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Katsiki AD, Karatzas PE, De Lastic HX, Georgakilas AG, Tsitsilonis O, Vorgias CE. DExplore: An Online Tool for Detecting Differentially Expressed Genes from mRNA Microarray Experiments. BIOLOGY 2024; 13:351. [PMID: 38785833 PMCID: PMC11117493 DOI: 10.3390/biology13050351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 05/09/2024] [Accepted: 05/13/2024] [Indexed: 05/25/2024]
Abstract
Microarray experiments, a mainstay in gene expression analysis for nearly two decades, pose challenges due to their complexity. To address this, we introduce DExplore, a user-friendly web application enabling researchers to detect differentially expressed genes using data from NCBI's GEO. Developed with R, Shiny, and Bioconductor, DExplore integrates WebGestalt for functional enrichment analysis. It also provides visualization plots for enhanced result interpretation. With a Docker image for local execution, DExplore accommodates unpublished data. To illustrate its utility, we showcase two case studies on cancer cells treated with chemotherapeutic drugs. DExplore streamlines microarray data analysis, empowering molecular biologists to focus on genes of biological significance.
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Affiliation(s)
- Anna D. Katsiki
- Department of Biology, School of Science, National and Kapodistrian University of Athens, 15784 Athens, Greece
| | - Pantelis E. Karatzas
- Unit of Process Control and Informatics, Department of Process Analysis and Plant Design, School of Chemical Engineering, National Technical University of Athens (NTUA), Zografou Campus, 15780 Athens, Greece
| | - Hector-Xavier De Lastic
- DNA Damage Laboratory, Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens (NTUA), Zografou Campus, 15780 Athens, Greece
| | - Alexandros G. Georgakilas
- DNA Damage Laboratory, Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens (NTUA), Zografou Campus, 15780 Athens, Greece
| | - Ourania Tsitsilonis
- Department of Biology, School of Science, National and Kapodistrian University of Athens, 15784 Athens, Greece
| | - Constantinos E. Vorgias
- Department of Biology, School of Science, National and Kapodistrian University of Athens, 15784 Athens, Greece
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Lachmansingh DA, Valderrama B, Bastiaanssen T, Cryan J, Clarke G, Lavelle A. Impact of dietary fiber on gut microbiota composition, function and gut-brain-modules in healthy adults - a systematic review protocol. HRB Open Res 2024; 6:62. [PMID: 38525261 PMCID: PMC10958149 DOI: 10.12688/hrbopenres.13794.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/23/2024] [Indexed: 03/26/2024] Open
Abstract
Background The gut microbiota has been extensively implicated in health and disease. The functional outputs of the gut microbiota, such as microbial metabolites, are considered particularly important in this regard. Significant associations exist between alterations in the relative abundance of specific microbial taxa and mental health disorders. Dietary fiber has the potential to alter gut microbiota composition and function, modifying bacterial enzymatic function and the production of metabolites. As many taxa of microorganisms have enzymes capable of producing or degrading neurochemicals i.e. neuroactive gut brain modules, new predictive tools can be applied to existing datasets such as those harvested from dietary fiber interventions. We endeavor to perform a systematic review in order to identify studies reporting compositional gut microbiota alterations after interventions with dietary fiber in healthy individuals. We aim to also extract from the selected studies publicly available microbial genomic sequence datasets for reanalysis with a consistent bioinformatics pipeline, with the ultimate intention of identifying altered gut brain modules following dietary fiber interventions. Methods Interventional trials and randomized controlled studies that are originally published, including cross-over and non-crossover design and involving healthy adult humans will be included. A systematic search of PubMed/MEDLINE and EMBASE, two electronic databases, will be completed. Discussion Various types of dietary fiber have an impact on the gut microbiota composition, with some promoting the growth of particular taxa while others are reduced in relative abundance. Our search focuses on the impact of this food component on the microbiota of healthy individuals. Compositional gut microbial changes have been reported and our review will compile and update these observations after reanalysis of their datasets with a consistent bioinformatic pipeline. From this it may be possible to predict more detailed functional consequences in terms of neuroactive gut brain modules, of the compositional alterations in gut microbial taxa.
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Affiliation(s)
- David Antoine Lachmansingh
- Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, County Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, County Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Cork, County Cork, Ireland
| | - Benjamin Valderrama
- APC Microbiome Ireland, University College Cork, Cork, County Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Cork, County Cork, Ireland
| | - Thomaz Bastiaanssen
- APC Microbiome Ireland, University College Cork, Cork, County Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Cork, County Cork, Ireland
| | - John Cryan
- APC Microbiome Ireland, University College Cork, Cork, County Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Cork, County Cork, Ireland
| | - Gerard Clarke
- Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, County Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, County Cork, Ireland
| | - Aonghus Lavelle
- APC Microbiome Ireland, University College Cork, Cork, County Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Cork, County Cork, Ireland
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Shin S, Choi EJ, Moon SW, Lee SB, Chung YJ, Lee SH. Leprosy-specific subsets of macrophages and Schwann cells identified by single-cell RNA-sequencing. Pathol Res Pract 2023; 250:154821. [PMID: 37757621 DOI: 10.1016/j.prp.2023.154821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/10/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023]
Abstract
In Mycobacterium leprae (M. leprae)-infection, inflammatory cells' subsets and dynamics as well as the interactions with Schwann cells have remained elusive. We investigated individual cells in M. leprae-inoculated nude mice by single-cell RNA-sequencing (scRNA-seq). For macrophages, we dissected two M1-like subsets and five M2-like subsets, where lipid-associated signatures were pervasive in both M1-like and M2-like subsets. There were four macrophage trajectories showing: (i) pro-inflammatory (M1), (ii) lipid metabolism-related (M2), (iii) anti-inflammatory (M2), and (iv) interferon-stimulated gene-related (M2) fates. They displayed early divergence without ever rejoining along the paths, suggesting simultaneous or continuous stimuli for macrophage activation in leprosy. The scRNA-seq predicted Schwann cell-macrophage interactions (Notch1-Jag1, Plxnb1-Sema4d interactions). An immature Schwann cell subset showing Tfap2a expression was identified, indicating Schwann cell dedifferentiation in leprosy tissues. Expressions of Notch1, Jag1, Plxnb1, Sema4d, and Tfap2a were validated in mouse or human leprosy tissues by immunohistochemistry. We identified both pro-inflammatory and inflammation-resolution signatures, where lipid-associated signatures were pervasive to the macrophages, representing leprosy-specific macrophage states for prolonged and repeated episodes of inflammation and resolution. Our study identified refined molecular states and interactions of macrophages and Schwann cells, suggesting novel insights into the pathogenesis of unhealed inflammation with neuropathy and potential therapeutic targets for leprosy.
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Affiliation(s)
- Sun Shin
- Departments of Microbiology, College of Medicine, The Catholic University of Korea, Republic of Korea; Integrated Research Center for Genome Polymorphism, College of Medicine, The Catholic University of Korea, Republic of Korea
| | - Eun Ji Choi
- Departments of Pathology, College of Medicine, The Catholic University of Korea, Republic of Korea
| | - Seong Won Moon
- Departments of Pathology, College of Medicine, The Catholic University of Korea, Republic of Korea; Departments of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Republic of Korea
| | - Seong-Beom Lee
- Institute of Hansen's Disease, College of Medicine, The Catholic University of Korea, Republic of Korea; Departments of Pathology, College of Medicine, The Catholic University of Korea, Republic of Korea
| | - Yeun-Jun Chung
- Departments of Microbiology, College of Medicine, The Catholic University of Korea, Republic of Korea; Integrated Research Center for Genome Polymorphism, College of Medicine, The Catholic University of Korea, Republic of Korea; Cancer Evolution Research Center, College of Medicine, The Catholic University of Korea, Republic of Korea.
| | - Sug Hyung Lee
- Departments of Pathology, College of Medicine, The Catholic University of Korea, Republic of Korea; Departments of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Republic of Korea; Cancer Evolution Research Center, College of Medicine, The Catholic University of Korea, Republic of Korea.
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Visentin L, Scarpellino G, Chinigò G, Munaron L, Ruffinatti FA. BioTEA: Containerized Methods of Analysis for Microarray-Based Transcriptomics Data. BIOLOGY 2022; 11:biology11091346. [PMID: 36138825 PMCID: PMC9495986 DOI: 10.3390/biology11091346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 08/29/2022] [Accepted: 09/08/2022] [Indexed: 11/16/2022]
Abstract
Tens of thousands of gene expression data sets describing a variety of model organisms in many different pathophysiological conditions are currently stored in publicly available databases such as the Gene Expression Omnibus (GEO) and ArrayExpress (AE). As microarray technology is giving way to RNA-seq, it becomes strategic to develop high-level tools of analysis to preserve access to this huge amount of information through the most sophisticated methods of data preparation and processing developed over the years, while ensuring, at the same time, the reproducibility of the results. To meet this need, here we present bioTEA (biological Transcript Expression Analyzer), a novel software tool that combines ease of use with the versatility and power of an R/Bioconductor-based differential expression analysis, starting from raw data retrieval and preparation to gene annotation. BioTEA is an R-coded pipeline, wrapped in a Python-based command line interface and containerized with Docker technology. The user can choose among multiple options—including gene filtering, batch effect handling, sample pairing, statistical test type—to adapt the algorithm flow to the structure of the particular data set. All these options are saved in a single text file, which can be easily shared between different laboratories to deterministically reproduce the results. In addition, a detailed log file provides accurate information about each step of the analysis. Overall, these features make bioTEA an invaluable tool for both bioinformaticians and wet-lab biologists interested in transcriptomics. BioTEA is free and open-source.
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Ferreira H, Leal-Calvo T, Mendes MA, Avanzi C, Busso P, Benjak A, Sales AM, Ferreira CP, de Berrêdo-Pinho M, Cole ST, Sarno EN, Moraes MO, Pinheiro RO. Gene expression patterns associated with multidrug therapy in multibacillary leprosy. Front Cell Infect Microbiol 2022; 12:917282. [PMID: 35937686 PMCID: PMC9354612 DOI: 10.3389/fcimb.2022.917282] [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: 04/11/2022] [Accepted: 06/28/2022] [Indexed: 11/13/2022] Open
Abstract
Multidrug therapy (MDT) has been successfully used in the treatment of leprosy. However, although patients are cured after the completion of MDT, leprosy reactions, permanent disability, and occasional relapse/reinfection are frequently observed in patients. The immune system of multibacillary patients (MB) is not able to mount an effective cellular immune response against M. leprae. Consequently, clearance of bacilli from the body is a slow process and after 12 doses of MDT not all MB patients reduce bacillary index (BI). In this context, we recruited MB patients at the uptake and after 12-month of MDT. Patients were stratified according to the level of reduction of the BI after 12 doses MDT. A reduction of at least one log in BI was necessary to be considered a responder patient. We evaluated the pattern of host gene expression in skin samples with RNA sequencing before and after MDT and between samples from patients with or without one log reduction in BI. Our results demonstrated that after 12 doses of MDT there was a reduction in genes associated with lipid metabolism, inflammatory response, and cellular immune response among responders (APOBEC3A, LGALS17A, CXCL13, CXCL9, CALHM6, and IFNG). Also, by comparing MB patients with lower BI reduction versus responder patients, we identified high expression of CDH19, TMPRSS4, PAX3, FA2H, HLA-V, FABP7, and SERPINA11 before MDT. From the most differentially expressed genes, we observed that MDT modulates pathways related to immune response and lipid metabolism in skin cells from MB patients after MDT, with higher expression of genes like CYP11A1, that are associated with cholesterol metabolism in the group with the worst response to treatment. Altogether, the data presented contribute to elucidate gene signatures and identify differentially expressed genes associated with MDT outcomes in MB patients.
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Affiliation(s)
- Helen Ferreira
- Leprosy Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Thyago Leal-Calvo
- Leprosy Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Mayara Abud Mendes
- Leprosy Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Charlotte Avanzi
- Global Health Institute, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Philippe Busso
- Global Health Institute, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Andrej Benjak
- Global Health Institute, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Anna Maria Sales
- Leprosy Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Cássio Porto Ferreira
- Leprosy Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Márcia de Berrêdo-Pinho
- Cellular Microbiology Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Stewart Thomas Cole
- Global Health Institute, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Institut Pasteur, Paris, France
| | - Euzenir Nunes Sarno
- Leprosy Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Milton Ozório Moraes
- Leprosy Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Roberta Olmo Pinheiro
- Leprosy Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
- *Correspondence: Roberta Olmo Pinheiro,
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Bayat Z, Ahmadi-Motamayel F, Parsa MS, Taherkhani A. Potential biomarkers and signaling pathways associated with the pathogenesis of primary salivary gland carcinoma: a bioinformatics study. Genomics Inform 2022; 19:e42. [PMID: 35012286 PMCID: PMC8752977 DOI: 10.5808/gi.21052] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 12/08/2021] [Indexed: 01/21/2023] Open
Abstract
Salivary gland carcinoma (SGC) is rare cancer, constituting 6% of neoplasms in the head and neck area. The most responsible genes and pathways involved in the pathology of this disorder have not been fully understood. We aimed to identify differentially expressed genes (DEGs), the most critical hub genes, transcription factors, signaling pathways, and biological processes (BPs) associated with the pathogenesis of primary SGC. The mRNA dataset GSE153283 in the Gene Expression Omnibus database was re-analyzed for determining DEGs in cancer tissue of patients with primary SGC compared to the adjacent normal tissue (adjusted p-value < 0.001; |Log2 fold change| > 1). A protein interaction map (PIM) was built, and the main modules within the network were identified and focused on the different pathways and BP analyses. The hub genes of PIM were discovered, and their associated gene regulatory network was built to determine the master regulators involved in the pathogenesis of primary SGC. A total of 137 genes were found to be differentially expressed in primary SGC. The most significant pathways and BPs that were deregulated in the primary disease condition were associated with the cell cycle and fibroblast proliferation procedures. TP53, EGF, FN1, NOTCH1, EZH2, COL1A1, SPP1, CDKN2A, WNT5A, PDGFRB, CCNB1, and H2AFX were demonstrated to be the most critical genes linked with the primary SGC. SPIB, FOXM1, and POLR2A significantly regulate all the hub genes. This study illustrated several hub genes and their master regulators that might be appropriate targets for the therapeutic aims of primary SGC.
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Affiliation(s)
- Zeynab Bayat
- Department of Oral and Maxillofacial Medicine, Faculty of Dentistry, Hamadan University of Medical Sciences, Hamadan 6517838678, Iran
| | - Fatemeh Ahmadi-Motamayel
- Dental Implants Research Center and Dental Research Center, Department of Oral Medicine, Hamadan University of Medical Sciences, Hamadan 6517838678, Iran
| | - Mohadeseh Salimi Parsa
- Department of Oral and Maxillofacial Medicine, Faculty of Dentistry, Hamadan University of Medical Sciences, Hamadan 6517838678, Iran
| | - Amir Taherkhani
- Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan 6517838678, Iran
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Tavares IF, Dos Santos JB, Pacheco FDS, Gandini M, Mariante RM, Rodrigues TF, Sales AM, Moraes MO, Sarno EN, Schmitz V. Mycobacterium leprae Induces Neutrophilic Degranulation and Low-Density Neutrophil Generation During Erythema Nodosum Leprosum. Front Med (Lausanne) 2021; 8:711623. [PMID: 34692720 PMCID: PMC8531262 DOI: 10.3389/fmed.2021.711623] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 09/09/2021] [Indexed: 11/13/2022] Open
Abstract
Erythema Nodosum Leprosum (ENL) is a recurrent acute inflammatory complication of leprosy affecting up to 50% of all Borderline Lepromatous and Lepromatous Leprosy (BL/LL) patients. Although ENL is described as an immune reaction mediated by neutrophils, studies demonstrating the direct role of neutrophils in ENL are still rare. One subpopulation of low-density neutrophils (LDNs), present within the fraction of peripheral blood mononuclear cells (PBMC), has been associated with the pathogenesis and severity of diseases like sepsis, lupus, and tuberculosis. We herein analyzed LDNs and high-density neutrophils (HDNs) in terms of frequency, phenotype, and morphology. Serum levels of MMP-9 (a neutrophilic degranulation marker) were evaluated by ELISA; and LDNs were generated in vitro by stimulating healthy-donor, whole-blood cultures. PBMC layers of ENL patients presented segmented/hypersegmented cells that were morphologically compatible with neutrophils. Immunofluorescence analyses identified LDNs in ENL. Flow cytometry confirmed the elevated frequency of circulating LDNs (CD14−CD15+) in ENL patients compared to healthy donors and nonreactional Borderline Tuberculoid (BT) patients. Moreover, flow cytometry analyses revealed that ENL LDNs had a neutrophilic-activated phenotype. ENL patients under thalidomide treatment presented similar frequency of LDNs as observed before treatment but its activation status was lower. In addition, Mycobacterium leprae induced in vitro generation of LDNs in whole blood in a dose-dependent fashion; and TGF-β, an inhibitor of neutrophilic degranulation, prevented LDNs generation. MMP-9 serum levels of BL/LL patients with or without ENL correlated with LDNs frequency at the same time that ultrastructural observations of ENL LDNs showed suggestive signs of degranulation. Together, our data provide new insights into the knowledge and understanding of the pathogenesis of ENL while enriching the role of neutrophils in leprosy.
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Affiliation(s)
| | | | | | - Mariana Gandini
- Laboratory of Cellular Microbiology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Rafael M Mariante
- Laboratory of Structural Biology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | | | - Anna Maria Sales
- Leprosy Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Milton Ozório Moraes
- Leprosy Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Euzenir Nunes Sarno
- Leprosy Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Veronica Schmitz
- Leprosy Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
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Leal-Calvo T, Avanzi C, Mendes MA, Benjak A, Busso P, Pinheiro RO, Sarno EN, Cole ST, Moraes MO. A new paradigm for leprosy diagnosis based on host gene expression. PLoS Pathog 2021; 17:e1009972. [PMID: 34695167 PMCID: PMC8568100 DOI: 10.1371/journal.ppat.1009972] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 11/04/2021] [Accepted: 09/28/2021] [Indexed: 11/18/2022] Open
Abstract
Transcriptional profiling is a powerful tool to investigate and detect human diseases. In this study, we used bulk RNA-sequencing (RNA-Seq) to compare the transcriptomes in skin lesions of leprosy patients or controls affected by other dermal conditions such as granuloma annulare, a confounder for paucibacillary leprosy. We identified five genes capable of accurately distinguishing multibacillary and paucibacillary leprosy from other skin conditions. Indoleamine 2,3-dioxygenase 1 (IDO1) expression alone was highly discriminatory, followed by TLR10, BLK, CD38, and SLAMF7, whereas the HS3ST2 and CD40LG mRNA separated multi- and paucibacillary leprosy. Finally, from the main differentially expressed genes (DEG) and enriched pathways, we conclude that paucibacillary disease is characterized by epithelioid transformation and granuloma formation, with an exacerbated cellular immune response, while multibacillary leprosy features epithelial-mesenchymal transition with phagocytic and lipid biogenesis patterns in the skin. These findings will help catalyze the development of better diagnostic tools and potential host-based therapeutic interventions. Finally, our data may help elucidate host-pathogen interplay driving disease clinical manifestations.
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Affiliation(s)
- Thyago Leal-Calvo
- Laboratório de Hanseníase, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Charlotte Avanzi
- Global Health Institute, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Mayara Abud Mendes
- Laboratório de Hanseníase, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Andrej Benjak
- Global Health Institute, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Philippe Busso
- Global Health Institute, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Roberta Olmo Pinheiro
- Laboratório de Hanseníase, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Euzenir Nunes Sarno
- Laboratório de Hanseníase, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Stewart Thomas Cole
- Global Health Institute, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Institut Pasteur, Paris, France
| | - Milton Ozório Moraes
- Laboratório de Hanseníase, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
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Sahu S, Sharma K, Sharma M, Narang T, Dogra S, Minz RW, Chhabra S. Neutrophil NETworking in ENL: Potential as a Putative Biomarker: Future Insights. Front Med (Lausanne) 2021; 8:697804. [PMID: 34336901 PMCID: PMC8316588 DOI: 10.3389/fmed.2021.697804] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 06/17/2021] [Indexed: 12/11/2022] Open
Abstract
Erythema nodosum leprosum (ENL), also known as type 2 reaction (T2R) is an immune complex mediated (type III hypersensitivity) reactional state encountered in patients with borderline lepromatous and lepromatous leprosy (BL and LL) either before, during, or after the institution of anti-leprosy treatment (ALT). The consequences of ENL may be serious, leading to permanent nerve damage and deformities, constituting a major cause of leprosy-related morbidity. The incidence of ENL is increasing with the increasing number of multibacillary cases. Although the diagnosis of ENL is not difficult to make for physicians involved in the care of leprosy patients, its management continues to be a most challenging aspect of the leprosy eradication program: the chronic and recurrent painful skin lesions, neuritis, and organ involvement necessitates prolonged treatment with prednisolone, thalidomide, and anti-inflammatory and immunosuppressive drugs, which further adds to the existing morbidity. In addition, the use of immunosuppressants like methotrexate, azathioprine, cyclosporine, or biologics carries a risk of reactivation of persisters (Mycobacterium leprae), apart from their own end-organ toxicities. Most ENL therapeutic guidelines are primarily designed for acute episodes and there is scarcity of literature on management of patients with chronic and recurrent ENL. It is difficult to predict which patients will develop chronic or recurrent ENL and plan the treatment accordingly. We need simple point-of-care or ELISA-based tests from blood or skin biopsy samples, which can help us in identifying patients who are likely to require prolonged treatment and also inform us about the prognosis of reactions so that appropriate therapy may be started and continued for better ENL control in such patients. There is a significant unmet need for research for better understanding the immunopathogenesis of, and biomarkers for, ENL to improve clinical stratification and therapeutics. In this review we will discuss the potential of neutrophils (polymorphonuclear granulocytes) as putative diagnostic and prognostic biomarkers by virtue of their universal abundance in human blood, functional versatility, phenotypic heterogeneity, metabolic plasticity, differential hierarchical cytoplasmic granule mobilization, and their ability to form NETs (neutrophil extracellular traps). We will touch upon the various aspects of neutrophil biology relevant to ENL pathophysiology in a step-wise manner. We also hypothesize about an element of metabolic reprogramming of neutrophils by M. leprae that could be investigated and exploited for biomarker discovery. In the end, a potential role for neutrophil derived exosomes as a novel biomarker for ENL will also be explored.
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Affiliation(s)
- Smrity Sahu
- Department of Immunopathology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Keshav Sharma
- Department of Immunopathology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Maryada Sharma
- Department of Otolaryngology and Head and Neck Surgery, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Tarun Narang
- Department of Dermatology, Venereology and Leprology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Sunil Dogra
- Department of Dermatology, Venereology and Leprology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Ranjana Walker Minz
- Department of Immunopathology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Seema Chhabra
- Department of Immunopathology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
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Tió-Coma M, Kiełbasa SM, van den Eeden SJF, Mei H, Roy JC, Wallinga J, Khatun M, Soren S, Chowdhury AS, Alam K, van Hooij A, Richardus JH, Geluk A. Blood RNA signature RISK4LEP predicts leprosy years before clinical onset. EBioMedicine 2021; 68:103379. [PMID: 34090257 PMCID: PMC8182229 DOI: 10.1016/j.ebiom.2021.103379] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 04/16/2021] [Accepted: 04/19/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Leprosy, a chronic infectious disease caused by Mycobacterium leprae, is often late- or misdiagnosed leading to irreversible disabilities. Blood transcriptomic biomarkers that prospectively predict those who progress to leprosy (progressors) would allow early diagnosis, better treatment outcomes and facilitate interventions aimed at stopping bacterial transmission. To identify potential risk signatures of leprosy, we collected whole blood of household contacts (HC, n=5,352) of leprosy patients, including individuals who were diagnosed with leprosy 4-61 months after sample collection. METHODS We investigated differential gene expression (DGE) by RNA-Seq between progressors before presence of symptoms (n=40) and HC (n=40), as well as longitudinal DGE within each progressor. A prospective leprosy signature was identified using a machine learning approach (Random Forest) and validated using reverse transcription quantitative PCR (RT-qPCR). FINDINGS Although no significant intra-individual longitudinal variation within leprosy progressors was identified, 1,613 genes were differentially expressed in progressors before diagnosis compared to HC. We identified a 13-gene prospective risk signature with an Area Under the Curve (AUC) of 95.2%. Validation of this RNA-Seq signature in an additional set of progressors (n=43) and HC (n=43) by RT-qPCR, resulted in a final 4-gene signature, designated RISK4LEP (MT-ND2, REX1BD, TPGS1, UBC) (AUC=86.4%). INTERPRETATION This study identifies for the first time a prospective transcriptional risk signature in blood predicting development of leprosy 4 to 61 months before clinical diagnosis. Assessment of this signature in contacts of leprosy patients can function as an adjunct diagnostic tool to target implementation of interventions to restrain leprosy development. FUNDING This study was supported by R2STOP Research grant, the Order of Malta-Grants-for-Leprosy-Research, the Q.M. Gastmann-Wichers Foundation and the Leprosy Research Initiative (LRI) together with the Turing Foundation (ILEP# 702.02.73 and # 703.15.07).
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Affiliation(s)
- Maria Tió-Coma
- Department of Infectious Diseases and Leiden University Medical Center, Leiden, The Netherlands
| | - Szymon M Kiełbasa
- Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Susan J F van den Eeden
- Department of Infectious Diseases and Leiden University Medical Center, Leiden, The Netherlands
| | - Hailiang Mei
- Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Johan Chandra Roy
- Rural Health Program, The Leprosy Mission International Bangladesh, Nilphamari, Bangladesh
| | - Jacco Wallinga
- Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands; Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Marufa Khatun
- Rural Health Program, The Leprosy Mission International Bangladesh, Nilphamari, Bangladesh
| | - Sontosh Soren
- Rural Health Program, The Leprosy Mission International Bangladesh, Nilphamari, Bangladesh
| | - Abu Sufian Chowdhury
- Rural Health Program, The Leprosy Mission International Bangladesh, Nilphamari, Bangladesh
| | - Khorshed Alam
- Rural Health Program, The Leprosy Mission International Bangladesh, Nilphamari, Bangladesh
| | - Anouk van Hooij
- Department of Infectious Diseases and Leiden University Medical Center, Leiden, The Netherlands
| | - Jan Hendrik Richardus
- Department of Public Health, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Annemieke Geluk
- Department of Infectious Diseases and Leiden University Medical Center, Leiden, The Netherlands.
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11
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Oliveira MF, Medeiros RCA, Mietto BS, Calvo TL, Mendonça APM, Rosa TLSA, Silva DSD, Vasconcelos KGDCD, Pereira AMR, de Macedo CS, Pereira GMB, Moreira MDBP, Pessolani MCV, Moraes MO, Lara FA. Reduction of host cell mitochondrial activity as Mycobacterium leprae's strategy to evade host innate immunity. Immunol Rev 2021; 301:193-208. [PMID: 33913182 PMCID: PMC10084840 DOI: 10.1111/imr.12962] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 12/20/2022]
Abstract
Leprosy is a much-feared incapacitating infectious disease caused by Mycobacterium leprae or M lepromatosis, annually affecting roughly 200,000 people worldwide. During host-pathogen interaction, M leprae subverts the immune response, leading to development of disease. Throughout the last few decades, the impact of energy metabolism on the control of intracellular pathogens and leukocytic differentiation has become more evident. Mitochondria play a key role in regulating newly-discovered immune signaling pathways by controlling redox metabolism and the flow of energy besides activating inflammasome, xenophagy, and apoptosis. Likewise, this organelle, whose origin is probably an alphaproteobacterium, directly controls the intracellular pathogens attempting to invade its niche, a feature conquered at the expense of billions of years of coevolution. In the present review, we discuss the role of reduced host cell mitochondrial activity during M leprae infection and the consequential fates of M leprae and host innate immunity. Conceivably, inhibition of mitochondrial energy metabolism emerges as an overlooked and novel mechanism developed by M leprae to evade xenophagy and the host immune response.
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Affiliation(s)
- Marcus Fernandes Oliveira
- Laboratório de Bioquímica de Resposta ao Estresse, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Bruno Siqueira Mietto
- Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Minas Gerais, Brazil
| | - Thyago Leal Calvo
- Laboratório de Hanseníase, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Ana Paula Miranda Mendonça
- Laboratório de Bioquímica de Resposta ao Estresse, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | | | | | - Cristiana Santos de Macedo
- Laboratório de Microbiologia Celular, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.,Centro de Desenvolvimento Tecnológico em Saúde, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | | | | | | | | | - F A Lara
- Laboratório de Microbiologia Celular, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
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12
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Leal-Calvo T, Martins BL, Bertoluci DF, Rosa PS, de Camargo RM, Germano GV, Brito de Souza VN, Pereira Latini AC, Moraes MO. Large-Scale Gene Expression Signatures Reveal a Microbicidal Pattern of Activation in Mycobacterium leprae-Infected Monocyte-Derived Macrophages With Low Multiplicity of Infection. Front Immunol 2021; 12:647832. [PMID: 33936067 PMCID: PMC8085500 DOI: 10.3389/fimmu.2021.647832] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 03/31/2021] [Indexed: 12/17/2022] Open
Abstract
Leprosy is a disease with a clinical spectrum of presentations that is also manifested in diverse histological features. At one pole, lepromatous lesions (L-pole) have phagocytic foamy macrophages heavily parasitized with freely multiplying intracellular Mycobacterium leprae. At the other pole, the presence of epithelioid giant cells and granulomatous formation in tuberculoid lesions (T-pole) lead to the control of M. leprae replication and the containment of its spread. The mechanism that triggers this polarization is unknown, but macrophages are central in this process. Over the past few years, leprosy has been studied using large scale techniques to shed light on the basic pathways that, upon infection, rewire the host cellular metabolism and gene expression. M. leprae is particularly peculiar as it invades Schwann cells in the nerves, reprogramming their gene expression leading to a stem-like cell phenotype. This modulatory behavior exerted by M. leprae is also observed in skin macrophages. Here, we used live M. leprae to infect (10:1 multiplicity of infection) monocyte-derived macrophages (MDMs) for 48 h and analyzed the whole gene expression profile using microarrays. In this model, we observe an intense upregulation of genes consistent with a cellular immune response, with enriched pathways including peptide and protein secretion, leukocyte activation, inflammation, and cellular divalent inorganic cation homeostasis. Among the most differentially expressed genes (DEGs) are CCL5/RANTES and CYP27B1, and several members of the metallothionein and metalloproteinase families. This is consistent with a proinflammatory state that would resemble macrophage rewiring toward granulomatous formation observed at the T-pole. Furthermore, a comparison with a dataset retrieved from the Gene Expression Omnibus of M. leprae-infected Schwann cells (MOI 100:1) showed that the patterns among the DEGs are highly distinct, as the Schwann cells under these conditions had a scavenging and phagocytic gene profile similar to M2-like macrophages, with enriched pathways rearrangements in the cytoskeleton, lipid and cholesterol metabolism and upregulated genes including MVK, MSMO1, and LACC1/FAMIN. In summary, macrophages may have a central role in defining the paradigmatic cellular (T-pole) vs. humoral (L-pole) responses and it is likely that the multiplicity of infection and genetic polymorphisms in key genes are gearing this polarization.
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Affiliation(s)
- Thyago Leal-Calvo
- Laboratório de Hanseníase, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Bruna Leticia Martins
- Divisão de Pesquisa e Ensino, Instituto Lauro de Souza Lima, Bauru, Brazil.,Departamento de Doenças Tropicais, Faculdade de Medicina de Botucatu, Universidade Estadual Paulista, Botucatu, Brazil
| | - Daniele Ferreira Bertoluci
- Divisão de Pesquisa e Ensino, Instituto Lauro de Souza Lima, Bauru, Brazil.,Departamento de Doenças Tropicais, Faculdade de Medicina de Botucatu, Universidade Estadual Paulista, Botucatu, Brazil
| | | | - Rodrigo Mendes de Camargo
- Divisão de Pesquisa e Ensino, Instituto Lauro de Souza Lima, Bauru, Brazil.,Departamento de Doenças Tropicais, Faculdade de Medicina de Botucatu, Universidade Estadual Paulista, Botucatu, Brazil
| | - Giovanna Vale Germano
- Divisão de Pesquisa e Ensino, Instituto Lauro de Souza Lima, Bauru, Brazil.,Departamento de Doenças Tropicais, Faculdade de Medicina de Botucatu, Universidade Estadual Paulista, Botucatu, Brazil
| | - Vania Nieto Brito de Souza
- Divisão de Pesquisa e Ensino, Instituto Lauro de Souza Lima, Bauru, Brazil.,Departamento de Doenças Tropicais, Faculdade de Medicina de Botucatu, Universidade Estadual Paulista, Botucatu, Brazil
| | - Ana Carla Pereira Latini
- Divisão de Pesquisa e Ensino, Instituto Lauro de Souza Lima, Bauru, Brazil.,Departamento de Doenças Tropicais, Faculdade de Medicina de Botucatu, Universidade Estadual Paulista, Botucatu, Brazil
| | - Milton Ozório Moraes
- Laboratório de Hanseníase, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
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13
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van Hooij A, Geluk A. In search of biomarkers for leprosy by unraveling the host immune response to Mycobacterium leprae. Immunol Rev 2021; 301:175-192. [PMID: 33709405 PMCID: PMC8251784 DOI: 10.1111/imr.12966] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 02/23/2021] [Indexed: 12/18/2022]
Abstract
Mycobacterium leprae, the causative agent of leprosy, is still actively transmitted in endemic areas reflected by the fairly stable number of new cases detected each year. Recognizing the signs and symptoms of leprosy is challenging, especially at an early stage. Improved diagnostic tools, based on sensitive and specific biomarkers, that facilitate diagnosis of leprosy are therefore urgently needed. In this review, we address the challenges that leprosy biomarker research is facing by reviewing cell types reported to be involved in host immunity to M leprae. These cell types can be associated with different possible fates of M leprae infection being either protective immunity, or pathogenic immune responses inducing nerve damage. Unraveling these responses will facilitate the search for biomarkers. Implications for further studies to disentangle the complex interplay between host responses that lead to leprosy disease are discussed, providing leads for the identification of new biomarkers to improve leprosy diagnostics.
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Affiliation(s)
- Anouk van Hooij
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Annemieke Geluk
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
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14
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Abstract
Coronavirus Disease 2019 (COVID-19), a disease caused by the betacoronavirus Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), has only recently emerged, while Mycobacterium leprae, the etiological agent of leprosy, has endured for more than 2,000 years. As soon as the initial reports of COVID-19 became public, several entities, including the Brazilian Leprosy Society, warned about the possible impact of COVID-19 on leprosy patients. It has been verified that COVID-19 carriers can be either asymptomatic or present varying degrees of severe respiratory failure in association with cytokine storm and death, among other diseases. Severe COVID-19 patients show increased numbers of neutrophils and serum neutrophil extracellular trap (NET) markers, in addition to alterations in the neutrophil-to-lymphocyte ratio (NLR). The absence of antiviral drugs and the speed of COVID-19 transmission have had a major impact on public health systems worldwide, leading to the almost total collapse of many national and local healthcare services. Leprosy, an infectious neurological and dermatological illness, is widely considered to be the most frequent cause of physical disabilities globally. The chronic clinical course of the disease may be interrupted by acute inflammatory episodes, named leprosy reactions. These serious immunological complications, characterized by cytokine storms, are responsible for amplifying peripheral nerve damage. From 30% to 40% of all multibacillary leprosy (MB) patients experience erythema nodosum leprosum (ENL), a neutrophilic immune-mediated condition. ENL patients often present these same COVID-19-like symptoms, including high levels of serum NET markers, altered NLR, and neutrophilia. Moreover, the consequences of a M. leprae-SARS-CoV-2 coinfection have yet to be fully investigated. The goal of the present viewpoint is to describe some of the similarities that may be found between COVID-19 and leprosy disease in the context of neutrophilic biology.
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Affiliation(s)
- Veronica Schmitz
- Laboratório de Hanseníase, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Brazil
| | - Jéssica Brandão dos Santos
- Laboratório de Hanseníase, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Brazil
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