Proteomic Analysis Reveals a Predominant NFE2L2 (NRF2) Signature in Canonical Pathway and Upstream Regulator Analysis of Leishmania-Infected Macrophages

Submitted by Ana Maria Fiscina Sampaio ([email protected]) on 2019-07-16T11:56:06Z No. of bitstreams: 1 Menezes, J.P. Proteomic Analysi...2019.pdf: 2216682 bytes, checksum: 42cced00b8b12eaae7f24baeecf4ae90 (MD5)Approved for entry into archive by Ana Maria Fiscina Sampaio ([email protected]) on 2019-07-16T12:33:35Z (GMT) No. of bitstreams: 1 Menezes, J.P. Proteomic Analysi...2019.pdf: 2216682 bytes, checksum: 42cced00b8b12eaae7f24baeecf4ae90 (MD5)Made available in DSpace on 2019-07-16T12:33:35Z (GMT). No. of bitstreams: 1 Menezes, J.P. Proteomic Analysi...2019.pdf: 2216682 bytes, checksum: 42cced00b8b12eaae7f24baeecf4ae90 (MD5) Previous issue date: 2019Fundação de Amparo à Pesquisa do Estado da Bahia (PV http://www.fapesb.ba.gov.br), Conselho Nacional de Pesquisa e Desenvolvimento Científico (PV http://www.cnpq.br) and National Institute of Science and Technology of Tropical Disease (PV http://inct.cnpq.br/ web/inct-dt). VB, PV, and UL are senior investigators funded by CNPq.Fundação Oswaldo Cruz. Instituto Gonçalo Moniz. Laboratório de Interação Hospedeiro-Parasita e Epidemiologia. Salvador, BA, Brasil.Fundação Oswaldo Cruz. Instituto Gonçalo Moniz. Laboratório de Doenças Infecciosas de Vetores. Salvador, BA, Brasil / Federal University of Bahia. Faculty of Medicine. Legal Medicine. Salvador, BA, Brazil.Fundação Oswaldo Cruz. Instituto Gonçalo Moniz. Laboratório de Interação Hospedeiro-Parasita e Epidemiologia. Salvador, BA, Brasil.Fundação Oswaldo Cruz. Instituto Gonçalo Moniz. Laboratório de Interação Hospedeiro-Parasita e Epidemiologia. Salvador, BA, Brasil.Fundação Oswaldo Cruz. Instituto Gonçalo Moniz. Laboratório de Interação Hospedeiro-Parasita e Epidemiologia. Salvador, BA, Brasil / Federal University of Rio de Janeiro. Laboratory of Physiopathology. Department of Pathology. Macaé, RJ, Brazil.Fundação Oswaldo Cruz. Instituto Gonçalo Moniz. Laboratório de Interação Hospedeiro-Parasita e Epidemiologia. Salvador, BA, Brasil.Fundação Oswaldo Cruz. Instituto Gonçalo Moniz. Laboratório de Interação Hospedeiro-Parasita e Epidemiologia. Salvador, BA, Brasil.Fundação Oswaldo Cruz. Instituto Gonçalo Moniz. Laboratório de Interação Hospedeiro-Parasita e Epidemiologia. Salvador, BA, Brasil.Fundação Oswaldo Cruz. Instituto Gonçalo Moniz. Laboratório de Inflamação e Biomarcadores. Salvador, BA, Brasil.Federal University of the Western of Bahia. Centro de Ciências Biológicas e da Saúde. Barreiras, BA, Brazil.Fundação Oswaldo Cruz. Centro de Integração de Dados e Conhecimento para a Saúde. Salvador, BA, Brasil.Fundação Oswaldo Cruz. Instituto René Rachou. Minas Gerais, BH, Brasil.Fundação Oswaldo Cruz. Instituto René Rachou. Minas Gerais, BH, Brasil.Virginia Commonwealth University. Department of Microbiology and Immunology. Richmond, VA, United States.Fundação Oswaldo Cruz. Instituto Carlos Chagas. Paraná, PR, Brasil.Federal University of Rio de Janeiro. Carlos Chagas Filho Biophysics Institute. Laboratory of Molecular Parasitology. Center of Health Science. Rio de Janeiro, RJ, Brazil.Federal University of Rio de Janeiro. Carlos Chagas Filho Biophysics Institute. Laboratory of Molecular Parasitology. Center of Health Science. Rio de Janeiro, RJ, Brazil.Fundação Oswaldo Cruz. Instituto Gonçalo Moniz. Laboratório de Doenças Infecciosas de Vetores. Salvador, BA, Brasil.Fundação Oswaldo Cruz. Instituto Gonçalo Moniz. Laboratório de Interação Hospedeiro-Parasita e Epidemiologia. Salvador, BA, Brasil / National Institute of Science and Technology of Tropical Disease. Patos, Brazil.CBA mice macrophages (MØ) control infection by Leishmania major and are susceptive to Leishmania amazonensis, suggesting that both parasite species induce distinct responses that play important roles in infection outcome. To evaluate the MØ responses to infection arising from these two Leishmania species, a proteomic study using a Multidimensional Protein Identification Technology (MudPIT) approach with liquid chromatography tandem mass spectrometry (LC-MS/MS) was carried out on CBA mice bone-marrow MØ (BMMØ). Following SEQUEST analysis, which revealed 2,838 proteins detected in BMMØ, data mining approach found six proteins significantly associated with the tested conditions. To investigate their biological significance, enrichment analysis was performed using Ingenuity Pathway Analysis (IPA). A three steps IPA approach revealed 4 Canonical Pathways (CP) and 7 Upstream Transcriptional Factors (UTFs) strongly associated with the infection process. NRF2 signatures were present in both CPs and UTFs pathways. Proteins involved in iron metabolism, such as heme oxigenase 1 (HO-1) and ferritin besides sequestosome (SQSMT1 or p62) were found in the NRF2 CPs and the NRF2 UTFs. Differences in the involvement of iron metabolism pathway in Leishmania infection was revealed by the presence of HO-1 and ferritin. Noteworty, HO-1 was strongly associated with L. amazonensis infection, while ferritin was regulated by both species. As expected, higher HO-1 and p62 expressions were validated in L. amazonensis-infected BMMØ, in addition to decreased expression of ferritin and nitric oxide production. Moreover, BMMØ incubated with L. amazonensis LPG also expressed higher levels of HO-1 in comparison to those stimulated with L. major LPG. In addition, L. amazonensis-induced uptake of holoTf was higher than that induced by L. major in BMMØ, and holoTf was also detected at higher levels in vacuoles induced by L. amazonensis. Taken together, these findings indicate that NRF2 pathway activation and increased HO-1 production, together with higher levels of holoTf uptake, may promote permissiveness to L. amazonensis infection. In this context, differences in protein signatures triggered in the host by L. amazonensis and L. major infection could drive the outcomes in distinct clinical forms of leishmaniasis

Data from: Proteomic analysis reveals a predominant NFE2L2 (NRF2) signature in the ​canonical pathway and upstream regulator analysis of Leishmania-infected macrophages

CBA mice macrophages (MØ) control infection by Leishmania major and are susceptive to Leishmania amazonensis, suggesting that both parasite species induce distinct responses that play important roles in infection outcome. To evaluate the MØ responses to infection arising from these two Leishmania species, a proteomic study using a Multidimensional Protein Identification Technology (MudPIT) approach with liquid chromatography tandem mass spectrometry (LC-MS/MS) was carried out on CBA mice bone-marrow MØ (BMMØ). Following SEQUEST analysis, which revealed 2,838 proteins detected in BMMØ, data mining approach found six proteins significantly associated with the tested conditions. To investigate their biological significance, enrichment analysis was performed using Ingenuity Pathway Analysis (IPA). A three steps IPA approach revealed 4 Canonical Pathways (CP) and 7 Upstream Transcriptional Factors (UTFs) strongly associated with the infection process. NRF2 signatures were present in both CPs and UTFs pathways. Proteins involved in iron metabolism, such as heme oxigenase 1 (HO-1) and ferritin besides sequestosome (SQSMT1 or p62) were found in the NRF2 CPs and the NRF2 UTFs. Differences in the involvement of iron metabolism pathway in Leishmania infection was revealed by the presence of HO-1 and ferritin. Noteworty, HO-1 was strongly associated with L. amazonensis infection, while ferritin was regulated by both species. As expected, higher HO-1 and p62 expressions were validated in L. amazonensis-infected BMMØ, in addition to decreased expression of ferritin and nitric oxide production. Moreover, BMMØ incubated with L. amazonensis LPG also expressed higher levels of HO-1 in comparison to those stimulated with L. major LPG. In addition, L. amazonensis-induced uptake of holoTf was higher than that induced by L. major in BMMØ, and holoTf was also detected at higher levels in vacuoles induced by L. amazonensis. Taken together, these findings indicate that NRF2 pathway activation and increased HO-1 production, together with higher levels of holoTf uptake, may promote permissiveness to L. amazonensis infection. In this context, differences in protein signatures triggered in the host by L. amazonensis and L. major infection could drive the outcomes in distinct clinical forms of leishmaniasis

A Comparison of Advanced Monte Carlo Methods for Open Systems: CFCMC vs CBMC

Two state-of-the-art simulation methods for computing adsorption properties in porous materials like zeolites and metal-organic frameworks are compared: the configurational bias Monte Carlo (CBMC) method and the recently proposed continuous fractional component Monte Carlo (CFCMC) method. We show that CFCMC is a very significant improvement over CBMC, and we can recommend it as our preferred method of choice. It is faster, more reliable, and (in contrast to CBMC) provides insight on whether or not the results are properly equilibrated. We also show that it is possible to combine the methods in a new CB/CFCMC hybrid method and derive the acceptance rules. This method achieves even higher insertion acceptance ratios