1
|
Wei L, Liu L, Meng Z, Qi K, Gao X, Feng J, Luo J. Recognition of Mycobacterium tuberculosis by macrophage Toll-like receptor and its role in autophagy. Inflamm Res 2024; 73:753-770. [PMID: 38563966 DOI: 10.1007/s00011-024-01864-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 12/25/2023] [Accepted: 02/20/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND The pathogen responsible for tuberculosis is called Mycobacterium tuberculosis. Its interaction with macrophages has a significant impact on the onset and progression of the disease. METHODS The respiratory pathway allows Mycobacterium tuberculosis to enter the body's lungs where it battles immune cells before being infected latently or actively. In the progress of tuberculosis, Mycobacterium tuberculosis activates the body's immune system and creates inflammatory factors, which cause tissue inflammation to infiltrate and the creation of granulomas, which seriously harms the body. Toll-like receptors of macrophage can mediate host recognition of Mycobacterium tuberculosis, initiate immune responses, and participate in macrophage autophagy. New host-directed therapeutic approaches targeting autophagy for drug-resistant Mycobacterium tuberculosis have emerged, providing new ideas for the effective treatment of tuberculosis. CONCLUSIONS In-depth understanding of the mechanisms by which macrophage autophagy interacts with intracellular Mycobacterium tuberculosis, as well as the study of potent and specific autophagy-regulating molecules, will lead to much-needed advances in drug discovery and vaccine design, which will improve the prevention and treatment of human tuberculosis.
Collapse
Affiliation(s)
- Linna Wei
- Department of Immunology, Zunyi Medical University, Zunyi, 563000, China
| | - Liping Liu
- Department of Immunology, Zunyi Medical University, Zunyi, 563000, China
| | - Zudi Meng
- Department of Immunology, Zunyi Medical University, Zunyi, 563000, China
| | - Kai Qi
- Department of Immunology, Zunyi Medical University, Zunyi, 563000, China
| | - Xuehan Gao
- Department of Immunology, Zunyi Medical University, Zunyi, 563000, China
| | - Jihong Feng
- Department of Oncology, Lishui People's Hospital, Sixth Affiliated Hospital of Wenzhou Medical University, Lishui, 323000, Zhejiang, China
| | - Junmin Luo
- Department of Immunology, Zunyi Medical University, Zunyi, 563000, China.
| |
Collapse
|
2
|
Hemmati S, Saeidikia Z, Seradj H, Mohagheghzadeh A. Immunomodulatory Peptides as Vaccine Adjuvants and Antimicrobial Agents. Pharmaceuticals (Basel) 2024; 17:201. [PMID: 38399416 PMCID: PMC10892805 DOI: 10.3390/ph17020201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Revised: 01/26/2024] [Accepted: 01/28/2024] [Indexed: 02/25/2024] Open
Abstract
The underdevelopment of adjuvant discovery and diversity, compared to core vaccine technology, is evident. On the other hand, antibiotic resistance is on the list of the top ten threats to global health. Immunomodulatory peptides that target a pathogen and modulate the immune system simultaneously are promising for the development of preventive and therapeutic molecules. Since investigating innate immunity in insects has led to prominent achievements in human immunology, such as toll-like receptor (TLR) discovery, we used the capacity of the immunomodulatory peptides of arthropods with concomitant antimicrobial or antitumor activity. An SVM-based machine learning classifier identified short immunomodulatory sequences encrypted in 643 antimicrobial peptides from 55 foe-to-friend arthropods. The critical features involved in efficacy and safety were calculated. Finally, 76 safe immunomodulators were identified. Then, molecular docking and simulation studies defined the target of the most optimal peptide ligands among all human cell-surface TLRs. SPalf2-453 from a crab is a cell-penetrating immunoadjuvant with antiviral properties. The peptide interacts with the TLR1/2 heterodimer. SBsib-711 from a blackfly is a TLR4/MD2 ligand used as a cancer vaccine immunoadjuvant. In addition, SBsib-711 binds CD47 and PD-L1 on tumor cells, which is applicable in cancer immunotherapy as a checkpoint inhibitor. MRh4-679 from a shrimp is a broad-spectrum or universal immunoadjuvant with a putative Th1/Th2-balanced response. We also implemented a pathway enrichment analysis to define fingerprints or immunological signatures for further in vitro and in vivo immunogenicity and reactogenicity measurements. Conclusively, combinatorial machine learning, molecular docking, and simulation studies, as well as systems biology, open a new opportunity for the discovery and development of multifunctional prophylactic and therapeutic lead peptides.
Collapse
Affiliation(s)
- Shiva Hemmati
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz 71345-1583, Iran
- Biotechnology Research Center, Shiraz University of Medical Sciences, Shiraz 71345-1583, Iran
- Department of Pharmaceutical Biology, Faculty of Pharmaceutical Sciences, UCSI University, Cheras, Kuala Lumpur 56000, Malaysia
| | - Zahra Saeidikia
- Student Research Committee, Shiraz University of Medical Sciences, Shiraz 71345-1583, Iran;
| | - Hassan Seradj
- Department of Medicinal Chemistry, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz 71345-1583, Iran;
| | - Abdolali Mohagheghzadeh
- Department of Phytopharmaceuticals, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz 71345-1583, Iran;
| |
Collapse
|
3
|
Biswas VK, Sen K, Ahad A, Ghosh A, Verma S, Pati R, Prusty S, Nayak SP, Podder S, Kumar D, Gupta B, Raghav SK. NCoR1 controls Mycobacterium tuberculosis growth in myeloid cells by regulating the AMPK-mTOR-TFEB axis. PLoS Biol 2023; 21:e3002231. [PMID: 37590294 PMCID: PMC10465006 DOI: 10.1371/journal.pbio.3002231] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 08/29/2023] [Accepted: 07/04/2023] [Indexed: 08/19/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb) defends host-mediated killing by repressing the autophagolysosome machinery. For the first time, we report NCoR1 co-repressor as a crucial host factor, controlling Mtb growth in myeloid cells by regulating both autophagosome maturation and lysosome biogenesis. We found that the dynamic expression of NCoR1 is compromised in human peripheral blood mononuclear cells (PBMCs) during active Mtb infection, which is rescued upon prolonged anti-mycobacterial therapy. In addition, a loss of function in myeloid-specific NCoR1 considerably exacerbates the growth of M. tuberculosis in vitro in THP1 differentiated macrophages, ex vivo in bone marrow-derived macrophages (BMDMs), and in vivo in NCoR1MyeKO mice. We showed that NCoR1 depletion controls the AMPK-mTOR-TFEB signalling axis by fine-tuning cellular adenosine triphosphate (ATP) homeostasis, which in turn changes the expression of proteins involved in autophagy and lysosomal biogenesis. Moreover, we also showed that the treatment of NCoR1 depleted cells by Rapamycin, Antimycin-A, or Metformin rescued the TFEB activity and LC3 levels, resulting in enhanced Mtb clearance. Similarly, expressing NCoR1 exogenously rescued the AMPK-mTOR-TFEB signalling axis and Mtb killing. Overall, our data revealed a central role of NCoR1 in Mtb pathogenesis in myeloid cells.
Collapse
Affiliation(s)
- Viplov Kumar Biswas
- Immuno-genomics & Systems Biology Laboratory, Institute of Life Sciences (ILS), Bhubaneswar, India
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Bhubaneswar, India
| | - Kaushik Sen
- Immuno-genomics & Systems Biology Laboratory, Institute of Life Sciences (ILS), Bhubaneswar, India
- Regional Centre for Biotechnology, Faridabad, India
| | - Abdul Ahad
- Immuno-genomics & Systems Biology Laboratory, Institute of Life Sciences (ILS), Bhubaneswar, India
| | - Arup Ghosh
- Immuno-genomics & Systems Biology Laboratory, Institute of Life Sciences (ILS), Bhubaneswar, India
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Bhubaneswar, India
| | - Surbhi Verma
- Molecular Medicine: Cellular Immunology, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Rashmirekha Pati
- Immuno-genomics & Systems Biology Laboratory, Institute of Life Sciences (ILS), Bhubaneswar, India
| | - Subhasish Prusty
- Immuno-genomics & Systems Biology Laboratory, Institute of Life Sciences (ILS), Bhubaneswar, India
- Regional Centre for Biotechnology, Faridabad, India
| | - Sourya Prakash Nayak
- Immuno-genomics & Systems Biology Laboratory, Institute of Life Sciences (ILS), Bhubaneswar, India
| | - Sreeparna Podder
- Immuno-genomics & Systems Biology Laboratory, Institute of Life Sciences (ILS), Bhubaneswar, India
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Bhubaneswar, India
| | - Dhiraj Kumar
- Molecular Medicine: Cellular Immunology, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Bhawna Gupta
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Bhubaneswar, India
| | - Sunil Kumar Raghav
- Immuno-genomics & Systems Biology Laboratory, Institute of Life Sciences (ILS), Bhubaneswar, India
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Bhubaneswar, India
| |
Collapse
|
4
|
Sengupta S, Pattanaik KP, Mishra S, Sonawane A. Epigenetic orchestration of host immune defences by Mycobacterium tuberculosis. Microbiol Res 2023; 273:127400. [PMID: 37196490 DOI: 10.1016/j.micres.2023.127400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 04/09/2023] [Accepted: 05/02/2023] [Indexed: 05/19/2023]
Abstract
Being among the top 10 causes of adult deaths, tuberculosis (TB) disease is considered a major global public health concern to address. The human tuberculosis pathogen, Mycobacterium tuberculosis (Mtb), is an extremely competent and well-versed pathogen that promotes pathogenesis by evading the host immune systems through numerous tactics. Investigations revealed that Mtb could evade the host defense mechanisms by reconfiguring the host gene transcription and causing epigenetic changes. Although results indicate the link between epigenetics and disease manifestation in other bacterial infections, little is known regarding the kinetics of the epigenetic alterations in mycobacterial infection. This literature review discusses the studies in Mtb-induced epigenetic alterations inside the host and its contribution in the host immune evasion strategies. It also discusses how the Mtb-induced alterations could be used as 'epibiomarkers' to diagnose TB. Additionally, this review also discusses therapeutic interventions to be enhanced through remodification by 'epidrugs'.
Collapse
Affiliation(s)
- Srabasti Sengupta
- School of Biotechnology, Campus-11, KIIT Deemed to be University, Patia, Bhubaneswar 751024, India
| | - Kali Prasad Pattanaik
- School of Biotechnology, Campus-11, KIIT Deemed to be University, Patia, Bhubaneswar 751024, India
| | - Snehasish Mishra
- School of Biotechnology, Campus-11, KIIT Deemed to be University, Patia, Bhubaneswar 751024, India
| | - Avinash Sonawane
- Discipline of Biosciences and Biomedical Engineering, Indian Institutes of Technology Indore, Khandwa Road, Simrol, Indore 453552, India.
| |
Collapse
|
5
|
Bachanová P, Cheyne A, Broderick C, Newton SM, Levin M, Kaforou M. Comparative transcriptomic analysis of whole blood mycobacterial growth assays and tuberculosis patients' blood RNA profiles. Sci Rep 2022; 12:17684. [PMID: 36271270 PMCID: PMC9587058 DOI: 10.1038/s41598-022-20409-y] [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: 06/24/2022] [Accepted: 09/13/2022] [Indexed: 01/18/2023] Open
Abstract
In vitro whole blood infection models are used for elucidating the immune response to Mycobacterium tuberculosis (Mtb). They exhibit commonalities but also differences, to the in vivo blood transcriptional response during natural human Mtb disease. Here, we present a description of concordant and discordant components of the immune response in blood, quantified through transcriptional profiling in an in vitro whole blood infection model compared to whole blood from patients with tuberculosis disease. We identified concordantly and discordantly expressed gene modules and performed in silico cell deconvolution. A high degree of concordance of gene expression between both adult and paediatric in vivo-in vitro tuberculosis infection was identified. Concordance in paediatric in vivo vs in vitro comparison is largely characterised by immune suppression, while in adults the comparison is marked by concordant immune activation, particularly that of inflammation, chemokine, and interferon signalling. Discordance between in vitro and in vivo increases over time and is driven by T-cell regulation and monocyte-related gene expression, likely due to apoptotic depletion of monocytes and increasing relative fraction of longer-lived cell types, such as T and B cells. Our approach facilitates a more informed use of the whole blood in vitro model, while also accounting for its limitations.
Collapse
Affiliation(s)
- Petra Bachanová
- grid.7445.20000 0001 2113 8111Department of Infectious Disease, Imperial College London, London, UK
| | - Ashleigh Cheyne
- grid.7445.20000 0001 2113 8111Department of Infectious Disease, Imperial College London, London, UK ,grid.7445.20000 0001 2113 8111MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, UK
| | - Claire Broderick
- grid.7445.20000 0001 2113 8111Department of Infectious Disease, Imperial College London, London, UK
| | - Sandra M. Newton
- grid.7445.20000 0001 2113 8111Department of Infectious Disease, Imperial College London, London, UK ,grid.7445.20000 0001 2113 8111Centre for Paediatrics and Child Health, Imperial College London, London, UK
| | - Michael Levin
- grid.7445.20000 0001 2113 8111Department of Infectious Disease, Imperial College London, London, UK ,grid.7445.20000 0001 2113 8111Centre for Paediatrics and Child Health, Imperial College London, London, UK
| | - Myrsini Kaforou
- grid.7445.20000 0001 2113 8111Department of Infectious Disease, Imperial College London, London, UK ,grid.7445.20000 0001 2113 8111Centre for Paediatrics and Child Health, Imperial College London, London, UK
| |
Collapse
|
6
|
Lu Y, Ning H, Kang J, Bai G, Zhou L, Kang Y, Wu Z, Tian M, Zhao J, Ma Y, Bai Y. Cyclic-di-AMP Phosphodiesterase Elicits Protective Immune Responses Against Mycobacterium tuberculosis H37Ra Infection in Mice. Front Cell Infect Microbiol 2022; 12:871135. [PMID: 35811674 PMCID: PMC9256937 DOI: 10.3389/fcimb.2022.871135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 04/19/2022] [Indexed: 11/13/2022] Open
Abstract
Many antigens from Mycobacterium tuberculosis (M. tuberculosis) have been demonstrated as strong immunogens and proved to have application potential as vaccine candidate antigens. Cyclic di-AMP (c-di-AMP) as a bacterial second messenger regulates various bacterial processes as well as the host immune responses. Rv2837c, the c-di-AMP phosphodiesterase (CnpB), was found to be relative to virulence of M. tuberculosis and interference with host innate immune response. In this study, recombinant CnpB was administered subcutaneously to mice. We found that CnpB had strong immunogenicity and induced high levels of humoral response and lung mucosal immunity after M. tuberculosis intranasally infection. CnpB immunization stimulated splenocyte proliferation and the increasing number of activated NK cells but had little effects on Th1/Th2 cellular immune responses in spleens. However, CnpB induced significant Th1/Th2 cellular immune responses with a decreased number of T and B cells in the lungs, and significantly recruits of CD4+ and CD8+ T cells after M. tuberculosis attenuated strain H37Ra infection. Besides, we first reported that CnpB could stimulate IFN-β expression transitorily and inhibit the autophagy of macrophages in vitro. In mice intranasally infection model, CnpB immunization alleviated pathological changes and reduced M. tuberculosis H37Ra loads in the lungs. Thus, our results suggested that CnpB interferes with host innate and adaptive immune responses and confers protection against M. tuberculosis respiratory infection, which should be considered in vaccine development as well as a drug target.
Collapse
Affiliation(s)
- Yanzhi Lu
- Department of Microbiology and Pathogen Biology, Basic Medical School, Air Force Medical University, Xi’an, China
| | - Huanhuan Ning
- Department of Microbiology and Pathogen Biology, Basic Medical School, Air Force Medical University, Xi’an, China
| | - Jian Kang
- Department of Microbiology and Pathogen Biology, Basic Medical School, Air Force Medical University, Xi’an, China
| | - Guangchun Bai
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, NY, United States
| | - Lei Zhou
- Department of Clinical Laboratory, The First Affiliated Hospital, Air Force Medical University, Xi’an, China
| | - Yali Kang
- Department of Physiology, Basic Medical School, Ningxia Medical University, Yinchuan, China
| | - Zhengfeng Wu
- Student Brigade, Basic Medical School, Air Force Medical University, Xi’an, China
| | - Maolin Tian
- Student Brigade, Basic Medical School, Air Force Medical University, Xi’an, China
| | - Junhao Zhao
- Student Brigade, Basic Medical School, Air Force Medical University, Xi’an, China
| | - Yueyun Ma
- Department of Clinical Laboratory, The First Affiliated Hospital, Air Force Medical University, Xi’an, China
- Department of Clinical Laboratory, Air Force Medical Center, Air Force Medical University, Beijing, China
- *Correspondence: Yinlan Bai, ; Yueyun Ma,
| | - Yinlan Bai
- Department of Microbiology and Pathogen Biology, Basic Medical School, Air Force Medical University, Xi’an, China
- *Correspondence: Yinlan Bai, ; Yueyun Ma,
| |
Collapse
|
7
|
Hernández-Bazán S, Mata-Espinosa D, Lozano-Ordaz V, Ramos-Espinosa O, Barrios-Payán J, López-Casillas F, Hernández-Pando R. Immune regulatory effect of osteopontin gene therapy in a murine model of multi-drug resistant pulmonary tuberculosis. Hum Gene Ther 2022; 33:1037-1051. [PMID: 35615876 DOI: 10.1089/hum.2022.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Tuberculosis (TB) has been for many years a major public health problem since treatment is long and sometimes ineffective favoring the increase of multi-drug-resistant mycobacteria (MDR). Gene therapy is a novel and effective tool to regulate immune responses. In this study we evaluated the therapeutic effect of an adenoviral vector codifying osteopontin (AdOPN), a molecule known for their roles to favour Th1 and Th17 type-cytokine expression which are crucial in TB containment. A single-dose of AdOPN administration in BALB/c mice suffering late progressive pulmonary MDR-TB, produced significant lower bacterial load and pneumonia, due to higher expression of IFN-γ, IL-12 and IL-17 in coexistence with increase of granulomas in number and size, resulting in higher survival, in contrast with mice treated with the control adenovirus that codify the green fluorescent protein (AdGFP). Combined therapy of AdOPN with a regimen of 2nd line antibiotics produced a better control of bacterial load in lung during the first days of treatment, suggesting that AdOPN can shorten chemotherapy. Taken together, gene therapy with AdOPN leads to higher immune responses against TB infection, resulting in a new potential treatment against pulmonary TB that can co-adjuvant chemotherapy.
Collapse
Affiliation(s)
- Sujhey Hernández-Bazán
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubiran, 42559, Department of Pathology, Experimental Pathology Section, Tlalpan, CDMX, Mexico;
| | - Dulce Mata-Espinosa
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubiran, 42559, Department of Pathology, Experimental Pathology Section, Tlalpan, CDMX, Mexico;
| | - Vasti Lozano-Ordaz
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubiran, 42559, Department of Pathology, Experimental Pathology Section, Tlalpan, CDMX, Mexico;
| | - Octavio Ramos-Espinosa
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubiran, 42559, Department of Pathology, Experimental Pathology Section, Tlalpan, CDMX, Mexico;
| | - Jorge Barrios-Payán
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubiran, 42559, Department of Pathology, Experimental Pathology Section, Tlalpan, CDMX, Mexico;
| | - Fernando López-Casillas
- Universidad Nacional Autónoma de México Instituto de Fisiología Celular, 61739, Department of Cellular and Developmental Biology, Coyoacán, CDMX, Mexico;
| | - Rogelio Hernández-Pando
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubiran, 42559, Department of Pathology, Experimental Pathology Section, Tlalpan, CDMX, Mexico;
| |
Collapse
|
8
|
Arish M, Naz F. Macrophage plasticity as a therapeutic target in tuberculosis. Eur J Immunol 2022; 52:696-704. [DOI: 10.1002/eji.202149624] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 12/31/2021] [Accepted: 03/01/2022] [Indexed: 11/08/2022]
Affiliation(s)
- Mohd Arish
- JH‐Institute of Molecular Medicine Jamia Hamdard New Delhi India
- Carter Immunology Center University of Virginia United States
| | - Farha Naz
- Centre for Interdisciplinary Research in Basic Sciences (CIRBSc) Jamia Millia Islamia New Delhi India
- Division of Infectious Disease and International Health School of Medicine University of Virginia Health System United States
| |
Collapse
|
9
|
Vavougios GD, Zarogiannis S, Barh D, Breza M, Krogfelt KA, Stamoulis G, Gourgoulianis KI. Innate immunity and metal ion trafficking pathway perturbations in idiopathic Parkinson's disease and Tuberculosis: A comparative transcriptomics approach. BRAIN DISORDERS 2021. [DOI: 10.1016/j.dscb.2021.100025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
|
10
|
Chowdhury UN, Faruqe MO, Mehedy M, Ahmad S, Islam MB, Shoombuatong W, Azad A, Moni MA. Effects of Bacille Calmette Guerin (BCG) vaccination during COVID-19 infection. Comput Biol Med 2021; 138:104891. [PMID: 34624759 PMCID: PMC8479467 DOI: 10.1016/j.compbiomed.2021.104891] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 09/21/2021] [Accepted: 09/21/2021] [Indexed: 12/16/2022]
Abstract
The coronavirus disease 2019 (COVID-19) is caused by the infection of highly contagious severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), also known as the novel coronavirus. In most countries, the containment of this virus spread is not controlled, which is driving the pandemic towards a more difficult phase. In this study, we investigated the impact of the Bacille Calmette Guerin (BCG) vaccination on the severity and mortality of COVID-19 by performing transcriptomic analyses of SARS-CoV-2 infected and BCG vaccinated samples in peripheral blood mononuclear cells (PBMC). A set of common differentially expressed genes (DEGs) were identified and seeded into their functional enrichment analyses via Gene Ontology (GO)-based functional terms and pre-annotated molecular pathways databases, and their Protein-Protein Interaction (PPI) network analysis. We further analysed the regulatory elements, possible comorbidities and putative drug candidates for COVID-19 patients who have not been BCG-vaccinated. Differential expression analyses of both BCG-vaccinated and COVID-19 infected samples identified 62 shared DEGs indicating their discordant expression pattern in their respected conditions compared to control. Next, PPI analysis of those DEGs revealed 10 hub genes, namely ITGB2, CXCL8, CXCL1, CCR2, IFNG, CCL4, PTGS2, ADORA3, TLR5 and CD33. Functional enrichment analyses found significantly enriched pathways/GO terms including cytokine activities, lysosome, IL-17 signalling pathway, TNF-signalling pathways. Moreover, a set of identified TFs, miRNAs and potential drug molecules were further investigated to assess their biological involvements in COVID-19 and their therapeutic possibilities. Findings showed significant genetic interactions between BCG vaccination and SARS-CoV-2 infection, suggesting an interesting prospect of the BCG vaccine in relation to the COVID-19 pandemic. We hope it may potentially trigger further research on this critical phenomenon to combat COVID-19 spread.
Collapse
Affiliation(s)
- Utpala Nanda Chowdhury
- Department of Computer Science and Engineering, University of Rajshahi, Rajshahi, Bangladesh
| | - Md Omar Faruqe
- Department of Computer Science and Engineering, University of Rajshahi, Rajshahi, Bangladesh
| | - Md Mehedy
- Department of Computer Science and Engineering, University of Rajshahi, Rajshahi, Bangladesh
| | - Shamim Ahmad
- Department of Computer Science and Engineering, University of Rajshahi, Rajshahi, Bangladesh
| | - M. Babul Islam
- Department of Electrical and Electronic Engineering, University of Rajshahi, Rajshahi, Bangladesh
| | - Watshara Shoombuatong
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand
| | - A.K.M. Azad
- Faculty of Science, Engineering & Technology, Swinburne University of Technology Sydney, Australia
| | - Mohammad Ali Moni
- School of Health and Rehabilitation Sciences, Faculty of Health and Behavioural Sciences, The University of Queensland, Brisbane, QLD 4072, Australia,Corresponding author
| |
Collapse
|
11
|
Śliwka P, Ochocka M, Skaradzińska A. Applications of bacteriophages against intracellular bacteria. Crit Rev Microbiol 2021; 48:222-239. [PMID: 34428105 DOI: 10.1080/1040841x.2021.1960481] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Infectious diseases pose a significant threat to both human and animal populations. Intracellular bacteria are a group of pathogens that invade and survive within the interior of eukaryotic cells, which in turn protect them from antibacterial drugs and the host immune system. Limited penetration of antibacterials into host cells results in insufficient bacterial clearance and treatment failure. Bacteriophages have, over the decades, been proved to play an important role in combating bacterial infections (phage therapy), making them an important alternative to classical antibiotic strategies today. Phages have been found to be effective at killing various species of extracellular bacteria, but little is still known about how phages control intracellular infections. With advances in phage genomics and mechanisms of delivery and cell uptake, the development of phage-based antibacterial strategies to address the treatment of intracellular bacteria has general potential. In this review, we present the current state of knowledge regarding the application of bacteriophages against intracellular bacteria. We cover phage deployment against the most common intracellular pathogens with special attention to therapeutic and preventive strategies.
Collapse
Affiliation(s)
- Paulina Śliwka
- Department of Biotechnology and Food Microbiology, Faculty of Biotechnology and Food Science, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Marta Ochocka
- Department of Biotechnology and Food Microbiology, Faculty of Biotechnology and Food Science, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Aneta Skaradzińska
- Department of Biotechnology and Food Microbiology, Faculty of Biotechnology and Food Science, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| |
Collapse
|
12
|
Monastirioti A, Papadaki C, Rounis K, Kalapanida D, Mavroudis D, Agelaki S. A Prognostic Role for Circulating microRNAs Involved in Macrophage Polarization in Advanced Non-Small Cell Lung Cancer. Cells 2021; 10:cells10081988. [PMID: 34440757 PMCID: PMC8391493 DOI: 10.3390/cells10081988] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/02/2021] [Accepted: 08/03/2021] [Indexed: 12/12/2022] Open
Abstract
Circulating microRNAs (miRNAs) are key regulators of the crosstalk between tumor cells and immune response. In the present study, miRNAs (let-7c, miR-26a, miR-30d, miR-98, miR-195, miR-202) reported to be involved in the polarization of macrophages were examined for associations with the outcomes of non-small cell lung cancer (NSCLC) patients (N = 125) treated with first-line platinum-based chemotherapy. RT-qPCR was used to analyze miRNA expression levels in the plasma of patients prior to treatment. In our results, disease progression was correlated with high miR-202 expression (HR: 2.335; p = 0.040). Additionally, high miR-202 expression was characterized as an independent prognostic factor for shorter progression-free survival (PFS, HR: 1.564; p = 0.021) and overall survival (OS, HR: 1.558; p = 0.024). Moreover, high miR-202 independently predicted shorter OS (HR: 1.989; p = 0.008) in the non-squamous (non-SqCC) subgroup, and high miR-26a was correlated with shorter OS in the squamous (SqCC) subgroup (10.07 vs. 13.53 months, p = 0.033). The results of the present study propose that the expression levels of circulating miRNAs involved in macrophage polarization are correlated with survival measures in NSCLC patients, and their role as potential biomarkers merits further investigation.
Collapse
Affiliation(s)
- Alexia Monastirioti
- Laboratory of Translational Oncology, School of Medicine, University of Crete, Vassilika Vouton, 71003 Heraklion, Crete, Greece; (A.M.); (C.P.); (D.M.)
| | - Chara Papadaki
- Laboratory of Translational Oncology, School of Medicine, University of Crete, Vassilika Vouton, 71003 Heraklion, Crete, Greece; (A.M.); (C.P.); (D.M.)
| | - Konstantinos Rounis
- Department of Medical Oncology, University General Hospital of Heraklion, Vassilika Vouton, 71110 Heraklion, Crete, Greece; (K.R.); (D.K.)
| | - Despoina Kalapanida
- Department of Medical Oncology, University General Hospital of Heraklion, Vassilika Vouton, 71110 Heraklion, Crete, Greece; (K.R.); (D.K.)
| | - Dimitrios Mavroudis
- Laboratory of Translational Oncology, School of Medicine, University of Crete, Vassilika Vouton, 71003 Heraklion, Crete, Greece; (A.M.); (C.P.); (D.M.)
- Department of Medical Oncology, University General Hospital of Heraklion, Vassilika Vouton, 71110 Heraklion, Crete, Greece; (K.R.); (D.K.)
| | - Sofia Agelaki
- Laboratory of Translational Oncology, School of Medicine, University of Crete, Vassilika Vouton, 71003 Heraklion, Crete, Greece; (A.M.); (C.P.); (D.M.)
- Department of Medical Oncology, University General Hospital of Heraklion, Vassilika Vouton, 71110 Heraklion, Crete, Greece; (K.R.); (D.K.)
- Correspondence: ; Tel.: +30-281-0392438
| |
Collapse
|
13
|
Can miRNA Indicate Risk of Illness after Continuous Exposure to M. tuberculosis? Int J Mol Sci 2021; 22:ijms22073674. [PMID: 33916069 PMCID: PMC8036329 DOI: 10.3390/ijms22073674] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 02/16/2021] [Accepted: 02/17/2021] [Indexed: 12/21/2022] Open
Abstract
The role of regulatory elements such as small ncRNAs and their mechanisms are poorly understood in infectious diseases. Tuberculosis is one of the oldest infectious diseases of humans and it is still a challenge to prevent and treat. Control of the infection, as well as its diagnosis, are still complex and current treatments used are linked to several side effects. This study aimed to identify possible biomarkers for tuberculosis by applying NGS techniques to obtain global miRNA expression profiles from 22 blood samples of infected patients with tuberculosis (n = 9), their respective healthy physicians (n = 6) and external healthy individuals as controls (n = 7). Samples were run through a pipeline consisting of differential expression, target genes, gene set enrichment and miRNA-gene network analyses. We observed 153 altered miRNAs, among which only three DEmiRNAs (hsa-let-7g-5p, hsa-miR-486-3p and hsa-miR-4732-5p) were found between the investigated patients and their respective physicians. These DEmiRNAs are suggested to play an important role in granuloma regulation and their immune physiopathology. Our results indicate that miRNAs may be involved in immune modulation by regulating gene expression in cells of the immune system. Our findings encourage the application of miRNAs as potential biomarkers for tuberculosis.
Collapse
|
14
|
Crowther RR, Qualls JE. Metabolic Regulation of Immune Responses to Mycobacterium tuberculosis: A Spotlight on L-Arginine and L-Tryptophan Metabolism. Front Immunol 2021; 11:628432. [PMID: 33633745 PMCID: PMC7900187 DOI: 10.3389/fimmu.2020.628432] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 12/30/2020] [Indexed: 12/16/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), is a leading cause of death worldwide. Despite decades of research, there is still much to be uncovered regarding the immune response to Mtb infection. Here, we summarize the current knowledge on anti-Mtb immunity, with a spotlight on immune cell amino acid metabolism. Specifically, we discuss L-arginine and L-tryptophan, focusing on their requirements, regulatory roles, and potential use as adjunctive therapy in TB patients. By continuing to uncover the immune cell contribution during Mtb infection and how amino acid utilization regulates their functions, it is anticipated that novel host-directed therapies may be developed and/or refined, helping to eradicate TB.
Collapse
Affiliation(s)
- Rebecca R Crowther
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States.,Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Immunology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH, United States.,Medical Scientist Training Program, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Joseph E Qualls
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States.,Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| |
Collapse
|
15
|
Epithelial processed Mycobacterium avium subsp. paratuberculosis induced prolonged Th17 response and suppression of phagocytic maturation in bovine peripheral blood mononuclear cells. Sci Rep 2020; 10:21048. [PMID: 33273606 PMCID: PMC7713309 DOI: 10.1038/s41598-020-78113-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 11/19/2020] [Indexed: 02/06/2023] Open
Abstract
Johne’s disease (JD) caused by Mycobacterium avium subsp. paratuberculosis (MAP) is a chronic, wasting infectious disease in ruminants that causes enormous economic losses to the dairy and beef cattle industries. Understanding the mechanism of persistency of MAP is key to produce novel ideas for the development of new diagnostic methods or prevention techniques. We sought interactions between the host and MAP using epithelial passage model, which mimic initial stage of infection. From the transcriptomic analysis of bovine immune cells (PBMCs), it was suggested that infection through the epithelial cells elicited prolonged Th17-derived immune response, as indicated by upregulation of IL-17A, IL-17F and RORC until 120 h p.i., compared to directly infected PBMCs. Global downregulation of gene expression was observed after 72 h p.i., especially for genes encoding cell surface receptors of phagocytic cells, such as Toll-like receptors and MHC class II molecules. In addition, the cholesterol efflux transporters ABCA1, ABCG1, and APOE, which are regulated by the LXR/RXR pathway, were downregulated. In summary, it would be suggested that the host initiate immune response to activate Th17-derived cytokines, and MAP survives persistently by altering the host adaptive immune response by suppressing surface receptors and manipulating lipid metabolism in phagocytic cells.
Collapse
|
16
|
Insights into the molecular pathogenesis of ocular tuberculosis. Tuberculosis (Edinb) 2020; 126:102018. [PMID: 33202350 DOI: 10.1016/j.tube.2020.102018] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 11/02/2020] [Accepted: 11/04/2020] [Indexed: 11/23/2022]
Abstract
Unclear pathogenic mechanisms underlying the ocular tuberculosis (OTB) has resulted in perplexity related to the diagnosis and management of the disease. Developments in experimental research and innovations in molecular diagnostics have recently provided a new understanding of disease pathogenesis and natural history. The current review focuses on the new insights into OTB pathogenesis, derived from in vivo and in vitro studies on Mycobacterium tuberculosis dissemination and localization into the eye, in combination with histopathological studies on chorioretinal tissue and vascular network. Advances in the knowledge of OTB have influenced disease management in the clinical setting and lead to reconsideration of the role of existing treatments and suggesting potential new therapeutic approaches.
Collapse
|
17
|
O’Connor D, Pinto MV, Sheerin D, Tomic A, Drury RE, Channon‐Wells S, Galal U, Dold C, Robinson H, Kerridge S, Plested E, Hughes H, Stockdale L, Sadarangani M, Snape MD, Rollier CS, Levin M, Pollard AJ. Gene expression profiling reveals insights into infant immunological and febrile responses to group B meningococcal vaccine. Mol Syst Biol 2020; 16:e9888. [PMID: 33210468 PMCID: PMC7674973 DOI: 10.15252/msb.20209888] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 10/06/2020] [Accepted: 10/08/2020] [Indexed: 12/12/2022] Open
Abstract
Neisseria meningitidis is a major cause of meningitis and septicaemia. A MenB vaccine (4CMenB) was licensed by the European Medicines Agency in January 2013. Here we describe the blood transcriptome and proteome following infant immunisations with or without concomitant 4CMenB, to gain insight into the molecular mechanisms underlying post-vaccination reactogenicity and immunogenicity. Infants were randomised to receive control immunisations (PCV13 and DTaP-IPV-Hib) with or without 4CMenB at 2 and 4 months of age. Blood gene expression and plasma proteins were measured prior to, then 4 h, 24 h, 3 days or 7 days post-vaccination. 4CMenB vaccination was associated with increased expression of ENTPD7 and increased concentrations of 4 plasma proteins: CRP, G-CSF, IL-1RA and IL-6. Post-vaccination fever was associated with increased expression of SELL, involved in neutrophil recruitment. A murine model dissecting the vaccine components found the concomitant regimen to be associated with increased gene perturbation compared with 4CMenB vaccine alone with enhancement of pathways such as interleukin-3, -5 and GM-CSF signalling. Finally, we present transcriptomic profiles predictive of immunological and febrile responses following 4CMenB vaccine.
Collapse
Affiliation(s)
- Daniel O’Connor
- Department of PaediatricsUniversity of OxfordOxfordUK
- NIHR Oxford Biomedical Research CentreOxford University Hospitals NHS Foundation TrustOxfordUK
| | - Marta Valente Pinto
- Department of PaediatricsUniversity of OxfordOxfordUK
- NIHR Oxford Biomedical Research CentreOxford University Hospitals NHS Foundation TrustOxfordUK
| | - Dylan Sheerin
- Department of PaediatricsUniversity of OxfordOxfordUK
- NIHR Oxford Biomedical Research CentreOxford University Hospitals NHS Foundation TrustOxfordUK
| | - Adriana Tomic
- Department of PaediatricsUniversity of OxfordOxfordUK
- NIHR Oxford Biomedical Research CentreOxford University Hospitals NHS Foundation TrustOxfordUK
- Institute of Immunity, Transplantation and InfectionStanford University School of MedicineStanfordCAUSA
| | - Ruth E Drury
- Department of PaediatricsUniversity of OxfordOxfordUK
- NIHR Oxford Biomedical Research CentreOxford University Hospitals NHS Foundation TrustOxfordUK
| | - Samuel Channon‐Wells
- Department of PaediatricsUniversity of OxfordOxfordUK
- NIHR Oxford Biomedical Research CentreOxford University Hospitals NHS Foundation TrustOxfordUK
| | - Ushma Galal
- Nuffield Department of Primary Health CareClinical Trials UnitUniversity of OxfordOxfordUK
| | - Christina Dold
- Department of PaediatricsUniversity of OxfordOxfordUK
- NIHR Oxford Biomedical Research CentreOxford University Hospitals NHS Foundation TrustOxfordUK
| | - Hannah Robinson
- Department of PaediatricsUniversity of OxfordOxfordUK
- NIHR Oxford Biomedical Research CentreOxford University Hospitals NHS Foundation TrustOxfordUK
| | - Simon Kerridge
- Department of PaediatricsUniversity of OxfordOxfordUK
- NIHR Oxford Biomedical Research CentreOxford University Hospitals NHS Foundation TrustOxfordUK
| | - Emma Plested
- Department of PaediatricsUniversity of OxfordOxfordUK
- NIHR Oxford Biomedical Research CentreOxford University Hospitals NHS Foundation TrustOxfordUK
| | - Harri Hughes
- Department of PaediatricsUniversity of OxfordOxfordUK
- NIHR Oxford Biomedical Research CentreOxford University Hospitals NHS Foundation TrustOxfordUK
| | - Lisa Stockdale
- Department of PaediatricsUniversity of OxfordOxfordUK
- NIHR Oxford Biomedical Research CentreOxford University Hospitals NHS Foundation TrustOxfordUK
| | | | - Matthew D Snape
- Department of PaediatricsUniversity of OxfordOxfordUK
- NIHR Oxford Biomedical Research CentreOxford University Hospitals NHS Foundation TrustOxfordUK
| | - Christine S Rollier
- Department of PaediatricsUniversity of OxfordOxfordUK
- NIHR Oxford Biomedical Research CentreOxford University Hospitals NHS Foundation TrustOxfordUK
| | - Michael Levin
- Division of Infectious DiseasesDepartment of MedicineImperial College LondonLondonUK
| | - Andrew J Pollard
- Department of PaediatricsUniversity of OxfordOxfordUK
- NIHR Oxford Biomedical Research CentreOxford University Hospitals NHS Foundation TrustOxfordUK
| |
Collapse
|
18
|
Alipoor SD, Adcock IM, Tabarsi P, Folkerts G, Mortaz E. MiRNAs in tuberculosis: Their decisive role in the fate of TB. Eur J Pharmacol 2020; 886:173529. [PMID: 32919937 DOI: 10.1016/j.ejphar.2020.173529] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 08/28/2020] [Accepted: 08/28/2020] [Indexed: 12/20/2022]
Abstract
Tuberculosis (TB) is one of the most lethal global infectious diseases. Despite the availability of much higher levels of technology in health and medicine, tuberculosis still remains a serious global health problem. Mycobacterium tuberculosis has the capacity for prolonged survival inside macrophages by exploiting host metabolic and energy pathways and perturbing autophagy and apoptosis of infected cells. The mechanism(s) underlying this process are not completely understood but evidence suggests that mycobacteria subvert the host miRNA network to enable mycobacterial survival. We present here a comprehensive review on the role of miRNAs in TB immune escape mechanisms and the potential for miRNA-based TB therapeutics. Further validation studies are required to (i) elucidate the precise effect of TB on host miRNAs, (ii) determine the inhibition of mycobacterial burden using miRNA-based therapies and (iii) identify novel miRNA biomarkers that may prove useful in TB diagnosis and treatment monitoring.
Collapse
Affiliation(s)
- Shamila D Alipoor
- Department of Molecular Medicine, Institute of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Ian M Adcock
- National Heart and Lung Institute, Imperial College London, London, United Kingdom; Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, The University of Newcastle, Newcastle, NSW, Australia
| | - Payam Tabarsi
- Clinical Tuberculosis and Epidemiology Research Center, National Research Institute of Tuberculosis and Lung Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Gert Folkerts
- Division of Pharmacology, Faculty of Science, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands
| | - Esmaeil Mortaz
- Clinical Tuberculosis and Epidemiology Research Center, National Research Institute of Tuberculosis and Lung Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| |
Collapse
|
19
|
Vavougios GD, Zarogiannis SG, Krogfelt KA, Stamoulis G, Gourgoulianis KI. Epigenetic regulation of apoptosis via the PARK7 interactome in peripheral blood mononuclear cells donated by tuberculosis patients vs. healthy controls and the response to treatment: A systems biology approach. Tuberculosis (Edinb) 2020; 123:101938. [PMID: 32741527 DOI: 10.1016/j.tube.2020.101938] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 03/22/2020] [Accepted: 04/14/2020] [Indexed: 12/22/2022]
Abstract
AIMS The aims of our study were to determine for the first time differentially expressed genes (DEGs) and enriched molecular pathways involving the PARK7 interactome in PBMCs donated from tuberculosis patients. METHODS Data on a previously reconstructed PARK7 interactome (Vavougios et al., 2017) from datasets GDS4966 (Case-Control) and GDS4781 (Treatment Series) were retrieved from the Gene Expression Omnibus (GEO) repository. Gene Enrichment analysis was performed via the STRING algorithm and the GeneTrail2 software. RESULTS 17 and 22 PARK7 interactores were determined as DEGs in the active TB vs HD and Treatment Series subset analyses, correspondingly, associated with significantly enriched pathways (FDR <0.05) involving p53 and PTEN mediated, stress responsive apoptosis regulation pathways. The treatment subset was characterized by the emergence of an additional layer of transcriptional regulation mediated by polycomb proteins among others, as well as TLR-mediated and cytokine survival signaling. Finally, the enrichment of a Parkinson's disease signature including PARK7 interactors was determined by its differential regulation both in the exploratory analyses (FDR = 0.024), as well as the confirmatory analyses (FDR = 1.81e-243). CONCLUSIONS Our in silico analysis revealed for the first time the role of PARK7's interactome in regulating the epigenetics of the PBMC lifecycle and Mtb symbiosis.
Collapse
Affiliation(s)
- George D Vavougios
- Department of Neurology, Athens Naval Hospital, Deinokratous 70, 115 21, Athens, Greece; Department of Electrical and Computer Engineering, 37 Glavani - 28th October Street, Deligiorgi Building, 4th floor, 382 21, Volos, Greece.
| | - Sotirios G Zarogiannis
- Department of Pleural Physiology, Faculty of Medicine, University of Thessaly, BIOPOLIS, Mezourlo, 41500, Larisa, Greece
| | - Karen A Krogfelt
- Department of Science and Environment, Molecular and Medical Biology, Roskilde University, Universitetsvej 1, 28A.1, DK-4000, Roskilde, Denmark
| | - George Stamoulis
- Department of Electrical and Computer Engineering, 37 Glavani - 28th October Street, Deligiorgi Building, 4th floor, 382 21, Volos, Greece
| | - Konstantinos I Gourgoulianis
- Department of Respiratory Medicine, Faculty of Medicine, University of Thessaly, BIOPOLIS, Mezourlo, 41110, Larisa, Greece
| |
Collapse
|
20
|
Muefong CN, Sutherland JS. Neutrophils in Tuberculosis-Associated Inflammation and Lung Pathology. Front Immunol 2020; 11:962. [PMID: 32536917 PMCID: PMC7266980 DOI: 10.3389/fimmu.2020.00962] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 04/23/2020] [Indexed: 12/13/2022] Open
Abstract
Protective immunity to Mycobacterium tuberculosis (Mtb)—the causative agent of tuberculosis (TB)—is not fully understood but involves immune responses within the pulmonary airways which can lead to exacerbated inflammation and immune pathology. In humans, this inflammation results in lung damage; the extent of which depends on specific host pro-inflammatory processes. Neutrophils, though increasingly linked to the development of inflammatory disorders, have been less well studied in relation to TB-induced lung pathology. Neutrophils mode of action and their specialized functions can be directly linked to TB-specific lung tissue damage observed on patient chest X-rays at diagnosis and contribute to long-term pulmonary sequelae. This review discusses aspects of neutrophil activity associated with active TB, including the resulting inflammation and pulmonary impairment. It highlights the significance of neutrophil function on TB disease outcome and underlines the necessity of monitoring neutrophil function for better assessment of the immune response and severity of lung pathology associated with TB. Finally, we propose that some MMPs, ROS, MPO, S100A8/A9 and Glutathione are neutrophil-related inflammatory mediators with promising potential as targets for developing host-directed therapies for TB.
Collapse
Affiliation(s)
- Caleb N Muefong
- Vaccines and Immunity Theme, Medical Research Council Unit, The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Jayne S Sutherland
- Vaccines and Immunity Theme, Medical Research Council Unit, The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| |
Collapse
|
21
|
Singh N, Singh R, Sharma RK, Kumar A, Sharma SP, Agarwal A, Gupta V, Singh R, Katoch D. Mycobacterium Tuberculosis Modulates Fibroblast Growth Factor and Vascular Endothelial Growth Factor in Ocular Tuberculosis. Ocul Immunol Inflamm 2020; 29:1445-1451. [PMID: 32160084 DOI: 10.1080/09273948.2020.1734212] [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: 10/24/2022]
Abstract
Purpose: To evaluate the role of angiogenic growth factors in the pathogenesis of intraocular tuberculosis.Methods: Retinal Pigment Epithelium (RPE) cells were infected with varying dilution of Mycobacterium tuberculosis (MTB), ranging from several thousand to a few MTB bacilli to replicate paucibacillary conditions. Angiogenesis growth factors were evaluated using multiplex fluorescent bead based flow cytometry in the culture supernatant of RPE cells infected with MTB, vitreous fluids and tear samples of uveitis patients visiting retina clinic.Results: Vascular endothelial growth factor (VEGF) levels were elevated and fibroblast growth factors (FGFs) were down regulated in RPE-infected MTB cells. Similar pattern of VEGF and FGF was observed in the vitreous of IOTB patients. However, no changes were observed in tear samples.Conclusions: MTB exploits the angiogenesis growth factors for pathogenesis by decreasing FGF with concomitant surge of VEGF in MTB infected RPE as well in the vitreous of IOTB patients.
Collapse
Affiliation(s)
- Nirbhai Singh
- Advanced Eye Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Ravinder Singh
- Advanced Eye Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Ravi Kumar Sharma
- Advanced Eye Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Aman Kumar
- Advanced Eye Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Surya Prakash Sharma
- Advanced Eye Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Aniruddha Agarwal
- Advanced Eye Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Vishali Gupta
- Advanced Eye Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Ramandeep Singh
- Advanced Eye Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Deeksha Katoch
- Advanced Eye Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| |
Collapse
|
22
|
Lérias JR, de Sousa E, Paraschoudi G, Martins J, Condeço C, Figueiredo N, Carvalho C, Dodoo E, Maia A, Castillo-Martin M, Beltrán A, Ligeiro D, Rao M, Zumla A, Maeurer M. Trained Immunity for Personalized Cancer Immunotherapy: Current Knowledge and Future Opportunities. Front Microbiol 2020; 10:2924. [PMID: 31998254 PMCID: PMC6967396 DOI: 10.3389/fmicb.2019.02924] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 12/04/2019] [Indexed: 12/17/2022] Open
Abstract
Memory formation, guided by microbial ligands, has been reported for innate immune cells. Epigenetic imprinting plays an important role herein, involving histone modification after pathogen-/danger-associated molecular patterns (PAMPs/DAMPs) recognition by pattern recognition receptors (PRRs). Such "trained immunity" affects not only the nominal target pathogen, yet also non-related targets that may be encountered later in life. The concept of trained innate immunity warrants further exploration in cancer and how these insights can be implemented in immunotherapeutic approaches. In this review, we discuss our current understanding of innate immune memory and we reference new findings in this field, highlighting the observations of trained immunity in monocytic and natural killer cells. We also provide a brief overview of trained immunity in non-immune cells, such as stromal cells and fibroblasts. Finally, we present possible strategies based on trained innate immunity that may help to devise host-directed immunotherapies focusing on cancer, with possible extension to infectious diseases.
Collapse
Affiliation(s)
- Joana R Lérias
- ImmunoSurgery Unit, Champalimaud Centre for the Unknown, Lisbon, Portugal
| | - Eric de Sousa
- ImmunoSurgery Unit, Champalimaud Centre for the Unknown, Lisbon, Portugal
| | | | - João Martins
- ImmunoSurgery Unit, Champalimaud Centre for the Unknown, Lisbon, Portugal
| | - Carolina Condeço
- ImmunoSurgery Unit, Champalimaud Centre for the Unknown, Lisbon, Portugal
| | - Nuno Figueiredo
- Digestive Unit, Champalimaud Clinical Centre, Lisbon, Portugal
| | - Carlos Carvalho
- Digestive Unit, Champalimaud Clinical Centre, Lisbon, Portugal
| | - Ernest Dodoo
- ImmunoSurgery Unit, Champalimaud Centre for the Unknown, Lisbon, Portugal
| | - Andreia Maia
- Molecular and Experimental Pathology Laboratory, Champalimaud Centre for the Unknown, Lisbon, Portugal
| | - Mireia Castillo-Martin
- Molecular and Experimental Pathology Laboratory, Champalimaud Centre for the Unknown, Lisbon, Portugal.,Department of Pathology, Champalimaud Clinical Centre, Lisbon, Portugal
| | - Antonio Beltrán
- Department of Pathology, Champalimaud Clinical Centre, Lisbon, Portugal
| | - Dário Ligeiro
- Lisbon Centre for Blood and Transplantation, Instituto Português do Sangue e Transplantação, Lisbon, Portugal
| | - Martin Rao
- ImmunoSurgery Unit, Champalimaud Centre for the Unknown, Lisbon, Portugal
| | - Alimuddin Zumla
- Division of Infection and Immunity, NIHR Biomedical Research Centre, UCL Hospitals, NHS Foundation Trust, University College London, London, United Kingdom
| | - Markus Maeurer
- ImmunoSurgery Unit, Champalimaud Centre for the Unknown, Lisbon, Portugal
| |
Collapse
|
23
|
MicroRNAs as new immunity regulators in viral and bacterial infections. ACTA BIOLOGICA 2020. [DOI: 10.18276/ab.2020.27-09] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
24
|
Asai M, Li Y, Khara JS, Robertson BD, Langford PR, Newton SM. Galleria mellonella: An Infection Model for Screening Compounds Against the Mycobacterium tuberculosis Complex. Front Microbiol 2019; 10:2630. [PMID: 31824448 PMCID: PMC6882372 DOI: 10.3389/fmicb.2019.02630] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 10/29/2019] [Indexed: 01/08/2023] Open
Abstract
Drug screening models have a vital role in the development of novel antimycobacterial agents which are urgently needed to tackle drug-resistant tuberculosis (TB). We recently established the larvae of the insect Galleria mellonella (greater wax moth) as a novel infection model for the Mycobacterium tuberculosis complex. Here we demonstrate its use as a rapid and reproducible screen to evaluate antimycobacterial drug efficacy using larvae infected with bioluminescent Mycobacterium bovis BCG lux. Treatment improved larval survival outcome and, with the exception of pyrazinamide, was associated with a significant reduction in in vivo mycobacterial bioluminescence over a 96 h period compared to the untreated controls. Isoniazid and rifampicin displayed the greatest in vivo efficacy and survival outcome. Thus G. mellonella, infected with bioluminescent mycobacteria, can rapidly determine in vivo drug efficacy, and has the potential to significantly reduce and/or replace the number of animals used in TB research.
Collapse
Affiliation(s)
- Masanori Asai
- Section of Paediatric Infectious Diseases, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Yanwen Li
- Department of Pharmacy, National University of Singapore, Singapore, Singapore
| | - Jasmeet Singh Khara
- Section of Paediatric Infectious Diseases, Department of Infectious Disease, Imperial College London, London, United Kingdom.,Department of Pharmacy, National University of Singapore, Singapore, Singapore
| | - Brian D Robertson
- MRC Centre for Molecular Bacteriology and Infection, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Paul R Langford
- Section of Paediatric Infectious Diseases, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Sandra M Newton
- Section of Paediatric Infectious Diseases, Department of Infectious Disease, Imperial College London, London, United Kingdom
| |
Collapse
|
25
|
Popovic M, Yaparla A, Paquin‐Proulx D, Koubourli DV, Webb R, Firmani M, Grayfer L. Colony‐stimulating factor‐1‐ and interleukin‐34‐derived macrophages differ in their susceptibility to
Mycobacterium marinum. J Leukoc Biol 2019; 106:1257-1269. [DOI: 10.1002/jlb.1a0919-147r] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 09/02/2019] [Accepted: 09/06/2019] [Indexed: 12/22/2022] Open
Affiliation(s)
- Milan Popovic
- Department of Biological Sciences George Washington University Washington DC 20052 USA
| | - Amulya Yaparla
- Department of Biological Sciences George Washington University Washington DC 20052 USA
| | - Dominic Paquin‐Proulx
- Department of Microbiology Immunology and Tropical Medicine George Washington University Washington DC 20037 USA
| | - Daphne V. Koubourli
- Department of Biological Sciences George Washington University Washington DC 20052 USA
| | - Rose Webb
- Pathology Core Laboratory George Washington University Washington DC 20037 USA
| | - Marcia Firmani
- Department of Biomedical Laboratory Sciences George Washington University Washington DC 20037 USA
| | - Leon Grayfer
- Department of Biological Sciences George Washington University Washington DC 20052 USA
| |
Collapse
|
26
|
Mucosal boosting of H56:CAF01 immunization promotes lung-localized T cells and an accelerated pulmonary response to Mycobacterium tuberculosis infection without enhancing vaccine protection. Mucosal Immunol 2019; 12:816-826. [PMID: 30760832 DOI: 10.1038/s41385-019-0145-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Revised: 12/20/2018] [Accepted: 01/23/2019] [Indexed: 02/04/2023]
Abstract
T cell-mediated protection against Mycobacterium tuberculosis (Mtb) is dependent upon the ability to localize within the site of pulmonary infection and directly interact with infected cells. In turn, vaccine strategies to improve rapid T cell targeting of Mtb-infected cells after pulmonary exposure are being actively pursued. Given parenterally, the subunit vaccine H56:CAF01 elicits polyfunctional CD4 T cells that localize to the lung parenchyma and confer durable protection. Here, we find that airway mucosal boosting of parenteral H56:CAF01 immunization greatly enhances the population of long-lived lung-resident T cells (Trm) and increases early vaccine T cell responses to pulmonary Mtb challenge in multiple mouse models. However, mucosal boosting does not alter the Th1/17 vaccine signature typical of H56:CAF01 and does not further improve durable control of pulmonary infection following aerosol Mtb-challenge. Additional mucosal boosting with H56:CAF01 further enhances the Trm response without further improving protection, while blocking the recruitment of non-Trm with FTY720-treatment failed to exposed Trm-mediated protection in mucosally boosting animals. These results demonstrate the limitations of maximizing lung-localized Trm in vaccine control of pulmonary Mtb infection, especially within an immunization protocol that is already optimized for the induction of mucosal-homing Th17 cells.
Collapse
|
27
|
Curtale G, Rubino M, Locati M. MicroRNAs as Molecular Switches in Macrophage Activation. Front Immunol 2019; 10:799. [PMID: 31057539 PMCID: PMC6478758 DOI: 10.3389/fimmu.2019.00799] [Citation(s) in RCA: 118] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 03/26/2019] [Indexed: 12/25/2022] Open
Abstract
The efficacy of macrophage- mediated inflammatory response relies on the coordinated expression of key factors, which expression is finely regulated at both transcriptional and post-transcriptional level. Several studies have provided compelling evidence that microRNAs play pivotal roles in modulating macrophage activation, polarization, tissue infiltration, and resolution of inflammation. In this review, we highlight the essential molecular mechanisms underlying the different phases of inflammation that are targeted by microRNAs to inhibit or accelerate restoration to tissue integrity and homeostasis. We further review the impact of microRNA-dependent regulation of tumor-associated macrophages and the relative implication for tumor biology.
Collapse
Affiliation(s)
- Graziella Curtale
- Department of Medical Biotechnologies and Translational Medicine, University of Milan, Milan, Italy.,Humanitas Clinical and Research Center - IRCCS, Rozzano, Italy
| | - Marcello Rubino
- Humanitas Clinical and Research Center - IRCCS, Rozzano, Italy
| | - Massimo Locati
- Department of Medical Biotechnologies and Translational Medicine, University of Milan, Milan, Italy.,Humanitas Clinical and Research Center - IRCCS, Rozzano, Italy
| |
Collapse
|
28
|
Mycobacterium smegmatis But Not Mycobacterium avium subsp. hominissuis Causes Increased Expression of the Long Non-Coding RNA MEG3 in THP-1-Derived Human Macrophages and Associated Decrease of TGF-β. Microorganisms 2019; 7:microorganisms7030063. [PMID: 30818784 PMCID: PMC6463094 DOI: 10.3390/microorganisms7030063] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 02/13/2019] [Accepted: 02/26/2019] [Indexed: 11/16/2022] Open
Abstract
Pathogenic mycobacteria are able to persist intracellularly in macrophages, whereas non-pathogenic mycobacteria are effectively combated and eliminated after their phagocytosis. It is known that TGF-β plays an important role in this context. Infection with pathogenic mycobacteria such as Mycobacterium tuberculosis or M. avium leads to production of active TGF-β, which blocks the ability of IFN-γ and TNF-α to inhibit intracellular replication. On the other hand, it is known that the long non-coding RNA (lncRNA) maternally expressed 3 (MEG3) is involved in the regulation of TGF-β. In this study, we show how the infection of THP-1-derived human macrophages with the saprophytic M. smegmatis but not with the facultatively pathogenic M. avium subsp. hominissuis leads to increased MEG3 expression. This is associated with the downregulation of DNA methyltransferases (DNMT) 1 and 3b, which are known to regulate MEG3 expression via promoter hypermethylation. Consequently, we observe a significant downregulation of TGF-β in M. smegmatis-infected macrophages but not in M. avium subsp. hominissuis pointing to lncRNAs as novel mediators of host cell response during mycobacterial infections.
Collapse
|
29
|
Li Y, Spiropoulos J, Cooley W, Khara JS, Gladstone CA, Asai M, Bossé JT, Robertson BD, Newton SM, Langford PR. Galleria mellonella - a novel infection model for the Mycobacterium tuberculosis complex. Virulence 2018; 9:1126-1137. [PMID: 30067135 PMCID: PMC6086298 DOI: 10.1080/21505594.2018.1491255] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Animal models have long been used in tuberculosis research to understand disease pathogenesis and to evaluate novel vaccine candidates and anti-mycobacterial drugs. However, all have limitations and there is no single animal model which mimics all the aspects of mycobacterial pathogenesis seen in humans. Importantly mice, the most commonly used model, do not normally form granulomas, the hallmark of tuberculosis infection. Thus there is an urgent need for the development of new alternative in vivo models. The insect larvae, Galleria mellonella has been increasingly used as a successful, simple, widely available and cost-effective model to study microbial infections. Here we report for the first time that G. mellonella can be used as an infection model for members of the Mycobacterium tuberculosis complex. We demonstrate a dose-response for G. mellonella survival infected with different inocula of bioluminescent Mycobacterium bovis BCG lux, and demonstrate suppression of mycobacterial luminesence over 14 days. Histopathology staining and transmission electron microscopy of infected G. mellonella phagocytic haemocytes show internalization and aggregation of M. bovis BCG lux in granuloma-like structures, and increasing accumulation of lipid bodies within M. bovis BCG lux over time, characteristic of latent tuberculosis infection. Our results demonstrate that G. mellonella can act as a surrogate host to study the pathogenesis of mycobacterial infection and shed light on host-mycobacteria interactions, including latent tuberculosis infection.
Collapse
Affiliation(s)
- Yanwen Li
- a Section of Paediatric Infectious Diseases and Allergy, Department of Medicine , Imperial College London , London , UK
| | - John Spiropoulos
- b Department of Pathology , Animal and Plant Health Agency , Addlestone , UK
| | - William Cooley
- b Department of Pathology , Animal and Plant Health Agency , Addlestone , UK
| | - Jasmeet Singh Khara
- a Section of Paediatric Infectious Diseases and Allergy, Department of Medicine , Imperial College London , London , UK.,c Department of Pharmacy , National University of Singapore , Singapore
| | - Camilla A Gladstone
- a Section of Paediatric Infectious Diseases and Allergy, Department of Medicine , Imperial College London , London , UK
| | - Masanori Asai
- a Section of Paediatric Infectious Diseases and Allergy, Department of Medicine , Imperial College London , London , UK
| | - Janine T Bossé
- a Section of Paediatric Infectious Diseases and Allergy, Department of Medicine , Imperial College London , London , UK
| | - Brian D Robertson
- d MRC Centre for Molecular Bacteriology and Infection, Department of Medicine , Imperial College London , London , UK
| | - Sandra M Newton
- a Section of Paediatric Infectious Diseases and Allergy, Department of Medicine , Imperial College London , London , UK
| | - Paul R Langford
- a Section of Paediatric Infectious Diseases and Allergy, Department of Medicine , Imperial College London , London , UK
| |
Collapse
|
30
|
Ramsuran V, Ewy R, Nguyen H, Kulkarni S. Variation in the Untranslated Genome and Susceptibility to Infections. Front Immunol 2018; 9:2046. [PMID: 30245696 PMCID: PMC6137953 DOI: 10.3389/fimmu.2018.02046] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 08/20/2018] [Indexed: 12/11/2022] Open
Abstract
The clinical outcomes of infections are highly variable among individuals and are determined by complex host-pathogen interactions. Genome-wide association studies (GWAS) are powerful tools to unravel common genetic variations that are associated with disease risk and clinical outcomes. However, GWAS has only rarely revealed information on the exact genetic elements and their effects underlying an association because the majority of the hits are within non-coding regions. Some of the variants or the linked polymorphisms are now being discovered to have functional significance, such as regulatory elements in the promoter and enhancer regions or the microRNA binding sites in the 3′untranslated region of the protein-coding genes, which influence transcription, RNA stability, and translation of the protein-coding genes. However, only 3% of the entire transcriptome is protein-coding, signifying that non-coding RNAs represent most of the transcripts. Thus, a large portion of previously identified intergenic GWAS single nucleotide polymorphisms (SNPs) is in the non-coding RNAs. The non-coding RNAs form a large-scale regulatory network across the transcriptome, greatly expanding the complexity of gene regulation. Accumulating evidence also suggests that the “non-coding” genome regions actively regulate the highly dynamic three dimensional (3D) chromatin structures, which are critical for genome function. Epigenetic modulation like DNA methylation and histone modifications further affect chromatin accessibility and gene expression adding another layer of complexity to the functional interpretation of genetic variation associated with disease outcomes. We provide an overview of the current information on the influence of variation in these “untranslated” regions of the human genome on infectious diseases. The focus of this review is infectious disease-associated polymorphisms and gene regulatory mechanisms of pathophysiological relevance.
Collapse
Affiliation(s)
- Veron Ramsuran
- Centre for the AIDS Programme of Research in South Africa, KwaZulu-Natal Research Innovation and Sequencing Platform, School of Laboratory Medicine and Medical Sciences, Nelson R. Mandela School of Medicine, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Rodger Ewy
- Genetics Department, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Hoang Nguyen
- Genetics Department, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Smita Kulkarni
- Genetics Department, Texas Biomedical Research Institute, San Antonio, TX, United States
| |
Collapse
|
31
|
Dallmann-Sauer M, Correa-Macedo W, Schurr E. Human genetics of mycobacterial disease. Mamm Genome 2018; 29:523-538. [PMID: 30116885 PMCID: PMC6132723 DOI: 10.1007/s00335-018-9765-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 07/23/2018] [Indexed: 12/18/2022]
Abstract
Mycobacterial diseases are caused by members of the genus Mycobacterium, acid-fast bacteria characterized by the presence of mycolic acids within their cell walls. Claiming almost 2 million lives every year, tuberculosis (TB) is the most common mycobacterial disease and is caused by infection with M. tuberculosis and, in rare cases, by M. bovis or M. africanum. The second and third most common mycobacterial diseases are leprosy and buruli ulcer (BU), respectively. Both diseases affect the skin and can lead to permanent sequelae and deformities. Leprosy is caused by the uncultivable M. leprae while the etiological agent of BU is the environmental bacterium M. ulcerans. After exposure to these mycobacterial species, a majority of individuals will not progress to clinical disease and, among those who do, inter-individual variability in disease manifestation and outcome can be observed. Susceptibility to mycobacterial diseases carries a human genetic component and intense efforts have been applied over the past decades to decipher the exact nature of the genetic factors controlling disease susceptibility. While for BU this search was mostly conducted on the basis of candidate genes association studies, genome-wide approaches have been widely applied for TB and leprosy. In this review, we summarize some of the findings achieved by genome-wide linkage, association and transcriptome analyses in TB disease and leprosy and the recent genetic findings for BU susceptibility.
Collapse
Affiliation(s)
- Monica Dallmann-Sauer
- Program in Infectious Diseases and Immunity in Global Health, Research Institute, McGill University Health Centre, Montreal, QC, Canada.,The McGill International TB Centre, McGill University, Montreal, QC, Canada.,Departments of Human Genetics and Medicine, Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Wilian Correa-Macedo
- Program in Infectious Diseases and Immunity in Global Health, Research Institute, McGill University Health Centre, Montreal, QC, Canada.,The McGill International TB Centre, McGill University, Montreal, QC, Canada.,Department of Biochemistry, Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Erwin Schurr
- Program in Infectious Diseases and Immunity in Global Health, Research Institute, McGill University Health Centre, Montreal, QC, Canada. .,The McGill International TB Centre, McGill University, Montreal, QC, Canada. .,Departments of Human Genetics and Medicine, Faculty of Medicine, McGill University, Montreal, QC, Canada. .,Department of Biochemistry, Faculty of Medicine, McGill University, Montreal, QC, Canada.
| |
Collapse
|
32
|
Yang T, Ge B. miRNAs in immune responses to Mycobacterium tuberculosis infection. Cancer Lett 2018; 431:22-30. [PMID: 29803788 DOI: 10.1016/j.canlet.2018.05.028] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 05/16/2018] [Accepted: 05/17/2018] [Indexed: 12/21/2022]
Abstract
Tuberculosis (TB) is one of the most fatal infectious diseases, affecting one third of the world's population. The causative agent, Mycobacterium tuberculosis (Mtb), has a well-established ability to circumvent the host's immune system for its long-term intracellular survival. MicroRNAs (miRNAs) are crucial post-transcriptional regulators of immune response. They act by negatively regulating the expression levels of important genes in both innate and adaptive immunity. It has been established in recent studies that the host immune response against Mtb is regulated by many miRNAs, most of which are induced by Mtb infection. Moreover, differential expression of miRNA in tuberculosis (TB) patients may help distinguish between TB patients and healthy individuals or latent TB. In this review, we present the recent advancements on the miRNA regulation of the host responses against Mtb infection, as well as the potential of miRNAs to as biomarkers for TB diagnosis.
Collapse
Affiliation(s)
- Tianshu Yang
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China; Department of Microbiology and Immunology, Tongji University Medicine, Shanghai, China
| | - Baoxue Ge
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China; Department of Microbiology and Immunology, Tongji University Medicine, Shanghai, China.
| |
Collapse
|