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Shi L, Han X, Liu F, Long J, Jin Y, Chen S, Duan G, Yang H. Review on Long Non-Coding RNAs as Biomarkers and Potentially Therapeutic Targets for Bacterial Infections. Curr Issues Mol Biol 2024; 46:7558-7576. [PMID: 39057090 PMCID: PMC11276060 DOI: 10.3390/cimb46070449] [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: 06/19/2024] [Revised: 07/13/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024] Open
Abstract
The confrontation between humans and bacteria is ongoing, with strategies for combating bacterial infections continually evolving. With the advancement of RNA sequencing technology, non-coding RNAs (ncRNAs) associated with bacterial infections have garnered significant attention. Recently, long ncRNAs (lncRNAs) have been identified as regulators of sterile inflammatory responses and cellular defense against live bacterial pathogens. They are involved in regulating host antimicrobial immunity in both the nucleus and cytoplasm. Increasing evidence indicates that lncRNAs are critical for the intricate interactions between host and pathogen during bacterial infections. This paper emphatically elaborates on the potential applications of lncRNAs in clinical hallmarks, cellular damage, immunity, virulence, and drug resistance in bacterial infections in greater detail. Additionally, we discuss the challenges and limitations of studying lncRNAs in the context of bacterial infections and highlight clear directions for this promising field.
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Affiliation(s)
| | | | | | | | | | | | | | - Haiyan Yang
- Department of Epidemiology, School of Public Health, Zhengzhou University, Zhengzhou 450001, China; (L.S.); (X.H.); (F.L.); (J.L.); (Y.J.); (S.C.); (G.D.)
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Ramos EI, Veerapandian R, Das K, Chacon JA, Gadad SS, Dhandayuthapani S. Pathogenic mycoplasmas of humans regulate the long noncoding RNAs in epithelial cells. Noncoding RNA Res 2023; 8:282-293. [PMID: 36970372 PMCID: PMC10031284 DOI: 10.1016/j.ncrna.2023.03.002] [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: 11/10/2022] [Revised: 03/06/2023] [Accepted: 03/07/2023] [Indexed: 03/09/2023] Open
Abstract
Non-coding RNAs (ncRNAs), specifically long ncRNAs (lncRNAs), regulate cellular processes by affecting gene expression at the transcriptional, post-transcriptional, and epigenetic levels. Emerging evidence indicates that pathogenic microbes dysregulate the expression of host lncRNAs to suppress cellular defense mechanisms and promote survival. To understand whether the pathogenic human mycoplasmas dysregulate host lncRNAs, we infected HeLa cells with Mycoplasma genitalium (Mg) and Mycoplasma penumoniae (Mp) and assessed the expression of lncRNAs by directional RNA-seq analysis. HeLa cells infected with these species showed up-and-down regulation of lncRNAs expression, indicating that both species can modulate host lncRNAs. However, the number of upregulated (200 for Mg and 112 for Mp) and downregulated lncRNAs (30 for Mg and 62 for Mp) differ widely between these two species. GREAT analysis of the noncoding regions associated with differentially expressed lncRNAs showed that Mg and Mp regulate a discrete set of lncRNA plausibly related to transcription, metabolism, and inflammation. Further, signaling network analysis of the differentially regulated lncRNAs exhibited diverse pathways such as neurodegeneration, NOD-like receptor signaling, MAPK signaling, p53 signaling, and PI3K signaling, suggesting that both species primarily target signaling mechanisms. Overall, the study's results suggest that Mg and Mp modulate lncRNAs to promote their survival within the host but in distinct manners.
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Affiliation(s)
- Enrique I. Ramos
- Center of Emphasis in Cancer, Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, TX, 79905, USA
| | - Raja Veerapandian
- Center of Emphasis in Infectious Diseases, Paul L. Foster School of Medicine, Department of Molecular and Translational Medicine, Texas Tech University Health Sciences Center El Paso, TX, 79905, USA
| | - Kishore Das
- Center of Emphasis in Infectious Diseases, Paul L. Foster School of Medicine, Department of Molecular and Translational Medicine, Texas Tech University Health Sciences Center El Paso, TX, 79905, USA
| | - Jessica A. Chacon
- Department of Medical Education, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, TX, 79905, USA
| | - Shrikanth S. Gadad
- Center of Emphasis in Cancer, Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, TX, 79905, USA
- Frederick L. Francis Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center El Paso, Texas, 79905, USA
- Mays Cancer Center, UT Health San Antonio MD Anderson Cancer Center, San Antonio, TX, 78229, USA
| | - Subramanian Dhandayuthapani
- Center of Emphasis in Infectious Diseases, Paul L. Foster School of Medicine, Department of Molecular and Translational Medicine, Texas Tech University Health Sciences Center El Paso, TX, 79905, USA
- Frederick L. Francis Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center El Paso, Texas, 79905, USA
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Blotas C, Férec C, Moisan S. Tissue-Specific Regulation of CFTR Gene Expression. Int J Mol Sci 2023; 24:10678. [PMID: 37445855 DOI: 10.3390/ijms241310678] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/21/2023] [Accepted: 06/23/2023] [Indexed: 07/15/2023] Open
Abstract
More than 2000 variations are described within the CFTR (Cystic Fibrosis Transmembrane Regulator) gene and related to large clinical issues from cystic fibrosis to mono-organ diseases. Although these CFTR-associated diseases have been well documented, a large phenotype spectrum is observed and correlations between phenotypes and genotypes are still not well established. To address this issue, we present several regulatory elements that can modulate CFTR gene expression in a tissue-specific manner. Among them, cis-regulatory elements act through chromatin loopings and take part in three-dimensional structured organization. With tissue-specific transcription factors, they form chromatin modules and can regulate gene expression. Alterations of specific regulations can impact and modulate disease expressions. Understanding all those mechanisms highlights the need to expand research outside the gene to enhance our knowledge.
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Affiliation(s)
- Clara Blotas
- Univ Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France
| | - Claude Férec
- Univ Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France
| | - Stéphanie Moisan
- Univ Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France
- Laboratoire de Génétique Moléculaire et d'Histocompatibilité, CHU Brest, F-29200 Brest, France
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Ghigo A, De Santi C, Hart M, Mitash N, Swiatecka-Urban A. Cell signaling and regulation of CFTR expression in cystic fibrosis cells in the era of high efficiency modulator therapy. J Cyst Fibros 2023; 22 Suppl 1:S12-S16. [PMID: 36621372 DOI: 10.1016/j.jcf.2022.12.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 12/26/2022] [Accepted: 12/30/2022] [Indexed: 01/09/2023]
Abstract
Cystic fibrosis transmembrane conductance regulator (CFTR) is a cAMP- and protein kinase A (PKA)-regulated channel, expressed on the luminal surface of secretory and absorptive epithelial cells. CFTR has a complex, cell-specific regulatory network playing a major role in cAMP- and Ca2+-activated secretion of electrolytes. It secretes intracellular Cl- and bicarbonate and regulates absorption of electrolytes by differentially controlling the activity of the epithelial Na+ channel (ENaC) in colon, airways, and sweat ducts. The CFTR gene expression is regulated by cell-specific, time-dependent mechanisms reviewed elsewhere [1]. This review will focus on the transcriptional, post-transcriptional, and translational regulation of CFTR by cAMP-PKA, non-coding (nc)RNAs, and TGF-β signaling pathways in cystic fibrosis (CF) cells.
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Affiliation(s)
- Alessandra Ghigo
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Torino, Via Nizza 52, Torino 10126, Italy.
| | - Chiara De Santi
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, 111St Stephen's Green, Dublin 2, Ireland
| | - Merrill Hart
- Department of Pediatrics, University of Virginia Children's Hospital, Charlottesville, VA, United States
| | - Nilay Mitash
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, PA, United States
| | - Agnieszka Swiatecka-Urban
- Department of Pediatrics, University of Virginia Children's Hospital, Charlottesville, VA, United States
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Non-coding RNAs in human health and disease: potential function as biomarkers and therapeutic targets. Funct Integr Genomics 2023; 23:33. [PMID: 36625940 PMCID: PMC9838419 DOI: 10.1007/s10142-022-00947-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 01/11/2023]
Abstract
Human diseases have been a critical threat from the beginning of human history. Knowing the origin, course of action and treatment of any disease state is essential. A microscopic approach to the molecular field is a more coherent and accurate way to explore the mechanism, progression, and therapy with the introduction and evolution of technology than a macroscopic approach. Non-coding RNAs (ncRNAs) play increasingly important roles in detecting, developing, and treating all abnormalities related to physiology, pathology, genetics, epigenetics, cancer, and developmental diseases. Noncoding RNAs are becoming increasingly crucial as powerful, multipurpose regulators of all biological processes. Parallel to this, a rising amount of scientific information has revealed links between abnormal noncoding RNA expression and human disorders. Numerous non-coding transcripts with unknown functions have been found in addition to advancements in RNA-sequencing methods. Non-coding linear RNAs come in a variety of forms, including circular RNAs with a continuous closed loop (circRNA), long non-coding RNAs (lncRNA), and microRNAs (miRNA). This comprises specific information on their biogenesis, mode of action, physiological function, and significance concerning disease (such as cancer or cardiovascular diseases and others). This study review focuses on non-coding RNA as specific biomarkers and novel therapeutic targets.
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Qiao X, Ding Y, Wu D, Zhang A, Yin Y, Wang Q, Wang W, Kang J. The roles of long noncoding RNA-mediated macrophage polarization in respiratory diseases. Front Immunol 2023; 13:1110774. [PMID: 36685535 PMCID: PMC9849253 DOI: 10.3389/fimmu.2022.1110774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 12/16/2022] [Indexed: 01/06/2023] Open
Abstract
Macrophages play an essential role in maintaining the normal function of the innate and adaptive immune responses during host defence. Macrophages acquire diverse functional phenotypes in response to various microenvironmental stimuli, and are mainly classified into classically activated macrophages (M1) and alternatively activated macrophages (M2). Macrophage polarization participates in the inflammatory, fibrotic, and oncogenic processes of diverse respiratory diseases by changing phenotype and function. In recent decades, with the advent of broad-range profiling methods such as microarrays and next-generation sequencing, the discovery of RNA transcripts that do not encode proteins termed "noncoding RNAs (ncRNAs)" has become more easily accessible. As one major member of the regulatory ncRNA family, long noncoding RNAs (lncRNAs, transcripts >200 nucleotides) participate in multiple pathophysiological processes, including cell proliferation, differentiation, and apoptosis, and vary with different stimulants and cell types. Emerging evidence suggests that lncRNAs account for the regulation of macrophage polarization and subsequent effects on respiratory diseases. In this review, we summarize the current published literature from the PubMed database concerning lncRNAs relevant to macrophage polarization and the underlying molecular mechanisms during the occurrence and development of respiratory diseases. These differentially expressed lncRNAs are expected to be biomarkers and targets for the therapeutic regulation of macrophage polarization during disease development.
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Arunima A, van Schaik EJ, Samuel JE. The emerging roles of long non-coding RNA in host immune response and intracellular bacterial infections. Front Cell Infect Microbiol 2023; 13:1160198. [PMID: 37153158 PMCID: PMC10160451 DOI: 10.3389/fcimb.2023.1160198] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 04/07/2023] [Indexed: 05/09/2023] Open
Abstract
The long non-coding RNAs (lncRNAs) are evolutionarily conserved classes of non-coding regulatory transcripts of > 200 nucleotides in length. They modulate several transcriptional and post-transcriptional events in the organism. Depending on their cellular localization and interactions, they regulate chromatin function and assembly; and alter the stability and translation of cytoplasmic mRNAs. Although their proposed range of functionality remains controversial, there is increasing research evidence that lncRNAs play a regulatory role in the activation, differentiation and development of immune signaling cascades; microbiome development; and in diseases such as neuronal and cardiovascular disorders; cancer; and pathogenic infections. This review discusses the functional roles of different lncRNAs in regulation of host immune responses, signaling pathways during host-microbe interaction and infection caused by obligate intracellular bacterial pathogens. The study of lncRNAs is assuming significance as it could be exploited for development of alternative therapeutic strategies for the treatment of severe and chronic pathogenic infections caused by Mycobacterium, Chlamydia and Rickettsia infections, as well as commensal colonization. Finally, this review summarizes the translational potential of lncRNA research in development of diagnostic and prognostic tools for human diseases.
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Aiyer A, Das T, Whiteley GS, Glasbey T, Kriel FH, Farrell J, Manos J. The Efficacy of an N-Acetylcysteine-Antibiotic Combination Therapy on Achromobacter xylosoxidans in a Cystic Fibrosis Sputum/Lung Cell Model. Biomedicines 2022; 10:2886. [PMID: 36359406 PMCID: PMC9687303 DOI: 10.3390/biomedicines10112886] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 11/04/2022] [Accepted: 11/07/2022] [Indexed: 09/29/2023] Open
Abstract
Cystic fibrosis (CF) is a disorder causing dysfunctional ion transport resulting in the accumulation of viscous mucus. This environment fosters a chronic bacterial biofilm-associated infection in the airways. Achromobacter xylosoxidans, a gram-negative aerobic bacillus, has been increasingly associated with antibiotic resistance and chronic colonisation in CF. In this study, we aimed to create a reproducible model of CF infection using an artificial sputum medium (ASMDM-1) with bronchial (BEAS-2B) and macrophage (THP-1) cells to test A. xylosoxidans infection and treatment toxicity. This study was conducted in three distinct stages. First, the tolerance of BEAS-2B cell lines and two A. xylosoxidans strains against ASMDM-1 was optimised. Secondly, the cytotoxicity of combined therapy (CT) comprising N-acetylcysteine (NAC) and the antibiotics colistin or ciprofloxacin was tested on cells alone in the sputum model in both BEAS-2B and THP-1 cells. Third, the efficacy of CT was assessed in the context of a bacterial infection within the live cell/sputum model. We found that a model using 20% ASMDM-1 in both cell populations tolerated a colistin-NAC-based CT and could significantly reduce bacterial loads in vitro (~2 log10 CFU/mL compared to untreated controls). This pilot study provides the foundation to study other bacterial opportunists that infect the CF lung to observe infection and CT kinetics. This model also acts as a springboard for more complex co-culture models.
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Affiliation(s)
- Aditi Aiyer
- Charles Perkins Centre, Infection, Immunity and Inflammation, Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Theerthankar Das
- Charles Perkins Centre, Infection, Immunity and Inflammation, Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Gregory S. Whiteley
- Charles Perkins Centre, Infection, Immunity and Inflammation, Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
- Whiteley Corporation, Level 5, 12 Mount Street North Sydney, Sydney, NSW 2060, Australia
- School of Medicine, Western Sydney University, Sydney, NSW 2566, Australia
| | - Trevor Glasbey
- Whiteley Corporation, 19-23 Laverick Avenue, Tomago, NSW 2322, Australia
| | - Frederik H. Kriel
- Whiteley Corporation, 19-23 Laverick Avenue, Tomago, NSW 2322, Australia
| | - Jessica Farrell
- Charles Perkins Centre, Infection, Immunity and Inflammation, Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
- Whiteley Corporation, Level 5, 12 Mount Street North Sydney, Sydney, NSW 2060, Australia
| | - Jim Manos
- Charles Perkins Centre, Infection, Immunity and Inflammation, Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
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Zhao SS, Tao DL, Chen JM, Wu JP, Yang X, Song JK, Zhu XQ, Zhao GH. RNA sequencing reveals dynamic expression of lncRNAs and mRNAs in caprine endometrial epithelial cells induced by Neospora caninum infection. Parasit Vectors 2022; 15:297. [PMID: 35999576 PMCID: PMC9398501 DOI: 10.1186/s13071-022-05405-5] [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: 06/08/2022] [Accepted: 07/19/2022] [Indexed: 11/10/2022] Open
Abstract
Background The effective transmission mode of Neospora caninum, with infection leading to reproductive failure in ruminants, is vertical transmission. The uterus is an important reproductive organ that forms the maternal–fetal interface. Neospora caninum can successfully invade and proliferate in the uterus, but the molecular mechanisms underlying epithelial-pathogen interactions remain unclear. Accumulating evidence suggests that host long noncoding RNAs (lncRNAs) play important roles in cellular molecular regulatory networks, with reports that these RNA molecules are closely related to the pathogenesis of apicomplexan parasites. However, the expression profiles of host lncRNAs during N. caninum infection has not been reported. Methods RNA sequencing (RNA-seq) analysis was used to investigate the expression profiles of messenger RNAs (mRNAs) and lncRNAs in caprine endometrial epithelial cells (EECs) infected with N. caninum for 24 h (TZ_24h) and 48 h (TZ_48 h), and the potential functions of differentially expressed (DE) lncRNAs were predicted by using Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of their mRNA targets. Results RNA-seq analysis identified 1280.15 M clean reads in 12 RNA samples, including six samples infected with N. caninum for 24 h (TZ1_24h-TZ3_24h) and 48 h (TZ1_48h-TZ3_48h), and six corresponding control samples (C1_24h-C3_24h and C1_48h-C3_48h). Within the categories TZ_24h-vs-C_24h, TZ_48h-vs-C_48h and TZ_48h-vs-TZ_24h, there were 934 (665 upregulated and 269 downregulated), 1238 (785 upregulated and 453 downregulated) and 489 (252 upregulated and 237 downregulated) DEmRNAs, respectively. GO enrichment and KEGG analysis revealed that these DEmRNAs were mainly involved in the regulation of host immune response (e.g. TNF signaling pathway, MAPK signaling pathway, transforming growth factor beta signaling pathway, AMPK signaling pathway, Toll-like receptor signaling pathway, NOD-like receptor signaling pathway), signaling molecules and interaction (e.g. cytokine-cytokine receptor interaction, cell adhesion molecules and ECM-receptor interaction). A total of 88 (59 upregulated and 29 downregulated), 129 (80 upregulated and 49 downregulated) and 32 (20 upregulated and 12 downregulated) DElncRNAs were found within the categories TZ_24h-vs-C_24h, TZ_48h-vs-C_48h and TZ_48h-vs-TZ_24h, respectively. Functional prediction indicated that these DElncRNAs would be involved in signal transduction (e.g. MAPK signaling pathway, PPAR signaling pathway, ErbB signaling pathway, calcium signaling pathway), neural transmission (e.g. GABAergic synapse, serotonergic synapse, cholinergic synapse), metabolism processes (e.g. glycosphingolipid biosynthesis-lacto and neolacto series, glycosaminoglycan biosynthesis-heparan sulfate/heparin) and signaling molecules and interaction (e.g. cytokine-cytokine receptor interaction, cell adhesion molecules and ECM-receptor interaction). Conclusions This is the first investigation of global gene expression profiles of lncRNAs during N. caninum infection. The results provide valuable information for further studies of the roles of lncRNAs during N. caninum infection. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13071-022-05405-5.
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Affiliation(s)
- Shan-Shan Zhao
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - De-Liang Tao
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Jin-Ming Chen
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Jiang-Ping Wu
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xin Yang
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Jun-Ke Song
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xing-Quan Zhu
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801, Shanxi, China. .,Key Laboratory of Veterinary Public Health of Higher Education of Yunnan Province, College of Veterinary Medicine, Yunnan Agricultural University, Kunming, 650201, Yunnan, China.
| | - Guang-Hui Zhao
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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Qiao X, Hou G, He YL, Song DF, An Y, Altawil A, Zhou XM, Wang QY, Kang J, Yin Y. The Novel Regulatory Role of the lncRNA–miRNA–mRNA Axis in Chronic Inflammatory Airway Diseases. Front Mol Biosci 2022; 9:927549. [PMID: 35769905 PMCID: PMC9234692 DOI: 10.3389/fmolb.2022.927549] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 05/19/2022] [Indexed: 12/28/2022] Open
Abstract
Chronic inflammatory airway diseases, characterized by airway inflammation and airway remodelling, are increasing as a cause of morbidity and mortality for all age groups and races across the world. The underlying molecular mechanisms involved in chronic inflammatory airway diseases have not been fully explored. MicroRNAs (miRNAs) and long noncoding RNAs (lncRNAs) have recently attracted much attention for their roles in the regulation of a variety of biological processes. A number of studies have confirmed that both lncRNAs and miRNAs can regulate the initiation and progression of chronic airway diseases by targeting mRNAs and regulating different cellular processes, such as proliferation, apoptosis, inflammation, migration, and epithelial–mesenchymal transition (EMT). Recently, accumulative evidence has shown that the novel regulatory mechanism underlying the interaction among lncRNAs, miRNAs and messenger RNAs (mRNAs) plays a critical role in the pathophysiological processes of chronic inflammatory airway diseases. In this review, we comprehensively summarized the regulatory roles of the lncRNA–miRNA–mRNA network in different cell types and their potential roles as biomarkers, indicators of comorbidities or therapeutic targets for chronic inflammatory airway diseases, particularly chronic obstructive pulmonary disease (COPD) and asthma.
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Affiliation(s)
- Xin Qiao
- Department of Pulmonary and Critical Care Medicine, First Affiliated Hospital of China Medical University, Shenyang, China
| | - Gang Hou
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
| | - Yu-Lin He
- Department of Pulmonary and Critical Care Medicine, First Affiliated Hospital of China Medical University, Shenyang, China
| | - Dong-Fang Song
- Department of Pulmonary and Critical Care Medicine, First Affiliated Hospital of China Medical University, Shenyang, China
| | - Yi An
- Department of Pulmonary and Critical Care Medicine, First Affiliated Hospital of China Medical University, Shenyang, China
| | - Abdullah Altawil
- Department of Pulmonary and Critical Care Medicine, First Affiliated Hospital of China Medical University, Shenyang, China
| | - Xiao-Ming Zhou
- Respiratory Department, Center for Pulmonary Vascular Diseases, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
- *Correspondence: Xiao-Ming Zhou, ; Yan Yin,
| | - Qiu-Yue Wang
- Department of Pulmonary and Critical Care Medicine, First Affiliated Hospital of China Medical University, Shenyang, China
| | - Jian Kang
- Department of Pulmonary and Critical Care Medicine, First Affiliated Hospital of China Medical University, Shenyang, China
| | - Yan Yin
- Department of Pulmonary and Critical Care Medicine, First Affiliated Hospital of China Medical University, Shenyang, China
- *Correspondence: Xiao-Ming Zhou, ; Yan Yin,
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Zhang X, Moore CM, Harmacek LD, Domenico J, Rangaraj VR, Ideozu JE, Knapp JR, Woods KJ, Jump S, Jia S, Prokop JW, Bowler R, Hessner MJ, Gelfand EW, Levy H. CFTR-mediated monocyte/macrophage dysfunction revealed by cystic fibrosis proband-parent comparisons. JCI Insight 2022; 7:152186. [PMID: 35315363 PMCID: PMC8986072 DOI: 10.1172/jci.insight.152186] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 02/02/2022] [Indexed: 12/23/2022] Open
Abstract
Cystic fibrosis (CF) is an inherited disorder caused by biallelic mutations of the CF transmembrane conductance regulator (CFTR) gene. Converging evidence suggests that CF carriers with only 1 defective CFTR copy are at increased risk for CF-related conditions and pulmonary infections, but the molecular mechanisms underpinning this effect remain unknown. We performed transcriptomic profiling of peripheral blood mononuclear cells (PBMCs) of CF child-parent trios (proband, father, and mother) and healthy control (HC) PBMCs or THP-1 cells incubated with the plasma of these participants. Transcriptomic analyses revealed suppression of cytokine-enriched immune-related genes (IL-1β, CXCL8, CREM), implicating lipopolysaccharide tolerance in innate immune cells (monocytes) of CF probands and their parents. These data suggest that a homozygous as well as a heterozygous CFTR mutation can modulate the immune/inflammatory system. This conclusion is further supported by the finding of lower numbers of circulating monocytes in CF probands and their parents, compared with HCs, and the abundance of mononuclear phagocyte subsets, which correlated with Pseudomonas aeruginosa infection, lung disease severity, and CF progression in the probands. This study provides insight into demonstrated CFTR-related innate immune dysfunction in individuals with CF and carriers of a CFTR mutation that may serve as a target for personalized therapy.
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Affiliation(s)
- Xi Zhang
- Data Science program, Weinberg College of Arts and Sciences, Northwestern University, Evanston, Illinois, USA.,Division of Pediatric Pulmonary Medicine, Department of Pediatrics, and
| | - Camille M Moore
- Center for Genes, Environment and Health, National Jewish Health, Denver, Colorado, USA
| | - Laura D Harmacek
- Center for Genes, Environment and Health, National Jewish Health, Denver, Colorado, USA
| | - Joanne Domenico
- Division of Pediatric Pulmonary Medicine, Department of Pediatrics, and
| | - Vittobai Rashika Rangaraj
- Division of Pulmonary & Sleep Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
| | - Justin E Ideozu
- Genomic Medicine, Genomics Research Center, AbbVie, North Chicago, Illinois, USA
| | - Jennifer R Knapp
- Center for Genes, Environment and Health, National Jewish Health, Denver, Colorado, USA
| | - Katherine J Woods
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Stephanie Jump
- Department of Pediatrics, National Jewish Health, Denver, Colorado, USA
| | - Shuang Jia
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Max McGee Center for Juvenile Diabetes, Children's Research Institute, Children's Hospital of Wisconsin, Milwaukee, Wisconsin, USA
| | - Jeremy W Prokop
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan, USA
| | - Russell Bowler
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, and
| | - Martin J Hessner
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Max McGee Center for Juvenile Diabetes, Children's Research Institute, Children's Hospital of Wisconsin, Milwaukee, Wisconsin, USA
| | - Erwin W Gelfand
- Division of Cell Biology, Department of Pediatrics, National Jewish Health, Denver, Colorado, USA.,Division of Immunology, Microbiology and Pediatrics, Department of Pediatrics, University of Colorado School of Medicine, Denver, Colorado, USA
| | - Hara Levy
- Division of Pediatric Pulmonary Medicine, Department of Pediatrics, and
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12
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Luo C, Liu F, Su W, Long P, Liang J, Hou W, Jiang H, Long X, Su G. Prognostic value of LINC02560 in colorectal cancer correlates with tumor microenvironment immunity. J Cancer 2022; 12:7507-7517. [PMID: 35003370 PMCID: PMC8734400 DOI: 10.7150/jca.64940] [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: 07/14/2021] [Accepted: 10/23/2021] [Indexed: 12/24/2022] Open
Abstract
Background: LINC02560 is a new 477 bp long non-coding RNA located in 19q13.43. However, the expression of LINC02560 in colorectal cancer (CRC) has not been reported, and its correlation with tumor development and function is still unclear. Methods: The expression of LINC02560 in CRC was first analyzed in the cancer genome atlas (TCGA) combined with The Genotype-Tissue Expression(GTEx) databases and then validated by clinical CRC samples and cell lines. The association between LINC02560 expression and clinicopathologic variables was analyzed by the Wilcoxon Rank SUM test. Cox regression analysis and Kaplan-Meier plots were used to assess the prognostic value of LINC02560 in CRC. The correlation between the expression level of LINC02560 and the 24 immune cells in tumor microenvironment (TME) was analyzed by single sample gene set enrichment analysis (ssGSEA). Gene set enrichment analysis (GSEA) was conducted to detect potential biological processes associated with LINC02560 in CRC. Results: LINC02560 was significantly up-regulated in CRC in comparison to normal samples. There are significant differences in the expression of LINC02560 in different subgroups of N stage, M stage, carcinoembryonic antigen (CEA) level, residual tumor, TP53 status and pathological stage. The high LINC02560 expression indicated poor overall survival (OS) and progress free interval (PFI) in patients with CRC. Moreover, the multivariate Cox analysis demonstrated that the expression of LINC02560 was an independent prognosis-predicting factor for OS in CRC patients. GSEA indicated that high expression of LINC02560 was involved in MAPK, Wnt, and PPAR signaling pathways and participated in humoral immune processes. We also identified that LINC02560 expression had a negative correlation with 4 kinds of immune cells. Conclusions: In summary, our research results indicate that LINC02560 may be a potential prognostic biomarker. It is involved in the occurrence and development of CRC and may affect the prognosis of CRC patients by regulating immune cells in the TME.
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Affiliation(s)
- Chunying Luo
- Department of Cell Biology, Medical College of Guangxi University, Nanning 530004, Guangxi, PR China.,Department of Pathology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise 533000, Guangxi, PR China
| | - Fahui Liu
- Department of Pathology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise 533000, Guangxi, PR China
| | - Weichao Su
- Department of Gastrointestinal Surgery III, Xiamen Cancer Hospital, First Affiliated Hospital of Xiamen University, 55 Zhenhai Road, Xiamen 361003, China
| | - Puze Long
- Department of Pathology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise 533000, Guangxi, PR China
| | - Jiadong Liang
- Department of Pathology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise 533000, Guangxi, PR China
| | - Wanyun Hou
- Department of Pathology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise 533000, Guangxi, PR China
| | - Haifeng Jiang
- Department of Gastrointestinal Surgery III, Xiamen Cancer Hospital, First Affiliated Hospital of Xiamen University, 55 Zhenhai Road, Xiamen 361003, China
| | - Xidai Long
- Department of Pathology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise 533000, Guangxi, PR China
| | - Guoqiang Su
- Department of Cell Biology, Medical College of Guangxi University, Nanning 530004, Guangxi, PR China.,Department of Gastrointestinal Surgery III, Xiamen Cancer Hospital, First Affiliated Hospital of Xiamen University, 55 Zhenhai Road, Xiamen 361003, China
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13
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Soni DK, Biswas R. Role of Non-Coding RNAs in Post-Transcriptional Regulation of Lung Diseases. Front Genet 2021; 12:767348. [PMID: 34819948 PMCID: PMC8606426 DOI: 10.3389/fgene.2021.767348] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 10/25/2021] [Indexed: 12/16/2022] Open
Abstract
Non-coding RNAs (ncRNAs), notably microRNAs (miRNAs) and long noncoding RNAs (lncRNAs), have recently gained increasing consideration because of their versatile role as key regulators of gene expression. They adopt diverse mechanisms to regulate transcription and translation, and thereby, the function of the protein, which is associated with several major biological processes. For example, proliferation, differentiation, apoptosis, and metabolic pathways demand fine-tuning for the precise development of a specific tissue or organ. The deregulation of ncRNA expression is concomitant with multiple diseases, including lung diseases. This review highlights recent advances in the post-transcriptional regulation of miRNAs and lncRNAs in lung diseases such as asthma, chronic obstructive pulmonary disease, cystic fibrosis, and idiopathic pulmonary fibrosis. Further, we also discuss the emerging role of ncRNAs as biomarkers as well as therapeutic targets for lung diseases. However, more investigations are required to explore miRNAs and lncRNAs interaction, and their function in the regulation of mRNA expression. Understanding these mechanisms might lead to early diagnosis and the development of novel therapeutics for lung diseases.
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Affiliation(s)
- Dharmendra Kumar Soni
- Department of Anatomy, Physiology and Genetics, School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Roopa Biswas
- Department of Anatomy, Physiology and Genetics, School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
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14
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Zhang X, Liu Y, Lu Y, Li S, Liu J, Zhang Y, Wang L, Li M, Luo Y, Zhang W, Chen C, Li Y. N-3-(oxododecanoyl)-l-homoserine lactone suppresses dendritic cell maturation by upregulating the long noncoding RNA NRIR. J Biosci 2021. [DOI: 10.1007/s12038-021-00186-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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15
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Schmerer N, Schulte LN. Long noncoding RNAs in bacterial infection. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 12:e1664. [PMID: 33989449 DOI: 10.1002/wrna.1664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 04/19/2021] [Accepted: 04/22/2021] [Indexed: 11/10/2022]
Abstract
Infectious and inflammatory diseases remain major causes of mortality and morbidity worldwide. To combat bacterial infections, the mammalian immune system employs a myriad of regulators, which secure the effective initiation of inflammatory responses while preventing pathologies due to overshooting immunity. Recently, the human genome has been shown to be pervasively transcribed and to generate thousands of still poorly characterized long noncoding RNAs (lncRNAs). A growing body of literature suggests that lncRNAs play important roles in the regulatory circuitries controlling innate and adaptive immune responses to bacterial pathogens. This review provides an overview of the roles of lncRNAs in the interaction of human and rodent host cells with bacterial pathogens. Further decoding of the lncRNA networks that underlie pathological inflammation and immune subversion could provide new insights into the host cell mechanisms and microbial strategies that determine the outcome of bacterial infections. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Nils Schmerer
- Institute for Lung Research, Philipps-University, Marburg, Germany
| | - Leon N Schulte
- Institute for Lung Research, Philipps-University, Marburg, Germany.,German Center for Lung Research, Giessen, Germany
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16
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Wen Y, Chen H, Luo F, Zhou H, Li Z. Roles of long noncoding RNAs in bacterial infection. Life Sci 2020; 263:118579. [DOI: 10.1016/j.lfs.2020.118579] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/28/2020] [Accepted: 10/03/2020] [Indexed: 02/09/2023]
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17
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Dang H, Polineni D, Pace RG, Stonebraker JR, Corvol H, Cutting GR, Drumm ML, Strug LJ, O’Neal WK, Knowles MR. Mining GWAS and eQTL data for CF lung disease modifiers by gene expression imputation. PLoS One 2020; 15:e0239189. [PMID: 33253230 PMCID: PMC7703903 DOI: 10.1371/journal.pone.0239189] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 09/02/2020] [Indexed: 12/18/2022] Open
Abstract
Genome wide association studies (GWAS) have identified several genomic loci with candidate modifiers of cystic fibrosis (CF) lung disease, but only a small proportion of the expected genetic contribution is accounted for at these loci. We leveraged expression data from CF cohorts, and Genotype-Tissue Expression (GTEx) reference data sets from multiple human tissues to generate predictive models, which were used to impute transcriptional regulation from genetic variance in our GWAS population. The imputed gene expression was tested for association with CF lung disease severity. By comparing and combining results from alternative approaches, we identified 379 candidate modifier genes. We delved into 52 modifier candidates that showed consensus between approaches, and 28 of them were near known GWAS loci. A number of these genes are implicated in the pathophysiology of CF lung disease (e.g., immunity, infection, inflammation, HLA pathways, glycosylation, and mucociliary clearance) and the CFTR protein biology (e.g., cytoskeleton, microtubule, mitochondrial function, lipid metabolism, endoplasmic reticulum/Golgi, and ubiquitination). Gene set enrichment results are consistent with current knowledge of CF lung disease pathogenesis. HLA Class II genes on chr6, and CEP72, EXOC3, and TPPP near the GWAS peak on chr5 are most consistently associated with CF lung disease severity across the tissues tested. The results help to prioritize genes in the GWAS regions, predict direction of gene expression regulation, and identify new candidate modifiers throughout the genome for potential therapeutic development.
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Affiliation(s)
- Hong Dang
- Marsico Lung Institute, University of North Carolina at Chapel Hill School of Medicine Cystic Fibrosis/Pulmonary Research & Treatment Center, Chapel Hill, North Carolina, United States of America
| | - Deepika Polineni
- University of Kansas Medical Center, Kansas City, Kansas, United States of America
| | - Rhonda G. Pace
- Marsico Lung Institute, University of North Carolina at Chapel Hill School of Medicine Cystic Fibrosis/Pulmonary Research & Treatment Center, Chapel Hill, North Carolina, United States of America
| | - Jaclyn R. Stonebraker
- Marsico Lung Institute, University of North Carolina at Chapel Hill School of Medicine Cystic Fibrosis/Pulmonary Research & Treatment Center, Chapel Hill, North Carolina, United States of America
| | - Harriet Corvol
- Pediatric Pulmonary Department, Assistance Publique-Hôpitaux sde Paris (AP-HP), Hôpital Trousseau, Institut National de la Santé et la Recherche Médicale (INSERM) U938, Paris, France
- Sorbonne Universités, Université Pierre et Marie Curie (UPMC), Paris 6, Paris, France
| | - Garry R. Cutting
- McKusick-Nathans Institute of Genetic Medicine, Baltimore, Maryland, United States of America
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Mitchell L. Drumm
- Department of Pediatrics, School of Medicine, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Lisa J. Strug
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Wanda K. O’Neal
- Marsico Lung Institute, University of North Carolina at Chapel Hill School of Medicine Cystic Fibrosis/Pulmonary Research & Treatment Center, Chapel Hill, North Carolina, United States of America
| | - Michael R. Knowles
- Marsico Lung Institute, University of North Carolina at Chapel Hill School of Medicine Cystic Fibrosis/Pulmonary Research & Treatment Center, Chapel Hill, North Carolina, United States of America
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18
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Wei T, Sui H, Su Y, Cheng W, Liu Y, He Z, Ji Q, Xu C. Research advances in molecular mechanisms underlying the pathogenesis of cystic fibrosis: From technical improvement to clinical applications (Review). Mol Med Rep 2020; 22:4992-5002. [PMID: 33173976 PMCID: PMC7646950 DOI: 10.3892/mmr.2020.11607] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 09/17/2020] [Indexed: 12/11/2022] Open
Abstract
Cystic fibrosis (CF) is a chronic disease causing severe impairment to the respiratory system and digestive tracts. Currently, CF is incurable. As an autosomal recessive disorder, the morbidity of CF is significantly higher among Caucasians of European descent, whereas it is less pervasive among African and Asian populations. The disease is caused by identical mutations (homozygosity) or different mutations (heterozygosity) of an autosomal recessive mutation at position 7q31.2-q31.1 of chromosome 7. Diagnostic criteria and guidelines work concurrently with laboratory detection to facilitate precise CF detection. With technological advances, the understanding of CF pathogenesis has reached an unprecedented level, allowing for increasingly precise carrier screening, more effective early stage CF intervention and improved prognostic outcomes. These advances significantly increase the life quality and expectancy of patients with CF. Given the numerous improvements in the field of CF, the current review summarized the technical advances in the study of the molecular mechanisms underlying CF, as well as how these improvements facilitate the clinical outcomes of CF. Furthermore, challenges and obstacles to overcome are discussed.
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Affiliation(s)
- Tao Wei
- Department of Histology and Embryology, Shandong First Medical University and Shandong Academy of Medical Sciences, Tai'an, Shandong 271000, P.R. China
| | - Hongshu Sui
- Department of Histology and Embryology, Shandong First Medical University and Shandong Academy of Medical Sciences, Tai'an, Shandong 271000, P.R. China
| | - Yanping Su
- Department of Histology and Embryology, Shandong First Medical University and Shandong Academy of Medical Sciences, Tai'an, Shandong 271000, P.R. China
| | - Wanjing Cheng
- Department of Histology and Embryology, Shandong First Medical University and Shandong Academy of Medical Sciences, Tai'an, Shandong 271000, P.R. China
| | - Yunhua Liu
- Department of Histology and Embryology, Shandong First Medical University and Shandong Academy of Medical Sciences, Tai'an, Shandong 271000, P.R. China
| | - Zilin He
- Department of Histology and Embryology, Shandong First Medical University and Shandong Academy of Medical Sciences, Tai'an, Shandong 271000, P.R. China
| | - Qingchao Ji
- Department of Histology and Embryology, Shandong First Medical University and Shandong Academy of Medical Sciences, Tai'an, Shandong 271000, P.R. China
| | - Changlong Xu
- Reproductive Medical Center, Nanning Second People's Hospital, Nanning, Guangxi Zhuang Autonomous Region 530031, P.R. China
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19
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Laucirica DR, Garratt LW, Kicic A. Progress in Model Systems of Cystic Fibrosis Mucosal Inflammation to Understand Aberrant Neutrophil Activity. Front Immunol 2020; 11:595. [PMID: 32318073 PMCID: PMC7154161 DOI: 10.3389/fimmu.2020.00595] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 03/13/2020] [Indexed: 12/18/2022] Open
Abstract
In response to recurrent infection in cystic fibrosis (CF), powerful innate immune signals trigger polymorphonuclear neutrophil recruitment into the airway lumen. Exaggerated neutrophil proteolytic activity results in sustained inflammation and scarring of the airways. Consequently, neutrophils and their secretions are reliable clinical biomarkers of lung disease progression. As neutrophils are required to clear infection and yet a direct cause of airway damage, modulating adverse neutrophil activity while preserving their pathogen fighting function remains a key area of CF research. The factors that drive their pathological behavior are still under investigation, especially in early disease when aberrant neutrophil behavior first becomes evident. Here we examine the latest findings of neutrophils in pediatric CF lung disease and proposed mechanisms of their pathogenicity. Highlighted in this review are current and emerging experimental methods for assessing CF mucosal immunity and human neutrophil function in the laboratory.
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Affiliation(s)
- Daniel R Laucirica
- Faculty of Health and Medical Sciences, University of Western Australia, Nedlands, WA, Australia.,Telethon Kids Institute, University of Western Australia, Nedlands, WA, Australia
| | - Luke W Garratt
- Telethon Kids Institute, University of Western Australia, Nedlands, WA, Australia
| | - Anthony Kicic
- Faculty of Health and Medical Sciences, University of Western Australia, Nedlands, WA, Australia.,Telethon Kids Institute, University of Western Australia, Nedlands, WA, Australia.,Department of Respiratory and Sleep Medicine, Perth Children's Hospital, Nedlands, WA, Australia.,School of Public Health, Curtin University, Bentley, WA, Australia
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20
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Fan XC, Liu TL, Wang Y, Wu XM, Wang YX, Lai P, Song JK, Zhao GH. Genome-wide analysis of differentially expressed profiles of mRNAs, lncRNAs and circRNAs in chickens during Eimeria necatrix infection. Parasit Vectors 2020; 13:167. [PMID: 32245514 PMCID: PMC7118956 DOI: 10.1186/s13071-020-04047-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 03/27/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Eimeria necatrix, the most highly pathogenic coccidian in chicken small intestines, can cause high morbidity and mortality in susceptible birds and devastating economic losses in poultry production, but the underlying molecular mechanisms in interaction between chicken and E. necatrix are not entirely revealed. Accumulating evidence shows that the long-non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) are key regulators in various infectious diseases. However, the expression profiles and roles of these two non-coding RNAs (ncRNAs) during E. necatrix infection are still unclear. METHODS The expression profiles of mRNAs, lncRNAs and circRNAs in mid-segments of chicken small intestines at 108 h post-infection (pi) with E. necatrix were analyzed by using the RNA-seq technique. RESULTS After strict filtering of raw data, we putatively identified 49,183 mRNAs, 818 lncRNAs and 4153 circRNAs. The obtained lncRNAs were classified into four types, including 228 (27.87%) intergenic, 67 (8.19%) intronic, 166 (20.29%) anti-sense and 357 (43.64%) sense-overlapping lncRNAs; of these, 571 were found to be novel. Five types were also predicted for putative circRNAs, including 180 exonic, 54 intronic, 113 antisense, 109 intergenic and 3697 sense-overlapping circRNAs. Eimeria necatrix infection significantly altered the expression of 1543 mRNAs (707 upregulated and 836 downregulated), 95 lncRNAs (49 upregulated and 46 downregulated) and 13 circRNAs (9 upregulated and 4 downregulated). Target predictions revealed that 38 aberrantly expressed lncRNAs would cis-regulate 73 mRNAs, and 1453 mRNAs could be trans-regulated by 87 differentially regulated lncRNAs. Additionally, 109 potential sponging miRNAs were also identified for 9 circRNAs. GO and KEGG enrichment analysis of target mRNAs for lncRNAs, and sponging miRNA targets and source genes for circRNAs identified associations of both lncRNAs and circRNAs with host immune defense and pathogenesis during E. necatrix infection. CONCLUSIONS To the best of our knowledge, the present study provides the first genome-wide analysis of mRNAs, lncRNAs and circRNAs in chicken small intestines infected with E. necatrix. The obtained data will offer novel clues for exploring the interaction mechanisms between chickens and Eimeria spp.
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Affiliation(s)
- Xian-Cheng Fan
- Department of Parasitology, College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, China.,Center of Animal Disease Prevention and Control of Huyi District, Xi'an, 710300, China
| | - Ting-Li Liu
- Department of Parasitology, College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, China.,State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730000, China
| | - Yi Wang
- Department of Parasitology, College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, China
| | - Xue-Mei Wu
- Department of Parasitology, College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, China
| | - Yu-Xin Wang
- Department of Parasitology, College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, China
| | - Peng Lai
- Department of Parasitology, College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, China
| | - Jun-Ke Song
- Department of Parasitology, College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, China
| | - Guang-Hui Zhao
- Department of Parasitology, College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, China.
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21
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Wang Y, Huang L, Wang Y, Luo W, Li F, Xiao J, Qin S, Wang Z, Song X, Wang Y, Jin F, Wang Y. Single-cell RNA-sequencing analysis identifies host long noncoding RNA MAMDC2-AS1 as a co-factor for HSV-1 nuclear transport. Int J Biol Sci 2020; 16:1586-1603. [PMID: 32226304 PMCID: PMC7097924 DOI: 10.7150/ijbs.42556] [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: 12/09/2019] [Accepted: 02/02/2020] [Indexed: 12/29/2022] Open
Abstract
Herpes simplex virus (HSV) type 1 (HSV-1) infection exhibited high heterogeneity at individual cells level, including the different gene expression patterns and varying amounts of progeny virus. However, the underlying mechanism of such variability remains obscure. The importance of host long noncoding RNAs (lncRNAs) in virus infection had been recognized, while the contribution of lncRNAs to the heterogeneous infection remains unknown. Herein, a prior single-cell RNA sequencing data using HSV-1 reporter strain expressing ICP4-YFP was re-analyzed to obtain the differentially expressed lncRNA between the successfully initiated viral gene expression (ICP4-YFP+) cells and the aborted infection cells (ICP4-YFP-). The ICP4-YFP+ population show a higher abundance of MAMDC2 antisense 1 (MAMDC2-AS1) lncRNA than ICP4-YFP- population. MAMDC2-AS1 silencing reduces the expression of HSV-1 immediate early (IE) genes and limit HSV-1 infection in human host cells. Consistently, ectopic expression of MAMDC2-AS1 enhances HSV-1 IE genes transcription and facilitates the formation of HSV-1-induced plaques. Mechanically, both RNA-pull down and RNA immunoprecipitation assays show that MAMDC2-AS1 interacts with the RNA binding protein heat shock protein 90α (Hsp90α), a molecular chaperone involving in the nuclear import of HSV-1. The MAMDC2-AS1-Hsp90α interaction facilitates the nuclear transport of viral tegument protein VP16, the core factor initiating the expression of HSV-1 IE genes. The transcription factor YY1 mediates the induction of MAMDC2-AS1 upon HSV-1 infection. Our study elucidates the contribution of lncRNA to HSV-1 infection susceptibility in human cells and the role of Hsp90α RNA binding activity in HSV-1 infection.
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Affiliation(s)
- Yiliang Wang
- College of Life science and Technology, Guangzhou Jinan Biomedicine Research and Development Center, Jinan University, Guangzhou 510632, PR China
| | - Lianzhou Huang
- College of Life science and Technology, Guangzhou Jinan Biomedicine Research and Development Center, Jinan University, Guangzhou 510632, PR China.,College of Pharmacy, Jinan University, Guangzhou 510632, PR China
| | - Yun Wang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Jinan University, Guangzhou 510632, PR China
| | - Weisheng Luo
- College of Life science and Technology, Guangzhou Jinan Biomedicine Research and Development Center, Jinan University, Guangzhou 510632, PR China
| | - Feng Li
- College of Life science and Technology, Guangzhou Jinan Biomedicine Research and Development Center, Jinan University, Guangzhou 510632, PR China
| | - Ji Xiao
- College of Life science and Technology, Guangzhou Jinan Biomedicine Research and Development Center, Jinan University, Guangzhou 510632, PR China
| | - Shurong Qin
- College of Pharmacy, Jinan University, Guangzhou 510632, PR China
| | - Zhaoyang Wang
- College of Life science and Technology, Guangzhou Jinan Biomedicine Research and Development Center, Jinan University, Guangzhou 510632, PR China
| | - Xiaowei Song
- College of Pharmacy, Jinan University, Guangzhou 510632, PR China
| | - Yuan Wang
- College of Life science and Technology, Guangzhou Jinan Biomedicine Research and Development Center, Jinan University, Guangzhou 510632, PR China
| | - Fujun Jin
- Integrated Chinese and Western Medicine Postdoctoral Research Station, Jinan University, Guangzhou 510632, PR China
| | - Yifei Wang
- College of Life science and Technology, Guangzhou Jinan Biomedicine Research and Development Center, Jinan University, Guangzhou 510632, PR China
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22
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Kumar P, Sen C, Peters K, Frizzell RA, Biswas R. Comparative analyses of long non-coding RNA profiles in vivo in cystic fibrosis lung airway and parenchyma tissues. Respir Res 2019; 20:284. [PMID: 31842871 PMCID: PMC6916039 DOI: 10.1186/s12931-019-1259-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 12/09/2019] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Recent advances in the functional analyses of endogenous non-coding RNA (ncRNA) molecules, including long non-coding RNAs (LncRNAs), have provided a new perspective on the crucial roles of RNA in gene regulation. Consequently, LncRNA deregulation is a key factor in various diseases, including pulmonary disorders like Cystic Fibrosis (CF). CF is the most common life limiting recessive disease in the U.S., and is due to mutations in the CFTR gene. CF mutations, of which the most common is F508del-CFTR, prevents correct folding, trafficking and function of the mutant CFTR protein and is further manifested by the hyper-expression of pro-inflammatory cytokines and chemokines into the airway lumen leading to bronchiectasis and culminating in lung destruction. METHODS Here we report a distinct LncRNA signature and corresponding mRNAs that distinguishes CF lung (airway and parenchyma) tissues from matched non-CF controls (n = 4 each group), generated by microarray specific for LncRNAs which includes corresponding mRNA expressions. In silico analyses of the cellular processes that are impacted by these LncRNAs was performed using Gene Ontology (GO). A selected subset of LncRNAs were validated by quantitative real-time PCR. RESULTS We have identified 636 LncRNAs differentially expressed in CF airway epithelium and 1974 in CF lung parenchyma compared to matched non-CF controls (fold change ≥2, p < 0.05), majority of which (> 50%) are intergenic. Interestingly, 15 of these differentially expressed LncRNAs and 9 coding mRNAs are common to airway and parenchyma tissues. GO analyses indicates that signaling pathways and cell membrane functions are significantly affected by the alteration in LncRNA expressions in CF lung tissues. Seven of the differentially expressed LncRNAs, exhibit similar expression trends in CFBE41o- compared to control cells. CONCLUSION Understanding the mechanisms by which these LncRNAs regulate CF disease phenotype will help develop novel therapeutic targets for CF and related pulmonary diseases, such as COPD and Asthma.
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Affiliation(s)
- Parameet Kumar
- Department of Anatomy, Physiology and Genetics, School of Medicine, Uniformed Services University of the Health Sciences, Room B4024, 4301 Jones Bridge Road, Bethesda, MD, 20814, USA
| | - Chaitali Sen
- Department of Anatomy, Physiology and Genetics, School of Medicine, Uniformed Services University of the Health Sciences, Room B4024, 4301 Jones Bridge Road, Bethesda, MD, 20814, USA
| | - Kathryn Peters
- Departments of Pediatrics and Cell Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Raymond A Frizzell
- Departments of Pediatrics and Cell Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Roopa Biswas
- Department of Anatomy, Physiology and Genetics, School of Medicine, Uniformed Services University of the Health Sciences, Room B4024, 4301 Jones Bridge Road, Bethesda, MD, 20814, USA.
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23
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Finotti A, Fabbri E, Lampronti I, Gasparello J, Borgatti M, Gambari R. MicroRNAs and Long Non-coding RNAs in Genetic Diseases. Mol Diagn Ther 2019; 23:155-171. [PMID: 30610665 PMCID: PMC6469593 DOI: 10.1007/s40291-018-0380-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Since the discovery and classification of non-coding RNAs, their roles have gained great attention. In this respect, microRNAs and long non-coding RNAs have been firmly demonstrated to be linked to regulation of gene expression and onset of human diseases, including rare genetic diseases; therefore they are suitable targets for therapeutic intervention. This issue, in the context of rare genetic diseases, is being considered by an increasing number of research groups and is of key interest to the health community. In the case of rare genetic diseases, the possibility of developing personalized therapy in precision medicine has attracted the attention of researchers and clinicians involved in developing "orphan medicinal products" and proposing these to the European Medicines Agency (EMA) and to the Food and Drug Administration (FDA) Office of Orphan Products Development (OOPD) in the United States. The major focuses of these activities are the evaluation and development of products (drugs, biologics, devices, or medical foods) considered to be promising for diagnosis and/or treatment of rare diseases or conditions, including rare genetic diseases. In an increasing number of rare genetic diseases, analysis of microRNAs and long non-coding RNAs has been proven a promising strategy. These diseases include, but are not limited to, Duchenne muscular dystrophy, cystic fibrosis, Rett syndrome, and β-thalassemia. In conclusion, a large number of approaches based on targeting microRNAs and long non-coding RNAs are expected in the field of molecular diagnosis and therapy, with a facilitated technological transfer in the case of rare genetic diseases, in virtue of the existing regulation concerning these diseases.
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Affiliation(s)
- Alessia Finotti
- Department of Life Sciences and Biotechnology, Section of Biochemistry and Molecular Biology, University of Ferrara, Via Fossato di Mortara n.74, 44121, Ferrara, Italy
| | - Enrica Fabbri
- Department of Life Sciences and Biotechnology, Section of Biochemistry and Molecular Biology, University of Ferrara, Via Fossato di Mortara n.74, 44121, Ferrara, Italy
| | - Ilaria Lampronti
- Department of Life Sciences and Biotechnology, Section of Biochemistry and Molecular Biology, University of Ferrara, Via Fossato di Mortara n.74, 44121, Ferrara, Italy
| | - Jessica Gasparello
- Department of Life Sciences and Biotechnology, Section of Biochemistry and Molecular Biology, University of Ferrara, Via Fossato di Mortara n.74, 44121, Ferrara, Italy
| | - Monica Borgatti
- Department of Life Sciences and Biotechnology, Section of Biochemistry and Molecular Biology, University of Ferrara, Via Fossato di Mortara n.74, 44121, Ferrara, Italy
| | - Roberto Gambari
- Department of Life Sciences and Biotechnology, Section of Biochemistry and Molecular Biology, University of Ferrara, Via Fossato di Mortara n.74, 44121, Ferrara, Italy.
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Ideozu JE, Zhang X, McColley S, Levy H. Transcriptome Profiling and Molecular Therapeutic Advances in Cystic Fibrosis: Recent Insights. Genes (Basel) 2019; 10:genes10030180. [PMID: 30813620 PMCID: PMC6470978 DOI: 10.3390/genes10030180] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 02/20/2019] [Accepted: 02/21/2019] [Indexed: 12/16/2022] Open
Abstract
In cystic fibrosis (CF), mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene disrupt the capacity of the encoded protein to function as a channel to transport chloride ions and water across cell membranes. The consequences are deleterious, system-wide, and immensely variable, even among patients with the same CFTR genotype. This underscores the need to characterize the mechanisms contributing to CF pathophysiology. Gene replacement and gene editing therapies have been pursued intensively and are expected to provide a one-time treatment for CF. However, gene replacement therapy is limited by the lack of efficient vectors to deliver functional copies of CFTR to cells without immunological complications, while gene editing technologies such as CRISPR/Cas9 are still in their infancy, mainly useful in somatic cells and limited by off-target insertions. Small molecule treatments targeted at potentiating or correcting CFTR have shown clinical benefits, but they are limited to a few CFTR mutations and insufficient to overcome challenges related to clinical heterogeneity. Transcriptome profiling approaches have emerged as robust tools capable of characterizing phenotypic variability and revealing novel molecular targets with therapeutic potential for CF. We summarize current insights gained through transcriptome profiling approaches in CF studies and recent advances in molecular therapeutics.
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Affiliation(s)
- Justin E Ideozu
- Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL 60611, USA.
- Human Molecular Genetics Program, Stanley Manne Children's Research Institute, Chicago, IL 60614, USA.
- Feinberg School of Medicine at Northwestern University Chicago, Chicago, IL 60611, USA.
| | - Xi Zhang
- Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL 60611, USA.
- Human Molecular Genetics Program, Stanley Manne Children's Research Institute, Chicago, IL 60614, USA.
- Feinberg School of Medicine at Northwestern University Chicago, Chicago, IL 60611, USA.
| | - Susanna McColley
- Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL 60611, USA.
- Feinberg School of Medicine at Northwestern University Chicago, Chicago, IL 60611, USA.
| | - Hara Levy
- Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL 60611, USA.
- Human Molecular Genetics Program, Stanley Manne Children's Research Institute, Chicago, IL 60614, USA.
- Feinberg School of Medicine at Northwestern University Chicago, Chicago, IL 60611, USA.
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25
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Chen W, Hang Y, Xu W, Wu J, Chen L, Chen J, Mao Y, Song J, Song J, Wang H. BLACAT1 predicts poor prognosis and serves as oncogenic lncRNA in small-cell lung cancer. J Cell Biochem 2019; 120:2540-2546. [PMID: 30203450 DOI: 10.1002/jcb.27548] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 08/06/2018] [Indexed: 01/24/2023]
Abstract
Bladder cancer-associated transcript 1 (BLACAT1) is a novel identified long noncoding RNA (lncRNA) in bladder cancer, and has been suggested to function as an oncogenic lncRNA in several types of human cancer. However, its involvement in the progression of small-cell lung cancer (SCLC) remained unknown. The aim of our study was to investigate the clinical value and biological function in SCLC. In our results, BLACAT1 expression was increased in SCLC tissues and cell lines compared with paired adjacent normal tissues and bronchial epithelial cell lines, respectively. In addition, BLACAT1 high-expression was obviously associated with advanced clinical stage, large tumor size, more lymph node metastasis, present distant metastasis, and poor prognosis. Furthermore, multivariate analysis indicated that high-expression of BLACAT1 acted as an independent poor prognostic factor for overall survival in SCLC cases. The loss-of-function studies suggested that of BLACAT1 suppressed SCLC cell proliferation, migration, and invasion, and induced G0/G1 phase arrest. In conclusion, BLACAT1 is associated with the malignant status and prognosis in patients with SCLC, and functions as an oncogenic lncRNA in regulating cell proliferation and motility, suggesting BLACAT1 may act as a potential target for SCLC prevention and treatment.
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Affiliation(s)
- Weiwei Chen
- Department of Radiotherapy, Yancheng Third People's Hospital, The Affiliated Yancheng Hospital of Southeast University, The Sixth Affiliated Hospital of Nantong University, Yancheng, Jiangsu, China
| | - Ye Hang
- Department of Radiotherapy, Yancheng Third People's Hospital, The Affiliated Yancheng Hospital of Southeast University, The Sixth Affiliated Hospital of Nantong University, Yancheng, Jiangsu, China
| | - Weiwei Xu
- Department of Radiotherapy, Yancheng Third People's Hospital, The Affiliated Yancheng Hospital of Southeast University, The Sixth Affiliated Hospital of Nantong University, Yancheng, Jiangsu, China
| | - Jixiang Wu
- Department of Cardiothoracic Surgery, Yancheng Third People's Hospital, The Affiliated Yancheng Hospital of Southeast University, The Sixth Affiliated Hospital of Nantong University, Yancheng, Jiangsu, China
| | - Longyun Chen
- Department of Radiotherapy, Yancheng Third People's Hospital, The Affiliated Yancheng Hospital of Southeast University, The Sixth Affiliated Hospital of Nantong University, Yancheng, Jiangsu, China
| | - Jinzhong Chen
- Department of Radiotherapy, Yancheng Third People's Hospital, The Affiliated Yancheng Hospital of Southeast University, The Sixth Affiliated Hospital of Nantong University, Yancheng, Jiangsu, China
| | - Yixiang Mao
- Department of Radiotherapy, Yancheng Third People's Hospital, The Affiliated Yancheng Hospital of Southeast University, The Sixth Affiliated Hospital of Nantong University, Yancheng, Jiangsu, China
| | - Jin Song
- Department of Radiotherapy, Yancheng Third People's Hospital, The Affiliated Yancheng Hospital of Southeast University, The Sixth Affiliated Hospital of Nantong University, Yancheng, Jiangsu, China
| | - Jianxiang Song
- Department of Cardiothoracic Surgery, Yancheng Third People's Hospital, The Affiliated Yancheng Hospital of Southeast University, The Sixth Affiliated Hospital of Nantong University, Yancheng, Jiangsu, China
| | - Hanhua Wang
- Department of Radiotherapy, Yancheng Third People's Hospital, The Affiliated Yancheng Hospital of Southeast University, The Sixth Affiliated Hospital of Nantong University, Yancheng, Jiangsu, China
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Integrated Analysis of lncRNA and mRNA Transcriptomes Reveals New Regulators of Ubiquitination and the Immune Response in Silica-Induced Pulmonary Fibrosis. BIOMED RESEARCH INTERNATIONAL 2019; 2019:6305065. [PMID: 30756084 PMCID: PMC6348882 DOI: 10.1155/2019/6305065] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 12/19/2018] [Accepted: 12/26/2018] [Indexed: 12/13/2022]
Abstract
Objectives As an epigenetic player, long noncoding RNAs (LncRNAs) have been reported to participate in multiple biological processes; however, their biological functions in silica-induced pulmonary fibrosis (SIPF) occurrence and development remain incompletely understood. Methods Five case/control pairs were used to perform integrated transcriptomes analysis of lncRNA and mRNA. Prediction of lncRNA and mRNA functions was aided by the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Additionally, we constructed a coexpression network of lncRNAs and mRNAs to identify targets of regulation. Results In total, 1069 differentially expressed mRNAs and 366 lncRNAs were identified with the changes more than 2 times (p<0.05), of which 351 downregulated mRNA and 31 downregulated lncRNA were <0.5 (p<0.05) and those of 718 upregulated mRNAs and 335 upregulated lncRNA were >2 (p<0.05). The levels of 10 lncRNAs were measured via qRT-PCR; the results were consistent with the microarray data. Four genes named of FEM1B, TRIM39, TRIM32, and KLHL15 were enriched significantly with ubiquitination and immune response. Cytokine-cytokine receptor interaction was the most significantly enriched KEGG pathway in both mRNAs and lncRNAs. The coexpression network revealed that a single lncRNA can interact with multiple mRNAs, and vice versa. Conclusions lncRNA and mRNA expression were aberrant in patients with SIPF compared to controls, indicating that differentially expressed lncRNAs and mRNAs may play critical roles in SIPF development. Our study affords new insights into the molecular mechanisms of SIPF and identifies potential biomarkers and targets for SIPF diagnosis and treatment.
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Kamei S, Maruta K, Fujikawa H, Nohara H, Ueno-Shuto K, Tasaki Y, Nakashima R, Kawakami T, Eto Y, Suico MA, Suzuki S, Gruenert DC, Li JD, Kai H, Shuto T. Integrative expression analysis identifies a novel interplay between CFTR and linc-SUMF1-2 that involves CF-associated gene dysregulation. Biochem Biophys Res Commun 2018; 509:521-528. [PMID: 30598261 DOI: 10.1016/j.bbrc.2018.12.152] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Accepted: 12/21/2018] [Indexed: 12/19/2022]
Abstract
Cystic fibrosis transmembrane regulator (CFTR) is a cyclic AMP-dependent Cl- channel, and its dysfunction, due to CFTR gene mutations, causes the lethal inherited disorder cystic fibrosis (CF). To date, widespread dysregulation of certain coding genes in CF airway epithelial cells is well studied and considered as the driver of pulmonary abnormality. However, the involvement of non-coding genes, novel classes of functional RNAs with little or no protein-coding capacity, in the regulation of CF-associated gene dysregulation is poorly understood. Here, we utilized integrative analyses of human transcriptome array (HTA) and characterized 99 coding and 91 non-coding RNAs that are dysregulated in CFTR-defective CF bronchial epithelial cell line CFBE41o-. Among these genes, the expression level of linc-SUMF1-2, an intergenic non-coding RNA (lincRNA) whose function is unknown, was inversely correlated with that of WT-CFTR and consistently higher in primary human CF airway epithelial cells (DHBE-CF). Further integrative analyses under linc-SUMF1-knockdown condition determined MXRA5, SEMA5A, CXCL10, AK022877, CTGF, MYC, AREG and LAMB3 as both CFTR- and linc-SUMF1-2-dependent dysregulated gene sets in CF airway epithelial cells. Overall, our analyses reveal linc-SUMF1-2 as a dysregulated non-coding gene in CF as well as CFTR-linc-SUMF1-2 axis as a novel regulatory pathway involved in CF-associated gene dysregulation.
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Affiliation(s)
- Shunsuke Kamei
- Department of Molecular Medicine, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-Honmachi, Chuo-ku, Kumamoto, 862-0973, Japan; Program for Leading Graduate Schools "HIGO (Health Life Science: Interdisciplinary and Glocal Oriented) Program", Kumamoto University, 5-1 Oe-Honmachi, Chuo-ku, Kumamoto, 862-0973, Japan
| | - Kasumi Maruta
- Department of Molecular Medicine, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-Honmachi, Chuo-ku, Kumamoto, 862-0973, Japan
| | - Haruka Fujikawa
- Department of Molecular Medicine, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-Honmachi, Chuo-ku, Kumamoto, 862-0973, Japan; Program for Leading Graduate Schools "HIGO (Health Life Science: Interdisciplinary and Glocal Oriented) Program", Kumamoto University, 5-1 Oe-Honmachi, Chuo-ku, Kumamoto, 862-0973, Japan
| | - Hirofumi Nohara
- Department of Molecular Medicine, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-Honmachi, Chuo-ku, Kumamoto, 862-0973, Japan; Program for Leading Graduate Schools "HIGO (Health Life Science: Interdisciplinary and Glocal Oriented) Program", Kumamoto University, 5-1 Oe-Honmachi, Chuo-ku, Kumamoto, 862-0973, Japan
| | - Keiko Ueno-Shuto
- Laboratory of Pharmacology, Division of Life Science, Faculty of Pharmaceutical Sciences, Sojo University, 4-22-1 Ikeda, Nishi-ku, Kumamoto, 860-0082, Japan
| | - Yukihiro Tasaki
- Center for Inflammation, Immunity & Infection, Institute for Biomedical Sciences, Georgia State University, 714 Petit Science Center, 100 Piedmont Ave SE, Atlanta, GA30303, USA
| | - Ryunosuke Nakashima
- Department of Molecular Medicine, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-Honmachi, Chuo-ku, Kumamoto, 862-0973, Japan
| | - Taisei Kawakami
- Department of Molecular Medicine, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-Honmachi, Chuo-ku, Kumamoto, 862-0973, Japan
| | - Yuka Eto
- Department of Molecular Medicine, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-Honmachi, Chuo-ku, Kumamoto, 862-0973, Japan
| | - Mary Ann Suico
- Department of Molecular Medicine, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-Honmachi, Chuo-ku, Kumamoto, 862-0973, Japan
| | - Shingo Suzuki
- Institute of Molecular Medicine, University of Texas Health Science Center at Houston, 1825 Pressler St, Houston, TX77030, USA
| | - Dieter C Gruenert
- Head and Neck Stem Cell Lab, University of California, San Francisco, 2340 Sutter St, Box 1330, N331, San Francisco, CA, 94115, USA
| | - Jian-Dong Li
- Center for Inflammation, Immunity & Infection, Institute for Biomedical Sciences, Georgia State University, 714 Petit Science Center, 100 Piedmont Ave SE, Atlanta, GA30303, USA
| | - Hirofumi Kai
- Department of Molecular Medicine, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-Honmachi, Chuo-ku, Kumamoto, 862-0973, Japan
| | - Tsuyoshi Shuto
- Department of Molecular Medicine, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-Honmachi, Chuo-ku, Kumamoto, 862-0973, Japan.
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Abstract
Non-coding RNAs (ncRNAs) are an abundant class of RNAs that include small ncRNAs, long non-coding RNAs (lncRNA) and pseudogenes. The human ncRNA atlas includes thousands of these specialised RNA molecules that are further subcategorised based on their size or function. Two of the more well-known and widely studied ncRNA species are microRNAs (miRNAs) and lncRNAs. These are regulatory RNAs and their altered expression has been implicated in the pathogenesis of a variety of human diseases. Failure to express a functional cystic fibrosis (CF) transmembrane receptor (CFTR) chloride ion channel in epithelial cells underpins CF. Secondary to the CFTR defect, it is known that other pathways can be altered and these may contribute to the pathophysiology of CF lung disease in particular. For example, quantitative alterations in expression of some ncRNAs are associated with CF. In recent years, there has been a series of published studies exploring ncRNA expression and function in CF. The majority have focussed principally on miRNAs, with just a handful of reports to date on lncRNAs. The present study reviews what is currently known about ncRNA expression and function in CF, and discusses the possibility of applying this knowledge to the clinical management of CF in the near future.
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Affiliation(s)
- Arlene M.A. Glasgow
- Lung Biology Group, Department of Clinical Microbiology, Royal College of Surgeons in Ireland, Education and Research Centre, Beaumont Hospital, Dublin 9, Ireland
| | - Chiara De Santi
- Lung Biology Group, Department of Clinical Microbiology, Royal College of Surgeons in Ireland, Education and Research Centre, Beaumont Hospital, Dublin 9, Ireland
| | - Catherine M. Greene
- Lung Biology Group, Department of Clinical Microbiology, Royal College of Surgeons in Ireland, Education and Research Centre, Beaumont Hospital, Dublin 9, Ireland
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Hariprakash JM, Vellarikkal SK, Verma A, Ranawat AS, Jayarajan R, Ravi R, Kumar A, Dixit V, Sivadas A, Kashyap AK, Senthivel V, Sehgal P, Mahadevan V, Scaria V, Sivasubbu S. SAGE: a comprehensive resource of genetic variants integrating South Asian whole genomes and exomes. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2018; 2018:1-10. [PMID: 30184194 PMCID: PMC6146123 DOI: 10.1093/database/bay080] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 07/03/2018] [Indexed: 11/20/2022]
Abstract
South Asia is home to \documentclass[12pt]{minimal}
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}{}$\sim $\end{document}20% of the world population and characterized by distinct ethnic, linguistic, cultural and genetic lineages. Only limited representative samples from the region have found its place in large population-scale international genome projects. The recent availability of genome scale data from multiple populations and datasets from South Asian countries in public domain motivated us to integrate the data into a comprehensive resource. In the present study, we have integrated a total of six datasets encompassing 1213 human exomes and genomes to create a compendium of 154 814 557 genetic variants and adding a total of 69 059 255 novel variants. The variants were systematically annotated using public resources and along with the allele frequencies are available as a browsable-online resource South Asian genomes and exomes. As a proof of principle application of the data and resource for genetic epidemiology, we have analyzed the pathogenic genetic variants causing retinitis pigmentosa. Our analysis reveals the genetic landscape of the disease and suggests subset of genetic variants to be highly prevalent in South Asia.
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Affiliation(s)
- Judith Mary Hariprakash
- GN Ramachandran Knowledge Center for Genome Informatics, Council of Scientific and Industrial Research (CSIR) Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India
| | - Shamsudheen Karuthedath Vellarikkal
- Genomics & Molecular Medicine, Council of Scientific and Industrial Research (CSIR) Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India
| | - Ankit Verma
- Genomics & Molecular Medicine, Council of Scientific and Industrial Research (CSIR) Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India
| | - Anop Singh Ranawat
- GN Ramachandran Knowledge Center for Genome Informatics, Council of Scientific and Industrial Research (CSIR) Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India
| | - Rijith Jayarajan
- Genomics & Molecular Medicine, Council of Scientific and Industrial Research (CSIR) Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India
| | - Rowmika Ravi
- Genomics & Molecular Medicine, Council of Scientific and Industrial Research (CSIR) Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India
| | - Anoop Kumar
- Genomics & Molecular Medicine, Council of Scientific and Industrial Research (CSIR) Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India
| | - Vishal Dixit
- Genomics & Molecular Medicine, Council of Scientific and Industrial Research (CSIR) Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India
| | - Ambily Sivadas
- GN Ramachandran Knowledge Center for Genome Informatics, Council of Scientific and Industrial Research (CSIR) Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India
| | - Atul Kumar Kashyap
- Genomics & Molecular Medicine, Council of Scientific and Industrial Research (CSIR) Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India
| | - Vigneshwar Senthivel
- Genomics & Molecular Medicine, Council of Scientific and Industrial Research (CSIR) Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India
| | - Paras Sehgal
- Genomics & Molecular Medicine, Council of Scientific and Industrial Research (CSIR) Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India
| | - Vijayalakshmi Mahadevan
- School of Chemical & Biotechnology, Shanmugha Arts, Science, Technology and Research Academy (SASTRA) University, Thanjavur, Tamil Nadu 613402, India
| | - Vinod Scaria
- GN Ramachandran Knowledge Center for Genome Informatics, Council of Scientific and Industrial Research (CSIR) Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India
| | - Sridhar Sivasubbu
- Genomics & Molecular Medicine, Council of Scientific and Industrial Research (CSIR) Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India
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Narożna B, Langwiński W, Szczepankiewicz A. Non-Coding RNAs in Pediatric Airway Diseases. Genes (Basel) 2017; 8:genes8120348. [PMID: 29186897 PMCID: PMC5748666 DOI: 10.3390/genes8120348] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 11/18/2017] [Accepted: 11/21/2017] [Indexed: 12/18/2022] Open
Abstract
Non-coding RNAs (ncRNAs) are involved in the regulation of numerous biological processes and pathways and therefore have been extensively studied in human diseases. Previous reports have shown that non-coding RNAs play a crucial role in the pathogenesis and aberrant regulation of respiratory diseases. The altered expression of microRNAs (miRNAs) and long non-coding RNAs in blood and also locally in sputum or exhaled breath condensate influences lung function, immune response, and disease phenotype and may be used for the development of biomarkers specific for airway disease. In this review, we provide an overview of the recent works studying the non-coding RNAs in airway diseases, with a particular focus on chronic respiratory diseases of childhood. We have chosen the most common chronic respiratory condition—asthma—and the most severe, chronic disease of the airways—cystic fibrosis. Study of the altered expression of non-coding RNAs in these diseases may be key to better understanding their pathogenesis and improving diagnosis, while also holding promise for the development of therapeutic strategies using the regulatory potential of non-coding RNAs.
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Affiliation(s)
- Beata Narożna
- Laboratory of Molecular and Cell Biology, Department of Pediatric Pulmonology, Allergy and Clinical Immunology, Poznan University of Medical Sciences, 60-512 Poznan, Poland.
| | - Wojciech Langwiński
- Laboratory of Molecular and Cell Biology, Department of Pediatric Pulmonology, Allergy and Clinical Immunology, Poznan University of Medical Sciences, 60-512 Poznan, Poland.
| | - Aleksandra Szczepankiewicz
- Laboratory of Molecular and Cell Biology, Department of Pediatric Pulmonology, Allergy and Clinical Immunology, Poznan University of Medical Sciences, 60-512 Poznan, Poland.
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