1
|
Savardashtaki A, Khalili Alashti S, Vafadar A, Sadeghi M, Baneshi M, Hashemi KS, Karami J, Muro A, Manzano-Roman R, Rashidi S. An integrated bioinformatic analysis of microarray datasets to identify biomarkers and miRNA-based regulatory networks in leishmaniasis. Sci Rep 2024; 14:12981. [PMID: 38839916 PMCID: PMC11153516 DOI: 10.1038/s41598-024-63462-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 05/29/2024] [Indexed: 06/07/2024] Open
Abstract
Micro RNAs (miRNAs, miRs) and relevant networks might exert crucial functions during differential host cell infection by the different Leishmania species. Thus, a bioinformatic analysis of microarray datasets was developed to identify pivotal shared biomarkers and miRNA-based regulatory networks for Leishmaniasis. A transcriptomic analysis by employing a comprehensive set of gene expression profiling microarrays was conducted to identify the key genes and miRNAs relevant for Leishmania spp. infections. Accordingly, the gene expression profiles of healthy human controls were compared with those of individuals infected with Leishmania mexicana, L. major, L. donovani, and L. braziliensis. The enrichment analysis for datasets was conducted by utilizing EnrichR database, and Protein-Protein Interaction (PPI) network to identify the hub genes. The prognostic value of hub genes was assessed by using receiver operating characteristic (ROC) curves. Finally, the miRNAs that interact with the hub genes were identified using miRTarBase, miRWalk, TargetScan, and miRNet. Differentially expressed genes were identified between the groups compared in this study. These genes were significantly enriched in inflammatory responses, cytokine-mediated signaling pathways and granulocyte and neutrophil chemotaxis responses. The identification of hub genes of recruited datasets suggested that TNF, SOCS3, JUN, TNFAIP3, and CXCL9 may serve as potential infection biomarkers and could deserve value as prognostic biomarkers for leishmaniasis. Additionally, inferred data from miRWalk revealed a significant degree of interaction of a number of miRNAs (hsa-miR-8085, hsa-miR-4673, hsa-miR-4743-3p, hsa-miR-892c-3p, hsa-miR-4644, hsa-miR-671-5p, hsa-miR-7106-5p, hsa-miR-4267, hsa-miR-5196-5p, and hsa-miR-4252) with the majority of the hub genes, suggesting such miRNAs play a crucial role afterwards parasite infection. The hub genes and hub miRNAs identified in this study could be potentially suggested as therapeutic targets or biomarkers for the management of leishmaniasis.
Collapse
Affiliation(s)
- Amir Savardashtaki
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
- Infertility Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Shayan Khalili Alashti
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
- Epilepsy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Asma Vafadar
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
- Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mahboubeh Sadeghi
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Maryam Baneshi
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Kimia Sadat Hashemi
- Department of Medical Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Jafar Karami
- Molecular and Medicine Research Center, Khomein University of Medical Sciences, Khomein, Iran
- Department of Medical Laboratory Sciences, Khomein University of Medical Sciences, Khomein, Iran
| | - Antonio Muro
- Infectious and Tropical Diseases Group (E-INTRO), Faculty of Pharmacy, Institute of Biomedical Research of Salamanca-Research Center for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), University of Salamanca, 37008, Salamanca, Spain
| | - Raúl Manzano-Roman
- Infectious and Tropical Diseases Group (E-INTRO), Faculty of Pharmacy, Institute of Biomedical Research of Salamanca-Research Center for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), University of Salamanca, 37008, Salamanca, Spain.
| | - Sajad Rashidi
- Molecular and Medicine Research Center, Khomein University of Medical Sciences, Khomein, Iran.
- Department of Medical Laboratory Sciences, Khomein University of Medical Sciences, Khomein, Iran.
| |
Collapse
|
2
|
Furci F, Allegra A, Tonacci A, Isola S, Senna G, Pioggia G, Gangemi S. Air Pollution and microRNAs: The Role of Association in Airway Inflammation. Life (Basel) 2023; 13:1375. [PMID: 37374157 DOI: 10.3390/life13061375] [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: 05/02/2023] [Revised: 05/29/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
Air pollution exposure plays a key role in the alteration of gene expression profiles, which can be regulated by microRNAs, inducing the development of various diseases. Moreover, there is also evidence of sensitivity of miRNAs to environmental factors, including tobacco smoke. Various diseases are related to specific microRNA signatures, suggesting their potential role in pathophysiological processes; considering their association with environmental pollutants, they could become novel biomarkers of exposure. Therefore, the aim of the present work is to analyse data reported in the literature on the role of environmental stressors on microRNA alterations and, in particular, to identify specific alterations that might be related to the development of airway diseases so as to propose future preventive, diagnostic, and therapeutic strategies.
Collapse
Affiliation(s)
- Fabiana Furci
- Allergy Unit and Asthma Center, Verona University Hospital, 37134 Verona, Italy
| | - Alessandro Allegra
- Division of Hematology, Department of Human Pathology in Adulthood and Childhood "Gaetano Barresi", University of Messina, 98124 Messina, Italy
| | - Alessandro Tonacci
- Clinical Physiology Institute, National Research Council of Italy (IFC-CNR), 56124 Pisa, Italy
| | - Stefania Isola
- School and Operative Unit of Allergy and Clinical Immunology, Department of Clinical and Experimental Medicine, University of Messina, 98124 Messina, Italy
| | - Gianenrico Senna
- Allergy Unit and Asthma Center, Verona University Hospital, 37134 Verona, Italy
- Department of Medicine, Verona University Hospital, 37134 Verona, Italy
| | - Giovanni Pioggia
- Institute for Biomedical Research and Innovation (IRIB), National Research Council of Italy (CNR), 98164 Messina, Italy
| | - Sebastiano Gangemi
- School and Operative Unit of Allergy and Clinical Immunology, Department of Clinical and Experimental Medicine, University of Messina, 98124 Messina, Italy
| |
Collapse
|
3
|
DnaJ, a promising vaccine candidate against Ureaplasma urealyticum infection. Appl Microbiol Biotechnol 2022; 106:7643-7659. [PMID: 36269329 PMCID: PMC9589543 DOI: 10.1007/s00253-022-12230-4] [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: 05/17/2022] [Revised: 09/20/2022] [Accepted: 10/05/2022] [Indexed: 11/08/2022]
Abstract
Abstract
Ureaplasma urealyticum (U. urealyticum, Uu) is a common sexually transmitted pathogen that is responsible for diseases such as non-gonococcal urethritis, chorioamnionitis, and neonatal respiratory diseases. The rapid emergence of multidrug-resistant bacteria threatens the effective treatment of Uu infections. Considering this, vaccination could be an efficacious medical intervention to prevent Uu infection and disease. As a highly conserved molecular chaperone, DnaJ is expressed and upregulated by pathogens soon after infection. Here, we assessed the vaccine potential of recombinant Uu-DnaJ in a mouse model and dendritic cells. Results showed that intramuscular administration of DnaJ induced robust humoral- and T helper (Th) 1 cell-mediated immune responses and protected against genital tract infection, inflammation, and the pathologic sequelae after Uu infection. Importantly, the DnaJ protein also induced the maturation of mouse bone marrow–derived dendritic cells (BMDCs), ultimately promoting naïve T cell differentiation toward the Th1 phenotype. In addition, adoptive immunization of DnaJ-pulsed BMDCs elicited antigen-specific Immunoglobulin G2 (IgG2) antibodies as well as a Th1-biased cellular response in mice. These results support DnaJ as a promising vaccine candidate to control Uu infections. Key points • A novel recombinant vaccine was constructed against U. urealyticum infection. • Antigen-specific humoral and cellular immune responses after DnaJ vaccination. • Dendritic cells are activated by Uu-DnaJ, which results in a Th1-biased immune response. Supplementary Information The online version contains supplementary material available at 10.1007/s00253-022-12230-4.
Collapse
|
4
|
Volpedo G, Pacheco-Fernandez T, Holcomb EA, Zhang WW, Lypaczewski P, Cox B, Fultz R, Mishan C, Verma C, Huston RH, Wharton AR, Dey R, Karmakar S, Oghumu S, Hamano S, Gannavaram S, Nakhasi HL, Matlashewski G, Satoskar AR. Centrin-deficient Leishmania mexicana confers protection against New World cutaneous leishmaniasis. NPJ Vaccines 2022; 7:32. [PMID: 35236861 PMCID: PMC8891280 DOI: 10.1038/s41541-022-00449-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 01/27/2022] [Indexed: 01/01/2023] Open
Abstract
Leishmaniasis is a neglected protozoan disease affecting over 12 million people globally with no approved vaccines for human use. New World cutaneous leishmaniasis (CL) caused by L. mexicana is characterized by the development of chronic non-healing skin lesions. Using the CRISPR/Cas9 technique, we have generated live attenuated centrin knockout L. mexicana (LmexCen-/-) parasites. Centrin is a cytoskeletal protein important for cellular division in eukaryotes and, in Leishmania, is required only for intracellular amastigote replication. We have investigated the safety and immunogenicity characteristics of LmexCen-/- parasites by evaluating their survival and the cytokine production in bone-marrow-derived macrophages (BMDMs) and dendritic cells (BMDCs) in vitro. Our data shows that LmexCen-/- amastigotes present a growth defect, which results in significantly lower parasitic burdens and increased protective cytokine production in infected BMDMs and BMDCs, compared to the wild type (WT) parasites. We have also determined the safety and efficacy of LmexCen-/- in vivo using experimental murine models of L. mexicana. We demonstrate that LmexCen-/- parasites are safe and do not cause lesions in susceptible mouse models. Immunization with LmexCen-/- is also efficacious against challenge with WT L. mexicana parasites in genetically different BALB/c and C57BL/6 mouse models. Vaccinated mice did not develop cutaneous lesions, displayed protective immunity, and showed significantly lower parasitic burdens at the infection site and draining lymph nodes compared to the control group. Overall, we demonstrate that LmexCen-/- parasites are safe and efficacious against New World cutaneous leishmaniasis in pre-clinical models.
Collapse
Affiliation(s)
- Greta Volpedo
- Department of Microbiology, The Ohio State University, Columbus, OH, 43210, USA.,Department of Pathology, Wexner Medical Center, The Ohio State University, Columbus, OH, 43210, USA
| | - Thalia Pacheco-Fernandez
- Department of Pathology, Wexner Medical Center, The Ohio State University, Columbus, OH, 43210, USA
| | - Erin A Holcomb
- Department of Pathology, Wexner Medical Center, The Ohio State University, Columbus, OH, 43210, USA
| | - Wen-Wei Zhang
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Patrick Lypaczewski
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Blake Cox
- Department of Pathology, Wexner Medical Center, The Ohio State University, Columbus, OH, 43210, USA
| | - Rebecca Fultz
- Department of Pathology, Wexner Medical Center, The Ohio State University, Columbus, OH, 43210, USA
| | - Chelsea Mishan
- Department of Pathology, Wexner Medical Center, The Ohio State University, Columbus, OH, 43210, USA
| | - Chaitenya Verma
- Department of Pathology, Wexner Medical Center, The Ohio State University, Columbus, OH, 43210, USA
| | - Ryan H Huston
- Department of Pathology, Wexner Medical Center, The Ohio State University, Columbus, OH, 43210, USA
| | - Abigail R Wharton
- Department of Pathology, Wexner Medical Center, The Ohio State University, Columbus, OH, 43210, USA
| | - Ranadhir Dey
- Division of Emerging and Transfusion Transmitted Diseases, CBER, FDA, Silver Spring, MD, USA
| | - Subir Karmakar
- Division of Emerging and Transfusion Transmitted Diseases, CBER, FDA, Silver Spring, MD, USA
| | - Steve Oghumu
- Department of Pathology, Wexner Medical Center, The Ohio State University, Columbus, OH, 43210, USA
| | - Shinjiro Hamano
- Department of Parasitology, Institute of Tropical Medicine (NEKKEN), The Joint Usage/Research Center on Tropical Disease, Nagasaki University, Nagasaki University Graduate School of Biomedical Sciences Doctoral Leadership Program, Nagasaki, Japan
| | - Sreenivas Gannavaram
- Division of Emerging and Transfusion Transmitted Diseases, CBER, FDA, Silver Spring, MD, USA
| | - Hira L Nakhasi
- Division of Emerging and Transfusion Transmitted Diseases, CBER, FDA, Silver Spring, MD, USA.
| | - Greg Matlashewski
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada.
| | - Abhay R Satoskar
- Department of Microbiology, The Ohio State University, Columbus, OH, 43210, USA. .,Department of Pathology, Wexner Medical Center, The Ohio State University, Columbus, OH, 43210, USA.
| |
Collapse
|
5
|
Volpedo G, Pacheco-Fernandez T, Bhattacharya P, Oljuskin T, Dey R, Gannavaram S, Satoskar AR, Nakhasi HL. Determinants of Innate Immunity in Visceral Leishmaniasis and Their Implication in Vaccine Development. Front Immunol 2021; 12:748325. [PMID: 34712235 PMCID: PMC8546207 DOI: 10.3389/fimmu.2021.748325] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 09/24/2021] [Indexed: 12/22/2022] Open
Abstract
Leishmaniasis is endemic to the tropical and subtropical regions of the world and is transmitted by the bite of an infected sand fly. The multifaceted interactions between Leishmania, the host innate immune cells, and the adaptive immunity determine the severity of pathogenesis and disease development. Leishmania parasites establish a chronic infection by subversion and attenuation of the microbicidal functions of phagocytic innate immune cells such as neutrophils, macrophages and dendritic cells (DCs). Other innate cells such as inflammatory monocytes, mast cells and NK cells, also contribute to resistance and/or susceptibility to Leishmania infection. In addition to the cytokine/chemokine signals from the innate immune cells, recent studies identified the subtle shifts in the metabolic pathways of the innate cells that activate distinct immune signal cascades. The nexus between metabolic pathways, epigenetic reprogramming and the immune signaling cascades that drive the divergent innate immune responses, remains to be fully understood in Leishmania pathogenesis. Further, development of safe and efficacious vaccines against Leishmaniasis requires a broader understanding of the early interactions between the parasites and innate immune cells. In this review we focus on the current understanding of the specific role of innate immune cells, the metabolomic and epigenetic reprogramming and immune regulation that occurs during visceral leishmaniasis, and the strategies used by the parasite to evade and modulate host immunity. We highlight how such pathways could be exploited in the development of safe and efficacious Leishmania vaccines.
Collapse
Affiliation(s)
- Greta Volpedo
- Departments of Pathology and Microbiology, Wexner Medical Center, The Ohio State University, Columbus, OH, United States
| | - Thalia Pacheco-Fernandez
- Departments of Pathology and Microbiology, Wexner Medical Center, The Ohio State University, Columbus, OH, United States
| | - Parna Bhattacharya
- Laboratory of Emerging Pathogens, Division of Emerging and Transfusion Transmitted Diseases, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, United States
| | - Timur Oljuskin
- Laboratory of Emerging Pathogens, Division of Emerging and Transfusion Transmitted Diseases, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, United States
| | - Ranadhir Dey
- Laboratory of Emerging Pathogens, Division of Emerging and Transfusion Transmitted Diseases, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, United States
| | - Sreenivas Gannavaram
- Laboratory of Emerging Pathogens, Division of Emerging and Transfusion Transmitted Diseases, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, United States
| | - Abhay R Satoskar
- Departments of Pathology and Microbiology, Wexner Medical Center, The Ohio State University, Columbus, OH, United States
| | - Hira L Nakhasi
- Laboratory of Emerging Pathogens, Division of Emerging and Transfusion Transmitted Diseases, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, United States
| |
Collapse
|