenable to therapeutic targeting, for example through gene therapy. Here, we provide an overview of ncRNAs and review technological advances that enable their study and hold substantial promise for the future. We provide context-specific examples by examining the associations of ncRNAs with four prototypical human autoimmune diseases, specifically rheumatoid arthritis, psoriasis, inflammatory bowel disease and multiple sclerosis. We anticipate that the utility and mechanistic roles of these ncRNAs in autoimmunity will be further elucidated in the near future.
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Affiliation(s)
- Dhaneshwar Kumar
- Immunoregulation Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, MD, USA
| | - Subhransu Sekhar Sahoo
- Departments of Biochemistry and Computer Science, Purdue University, West Lafayette, IN, USA
| | - Daniel Chauss
- Immunoregulation Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, MD, USA
| | - Majid Kazemian
- Departments of Biochemistry and Computer Science, Purdue University, West Lafayette, IN, USA
| | - Behdad Afzali
- Immunoregulation Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, MD, USA.
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10
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Valyaeva AA, Tikhomirova MA, Potashnikova DM, Bogomazova AN, Snigiryova GP, Penin AA, Logacheva MD, Arifulin EA, Shmakova AA, Germini D, Kachalova AI, Saidova AA, Zharikova AA, Musinova YR, Mironov AA, Vassetzky YS, Sheval EV. Ectopic expression of HIV-1 Tat modifies gene expression in cultured B cells: implications for the development of B-cell lymphomas in HIV-1-infected patients. PeerJ 2022; 10:e13986. [PMID: 36275462 PMCID: PMC9586123 DOI: 10.7717/peerj.13986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 08/11/2022] [Indexed: 01/19/2023] Open
Abstract
An increased frequency of B-cell lymphomas is observed in human immunodeficiency virus-1 (HIV-1)-infected patients, although HIV-1 does not infect B cells. Development of B-cell lymphomas may be potentially due to the action of the HIV-1 Tat protein, which is actively released from HIV-1-infected cells, on uninfected B cells. The exact mechanism of Tat-induced B-cell lymphomagenesis has not yet been precisely identified. Here, we ectopically expressed either Tat or its TatC22G mutant devoid of transactivation activity in the RPMI 8866 lymphoblastoid B cell line and performed a genome-wide analysis of host gene expression. Stable expression of both Tat and TatC22G led to substantial modifications of the host transcriptome, including pronounced changes in antiviral response and cell cycle pathways. We did not find any strong action of Tat on cell proliferation, but during prolonged culturing, Tat-expressing cells were displaced by non-expressing cells, indicating that Tat expression slightly inhibited cell growth. We also found an increased frequency of chromosome aberrations in cells expressing Tat. Thus, Tat can modify gene expression in cultured B cells, leading to subtle modifications in cellular growth and chromosome instability, which could promote lymphomagenesis over time.
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Affiliation(s)
- Anna A. Valyaeva
- School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia,Department of Cell Biology and Histology, School of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Maria A. Tikhomirova
- School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia,Koltzov Institute of Developmental Biology, Moscow, Russia
| | - Daria M. Potashnikova
- Department of Cell Biology and Histology, School of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Alexandra N. Bogomazova
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | | | | | - Maria D. Logacheva
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia,Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Eugene A. Arifulin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Anna A. Shmakova
- Koltzov Institute of Developmental Biology, Moscow, Russia,UMR9018 (CNRS – Institut Gustave Roussy – Université Paris Saclay), Centre National de Recherche Scientifique, Villejuif, France, France
| | - Diego Germini
- UMR9018 (CNRS – Institut Gustave Roussy – Université Paris Saclay), Centre National de Recherche Scientifique, Villejuif, France, France
| | - Anastasia I. Kachalova
- Department of Cell Biology and Histology, School of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Aleena A. Saidova
- Department of Cell Biology and Histology, School of Biology, Lomonosov Moscow State University, Moscow, Russia,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Moscow, Russia
| | - Anastasia A. Zharikova
- School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Yana R. Musinova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia,Koltzov Institute of Developmental Biology, Moscow, Russia
| | - Andrey A. Mironov
- School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia,Institute for Information Transmission Problems, Moscow, Russia
| | - Yegor S. Vassetzky
- Koltzov Institute of Developmental Biology, Moscow, Russia,UMR9018 (CNRS – Institut Gustave Roussy – Université Paris Saclay), Centre National de Recherche Scientifique, Villejuif, France, France
| | - Eugene V. Sheval
- School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia,Department of Cell Biology and Histology, School of Biology, Lomonosov Moscow State University, Moscow, Russia
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11
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McMillan JKP, O’Donnell P, Chang SP. Pattern recognition receptor ligand-induced differentiation of human transitional B cells. PLoS One 2022; 17:e0273810. [PMID: 36040923 PMCID: PMC9426890 DOI: 10.1371/journal.pone.0273810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 08/15/2022] [Indexed: 12/01/2022] Open
Abstract
B cells represent a critical component of the adaptive immune response whose development and differentiation are determined by antigen-dependent and antigen-independent interactions. In this study, we explored the effects of IL-4 and pattern-recognition receptor (PRR) ligands on B cell development and differentiation by investigating their capacity to drive the in vitro maturation of human transitional B cells. In the presence of IL-4, ligands for TLR7/8, TLR9, and NOD1 were effective in driving the in vitro maturation of cord blood transitional B cells into mature, naïve B cells as measured by CD23 expression, ABCB1 transporter activation and upregulation of sIgM and sIgD. In addition, several stimulation conditions, including TLR9 ligand alone, favored an expansion of CD27+ IgM memory B cells. Transitional B cells stimulated with TLR7/8 ligand + IL-4 or TLR9 ligand, with or without IL-4, induced a significant subpopulation of CD23+CD27+ B cells expressing high levels of sIgM and sIgD, a minor B cell subpopulation found in human peripheral blood. These studies illustrate the heterogeneity of the B cell populations induced by cytokine and PRR ligand stimulation. A comparison of transitional and mature, naïve B cells transcriptomes to identify novel genes involved in B cell maturation revealed that mature, naïve B cells were less transcriptionally active than transitional B cells. Nevertheless, a subset of differentially expressed genes in mature, naïve B cells was identified including genes associated with the IL-4 signaling pathway, PI3K signaling in B lymphocytes, the NF-κB signaling pathway, and the TNFR superfamily. When transitional B cells were stimulated in vitro with IL-4 and PRR ligands, gene expression was found to be dependent on the nature of the stimulants, suggesting that exposure to these stimulants may alter the developmental fate of transitional B cells. The influence of IL-4 and PRR signaling on transitional B cell maturation illustrates the potential synergy that may be achieved when certain PRR ligands are incorporated as adjuvants in vaccine formulations and presented to developing B cells in the context of an inflammatory cytokine environment. These studies demonstrate the potential of the PRR ligands to drive transitional B cell differentiation in the periphery during infection or vaccination independently of antigen mediated BCR signaling.
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Affiliation(s)
- Jourdan K. P. McMillan
- Department of Tropical Medicine, Medical Microbiology and Pharmacology, John A Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI, United States of America
- * E-mail:
| | - Patrick O’Donnell
- Kapiolani Medical Center for Women and Children, Hawaii Pacific Health, Honolulu, HI, United States of America
| | - Sandra P. Chang
- Department of Tropical Medicine, Medical Microbiology and Pharmacology, John A Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI, United States of America
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12
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王 冲, 黄 海, 王 宏, 李 椿, 刘 晓. [Research progress on the relationship between lncRNA and the pathogenesis of allergic rhinitis]. LIN CHUANG ER BI YAN HOU TOU JING WAI KE ZA ZHI = JOURNAL OF CLINICAL OTORHINOLARYNGOLOGY, HEAD, AND NECK SURGERY 2022; 36:233-238. [PMID: 35193349 PMCID: PMC10128298 DOI: 10.13201/j.issn.2096-7993.2022.03.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 10/11/2021] [Indexed: 04/30/2023]
Abstract
Long non-coding RNA(lncRNA) belongs to the category of non-coding RNA, which length exceeds 200 nucleotides and can hardly encode the expression of proteins. Based on the data from several clinical researches, it is considered that lncRNA not only plays the biological role in epigenetics, transcriptional and post-transcriptional levels, but also abnormally expresses in inflammatory response and the related diseases. In recent years, with the intensive study of gene expression regulation of allergic rhinitis(AR), it has been found that a variety of non-coding RNA, including lncRNA, have close relationship with the occurrence and development of AR. This review mainly summarized the biological function, immunomodulatory effect of lncRNA and the relationship between the lncRNA and the pathogenesis of AR, providing new thoughts and strategies for the further research, prevention as well as the treatment of AR.
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13
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Farooq A, Trøen G, Delabie J, Wang J. Integrating whole genome sequencing, methylation, gene expression, topological associated domain information in regulatory mutation prediction: a study of follicular lymphoma. Comput Struct Biotechnol J 2022; 20:1726-1742. [PMID: 35495111 PMCID: PMC9024376 DOI: 10.1016/j.csbj.2022.03.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 03/22/2022] [Accepted: 03/22/2022] [Indexed: 11/13/2022] Open
Abstract
A major challenge in human genetics is of the analysis of the interplay between genetic and epigenetic factors in a multifactorial disease like cancer. Here, a novel methodology is proposed to investigate genome-wide regulatory mechanisms in cancer, as studied with the example of follicular Lymphoma (FL). In a first phase, a new machine-learning method is designed to identify Differentially Methylated Regions (DMRs) by computing six attributes. In a second phase, an integrative data analysis method is developed to study regulatory mutations in FL, by considering differential methylation information together with DNA sequence variation, differential gene expression, 3D organization of genome (e.g., topologically associated domains), and enriched biological pathways. Resulting mutation block-gene pairs are further ranked to find out the significant ones. By this approach, BCL2 and BCL6 were identified as top-ranking FL-related genes with several mutation blocks and DMRs acting on their regulatory regions. Two additional genes, CDCA4 and CTSO, were also found in top rank with significant DNA sequence variation and differential methylation in neighboring areas, pointing towards their potential use as biomarkers for FL. This work combines both genomic and epigenomic information to investigate genome-wide gene regulatory mechanisms in cancer and contribute to devising novel treatment strategies.
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14
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Stage-Specific Non-Coding RNA Expression Patterns during In Vitro Human B Cell Differentiation into Antibody Secreting Plasma Cells. Noncoding RNA 2022; 8:ncrna8010015. [PMID: 35202088 PMCID: PMC8878715 DOI: 10.3390/ncrna8010015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/31/2022] [Accepted: 02/03/2022] [Indexed: 11/17/2022] Open
Abstract
The differentiation of B cells into antibody secreting plasma cells (PCs) is governed by a strict regulatory network that results in expression of specific transcriptomes along the activation continuum. In vitro models yielding significant numbers of PCs phenotypically identical to the in vivo state enable investigation of pathways, metabolomes, and non-coding (ncRNAs) not previously identified. The objective of our study was to characterize ncRNA expression during human B cell activation and differentiation. To achieve this, we used an in vitro system and performed RNA-seq on resting and activated B cells and PCs. Characterization of coding gene transcripts, including immunoglobulin (Ig), validated our system and also demonstrated that memory B cells preferentially differentiated into PCs. Importantly, we identified more than 980 ncRNA transcripts that are differentially expressed across the stages of activation and differentiation, some of which are known to target transcription, proliferation, cytoskeletal, autophagy and proteasome pathways. Interestingly, ncRNAs located within Ig loci may be targeting both Ig and non-Ig-related transcripts. ncRNAs associated with B cell malignancies were also identified. Taken together, this system provides a platform to study the role of specific ncRNAs in B cell differentiation and altered expression of those ncRNAs involved in B cell malignancies.
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15
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Xia J, Wang M, Zhu Y, Bu C, Li T. Differential mRNA and long noncoding RNA expression profiles in pediatric B-cell acute lymphoblastic leukemia patients. BMC Pediatr 2022; 22:10. [PMID: 34980027 PMCID: PMC8722040 DOI: 10.1186/s12887-021-03073-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 12/10/2021] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) are transcripts longer than 200 nucleotides (nt) that are involved in the pathogenesis and development of various cancers including B cell acute lymphoblastic leukemia (B-ALL). To determine the potential roles of lncRNAs involved in pathogenesis of B-ALL, we analyzed the expression profile of lncRNAs and mRNAs in B-ALL, respectively, and constructed lncRNAs/mRNAs interaction network. METHODS We performed RNA sequencing of 10 non-leukemic blood disease donors and 10 B-ALL patients for Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Interactions among mRNAs were predicted using the STRING database. Quantitative real time PCR (qRT-PCR) was performed to verify the RNA-seq data of lncRNAs and mRNAs. Potential functions of subtype-specific lncRNAs were determined by using coexpression-based analysis on distally (trans-pattern) located protein-coding genes. RESULTS A total of 1813 differentially expressed transcripts (DETs) and 2203 lncRNAs were identified. Moreover, 10 dysregulated lncRNAs and 10 mRNAs were randomly selected, and further assessed by RT-qPCR in vitro. Go and KEGG analysis demonstrated that the differentially expressed mRNAs were most closely associated with myeloid leukocyte activation and in transcriptional misregulation in cancer, respectively. In addition, co-expression analysis demonstrated that these lncRNAs, including MSTRG.27994.3, MSTRG.21740.1, ENST00000456341, MSTRG.14224.1 and MSTRG.20153.1, may mediate the pathogenesis and development of B-ALL via lncRNA-mRNA network interactions. CONCLUSIONS These results showed that several mRNAs and lncRNAs are aberrantly expressed in the bone marrow of B-ALL patients and play potential roles in B-ALL development, and be useful for diagnostic and/or prognostic purposes in pediatric B-ALL. DATA AVAILABILITY The datasets used during our study are available through HARVARD Dataverse Persistent ID doi: https://doi.org/10.7910/DVN/LK9T4Z .
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Affiliation(s)
- Jing Xia
- Department of Pediatric Laboratory, The Affiliated Wuxi Children's Hospital of Nanjing Medical University, Wuxi, 214000, Jiangsu, China
| | - Mengjie Wang
- Department of hematology & oncology, The Affiliated Wuxi Children's Hospital of Nanjing Medical University, Wuxi, 214000, Jiangsu, China
| | - Yi Zhu
- Department of hematology & oncology, The Affiliated Wuxi Children's Hospital of Nanjing Medical University, Wuxi, 214000, Jiangsu, China
| | - Chaozhi Bu
- Center of Reproductive Medicine, State Key Laboratory of Reproductive Medicine, Research Institute for Reproductive Health and Genetic Diseases, The Affiliated Wuxi Matemity and Child Health Care Hospital of Nanjing Medical University, Wuxi, 214002, Jiangsu, China.
| | - Tianyu Li
- Department of hematology & oncology, The Affiliated Wuxi Children's Hospital of Nanjing Medical University, Wuxi, 214000, Jiangsu, China.
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16
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Fernandes M, Marques H, Teixeira AL, Medeiros R. Competitive Endogenous RNA Network Involving miRNA and lncRNA in Non-Hodgkin Lymphoma: Current Advances and Clinical Perspectives. Biomedicines 2021; 9:1934. [PMID: 34944752 PMCID: PMC8698845 DOI: 10.3390/biomedicines9121934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/14/2021] [Accepted: 12/16/2021] [Indexed: 11/18/2022] Open
Abstract
Non-Hodgkin lymphoma (NHL) is a heterogeneous malignancy with variable patient outcomes. There is still a lack of understanding about the different players involved in lymphomagenesis, and the identification of new diagnostic and prognostic biomarkers is urgent. MicroRNAs and long non-coding RNAs emerged as master regulators of B-cell development, and their deregulation has been associated with the initiation and progression of lymphomagenesis. They can function by acting alone or, as recently proposed, by creating competing endogenous RNA (ceRNA) networks. Most studies have focused on individual miRNAs/lncRNAs function in lymphoma, and there is still limited data regarding their interactions in lymphoma progression. The study of miRNAs' and lncRNAs' deregulation in NHL, either alone or as ceRNAs networks, offers new insights into the molecular mechanisms underlying lymphoma pathogenesis and opens a window of opportunity to identify potential diagnostic and prognostic biomarkers. In this review, we summarized the current knowledge regarding the role of miRNAs and lncRNAs in B-cell lymphoma, including their interactions and regulatory networks. Finally, we summarized the studies investigating the potential of miRNAs and lncRNAs as clinical biomarkers, with a special focus on the circulating profiles, to be applied as a non-invasive, easy-to-obtain, and reproducible liquid biopsy for dynamic management of NHL patients.
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Affiliation(s)
- Mara Fernandes
- Molecular Oncology and Viral Pathology Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center (Porto.CCC), 4200-072 Porto, Portugal; (M.F.); (A.L.T.)
- Research Department of the Portuguese League against Cancer Regional Nucleus of the North (LPCC-NRN), 4200-177 Porto, Portugal
- Faculty of Medicine, University of Porto (FMUP), 4200-319 Porto, Portugal
| | - Herlander Marques
- Life and Health Sciences Research Institute (ICVS), School of Medicine, Campus de Gualtar, University of Minho, 4710-057 Braga, Portugal;
- ICVS/3B’s–PT Government Associate Laboratory, 4805-017 Braga/Guimarães, Portugal
- Department of Oncology, Hospital de Braga, 4710-243 Braga, Portugal
- CINTESIS, Center for Health Technology and Services Research, Faculty of Medicine, University of Porto, 4200-450 Porto, Portugal
| | - Ana Luísa Teixeira
- Molecular Oncology and Viral Pathology Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center (Porto.CCC), 4200-072 Porto, Portugal; (M.F.); (A.L.T.)
- ICBAS—Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-513 Porto, Portugal
| | - Rui Medeiros
- Molecular Oncology and Viral Pathology Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center (Porto.CCC), 4200-072 Porto, Portugal; (M.F.); (A.L.T.)
- Research Department of the Portuguese League against Cancer Regional Nucleus of the North (LPCC-NRN), 4200-177 Porto, Portugal
- Faculty of Medicine, University of Porto (FMUP), 4200-319 Porto, Portugal
- ICBAS—Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-513 Porto, Portugal
- Biomedical Research Center (CEBIMED), Faculty of Health Sciences of Fernando Pessoa University (UFP), 4249-004 Porto, Portugal
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17
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Lin H, Xie Y, Kong Y, Yang L, Li M. Identification of Two Molecular Subtypes of Hepatocellular Carcinoma Based on Dysregulated Immune LncRNAs. Front Mol Biosci 2021; 8:625858. [PMID: 34888348 PMCID: PMC8650115 DOI: 10.3389/fmolb.2021.625858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 11/01/2021] [Indexed: 12/05/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) as important regulators of gene expression also have critical functions in immune regulation. This study identified lncRNA modulators of immune-related pathways as biomarkers for hepatocellular carcinoma (HCC). The profile of lncRNA regulation in immune pathways in HCC was comprehensively mapped. To determine lncRNAs with immunomodulatory functions specific to HCC, the enrichment of lncRNAs in a collection of 17 immune functions was calculated applying gene set enrichment analysis (GSEA). Unsupervised clustering of samples were performed in the R package ConsensusClusterPlus to analyze subtype survival and immunological characteristics. The enrichment of 3,134 lncRNA–immune pathway pairs in both diseased and normal samples showed a total of 1,984 immunoregulatory functional lncRNAs specific to HCC only. In addition, 18 immune-related lncRNAs were disordered in HCC and were significantly associated with immune cell infiltration. Functional enrichment analysis indicated that the 18 dysregulated immune lncRNAs were enriched in cytokines, cytokine receptors, TGFb family members, TNF family members, and TNF family member receptor pathways. Two molecular subtypes of hepatocellular carcinoma were identified based on 18 dysregulated immune lncRNAs. Immunological profiling showed that subtype 1 samples with higher levels of cytokine response had a better survival, but subtype 2 samples with higher levels of tumor proliferation had poorer survival. This study identified 18 HCC-specific dysregulated immune lncRNAs and two HCC molecular subtypes with significant prognostic differences and immune characteristics. The current findings help understand the function of lncRNAs and promote the identification of immunotherapy targets.
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Affiliation(s)
- Hongsheng Lin
- Guangxi University of Chinese Medicine, Nanning, China.,Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi University of Chinese Medicine, Nanning, China.,Guangxi Medical University, Nanning, China.,Department of Microbiology, School of Basic Medical Sciences, Guangxi Medical University, Nanning, China
| | - Yangyi Xie
- Guangxi University of Chinese Medicine, Nanning, China.,The First Clinical Faculty of Guangxi University of Chinese Medicine, Nanning, China
| | - Yinzhi Kong
- Guangxi University of Chinese Medicine, Nanning, China.,The First Clinical Faculty of Guangxi University of Chinese Medicine, Nanning, China
| | - Li Yang
- Guangxi University of Chinese Medicine, Nanning, China.,Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi University of Chinese Medicine, Nanning, China
| | - Mingfen Li
- Guangxi University of Chinese Medicine, Nanning, China.,Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi University of Chinese Medicine, Nanning, China
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18
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Park EG, Pyo SJ, Cui Y, Yoon SH, Nam JW. Tumor immune microenvironment lncRNAs. Brief Bioinform 2021; 23:6458113. [PMID: 34891154 PMCID: PMC8769899 DOI: 10.1093/bib/bbab504] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/15/2021] [Accepted: 11/02/2021] [Indexed: 01/17/2023] Open
Abstract
Long non-coding ribonucleic acids (RNAs) (lncRNAs) are key players in tumorigenesis and immune responses. The nature of their cell type-specific gene expression and other functional evidence support the idea that lncRNAs have distinct cellular functions in the tumor immune microenvironment (TIME). To date, the majority of lncRNA studies have heavily relied on bulk RNA-sequencing data in which various cell types contribute to an averaged signal, limiting the discovery of cell type-specific lncRNA functions. Single-cell RNA-sequencing (scRNA-seq) is a potential solution for tackling this limitation despite the lack of annotations for low abundance yet cell type-specific lncRNAs. Hence, updated annotations and further understanding of the cellular expression of lncRNAs will be necessary for characterizing cell type-specific functions of lncRNA genes in the TIME. In this review, we discuss lncRNAs that are specifically expressed in tumor and immune cells, summarize the regulatory functions of the lncRNAs at the cell type level and highlight how a scRNA-seq approach can help to study the cell type-specific functions of TIME lncRNAs.
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Affiliation(s)
- Eun-Gyeong Park
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
| | - Sung-Jin Pyo
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
| | - Youxi Cui
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
| | - Sang-Ho Yoon
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
| | - Jin-Wu Nam
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea.,Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul 04763, Republic of Korea.,Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
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19
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Attaway M, Chwat-Edelstein T, Vuong BQ. Regulatory Non-Coding RNAs Modulate Transcriptional Activation During B Cell Development. Front Genet 2021; 12:678084. [PMID: 34721515 PMCID: PMC8551670 DOI: 10.3389/fgene.2021.678084] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 09/29/2021] [Indexed: 01/07/2023] Open
Abstract
B cells play a significant role in the adaptive immune response by secreting immunoglobulins that can recognize and neutralize foreign antigens. They develop from hematopoietic stem cells, which also give rise to other types of blood cells, such as monocytes, neutrophils, and T cells, wherein specific transcriptional programs define the commitment and subsequent development of these different cell lineages. A number of transcription factors, such as PU.1, E2A, Pax5, and FOXO1, drive B cell development. Mounting evidence demonstrates that non-coding RNAs, such as microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), modulate the expression of these transcription factors directly by binding to the mRNA coding for the transcription factor or indirectly by modifying cellular pathways that promote expression of the transcription factor. Conversely, these transcription factors upregulate expression of some miRNAs and lncRNAs to determine cell fate decisions. These studies underscore the complex gene regulatory networks that control B cell development during hematopoiesis and identify new regulatory RNAs that require additional investigation. In this review, we highlight miRNAs and lncRNAs that modulate the expression and activity of transcriptional regulators of B lymphopoiesis and how they mediate this regulation.
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Affiliation(s)
- Mary Attaway
- Department of Biology, The City College of New York, New York, NY, United States
| | - Tzippora Chwat-Edelstein
- Department of Biology, The City College of New York, New York, NY, United States.,Macaulay Honors College, New York, NY, United States
| | - Bao Q Vuong
- Department of Biology, The City College of New York, New York, NY, United States.,The Graduate Center, The City University of New York, New York, NY, United States
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20
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Kersy O, Salmon-Divon M, Shpilberg O, Hershkovitz-Rokah O. Non-Coding RNAs in Normal B-Cell Development and in Mantle Cell Lymphoma: From Molecular Mechanism to Biomarker and Therapeutic Agent Potential. Int J Mol Sci 2021; 22:ijms22179490. [PMID: 34502399 PMCID: PMC8430640 DOI: 10.3390/ijms22179490] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/23/2021] [Accepted: 08/29/2021] [Indexed: 12/27/2022] Open
Abstract
B-lymphocytes are essential for an efficient immune response against a variety of pathogens. A large fraction of hematologic malignancies are of B-cell origin, suggesting that the development and activation of B cells must be tightly regulated. In recent years, differentially expressed non-coding RNAs have been identified in mantle cell lymphoma (MCL) tumor samples as opposed to their naive, normal B-cell compartment. These aberrantly expressed molecules, specifically microRNAs (miRNAs), circular RNAs (circRNAs) and long non-coding RNAs (lncRNAs), have a role in cellular growth and survival pathways in various biological models. Here, we provide an overview of current knowledge on the role of non-coding RNAs and their relevant targets in B-cell development, activation and malignant transformation, summarizing the current understanding of the role of aberrant expression of non-coding RNAs in MCL pathobiology with perspectives for clinical use.
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Affiliation(s)
- Olga Kersy
- Department of Molecular Biology, Faculty of Natural Sciences, Ariel University, Ariel 40700, Israel; (O.K.); (M.S.-D.)
- Translational Research Lab, Assuta Medical Centers, Tel-Aviv 6971028, Israel;
| | - Mali Salmon-Divon
- Department of Molecular Biology, Faculty of Natural Sciences, Ariel University, Ariel 40700, Israel; (O.K.); (M.S.-D.)
- Adelson School of Medicine, Ariel University, Ariel 40700, Israel
| | - Ofer Shpilberg
- Translational Research Lab, Assuta Medical Centers, Tel-Aviv 6971028, Israel;
- Adelson School of Medicine, Ariel University, Ariel 40700, Israel
- Institute of Hematology, Assuta Medical Centers, Tel-Aviv 6971028, Israel
| | - Oshrat Hershkovitz-Rokah
- Department of Molecular Biology, Faculty of Natural Sciences, Ariel University, Ariel 40700, Israel; (O.K.); (M.S.-D.)
- Translational Research Lab, Assuta Medical Centers, Tel-Aviv 6971028, Israel;
- Correspondence: ; Tel.: +972-3-764-4094
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21
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Fan Y, Wang L, Ding Y, Sheng Q, Zhang C, Li Y, Han C, Lu B, Dou X. Long non-coding RNA RP4-694A7.2 Promotes Hepatocellular Carcinoma Cell Proliferation and Metastasis through the Regulation of PSAT1. J Cancer 2021; 12:5633-5643. [PMID: 34405023 PMCID: PMC8364640 DOI: 10.7150/jca.59348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 07/10/2021] [Indexed: 11/05/2022] Open
Abstract
Background: Long noncoding RNAs (lncRNAs) have emerged as gene regulators in various cancers, including hepatocellular carcinoma (HCC). However, the biological roles and mechanisms of many lncRNAs in HCC tumorigenesis remain unknown. Aim: To identify novel lncRNAs associated with proliferation and metastasis in HCC. Methods: Expression profiles of lncRNAs were analyzed in HCC using two GSE datasets (GSE94660 and GSE104310). Functional studies were performed, including cell proliferation, colony formation, wound healing, and Transwell assays. Fluorescence in-situ hybridization (FISH), tandem mass tag (TMT) analyses, parallel reaction monitoring (PRM), and rescue assays were performed to evaluate the mechanisms underlying the effects of RP4-694A7.2. Results: RP4-694A7.2 levels were higher in HCC tissues than in normal liver tissues in published GSE datasets and were elevated in HCC cell lines. Cell function assays revealed that RP4-694A7.2 promotes cell proliferation, invasion, and migration. Furthermore, RP4-694A7.2 was primarily found to be located in the cytoplasm by FISH assay. Then, TMT assay was performed to predict proteins associated with RP4-694A7.2, and 28 cytoplastic proteins were identified by PRM. Finally, phosphoserine aminotransferase 1 (PSAT1) was found to be regulated by RP4-694A7.2 to modulate growth and metastasis in HCC cells using a rescue assay. Conclusions: These results suggested that RP4-694A7.2 promotes HCC cell proliferation and metastasis via PSAT1, providing a candidate therapeutic target for further research.
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Affiliation(s)
- Yaoxin Fan
- Department of Infectious Diseases, Shengjing Hospital of China Medical University, No. 39, Huaxiang Road, Shenyang Liaoning province, China.,Key Laboratory of Viral hepatitis, Shengjing Hospital of China Medical University, No. 39, Huaxiang Road, Shenyang Liaoning province, China
| | - Lin Wang
- Department of Health Management, Shengjing Hospital of China Medical University, No. 39, Huaxiang Road, Shenyang Liaoning province, China
| | - Yang Ding
- Department of Infectious Diseases, Shengjing Hospital of China Medical University, No. 39, Huaxiang Road, Shenyang Liaoning province, China.,Key Laboratory of Viral hepatitis, Shengjing Hospital of China Medical University, No. 39, Huaxiang Road, Shenyang Liaoning province, China
| | - Qiuju Sheng
- Department of Infectious Diseases, Shengjing Hospital of China Medical University, No. 39, Huaxiang Road, Shenyang Liaoning province, China.,Key Laboratory of Viral hepatitis, Shengjing Hospital of China Medical University, No. 39, Huaxiang Road, Shenyang Liaoning province, China
| | - Chong Zhang
- Department of Infectious Diseases, Shengjing Hospital of China Medical University, No. 39, Huaxiang Road, Shenyang Liaoning province, China.,Key Laboratory of Viral hepatitis, Shengjing Hospital of China Medical University, No. 39, Huaxiang Road, Shenyang Liaoning province, China
| | - Yanwei Li
- Department of Infectious Diseases, Shengjing Hospital of China Medical University, No. 39, Huaxiang Road, Shenyang Liaoning province, China.,Key Laboratory of Viral hepatitis, Shengjing Hospital of China Medical University, No. 39, Huaxiang Road, Shenyang Liaoning province, China
| | - Chao Han
- Department of Infectious Diseases, Shengjing Hospital of China Medical University, No. 39, Huaxiang Road, Shenyang Liaoning province, China.,Key Laboratory of Viral hepatitis, Shengjing Hospital of China Medical University, No. 39, Huaxiang Road, Shenyang Liaoning province, China
| | - Bingchao Lu
- Department of Infectious Diseases, Shengjing Hospital of China Medical University, No. 39, Huaxiang Road, Shenyang Liaoning province, China.,Key Laboratory of Viral hepatitis, Shengjing Hospital of China Medical University, No. 39, Huaxiang Road, Shenyang Liaoning province, China
| | - Xiaoguang Dou
- Department of Infectious Diseases, Shengjing Hospital of China Medical University, No. 39, Huaxiang Road, Shenyang Liaoning province, China.,Key Laboratory of Viral hepatitis, Shengjing Hospital of China Medical University, No. 39, Huaxiang Road, Shenyang Liaoning province, China
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22
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Waterlogging-Stress-Responsive LncRNAs, Their Regulatory Relationships with miRNAs and Target Genes in Cucumber ( Cucumis sativus L.). Int J Mol Sci 2021; 22:ijms22158197. [PMID: 34360961 PMCID: PMC8348067 DOI: 10.3390/ijms22158197] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 07/19/2021] [Accepted: 07/23/2021] [Indexed: 12/13/2022] Open
Abstract
Low oxygen level is a phenomenon often occurring during the cucumber cultivation period. Genes involved in adaptations to stress can be regulated by non-coding RNA. The aim was the identification of long non-coding RNAs (lncRNAs) involved in the response to long-term waterlogging stress in two cucumber haploid lines, i.e., DH2 (waterlogging tolerant—WL-T) and DH4 (waterlogging sensitive—WL-S). Plants, at the juvenile stage, were waterlogged for 7 days (non-primed, 1xH), and after a 14-day recovery period, plants were stressed again for another 7 days (primed, 2xH). Roots were collected for high-throughput RNA sequencing. Implementation of the bioinformatic pipeline made it possible to determine specific lncRNAs for non-primed and primed plants of both accessions, highlighting differential responses to hypoxia stress. In total, 3738 lncRNA molecules were identified. The highest number (1476) of unique lncRNAs was determined for non-primed WL-S plants. Seventy-one lncRNAs were depicted as potentially being involved in acquiring tolerance to hypoxia in cucumber. Understanding the mechanism of gene regulation under long-term waterlogging by lncRNAs and their interactions with miRNAs provides sufficient information in terms of adaptation to the oxygen deprivation in cucumber. To the best of our knowledge, this is the first report concerning the role of lncRNAs in the regulation of long-term waterlogging tolerance by priming application in cucumber.
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23
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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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24
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Chitneedi PK, Weikard R, Arranz JJ, Martínez-Valladares M, Kuehn C, Gutiérrez-Gil B. Identification of Regulatory Functions of LncRNAs Associated With T. circumcincta Infection in Adult Sheep. Front Genet 2021; 12:685341. [PMID: 34194481 PMCID: PMC8236958 DOI: 10.3389/fgene.2021.685341] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 05/20/2021] [Indexed: 12/13/2022] Open
Abstract
Several recent studies have demonstrated the role of long non-coding RNAs (lncRNAs) in regulating the defense mechanism against parasite infections, but no studies are available that investigated their relevance for immune response to nematode infection in sheep. Thus, the aim of the current study was to (i) detect putative lncRNAs that are expressed in the abomasal lymph node of adult sheep after an experimental infection with the gastrointestinal nematode (GIN) Teladorsagia circumcincta and (ii) to elucidate their potential functional role associated with the differential host immune response. We hypothesized that putative lncRNAs differentially expressed (DE) between samples from animals that differ in resistance to infection may play a significant regulatory role in response to nematode infection in adult sheep. To obtain further support for our hypothesis, we performed co-expression and functional gene enrichment analyses with the differentially expressed lncRNAs (DE lncRNAs). In a conservative approach, we included for this predictive analysis only those lncRNAs that are confirmed and supported by documentation of expression in gastrointestinal tissues in the current sheep gene atlas. We identified 9,105 putative lncRNA transcripts corresponding to 7,124 gene loci. Of these, 457 were differentially expressed lncRNA loci (DELs) with 683 lncRNA transcripts. Based on a gene co-expression analysis via weighted gene co-expression network analysis, 12 gene network modules (GNMs) were found significantly correlated with at least one of 10 selected target DE lncRNAs. Based on the principle of “guilt-by-association,” the DE genes from each of the three most significantly correlated GNMs were subjected to a gene enrichment analysis. The significant pathways associated with DE lncRNAs included ERK5 Signaling, SAPK/JNK Signaling, RhoGDI Signaling, EIF2 Signaling, Regulation of eIF4 and p70S6K Signaling and Oxidative Phosphorylation pathways. They belong to signaling pathway categories like Cellular Growth, Proliferation and Development, Cellular Stress and Injury, Intracellular and Second Messenger Signaling and Apoptosis. Overall, this lncRNA study conducted in adult sheep after GIN infection provided first insights into the potential functional role of lncRNAs in the differential host response to nematode infection.
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Affiliation(s)
| | - Rosemarie Weikard
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Juan J Arranz
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, León, Spain
| | - María Martínez-Valladares
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de León, León, Spain.,Instituto de Ganadería de Montaña, CSIC-Universidad de León, León, Spain
| | - Christa Kuehn
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany.,Faculty of Agricultural and Environmental Sciences, University of Rostock, Rostock, Germany
| | - Beatriz Gutiérrez-Gil
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, León, Spain
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25
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Diversity of Rainbow Trout Blood B Cells Revealed by Single Cell RNA Sequencing. BIOLOGY 2021; 10:biology10060511. [PMID: 34207643 PMCID: PMC8227096 DOI: 10.3390/biology10060511] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/03/2021] [Accepted: 06/06/2021] [Indexed: 01/13/2023]
Abstract
Simple Summary Although evolutionarily jawed fish constitute the first group of animals in which a complete adaptive immune system based on immunoglobulins (Igs) is present, many structural immune differences between fish and mammals predict important functional and phenotypical differences between B cells in these two animal groups. However, to date, very few tools are available to study B cell heterogeneity and functionality in fish. Hence, thus far, antibodies targeting the different Igs have been almost exclusively applied as tools to investigate B cell functionality in fish. In the current study, we used the newly developed 10× Genomics single cell RNA sequencing technology and used it to analyze the transcriptional pattern of single B cells from peripheral blood. The results obtained provide us with a transcriptional profile at single cell level of what seem to correspond to different B cell subsets or B cells in different stages of maturation or differentiation. The information provided will not only help us understand the biology of teleost B cells, but also provides us with a repertoire of potential markers that could be used in the future to differentiate trout B cell subsets. Abstract Single-cell sequencing technologies capable of providing us with immune information from dozens to thousands of individual cells simultaneously have revolutionized the field of immunology these past years. However, to date, most of these novel technologies have not been broadly applied to non-model organisms such as teleost fish. In this study, we used the 10× Genomics single cell RNA sequencing technology and used it to analyze for the first time in teleost fish the transcriptional pattern of single B cells from peripheral blood. The analysis of the data obtained in rainbow trout revealed ten distinct cell clusters that seem to be associated with different subsets and/or maturation/differentiation stages of circulating B cells. The potential characteristics and functions of these different B cell subpopulations are discussed on the basis of their transcriptomic profile. The results obtained provide us with valuable information to understand the biology of teleost B cells and offer us a repertoire of potential markers that could be used in the future to differentiate trout B cell subsets.
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26
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Grasseau A, Boudigou M, Michée-Cospolite M, Delaloy C, Mignen O, Jamin C, Cornec D, Pers JO, Le Pottier L, Hillion S. The diversity of the plasmablast signature across species and experimental conditions: A meta-analysis. Immunology 2021; 164:120-134. [PMID: 34041745 DOI: 10.1111/imm.13344] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 03/15/2021] [Accepted: 04/12/2021] [Indexed: 12/17/2022] Open
Abstract
Antibody-secreting cells (ASC) are divided into two principal subsets, including the long-lived plasma cell (PC) subset residing in the bone marrow and the short-lived subset, also called plasmablast (PB). PB are described as a proliferating subset circulating through the blood and ending its differentiation in tissues. Due to their inherent heterogeneity, the molecular signature of PB is not fully established. The purpose of this study was to decipher a specific PB signature in humans and mice through a comprehensive meta-analysis of different data sets exploring the PB differentiation in both species and across different experimental conditions. The present study used recent analyses using whole RNA sequencing in prdm1-GFP transgenic mice to define a reliable and accurate PB signature. Next, we performed similar analysis using current data sets obtained from human PB and PC. The PB-specific signature is composed of 155 and 113 genes in mouse and human being, respectively. Although only nine genes are shared between the human and mice PB signature, the loss of B-cell identity such as the down-regulation of PAX5, MS4A1, (CD20) CD22 and IL-4R is a conserved feature across species and across the different experimental conditions. Additionally, we observed that the IRF8 and IRF4 transcription factors have a specific dynamic range of expression in human PB. We thus demonstrated that IRF4/IRF8 intranuclear staining was useful to define PB in vivo and in vitro and able to discriminate between atypical PB populations and transient states.
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Affiliation(s)
| | | | | | - Céline Delaloy
- UMR U1236, INSERM, Etablissement Français du Sang (EFS) de Bretagne, Université de Rennes 1, Rennes, France
| | | | - Christophe Jamin
- UMR1227, LBAI, INSERM, Univ Brest, Brest, France.,UMR1227, LBAI, INSERM, CHU de Brest, Univ Brest, Brest, France
| | - Divi Cornec
- UMR1227, LBAI, INSERM, Univ Brest, Brest, France.,UMR1227, LBAI, INSERM, CHU de Brest, Univ Brest, Brest, France
| | - Jacques-Olivier Pers
- UMR1227, LBAI, INSERM, Univ Brest, Brest, France.,UMR1227, LBAI, INSERM, CHU de Brest, Univ Brest, Brest, France
| | | | - Sophie Hillion
- UMR1227, LBAI, INSERM, Univ Brest, Brest, France.,UMR1227, LBAI, INSERM, CHU de Brest, Univ Brest, Brest, France
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27
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Zeni PF, Mraz M. LncRNAs in adaptive immunity: role in physiological and pathological conditions. RNA Biol 2021; 18:619-632. [PMID: 33094664 PMCID: PMC8078528 DOI: 10.1080/15476286.2020.1838783] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 10/14/2020] [Accepted: 10/14/2020] [Indexed: 12/19/2022] Open
Abstract
The adaptive immune system is responsible for generating immunological response and immunological memory. Regulation of adaptive immunity including B cell and T cell biology was mainly understood from the protein and microRNA perspective. However, long non-coding RNAs (lncRNAs) are an emerging class of non-coding RNAs (ncRNAs) that influence key factors in lymphocyte biology such as NOTCH, PAX5, MYC and EZH2. LncRNAs were described to modulate lymphocyte activation by regulating pathways such as NFAT, NFκB, MYC, interferon and TCR/BCR signalling (NRON, NKILA, BCALM, GAS5, PVT1), and cell effector functions (IFNG-AS1, TH2-LCR). Here we review lncRNA involvement in adaptive immunity and the implications for autoimmune diseases (multiple sclerosis, inflammatory bowel disease, rheumatoid arthritis) and T/B cell leukaemias and lymphomas (CLL, MCL, DLBCL, T-ALL). It is becoming clear that lncRNAs are important in adaptive immune response and provide new insights into its orchestration.
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Affiliation(s)
- Pedro Faria Zeni
- Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Department of Internal Medicine, Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
- Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Marek Mraz
- Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Department of Internal Medicine, Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
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28
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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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29
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Díez P, Pérez-Andrés M, Bøgsted M, Azkargorta M, García-Valiente R, Dégano RM, Blanco E, Mateos-Gomez S, Bárcena P, Santa Cruz S, Góngora R, Elortza F, Landeira-Viñuela A, Juanes-Velasco P, Segura V, Manzano-Román R, Almeida J, Dybkaer K, Orfao A, Fuentes M. Dynamic Intracellular Metabolic Cell Signaling Profiles During Ag-Dependent B-Cell Differentiation. Front Immunol 2021; 12:637832. [PMID: 33859640 PMCID: PMC8043114 DOI: 10.3389/fimmu.2021.637832] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 03/10/2021] [Indexed: 11/23/2022] Open
Abstract
Human B-cell differentiation has been extensively investigated on genomic and transcriptomic grounds; however, no studies have accomplished so far detailed analysis of antigen-dependent maturation-associated human B-cell populations from a proteomic perspective. Here, we investigate for the first time the quantitative proteomic profiles of B-cells undergoing antigen-dependent maturation using a label-free LC-MS/MS approach applied on 5 purified B-cell subpopulations (naive, centroblasts, centrocytes, memory and plasma B-cells) from human tonsils (data are available via ProteomeXchange with identifier PXD006191). Our results revealed that the actual differences among these B-cell subpopulations are a combination of expression of a few maturation stage-specific proteins within each B-cell subset and maturation-associated changes in relative protein expression levels, which are related with metabolic regulation. The considerable overlap of the proteome of the 5 studied B-cell subsets strengthens the key role of the regulation of the stoichiometry of molecules associated with metabolic regulation and programming, among other signaling cascades (such as antigen recognition and presentation and cell survival) crucial for the transition between each B-cell maturation stage.
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Affiliation(s)
- Paula Díez
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain.,Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Martín Pérez-Andrés
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Martin Bøgsted
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
| | - Mikel Azkargorta
- Proteomics Platform, CIC bioGUNE, CIBERehd, ProteoRed-ISCIII, Derio, Spain
| | | | - Rosa M Dégano
- Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Elena Blanco
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Sheila Mateos-Gomez
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Paloma Bárcena
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Santiago Santa Cruz
- Service of Otolaryngology and Cervical Facial Pathology, University Hospital of Salamanca, Salamanca, Spain
| | - Rafael Góngora
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Félix Elortza
- Proteomics Platform, CIC bioGUNE, CIBERehd, ProteoRed-ISCIII, Derio, Spain
| | - Alicia Landeira-Viñuela
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Pablo Juanes-Velasco
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Victor Segura
- Division of Hepatology and Gene Therapy, Proteomics and BioInformatics Unit, Centre for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
| | - Raúl Manzano-Román
- Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Julia Almeida
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Karen Dybkaer
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
| | - Alberto Orfao
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Manuel Fuentes
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain.,Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
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30
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Maul RW, Catalina MD, Kumar V, Bachali P, Grammer AC, Wang S, Yang W, Hasni S, Ettinger R, Lipsky PE, Gearhart PJ. Transcriptome and IgH Repertoire Analyses Show That CD11c hi B Cells Are a Distinct Population With Similarity to B Cells Arising in Autoimmunity and Infection. Front Immunol 2021; 12:649458. [PMID: 33815408 PMCID: PMC8017342 DOI: 10.3389/fimmu.2021.649458] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 02/24/2021] [Indexed: 01/14/2023] Open
Abstract
A distinct B cell population marked by elevated CD11c expression is found in patients with systemic lupus erythematosus (SLE). Cells with a similar phenotype have been described during chronic infection, but variable gating strategies and nomenclature have led to uncertainty of their relationship to each other. We isolated CD11chi cells from peripheral blood and characterized them using transcriptome and IgH repertoire analyses. Gene expression data revealed the CD11chi IgD+ and IgD- subsets were highly similar to each other, but distinct from naive, memory, and plasma cell subsets. Although CD11chi B cells were enriched in some germinal center (GC) transcripts and expressed numerous negative regulators of B cell receptor (BCR) activation, they were distinct from GC B cells. Gene expression patterns from SLE CD11chi B cells were shared with other human diseases, but not with mouse age-associated B cells. IgH V-gene sequencing analysis showed IgD+ and IgD- CD11chi B cells had somatic hypermutation and were clonally related to each other and to conventional memory and plasma cells. However, the IgH repertoires expressed by the different subsets suggested that defects in negative selection during GC transit could contribute to autoimmunity. The results portray a pervasive B cell population that accumulates during autoimmunity and chronic infection and is refractory to BCR signaling.
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Affiliation(s)
- Robert W Maul
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
| | - Michelle D Catalina
- AMPEL BioSolutions LLC, Charlottesville, VA, United States.,RILITE Foundation, Charlottesville, VA, United States
| | - Varsha Kumar
- Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, United States
| | - Prathyusha Bachali
- AMPEL BioSolutions LLC, Charlottesville, VA, United States.,RILITE Foundation, Charlottesville, VA, United States
| | - Amrie C Grammer
- AMPEL BioSolutions LLC, Charlottesville, VA, United States.,RILITE Foundation, Charlottesville, VA, United States
| | - Shu Wang
- Viela Bio, Gaithersburg, MD, United States
| | - William Yang
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
| | - Sarfaraz Hasni
- Lupus Clinical Research Program, Office of the Clinical Director, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD, United States
| | | | - Peter E Lipsky
- AMPEL BioSolutions LLC, Charlottesville, VA, United States.,RILITE Foundation, Charlottesville, VA, United States
| | - Patricia J Gearhart
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
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Drillis G, Goulielmaki M, Spandidos DA, Aggelaki S, Zoumpourlis V. Non-coding RNAs (miRNAs and lncRNAs) and their roles in lymphogenesis in all types of lymphomas and lymphoid malignancies. Oncol Lett 2021; 21:393. [PMID: 33777216 PMCID: PMC7988683 DOI: 10.3892/ol.2021.12654] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 02/26/2021] [Indexed: 12/16/2022] Open
Abstract
Contemporary developments in molecular biology have been combined with discoveries on the analysis of the role of all non-coding RNAs (ncRNAs) in human diseases, particularly in cancer, by examining their roles in cells. Currently, included among these common types of cancer, are all the lymphomas and lymphoid malignancies, which represent a diverse group of neoplasms and malignant disorders. Initial data suggest that non-coding RNAs, particularly long ncRNAs (lncRNAs), play key roles in oncogenesis and that lncRNA-mediated biology is an important key pathway to cancer progression. Other non-coding RNAs, termed microRNAs (miRNAs or miRs), are very promising cancer molecular biomarkers. They can be detected in tissues, cell lines, biopsy material and all biological fluids, such as blood. With the number of well-characterized cancer-related lncRNAs and miRNAs increasing, the study of the roles of non-coding RNAs in cancer is bringing forth new hypotheses of the biology of cancerous cells. For the first time, to the best of our knowledge, the present review provides an up-to-date summary of the recent literature referring to all diagnosed ncRNAs that mediate the pathogenesis of all types of lymphomas and lymphoid malignancies.
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Affiliation(s)
- Georgios Drillis
- 1st Internal Medicine Clinic, Medical School, Laiko University Hospital of Athens, 115 27 Athens, Greece
| | - Maria Goulielmaki
- Biomedical Applications Unit, Institute of Chemical Biology, National Hellenic Research Foundation (NHRF), 116 35 Athens, Greece
| | - Demetrios A Spandidos
- Laboratory of Clinical Virology, Medical School, University of Crete, 71003 Heraklion, Greece
| | - Sofia Aggelaki
- Oncology Unit, Medical School, University of Crete, 71003 Heraklion, Greece
| | - Vassilios Zoumpourlis
- Biomedical Applications Unit, Institute of Chemical Biology, National Hellenic Research Foundation (NHRF), 116 35 Athens, Greece
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The LncRNA RP11-301G19.1/miR-582-5p/HMGB2 axis modulates the proliferation and apoptosis of multiple myeloma cancer cells via the PI3K/AKT signalling pathway. Cancer Gene Ther 2021; 29:292-303. [PMID: 33707625 DOI: 10.1038/s41417-021-00309-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 01/26/2021] [Accepted: 02/05/2021] [Indexed: 12/15/2022]
Abstract
Long non-coding RNAs (lncRNAs) have recently been reported to act as crucial regulators and prognostic biomarkers of human tumorigenesis. Based on microarray data, RP11-301G19.1 was previously identified as an upregulated lncRNA during B cell development. However, the effect of RP11-301G19.1 on multiple myeloma (MM) cells remains unclear. In the present study, the effects of RP11-301G19.1 on tumour progression were ascertained both in vitro and in vivo. Our results demonstrated that RP11-301G19.1 was upregulated in MM cell lines and that its downregulation inhibited the proliferation and cell cycle progression and promoted the apoptosis of MM cells. Bioinformatic analysis and luciferase reporter assay results revealed that RP11-301G19.1 can upregulate the miR-582-5p-targeted gene HMGB2 as a competing endogenous RNA (ceRNA). Furthermore, Western blot results indicated that RP11-301G19.1 knockdown decreased the levels of PI3K and AKT phosphorylation without affecting their total protein levels. Additionally, in a xenograft model of human MM, RP11-301G19.1 knockdown significantly inhibited tumour growth by downregulating HMGB2. Overall, our data demonstrated that RP11-301G19.1 is involved in MM cell proliferation by sponging miR-582-5p and may serve as a therapeutic target for MM.
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LUBAC accelerates B-cell lymphomagenesis by conferring resistance to genotoxic stress on B cells. Blood 2021; 136:684-697. [PMID: 32325488 DOI: 10.1182/blood.2019002654] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 03/30/2020] [Indexed: 02/07/2023] Open
Abstract
The linear ubiquitin chain assembly complex (LUBAC) is a key regulator of NF-κB signaling. Activating single-nucleotide polymorphisms of HOIP, the catalytic subunit of LUBAC, are enriched in patients with activated B-cell-like (ABC) diffuse large B-cell lymphoma (DLBCL), and expression of HOIP, which parallels LUBAC activity, is elevated in ABC-DLBCL samples. Thus, to clarify the precise roles of LUBAC in lymphomagenesis, we generated a mouse model with augmented expression of HOIP in B cells. Interestingly, augmented HOIP expression facilitated DLBCL-like B-cell lymphomagenesis driven by MYD88-activating mutation. The developed lymphoma cells partly shared somatic gene mutations with human DLBCLs, with increased frequency of a typical AID mutation pattern. In vitro analysis revealed that HOIP overexpression protected B cells from DNA damage-induced cell death through NF-κB activation, and analysis of the human DLBCL database showed that expression of HOIP positively correlated with gene signatures representing regulation of apoptosis signaling, as well as NF-κB signaling. These results indicate that HOIP facilitates lymphomagenesis by preventing cell death and augmenting NF-κB signaling, leading to accumulation of AID-mediated mutations. Furthermore, a natural compound that specifically inhibits LUBAC was shown to suppress the tumor growth in a mouse transplantation model. Collectively, our data indicate that LUBAC is crucially involved in B-cell lymphomagenesis through protection against DNA damage-induced cell death and is a suitable therapeutic target for B-cell lymphomas.
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Arora L, Pal D. Remodeling of Stromal Cells and Immune Landscape in Microenvironment During Tumor Progression. Front Oncol 2021; 11:596798. [PMID: 33763348 PMCID: PMC7982455 DOI: 10.3389/fonc.2021.596798] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 01/29/2021] [Indexed: 12/12/2022] Open
Abstract
The molecular understanding of carcinogenesis and tumor progression rests in intra and inter-tumoral heterogeneity. Solid tumors confined with vast diversity of genetic abnormalities, epigenetic modifications, and environmental cues that differ at each stage from tumor initiation, progression, and metastasis. Complexity within tumors studied by conventional molecular techniques fails to identify different subclasses in stromal and immune cells in individuals and that affects immunotherapies. Here we focus on diversity of stromal cell population and immune inhabitants, whose subtypes create the complexity of tumor microenvironment (TME), leading primary tumors towards advanced-stage cancers. Recent advances in single-cell sequencing (epitope profiling) approach circumscribes phenotypic markers, molecular pathways, and evolutionary trajectories of an individual cell. We discussed the current knowledge of stromal and immune cell subclasses at different stages of cancer development with the regulatory role of non-coding RNAs. Finally, we reported the current therapeutic options in immunotherapies, advances in therapies targeting heterogeneity, and possible outcomes.
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Affiliation(s)
- Leena Arora
- Tissue Engineering and Regenerative Medicine Lab, Indian Institute of Technology Ropar, Rupnagar, India
| | - Durba Pal
- Tissue Engineering and Regenerative Medicine Lab, Indian Institute of Technology Ropar, Rupnagar, India
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Rodriguez PD, Paculova H, Kogut S, Heath J, Schjerven H, Frietze S. Non-Coding RNA Signatures of B-Cell Acute Lymphoblastic Leukemia. Int J Mol Sci 2021; 22:ijms22052683. [PMID: 33799946 PMCID: PMC7961854 DOI: 10.3390/ijms22052683] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/01/2021] [Accepted: 03/03/2021] [Indexed: 12/15/2022] Open
Abstract
Non-coding RNAs (ncRNAs) comprise a diverse class of non-protein coding transcripts that regulate critical cellular processes associated with cancer. Advances in RNA-sequencing (RNA-Seq) have led to the characterization of non-coding RNA expression across different types of human cancers. Through comprehensive RNA-Seq profiling, a growing number of studies demonstrate that ncRNAs, including long non-coding RNA (lncRNAs) and microRNAs (miRNA), play central roles in progenitor B-cell acute lymphoblastic leukemia (B-ALL) pathogenesis. Furthermore, due to their central roles in cellular homeostasis and their potential as biomarkers, the study of ncRNAs continues to provide new insight into the molecular mechanisms of B-ALL. This article reviews the ncRNA signatures reported for all B-ALL subtypes, focusing on technological developments in transcriptome profiling and recently discovered examples of ncRNAs with biologic and therapeutic relevance in B-ALL.
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Affiliation(s)
- Princess D. Rodriguez
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA; (P.D.R.); (H.P.); (S.K.)
| | - Hana Paculova
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA; (P.D.R.); (H.P.); (S.K.)
| | - Sophie Kogut
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA; (P.D.R.); (H.P.); (S.K.)
| | - Jessica Heath
- The University of Vermont Cancer Center, University of Vermont, Burlington, VT 05405, USA;
- Department of Biochemistry, University of Vermont, Burlington, VT 05405, USA
- Department of Pediatrics, University of Vermont, Burlington, VT 05405, USA
| | - Hilde Schjerven
- Department of Laboratory Medicine, University of California, San Francisco, CA 94143, USA;
| | - Seth Frietze
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA; (P.D.R.); (H.P.); (S.K.)
- The University of Vermont Cancer Center, University of Vermont, Burlington, VT 05405, USA;
- Department of Biochemistry, University of Vermont, Burlington, VT 05405, USA
- Correspondence:
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Epigenetic suppression of SLFN11 in germinal center B-cells during B-cell development. PLoS One 2021; 16:e0237554. [PMID: 33513156 PMCID: PMC7846023 DOI: 10.1371/journal.pone.0237554] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 12/07/2020] [Indexed: 02/06/2023] Open
Abstract
Background SLFN11 has recently been reported to execute cancer cells harboring replicative stress induced by DNA damaging agents. However, the roles of SLFN11 under physiological conditions remain poorly understood. Germinal center B-cells (GCBs) undergo somatic hypermutations and class-switch recombination, which can cause physiological genotoxic stress. Hence, we tested whether SLFN11 expression needs to be suppressed in GCBs during B-cell development. Objective To clarify the expression profile of SLFN11 in different developmental stages of B-cells and B-cell-derived cancers. Methods We analyzed the expression of SLFN11 by mining cell line databases for different stages of normal B-cells and various types of B-cell-derived cancer cell lines. We performed dual immunohistochemical staining for SLFN11 and B-cell specific markers in normal human lymphatic tissues. We tested the effects of two epigenetic modifiers, an EZH2 inhibitor, tazemetostat (EPZ6438) and a histone deacetylase inhibitor, panobinostat (LBH589) on SLFN11 expression in GCB-derived lymphoma cell lines. We also examined the therapeutic efficacy of these drugs in combination with cytosine arabinoside and the effects of SLFN11 on the efficacy of cytosine arabinoside in SLFN11-overexpressing cells. Results SLFN11 mRNA level was found low in both normal GCBs and GCB-DLBCL (GCB like-diffuse large B-cell lymphoma). Immunohistochemical staining showed low SLFN11 expression in GCBs and high SLFN11 expression in plasmablasts and plasmacytes. The EZH2 and HDAC epigenetic modifiers upregulated SLFN11 expression in GCB-derived lymphoma cells and made them more susceptible to cytosine arabinoside. SLFN11 overexpression further sensitized GCB-derived lymphoma cells to cytosine arabinoside. Conclusions The expression of SLFN11 is epigenetically suppressed in normal GCBs and GCB-derived lymphomas. GCB-derived lymphomas with low SLFN11 expression can be treated by the combination of epigenetic modifiers and cytosine arabinoside.
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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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [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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Gao Q, Li Z, Meng L, Ma J, Xi Y, Wang T. Transcriptome profiling reveals an integrated mRNA-lncRNA signature with predictive value for long-term survival in diffuse large B-cell lymphoma. Aging (Albany NY) 2020; 12:23275-23295. [PMID: 33221755 PMCID: PMC7746345 DOI: 10.18632/aging.104100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 09/14/2020] [Indexed: 12/19/2022]
Abstract
For patients with diffuse large B-cell lymphoma (DLBCL), survival at 24 months is a milestone for long-term survival. The purpose of this study was to develop a multigene risk score (MGRS) to refine the International Prognostic Index (IPI) model to identify patients with DLBCL at high risk of death within 24 months. Using a robust statistical strategy, we built a MGRS incorporating nine mRNAs and two lncRNAs. Stratification and multivariable Cox regression analysis confirmed the MGRS as an independent risk factor. A nomogram based on IPI+MGRS model was constructed and its calibration plot showed close agreement between predicted 2-year survival rate and observed rate. The 2-year AUC was bigger with the IPI+MGRS model (ΔAUC=0.162; 95%CI 0.1295–0.1903) than with the IPI model, and the IPI+MGRS model more accurately predicted the prognostic risk of DLBCL. The 2-year survival decision curve revealed the IPI+MGRS model was more useful clinically than the IPI model. Functional enrichment analysis showed that the MGRS correlated with cell cycle, DNA replication and repair. The results were validated using an independent external dataset. In conclusion, we successfully developed an integrated mRNA–lncRNA signature to refine the IPI model for predicting long-term survival of patients with DLBCL.
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Affiliation(s)
- Qian Gao
- Department of Health Statistics, School of Public Health, Shanxi Medical University, Taiyuan 030001, China
| | - Zhiyao Li
- Department of Health Statistics, School of Public Health, Shanxi Medical University, Taiyuan 030001, China
| | - Lingxian Meng
- Department of Health Statistics, School of Public Health, Shanxi Medical University, Taiyuan 030001, China
| | - Jinsha Ma
- Department of Health Statistics, School of Public Health, Shanxi Medical University, Taiyuan 030001, China
| | - Yanfeng Xi
- Department of Pathology, Shanxi Cancer Hospital, Taiyuan 030013, China
| | - Tong Wang
- Department of Health Statistics, School of Public Health, Shanxi Medical University, Taiyuan 030001, China
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Moroney JB, Vasudev A, Pertsemlidis A, Zan H, Casali P. Integrative transcriptome and chromatin landscape analysis reveals distinct epigenetic regulations in human memory B cells. Nat Commun 2020; 11:5435. [PMID: 33116135 PMCID: PMC7595102 DOI: 10.1038/s41467-020-19242-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Accepted: 10/01/2020] [Indexed: 01/08/2023] Open
Abstract
Memory B cells (MBCs) are long-lived and produce high-affinity, generally, class-switched antibodies. Here, we use a multiparameter approach involving CD27 to segregate naïve B cells (NBC), IgD+ unswitched (unsw)MBCs and IgG+ or IgA+ class-switched (sw)MBCs from humans of different age, sex and race. Conserved antibody variable gene expression indicates that MBCs emerge through unbiased selection from NBCs. Integrative analyses of mRNAs, miRNAs, lncRNAs, chromatin accessibility and cis-regulatory elements uncover a core mRNA-ncRNA transcriptional signature shared by IgG+ and IgA+ swMBCs and distinct from NBCs, while unswMBCs display a transitional transcriptome. Some swMBC transcriptional signature loci are accessible but not expressed in NBCs. Profiling miRNAs reveals downregulated MIR181, and concomitantly upregulated MIR181 target genes such as RASSF6, TOX, TRERF1, TRPV3 and RORα, in swMBCs. Finally, lncRNAs differentially expressed in swMBCs cluster proximal to the IgH chain locus on chromosome 14. Our findings thus provide new insights into MBC transcriptional programs and epigenetic regulation, opening new investigative avenues on these critical cell elements in human health and disease. Human memory B cells differentiate from naïve B cells and can express different immunoglobulin (Ig) isotypes resulted from class-switch recombination. Here the authors describe, using transcriptional and epigenetic data from human memory B cells and integrated multi-omics analyses, the differentiation regulation and trajectory of IgG+, IgA+ and IgD+ memory B cells.
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Affiliation(s)
- Justin B Moroney
- Department of Microbiology, Immunology & Molecular Genetics, University of Texas Long School of Medicine, UT Health Science Center, San Antonio, TX, 78229, USA
| | - Anusha Vasudev
- Department of Microbiology, Immunology & Molecular Genetics, University of Texas Long School of Medicine, UT Health Science Center, San Antonio, TX, 78229, USA
| | - Alexander Pertsemlidis
- Greehey Children's Cancer Research Institute, University of Texas Long School of Medicine, UT Health Science Center, San Antonio, TX, 78229, USA
| | - Hong Zan
- Department of Microbiology, Immunology & Molecular Genetics, University of Texas Long School of Medicine, UT Health Science Center, San Antonio, TX, 78229, USA
| | - Paolo Casali
- Department of Microbiology, Immunology & Molecular Genetics, University of Texas Long School of Medicine, UT Health Science Center, San Antonio, TX, 78229, USA.
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Li J, Zou J, Wan X, Sun C, Peng F, Chu Z, Hu Y. The Role of Noncoding RNAs in B-Cell Lymphoma. Front Oncol 2020; 10:577890. [PMID: 33194698 PMCID: PMC7645065 DOI: 10.3389/fonc.2020.577890] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 08/20/2020] [Indexed: 12/19/2022] Open
Abstract
In recent years, emerging evidence has suggested that noncoding RNAs (ncRNAs) participate in nearly every aspect of biological processes and play a crucial role in the genesis and progression of numerous tumors, including B-cell lymphoma. The exploration of ncRNA dysregulations and their functions in B-cell lymphoma provides new insights into lymphoma pathogenesis and is essential for indicating future clinical trials and optimizing the diagnostic and therapeutic strategies. In this review, we summarize the role of ncRNAs in B-cell lymphoma and discuss their potential in clinical applications.
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Affiliation(s)
- Jingwen Li
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jing Zou
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoyue Wan
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chunyan Sun
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Collaborative Innovation Center of Hematology, Huazhong University of Science and Technology, Wuhan, China
| | - Fei Peng
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhangbo Chu
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yu Hu
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Collaborative Innovation Center of Hematology, Huazhong University of Science and Technology, Wuhan, China
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lncRNAs-mRNAs Co-Expression Network Underlying Childhood B-Cell Acute Lymphoblastic Leukaemia: A Pilot Study. Cancers (Basel) 2020; 12:cancers12092489. [PMID: 32887470 PMCID: PMC7564554 DOI: 10.3390/cancers12092489] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 08/24/2020] [Accepted: 08/31/2020] [Indexed: 02/01/2023] Open
Abstract
Simple Summary Acute lymphoblastic leukemia (ALL) is one of the most common childhood cancers. The ALL onset involves abnormal proliferation and arrest of differentiation of B or T cell progenitors. Recently, long non–coding RNAs (lncRNAs) gained great interest in the B–ALL leukemogenesis, however, so far few “omic” studies investigate lncRNAs and protein–coding gene networks. In our retrospective study, we conceived an integrated bioinformatic approach, by using NGS platform, to discover lncRNAs strongly correlated with aberrantly expressed protein–coding genes. We provided dysregulated lncRNA–mRNA pairs potentially underlying B–ALL pathogenesis. Diagnosis incidence peak of ALL appears approximatively between 1 and 19 years old. lncRNAs may be of clinical utility as non–invasive biomarker for B–ALL onset or therapy response in support of precision medicine. The identification of lncRNA as key regulators in B–ALL could lead to the identification of the altered pathways able to sustain the leukemic growth. Abstract Long non–coding RNAs (lncRNAs) are emerging as key gene regulators in the pathogenesis and development of various cancers including B lymphoblastic leukaemia (B–ALL). In this pilot study, we used RNA–Seq transcriptomic data for identifying novel lncRNA–mRNA cooperative pairs involved in childhood B–ALL pathogenesis. We conceived a bioinformatic pipeline based on unsupervised PCA feature extraction approach and stringent statistical criteria to extract potential childhood B–ALL lncRNA signatures. We then constructed a co–expression network of the aberrantly expressed lncRNAs (30) and protein–coding genes (754). We cross–validated our in–silico findings on an independent dataset and assessed the expression levels of the most differentially expressed lncRNAs and their co–expressed mRNAs through ex vivo experiments. Using the guilt–by–association approach, we predicted lncRNA functions based on their perfectly co–expressed mRNAs (Spearman’s correlation) that resulted closely disease–associated. We shed light on 24 key lncRNAs and their co–expressed mRNAs which may play an important role in B–ALL pathogenesis. Our results may be of clinical utility for diagnostic and/or prognostic purposes in paediatric B–ALL management.
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Sayad A, Ghafouri-Fard S, Sadeghpour S, Mirzajani S, Taheri M, Arsang-Jang S, Raji MA, Houshmand B, Amid R, Gholami L, Shams B. Dysregulation of GAS5 and OIP5-AS1 lncRNAs in periodontitis. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2020.100712] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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43
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Dutta A, Roy A, Chatterjee S. Long noncoding RNAs in cancer immunity: a new avenue in drug discovery. Drug Discov Today 2020; 26:264-272. [PMID: 32827755 DOI: 10.1016/j.drudis.2020.07.026] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 06/18/2020] [Accepted: 07/22/2020] [Indexed: 12/23/2022]
Abstract
The central role of the nonprotein-coding portion of the genome, such as long noncoding (lnc)RNAs is emerging as a hidden player manipulating the immune system in cancer. lncRNAs, in association with their interacting partners, regulate the expression of various immune system genes, which are perturbed during cancer. The tissue-specific expression of lncRNAs and their importance in cellular proliferation, the tumor microenvironment (TME), epithelial-mesenchymal transition (EMT), and modulation of the cells of the innate and adaptive immune system have novel therapeutic implications in establishing lncRNAs as biomarkers and targets to overcome cancer-associated immunosuppression. In this review, we establish and strengthen the link between lncRNAs and cancer immunity.
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Affiliation(s)
- Anindya Dutta
- Department of Biophysics, Bose Institute, P-1/12, CIT Scheme VIIM, Kankurgachi, Kolkata 700054, West Bengal, India
| | - Ananya Roy
- Department of Biophysics, Bose Institute, P-1/12, CIT Scheme VIIM, Kankurgachi, Kolkata 700054, West Bengal, India
| | - Subhrangsu Chatterjee
- Department of Biophysics, Bose Institute, P-1/12, CIT Scheme VIIM, Kankurgachi, Kolkata 700054, West Bengal, India.
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Inamo J, Suzuki K, Takeshita M, Kassai Y, Takiguchi M, Kurisu R, Okuzono Y, Tasaki S, Yoshimura A, Takeuchi T. Identification of novel genes associated with dysregulation of B cells in patients with primary Sjögren's syndrome. Arthritis Res Ther 2020; 22:153. [PMID: 32571405 PMCID: PMC7310138 DOI: 10.1186/s13075-020-02248-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 06/15/2020] [Indexed: 12/11/2022] Open
Abstract
Background The aim of this study was to identify the molecular mechanism of dysregulation of B cell subpopulations of primary Sjögren’s syndrome (pSS) at the transcriptome level. Methods We enrolled patients with pSS (n = 6) and healthy controls (HCs) (n = 6) in the discovery cohort using microarray and pSS (n = 14) and HCs (n = 12) in the validation cohort using quantitative PCR (qPCR). Peripheral B cells acquired from these subjects were separated by cell sorting into four subsets: CD38−IgD+ (Bm1), CD38+IgD+ (naive B cells), CD38highIgD+ (pre-germinal centre B cells) and CD38±IgD− (memory B cells). We performed differentially expressed gene (DEG) analysis and weighted gene co-expression network analysis (WGCNA). Results Expression of the long non-coding RNA LINC00487 was significantly upregulated in all B cell subsets, as was that of HLA and interferon (IFN) signature genes. Moreover, the normalized intensity value of LINC00487 significantly correlated with the disease activity score of all pSS B cell subsets. Studies of human B cell lines revealed that the expression of LINC00487 was strongly induced by IFNα. WGCNA revealed six gene clusters associated with the B cell subpopulation of pSS. Further, SOX4 was identified as an inter-module hub gene. Conclusion Our transcriptome analysis revealed key genes involved in the dysregulation of B cell subpopulations associated with pSS. Trial registration Not required.
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Affiliation(s)
- Jun Inamo
- Division of Rheumatology, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Katsuya Suzuki
- Division of Rheumatology, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Masaru Takeshita
- Division of Rheumatology, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Yoshiaki Kassai
- Immunology Unit, Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, Kanagawa, Japan
| | - Maiko Takiguchi
- Immunology Unit, Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, Kanagawa, Japan
| | - Rina Kurisu
- Immunology Unit, Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, Kanagawa, Japan
| | - Yuumi Okuzono
- Immunology Unit, Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, Kanagawa, Japan
| | - Shinya Tasaki
- Integrated Technology Research Laboratories, Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, Kanagawa, Japan.,Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, USA
| | - Akihiko Yoshimura
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan
| | - Tsutomu Takeuchi
- Division of Rheumatology, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan.
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45
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Taghizadeh E, Taheri F, Samadian MM, Soudyab M, Abi A, Gheibi Hayat SM. Role of long non-coding RNAs (LncRNAs) in multiple sclerosis: a brief review. Neurol Sci 2020; 41:2443-2451. [PMID: 32350675 DOI: 10.1007/s10072-020-04425-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 04/13/2020] [Indexed: 01/05/2023]
Abstract
Multiple sclerosis (MS) as chronic autoimmune inflammatory neurological disease of the central nervous system (CNS) occurs due to several environmental and genetic factors, whose pathogenesis is associated with genes with regulatory role in the immune system. Long non-coding RNAs (LncRNAs) are able to reportedly regulate responses of immune systems and expression of genes, and show the tissue specificity and complexity of biofunctions. Various studies have suggested that the aberrant LncRNA expression is an underlying factor involved in the incidence of MS and that the analysis of the expression profile of these molecules can be a specific biomarker of MS for preventing the course of the disease or responding to treatment. The purpose of this research was to review the recent studies for exploring the functions of LncRNAs in the processes leading to MS disease.
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Affiliation(s)
- Eskandar Taghizadeh
- Cellular and Molecular Research Center, Yasuj University of Medical Sciences, Yasuj, Iran
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Forough Taheri
- Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Mohammad Mahdi Samadian
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Soudyab
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Abbas Abi
- Department of Biotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Seyed Mohammad Gheibi Hayat
- Department of Medical Genetics, School of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran.
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Ahmad I, Valverde A, Ahmad F, Naqvi AR. Long Noncoding RNA in Myeloid and Lymphoid Cell Differentiation, Polarization and Function. Cells 2020; 9:cells9020269. [PMID: 31979061 PMCID: PMC7072530 DOI: 10.3390/cells9020269] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 01/15/2020] [Accepted: 01/20/2020] [Indexed: 12/13/2022] Open
Abstract
Long noncoding RNA (lncRNA) are a class of endogenous, non-protein coding RNAs that are increasingly being associated with various cellular functions and diseases. Yet, despite their ubiquity and abundance, only a minute fraction of these molecules has an assigned function. LncRNAs show tissue-, cell-, and developmental stage-specific expression, and are differentially expressed under physiological or pathological conditions. The role of lncRNAs in the lineage commitment of immune cells and shaping immune responses is becoming evident. Myeloid cells and lymphoid cells are two major classes of immune systems that work in concert to initiate and amplify innate and adaptive immunity in vertebrates. In this review, we provide mechanistic roles of lncRNA through which these noncoding RNAs can directly participate in the differentiation, polarization, and activation of myeloid (monocyte, macrophage, and dendritic cells) and lymphoid cells (T cells, B cells, and NK cells). While our knowledge on the role of lncRNA in immune cell differentiation and function has improved in the past decade, further studies are required to unravel the biological role of lncRNAs and identify novel mechanisms of lncRNA functions in immune cells. Harnessing the regulatory potential of lncRNAs can provide novel diagnostic and therapeutic targets in treating immune cell related diseases.
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Sun R, Sun X, Liu H, Li P. Knockdown of lncRNA TDRG1 Inhibits Tumorigenesis in Endometrial Carcinoma Through the PI3K/AKT/mTOR Pathway. Onco Targets Ther 2019; 12:10863-10872. [PMID: 31849490 PMCID: PMC6912007 DOI: 10.2147/ott.s228168] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 11/21/2019] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND AND OBJECTIVE Endometrial carcinoma (EC) is one of the most frequently diagnosed malignancies in females. Dysregulation of lncRNA TDRG1 has been widely documented in several cancers, including EC. However, the mechanism of this lncRNA involving in EC progression remains to be further elucidated. MATERIALS AND METHODS The enrichment levels of TDRG1 in EC tissues and cell lines were examined by RT-qPCR. Flow cytometry, cell counting kit-8 (CCK-8), transwell, and Western blot assays were conducted to assess whether TDRG1 knockdown could affect cell cycle arrest, proliferation, migration, invasion, and apoptosis of EC cells. The phosphorylation levels of mTOR, AKT and PI3K that associated with PI3K/Akt/mTOR pathway were determined by Western blot assay. RESULTS TDRG1 expression was markedly upregulated in EC tissues and cell lines. Knockdown of TDRG1 significantly induced cell cycle arrest and apoptosis, inhibited cell proliferation, restrained the invasion and migration abilities in EC cells. Moreover, TDRG1 silencing decreased the protein levels of p-AKT, p-PI3K, and p-mTOR of EC cells. CONCLUSION Our data underlined the implication of TDRG1 in EC progression, proposing that targeting TDRG1 might be a potential therapeutic avenue in EC.
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Affiliation(s)
- Ruimei Sun
- Department of Radiotherapy, The Affiliated Hospital of Weifang Medical University, Weifang261041, People’s Republic of China
| | - Xiujiang Sun
- Department of Thyroid and Breast Surgery, The Affiliated Hospital of Weifang Medical University, Weifang261041, People’s Republic of China
| | - Hua Liu
- Department of Gynaecology, The Affiliated Hospital of Weifang Medical University, Weifang261041, People’s Republic of China
| | - Peirui Li
- Department of Thyroid and Breast Surgery, The Affiliated Hospital of Weifang Medical University, Weifang261041, People’s Republic of China
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48
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A multiple myeloma classification system that associates normal B-cell subset phenotypes with prognosis. Blood Adv 2019; 2:2400-2411. [PMID: 30254104 DOI: 10.1182/bloodadvances.2018018564] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 07/17/2018] [Indexed: 12/22/2022] Open
Abstract
Despite the recent progress in treatment of multiple myeloma (MM), it is still an incurable malignant disease, and we are therefore in need of new risk stratification tools that can help us to understand the disease and optimize therapy. Here we propose a new subtyping of myeloma plasma cells (PCs) from diagnostic samples, assigned by normal B-cell subset associated gene signatures (BAGS). For this purpose, we combined fluorescence-activated cell sorting and gene expression profiles from normal bone marrow (BM) Pre-BI, Pre-BII, immature, naïve, memory, and PC subsets to generate BAGS for assignment of normal BM subtypes in diagnostic samples. The impact of the subtypes was analyzed in 8 available data sets from 1772 patients' myeloma PC samples. The resulting tumor assignments in available clinical data sets exhibited similar BAGS subtype frequencies in 4 cohorts from de novo MM patients across 1296 individual cases. The BAGS subtypes were significantly associated with progression-free and overall survival in a meta-analysis of 916 patients from 3 prospective clinical trials. The major impact was observed within the Pre-BII and memory subtypes, which had a significantly inferior prognosis compared with other subtypes. A multiple Cox proportional hazard analysis documented that BAGS subtypes added significant, independent prognostic information to the translocations and cyclin D classification. BAGS subtype analysis of patient cases identified transcriptional differences, including a number of differentially spliced genes. We identified subtype differences in myeloma at diagnosis, with prognostic impact and predictive potential, supporting an acquired B-cell trait and phenotypic plasticity as a pathogenetic hallmark of MM.
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Liao YW, Ho BC, Chen MH, Yu SL. Host relieves lnc-IRAK3-3-sequestered miR-891b to attenuate apoptosis in Enterovirus 71 infection. Cell Microbiol 2019; 21:e13043. [PMID: 31099182 DOI: 10.1111/cmi.13043] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 04/22/2019] [Accepted: 05/10/2019] [Indexed: 12/11/2022]
Abstract
Enterovirus 71 (EV71) is an emerging life-threatening pathogen particularly in the Asia-Pacific region. Apoptosis is a major pathogenic feature in EV71 infection. However, which molecular mechanism participating in EV71-induced apoptosis is not completely understood. Long noncoding RNAs (lncRNAs), a newly discovered class of regulatory RNA molecules, govern a wide range of biological functions through multiple regulatory mechanisms. Whether lncRNAs involved in EV71-induced apoptosis was investigated in this study. We conducted an apoptosis-oriented approach by integrating lncRNA and mRNA profilings. lnc-IRAK3-3 is down-regulated in EV71 infection and plays an important role in EV71 infection-induced apoptosis. Compensation of lnc-IRAK3-3 in EV71 infection promoted cell apoptosis wherein GADD45β expression was increased and further triggered caspase3 and PARP cleavage. Using bioinformatics analysis and functional assays, lnc-IRAK3-3 could functionally sequester miR-891b and GADD45β 3'UTR whereas miR-891b showed the inhibitory activity on GADD45β expression. Taken together, lnc-IRAK3-3 has the ability capturing miR-891b to enforce GADD45β expression and eventually promotes apoptosis. On the contrary, host cells suppress lnc-IRAK3-3 to relieve lnc-IRAK3-3-sequestered miR-891b, restrain GADD45β, and attenuate apoptosis in EV71 infection that prevent host cells from severe damages. We discover a new molecular mechanism by which host cells counteract EV71-induced apoptosis through the lnc-IRAK3-3/miR-891b/GADD45β axis partially.
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Affiliation(s)
- Yu-Wen Liao
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Bing-Ching Ho
- Centers of Genomic and Precision Medicine, National Taiwan University, Taipei, Taiwan
| | - Min-Hsuan Chen
- Centers of Genomic and Precision Medicine, National Taiwan University, Taipei, Taiwan
| | - Sung-Liang Yu
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan.,Centers of Genomic and Precision Medicine, National Taiwan University, Taipei, Taiwan.,Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan.,Institute of Medical Device and Imaging, College of Medicine, National Taiwan University, Taipei, Taiwan.,Graduate Institute of Pathology, College of Medicine, National Taiwan University, Taipei, Taiwan.,Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
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50
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LncRNAs with miRNAs in regulation of gastric, liver, and colorectal cancers: updates in recent years. Appl Microbiol Biotechnol 2019; 103:4649-4677. [PMID: 31062053 DOI: 10.1007/s00253-019-09837-5] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 04/07/2019] [Accepted: 04/08/2019] [Indexed: 12/15/2022]
Abstract
Long noncoding RNA (lncRNA) is a kind of RNAi molecule composed of hundreds to thousands of nucleotides. There are several major types of functional lncRNAs which participate in some important cellular pathways. LncRNA-RNA interaction controls mRNA translation and degradation or serves as a microRNA (miRNA) sponge for silencing. LncRNA-protein interaction regulates protein activity in transcriptional activation and silencing. LncRNA guide, decoy, and scaffold regulate transcription regulators of enhancer or repressor region of the coding genes for alteration of expression. LncRNA plays a role in cellular responses including the following activities: regulation of chromatin structural modification and gene expression for epigenetic and cell function control, promotion of hematopoiesis and maturation of immunity, cell programming in stem cell and somatic cell development, modulation of pathogen infection, switching glycolysis and lipid metabolism, and initiation of autoimmune diseases. LncRNA, together with miRNA, are considered the critical elements in cancer development. It has been demonstrated that tumorigenesis could be driven by homeostatic imbalance of lncRNA/miRNA/cancer regulatory factors resulting in biochemical and physiological alterations inside the cells. Cancer-driven lncRNAs with other cellular RNAs, epigenetic modulators, or protein effectors may change gene expression level and affect the viability, immortality, and motility of the cells that facilitate cancer cell cycle rearrangement, angiogenesis, proliferation, and metastasis. Molecular medicine will be the future trend for development. LncRNA/miRNA could be one of the potential candidates in this category. Continuous studies in lncRNA functional discrepancy between cancer cells and normal cells and regional and rational genetic differences of lncRNA profiles are critical for clinical research which is beneficial for clinical practice.
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