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Bhat AA, Afzal O, Agrawal N, Thapa R, Almalki WH, Kazmi I, Alzarea SI, Altamimi ASA, Kukreti N, Chakraborty A, Singh SK, Dua K, Gupta G. A comprehensive review on the emerging role of long non-coding RNAs in the regulation of NF-κB signaling in inflammatory lung diseases. Int J Biol Macromol 2023; 253:126951. [PMID: 37734525 DOI: 10.1016/j.ijbiomac.2023.126951] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/30/2023] [Accepted: 09/09/2023] [Indexed: 09/23/2023]
Abstract
Public health globally faces significant risks from conditions like acute respiratory distress syndrome (ARDS), chronic obstructive pulmonary disease (COPD), and various inflammatory lung disorders. The NF-κB signaling system partially controls lung inflammation, immunological responses, and remodeling. Non-coding RNAs (lncRNAs) are crucial in regulating gene expression. They are increasingly recognized for their involvement in NF-κB signaling and the development of inflammatory lung diseases. Disruption of lncRNA-NF-κB interactions is a potential cause and resolution factor for inflammatory respiratory conditions. This study explores the therapeutic potential of targeting lncRNAs and NF-κB signaling to alleviate inflammation and restore lung function. Understanding the intricate relationship between lncRNAs and NF-κB signaling could offer novel insights into disease mechanisms and identify therapeutic targets. Regulation of lncRNAs and NF-κB signaling holds promise as an effective approach for managing inflammatory lung disorders. This review aims to comprehensively analyze the interaction between lncRNAs and the NF-κB signaling pathway in the context of inflammatory lung diseases. It investigates the functional roles of lncRNAs in modulating NF-κB activity and the resulting inflammatory responses in lung cells, focusing on molecular mechanisms involving upstream regulators, inhibitory proteins, and downstream effectors.
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Affiliation(s)
- Asif Ahmad Bhat
- School of Pharmacy, Suresh Gyan Vihar University, Jagatpura 302017, Mahal Road, Jaipur, India
| | - Obaid Afzal
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al Kharj 11942, Saudi Arabia
| | - Neetu Agrawal
- Institute of Pharmaceutical Research, GLA University, Mathura, UP, India
| | - Riya Thapa
- School of Pharmacy, Suresh Gyan Vihar University, Jagatpura 302017, Mahal Road, Jaipur, India
| | - Waleed Hassan Almalki
- Department of Pharmacology, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Imran Kazmi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.
| | - Sami I Alzarea
- Department of Pharmacology, College of Pharmacy, Jouf University, Sakaka, Al-Jouf, Saudi Arabia
| | | | - Neelima Kukreti
- School of Pharmacy, Graphic Era Hill University, Dehradun 248007, India
| | - Amlan Chakraborty
- Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, Manchester M13 9PL, UK; Cardiovascular Disease Program, Biomedicine Discovery Institute and Department of Pharmacology, Monash University, Clayton, VIC 3800, Australia
| | - Sachin Kumar Singh
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab, 144411, India; Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney, Ultimo 2007, Australia
| | - Kamal Dua
- Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney, Ultimo 2007, Australia; Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, NSW 2007, Australia.
| | - Gaurav Gupta
- Center for Global Health research (CGHR), Saveetha Institute of Medical and Technical Science, Saveetha University, Chennai, India
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Stiens J, Tan YY, Joyce R, Arnvig KB, Kendall SL, Nobeli I. Using a whole genome co-expression network to inform the functional characterisation of predicted genomic elements from Mycobacterium tuberculosis transcriptomic data. Mol Microbiol 2023; 119:381-400. [PMID: 36924313 DOI: 10.1111/mmi.15055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 03/08/2023] [Accepted: 03/09/2023] [Indexed: 03/18/2023]
Abstract
A whole genome co-expression network was created using Mycobacterium tuberculosis transcriptomic data from publicly available RNA-sequencing experiments covering a wide variety of experimental conditions. The network includes expressed regions with no formal annotation, including putative short RNAs and untranslated regions of expressed transcripts, along with the protein-coding genes. These unannotated expressed transcripts were among the best-connected members of the module sub-networks, making up more than half of the 'hub' elements in modules that include protein-coding genes known to be part of regulatory systems involved in stress response and host adaptation. This data set provides a valuable resource for investigating the role of non-coding RNA, and conserved hypothetical proteins, in transcriptomic remodelling. Based on their connections to genes with known functional groupings and correlations with replicated host conditions, predicted expressed transcripts can be screened as suitable candidates for further experimental validation.
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Affiliation(s)
- Jennifer Stiens
- Institute of Structural and Molecular Biology, Biological Sciences, Birkbeck, University of London, London, UK
| | - Yen Yi Tan
- Institute of Structural and Molecular Biology, Biological Sciences, Birkbeck, University of London, London, UK
| | - Rosanna Joyce
- Institute of Structural and Molecular Biology, Biological Sciences, Birkbeck, University of London, London, UK
| | - Kristine B Arnvig
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, London, UK
| | - Sharon L Kendall
- Royal Veterinary College, Centre for Emerging, Endemic and Exotic Diseases, Pathobiology and Population Sciences, Hatfield, UK
| | - Irene Nobeli
- Institute of Structural and Molecular Biology, Biological Sciences, Birkbeck, University of London, London, UK
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Kaur K, Laal S, Ryndak MB. Mycobacterium tuberculosis transcriptome in intraocular tuberculosis. J Med Microbiol 2023; 72. [PMID: 36762529 DOI: 10.1099/jmm.0.001649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023] Open
Abstract
Introduction. Intraocular tuberculosis (IOTB) is a significant cause of visual morbidity in tuberculosis (TB)-endemic countries. Although Mycobacterium tuberculosis (M. tb) has been detected in both the retinal pigment epithelial (RPE) cells and in the intraocular fluid (IOF) in some cases, IOTB is paucibacillary in the vast majority of patients. As a result, M. tb pathogenesis in the ocular compartment is poorly defined.Hypothesis. The transcriptional profile of M. tb in the ocular compartment will differ from those of M. tb in environments that represent earlier stages of infection.Aim. Our aim is to shed light on the pathogenesis of M. tb in a clinically relevant but challenging environment to study.Methodology. Whole-genome microarray analysis was performed on M. tb grown in an IOF model (artificial IOF; AIOF) over 6 days against reference log phase bacteria grown in 7H9. Results were compared to published M. tb transcriptomes in other physiologically relevant environments, e.g. RPE cell line.Results. M. tb replicates slowly in AIOF. Genes involved in active replication and aerobic respiration as well as lipid metabolism were either downregulated or not differentially expressed. Yet, M. tb in AIOF downregulated genes of the DosR regulon, indicating the suppression of dormancy, similar to M. tb in RPE cells. This transcriptional profile is distinct from the active and virulent transcriptomes of M. tb in alveolar epithelial cells and blood.Conclusion. M. tb likely acquires a non-invasive and quiescent phenotype, between active infection and dormancy, upon reaching an extrapulmonary niche, i.e. the ocular environment.
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Affiliation(s)
- Kamaljit Kaur
- Department of Ophthalmology, Postgraduate Institute of Medical Education and Research, Chandigarh, India.,Present address: Public Health Research Institute, Rutgers University, New Jersey Medical School, The State University of New Jersey, Newark, NJ, USA
| | - Suman Laal
- Departments of Pathology and Microbiology, New York University Langone Medical Center, New York, NY, USA.,Veterans Affairs New York Harbor Healthcare System, New York, NY, NY, USA
| | - Michelle B Ryndak
- Department of Pathology, New York University Langone Medical Center, New York, NY, USA.,Present address: Columbia University, Vagelos College of Physicians and Surgeons, Office for Research, New York, NY, USA
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Rodríguez-García A, Sola-Landa A, Barreiro C. RNA Preparation and RNA-Seq Bioinformatics for Comparative Transcriptomics. Methods Mol Biol 2023; 2704:99-113. [PMID: 37642840 DOI: 10.1007/978-1-0716-3385-4_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
The principal transcriptome analysis is the determination of differentially expressed genes across experimental conditions. For this, the next-generation sequencing of RNA (RNA-seq) has several advantages over other techniques, such as the capability of detecting all the transcripts in one assay over RT-qPCR, such as its higher accuracy and broader dynamic range over microarrays or the ability to detect novel transcripts, including non-coding RNA molecules, at nucleotide-level resolution over both techniques. Despite these advantages, many microbiology laboratories have not yet applied RNA-seq analyses to their investigations. The high cost of the equipment for next-generation sequencing is no longer an issue since this intermediate part of the analysis can be provided by commercial or central services. Here, we detail a protocol for the first part of the analysis, the RNA extraction and an introductory protocol to the bioinformatics analysis of the sequencing data to generate the differential expression results.
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Affiliation(s)
- Antonio Rodríguez-García
- Área de Microbiología, Departamento de Biología Molecular, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, León, Spain.
- Instituto de Biotecnología de León, INBIOTEC, León, Spain.
| | - Alberto Sola-Landa
- Instituto de Biotecnología de León, INBIOTEC, León, Spain
- Fundación Cesefor, León, Spain
| | - Carlos Barreiro
- Instituto de Biotecnología de León, INBIOTEC, León, Spain
- Área de Bioquímica y Biología Molecular, Departamento de Biología Molecular, Facultad de Veterinaria, Universidad de León, León, Spain
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Almatroudi A. Non-Coding RNAs in Tuberculosis Epidemiology: Platforms and Approaches for Investigating the Genome's Dark Matter. Int J Mol Sci 2022; 23:ijms23084430. [PMID: 35457250 PMCID: PMC9024992 DOI: 10.3390/ijms23084430] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 04/05/2022] [Accepted: 04/14/2022] [Indexed: 02/07/2023] Open
Abstract
A growing amount of information about the different types, functions, and roles played by non-coding RNAs (ncRNAs) is becoming available, as more and more research is done. ncRNAs have been identified as potential therapeutic targets in the treatment of tuberculosis (TB), because they may be essential regulators of the gene network. ncRNA profiling and sequencing has recently revealed significant dysregulation in tuberculosis, primarily due to aberrant processes of ncRNA synthesis, including amplification, deletion, improper epigenetic regulation, or abnormal transcription. Despite the fact that ncRNAs may have a role in TB characteristics, the detailed mechanisms behind these occurrences are still unknown. The dark matter of the genome can only be explored through the development of cutting-edge bioinformatics and molecular technologies. In this review, ncRNAs' synthesis and functions are discussed in detail, with an emphasis on the potential role of ncRNAs in tuberculosis. We also focus on current platforms, experimental strategies, and computational analyses to explore ncRNAs in TB. Finally, a viewpoint is presented on the key challenges and novel techniques for the future and for a wide-ranging therapeutic application of ncRNAs.
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Affiliation(s)
- Ahmad Almatroudi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia
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