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Gonçalves LO, Pulido AFV, Mathias FAS, Enes AES, Carvalho MGR, de Melo Resende D, Polak ME, Ruiz JC. Expression Profile of Genes Related to the Th17 Pathway in Macrophages Infected by Leishmania major and Leishmania amazonensis: The Use of Gene Regulatory Networks in Modeling This Pathway. Front Cell Infect Microbiol 2022; 12:826523. [PMID: 35774406 PMCID: PMC9239034 DOI: 10.3389/fcimb.2022.826523] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 03/09/2022] [Indexed: 11/13/2022] Open
Abstract
Leishmania amazonensis and Leishmania major are the causative agents of cutaneous and mucocutaneous diseases. The infections‘ outcome depends on host–parasite interactions and Th1/Th2 response, and in cutaneous form, regulation of Th17 cytokines has been reported to maintain inflammation in lesions. Despite that, the Th17 regulatory scenario remains unclear. With the aim to gain a better understanding of the transcription factors (TFs) and genes involved in Th17 induction, in this study, the role of inducing factors of the Th17 pathway in Leishmania–macrophage infection was addressed through computational modeling of gene regulatory networks (GRNs). The Th17 GRN modeling integrated experimentally validated data available in the literature and gene expression data from a time-series RNA-seq experiment (4, 24, 48, and 72 h post-infection). The generated model comprises a total of 10 TFs, 22 coding genes, and 16 cytokines related to the Th17 immune modulation. Addressing the Th17 induction in infected and uninfected macrophages, an increase of 2- to 3-fold in 4–24 h was observed in the former. However, there was a decrease in basal levels at 48–72 h for both groups. In order to evaluate the possible outcomes triggered by GRN component modulation in the Th17 pathway. The generated GRN models promoted an integrative and dynamic view of Leishmania–macrophage interaction over time that extends beyond the analysis of single-gene expression.
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Affiliation(s)
- Leilane Oliveira Gonçalves
- Programa de Pós-graduação em Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
- Grupo Informática de Biossistemas, Instituto René Rachou, Fiocruz Minas, Belo Horizonte, Brazil
| | - Andrés F. Vallejo Pulido
- Systems Immunology Group, Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | | | - Alexandre Estevão Silvério Enes
- Programa de Pós-graduação em Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
- Grupo Informática de Biossistemas, Instituto René Rachou, Fiocruz Minas, Belo Horizonte, Brazil
| | | | - Daniela de Melo Resende
- Grupo Genômica Funcional de Parasitos, Instituto René Rachou, Fiocruz Minas, Belo Horizonte, Brazil
| | - Marta E. Polak
- Systems Immunology Group, Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
- *Correspondence: Jeronimo C. Ruiz, ; Marta E. Polak,
| | - Jeronimo C. Ruiz
- Grupo Informática de Biossistemas, Instituto René Rachou, Fiocruz Minas, Belo Horizonte, Brazil
- *Correspondence: Jeronimo C. Ruiz, ; Marta E. Polak,
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Smircich P, Forteza D, El-Sayed NM, Garat B. Genomic analysis of sequence-dependent DNA curvature in Leishmania. PLoS One 2013; 8:e63068. [PMID: 23646176 PMCID: PMC3639952 DOI: 10.1371/journal.pone.0063068] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Accepted: 03/27/2013] [Indexed: 11/26/2022] Open
Abstract
Leishmania major is a flagellated protozoan parasite of medical importance. Like other members of the Trypanosomatidae family, it possesses unique mechanisms of gene expression such as constitutive polycistronic transcription of directional gene clusters, gene amplification, mRNA trans-splicing, and extensive editing of mitochondrial transcripts. The molecular signals underlying most of these processes remain under investigation. In order to investigate the role of DNA secondary structure signals in gene expression, we carried out a genome-wide in silico analysis of the intrinsic DNA curvature. The L. major genome revealed a lower frequency of high intrinsic curvature regions as well as inter- and intra- chromosomal distribution heterogeneity, when compared to prokaryotic and eukaryotic organisms. Using a novel method aimed at detecting region-integrated intrinsic curvature (RIIC), high DNA curvature was found to be associated with regions implicated in transcription initiation. Those include divergent strand-switch regions between directional gene clusters and regions linked to markers of active transcription initiation such as acetylated H3 histone, TRF4 and SNAP50. These findings suggest a role for DNA curvature in transcription initiation in Leishmania supporting the relevance of DNA secondary structures signals.
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Affiliation(s)
- Pablo Smircich
- Laboratorio de Interacciones Moleculares, Facultad de Ciencias, Montevideo, Uruguay
- Departamento de Genética, Facultad de Medicina, Montevideo, Uruguay
| | - Diego Forteza
- Laboratorio de Interacciones Moleculares, Facultad de Ciencias, Montevideo, Uruguay
| | - Najib M. El-Sayed
- Department of Cell Biology and Molecular Genetics and Center for Bioinformatics and Computational Biology, University of Maryland College Park, Maryland, United States of America
| | - Beatriz Garat
- Laboratorio de Interacciones Moleculares, Facultad de Ciencias, Montevideo, Uruguay
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