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Mantovani N, Defelicibus A, da Silva IT, Cicero MF, Santana LC, Arnold R, de Castro DF, Duro RLS, Nishiyama-Jr MY, Junqueira-de-Azevedo ILM, da Silva BCM, da Silva Duarte AJ, Casseb J, de Barros Tenore S, Hunter J, Diaz RS, Komninakis SCV. Latency-associated DNA methylation patterns among HIV-1 infected individuals with distinct disease progression courses or antiretroviral virologic response. Sci Rep 2021; 11:22993. [PMID: 34837007 PMCID: PMC8626465 DOI: 10.1038/s41598-021-02463-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 11/10/2021] [Indexed: 11/09/2022] Open
Abstract
DNA methylation is one of the epigenetic modifications that configures gene transcription programs. This study describes the DNA methylation profile of HIV-infected individuals with distinct characteristics related to natural and artificial viremia control. Sheared DNA from circulating mononuclear cells was subjected to target enrichment bisulfite sequencing designed to cover CpG-rich genomic regions. Gene expression was assessed through RNA-seq. Hypermethylation in virologic responders was highly distributed closer to Transcription Start Sites (p-value = 0.03). Hyper and hypomethylation levels within TSS adjacencies varied according to disease progression status (Kruskal-Wallis, p < 0.001), and specific differentially methylated regions associated genes were identified for each group. The lower the promoter methylation, the higher the gene expression in subjects undergoing virologic failure (R = - 0.82, p = 0.00068). Among the inversely correlated genes, those supporting glycolysis and its related pathways were hypomethylated and up-regulated in virologic failures. Disease progression heterogeneity was associated with distinct DNA methylation patterns in terms of rates and distribution. Methylation was associated with the expression of genes sustaining intracellular glucose metabolism in subjects undergoing antiretroviral virologic failure. Our findings highlight that DNA methylation is associated with latency, disease progression, and fundamental cellular processes.
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Affiliation(s)
- Nathalia Mantovani
- Retrovirology Laboratory, Infectious Diseases Division, Federal University of São Paulo (UNIFESP), Rua Pedro de Toledo 669, Vila Clementino, Sao Paulo, SP, 04039-032, Brazil.
| | - Alexandre Defelicibus
- Laboratory of Bioinformatics and Computational Biology, A.C. Camargo Cancer Center, Rua Taguá, 440, São Paulo, SP, 01508-010, Brazil
| | - Israel Tojal da Silva
- Laboratory of Bioinformatics and Computational Biology, A.C. Camargo Cancer Center, Rua Taguá, 440, São Paulo, SP, 01508-010, Brazil
| | - Maira Ferreira Cicero
- Retrovirology Laboratory, Infectious Diseases Division, Federal University of São Paulo (UNIFESP), Rua Pedro de Toledo 669, Vila Clementino, Sao Paulo, SP, 04039-032, Brazil
| | - Luiz Claudio Santana
- Retrovirology Laboratory, Infectious Diseases Division, Federal University of São Paulo (UNIFESP), Rua Pedro de Toledo 669, Vila Clementino, Sao Paulo, SP, 04039-032, Brazil
| | - Rafael Arnold
- Retrovirology Laboratory, Infectious Diseases Division, Federal University of São Paulo (UNIFESP), Rua Pedro de Toledo 669, Vila Clementino, Sao Paulo, SP, 04039-032, Brazil
| | - Daniela Funayama de Castro
- Retrovirology Laboratory, Infectious Diseases Division, Federal University of São Paulo (UNIFESP), Rua Pedro de Toledo 669, Vila Clementino, Sao Paulo, SP, 04039-032, Brazil
| | - Rodrigo Lopes Sanz Duro
- Retrovirology Laboratory, Infectious Diseases Division, Federal University of São Paulo (UNIFESP), Rua Pedro de Toledo 669, Vila Clementino, Sao Paulo, SP, 04039-032, Brazil
| | - Milton Yutaka Nishiyama-Jr
- Laboratório de Toxinologia Aplicada, Instituto Butantan, Avenida Vital Brasil, 1500, São Paulo, SP, 05503-900, Brazil
| | | | - Bosco Christiano Maciel da Silva
- Laboratório de Investigação Médica 56 (LIM/56), Faculdade de Medicina FMUSP, Universidade de São Paulo, Avenida Dr. Enéas Carvalho de Aguiar, 470, São Paulo, SP, 05403-000, Brazil
| | - Alberto José da Silva Duarte
- Laboratório de Investigação Médica 56 (LIM/56), Faculdade de Medicina FMUSP, Universidade de São Paulo, Avenida Dr. Enéas Carvalho de Aguiar, 470, São Paulo, SP, 05403-000, Brazil
| | - Jorge Casseb
- Laboratório de Investigação Médica 56 (LIM/56), Faculdade de Medicina FMUSP, Universidade de São Paulo, Avenida Dr. Enéas Carvalho de Aguiar, 470, São Paulo, SP, 05403-000, Brazil
| | - Simone de Barros Tenore
- Retrovirology Laboratory, Infectious Diseases Division, Federal University of São Paulo (UNIFESP), Rua Pedro de Toledo 669, Vila Clementino, Sao Paulo, SP, 04039-032, Brazil
| | - James Hunter
- Retrovirology Laboratory, Infectious Diseases Division, Federal University of São Paulo (UNIFESP), Rua Pedro de Toledo 669, Vila Clementino, Sao Paulo, SP, 04039-032, Brazil
| | - Ricardo Sobhie Diaz
- Retrovirology Laboratory, Infectious Diseases Division, Federal University of São Paulo (UNIFESP), Rua Pedro de Toledo 669, Vila Clementino, Sao Paulo, SP, 04039-032, Brazil
| | - Shirley Cavalcante Vasconcelos Komninakis
- Retrovirology Laboratory, Infectious Diseases Division, Federal University of São Paulo (UNIFESP), Rua Pedro de Toledo 669, Vila Clementino, Sao Paulo, SP, 04039-032, Brazil
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Apoliano CF, Assone T, Maciel da Silva BC, Andreetta Corral M, de Oliveira ACP, Fonseca LAM, Duarte AJDS, Tang Y, Casseb J. Interferon-γ Secretion Enzyme-Linked Immunospot Assay Determined Among Human T Cell Lymphotropic Virus Type 1-Infected Subjects: A Potential Laboratory Marker for Early HTLV-1-Associated Myelopathy/Tropical Spastic Paraparesis Diagnosis. AIDS Res Hum Retroviruses 2020; 36:6-7. [PMID: 31474114 DOI: 10.1089/aid.2018.0290] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Carlos Fernando Apoliano
- Laboratory of Dermatology and Immunodeficiencies, Department of Dermatology, University of São Paulo Medical School, São Paulo, Brazil
- Institute of Tropical Medicine of São Paulo, São Paulo, Brazil
| | - Tatiane Assone
- Laboratory of Dermatology and Immunodeficiencies, Department of Dermatology, University of São Paulo Medical School, São Paulo, Brazil
- Institute of Tropical Medicine of São Paulo, São Paulo, Brazil
| | | | | | | | | | - Alberto José da Silva Duarte
- Laboratory of Dermatology and Immunodeficiencies, Department of Dermatology, University of São Paulo Medical School, São Paulo, Brazil
- Institute of Tropical Medicine of São Paulo, São Paulo, Brazil
| | - Yuyang Tang
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, California
| | - Jorge Casseb
- Laboratory of Dermatology and Immunodeficiencies, Department of Dermatology, University of São Paulo Medical School, São Paulo, Brazil
- Institute of Tropical Medicine of São Paulo, São Paulo, Brazil
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Lara BR, Melo MBDA, Paula CR, Arnoni MV, Simões CCN, Nakano S, Richini-Pereira VB, Garces HG, Maciel da Silva BC, Anversa L, Gonçalves Silva E, Auler ME, Oliveira Dos Santos RL, da Silva Ruiz L. Apiotrichum veenhuisii isolated from a pediatric patient with acute myeloid leukemia: The first case in humans. Mycologia 2019; 111:793-797. [PMID: 31385738 DOI: 10.1080/00275514.2019.1637645] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
This is the first report of the yeast Apiotrichum veenhuisii (formerly Trichosporon veenhuisii) causing disease in humans; its virulence and in vitro behavior against antifungals were also studied. The sample was isolated from biopsy fragments of disseminated lesions on the skin of a pediatric patient with acute myeloid leukemia. The studied virulence factors evidenced that the strain tested negative for secretion of the enzymes proteinase, phospholipase, and hemolysin. The isolate was characterized as low biofilm producer. Except for amphotericin B and voriconazole, the sample presented high minimum inhibitory concentration values against azole and echinocandins.
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Affiliation(s)
- Bruna Rossini Lara
- Núcleo de Ciências Biomédicas, Instituto Adolfo Lutz (IAL) , CLR II, Bauru , São Paulo , Brazil
| | | | | | | | | | - Shirley Nakano
- Hospital Infantil Darcy Vargas , São Paulo , São Paulo , Brazil
| | | | - Hans Garcia Garces
- Departamento de Microbiologia e Imunologia, Universidade Estadual Paulista , Botucatu , São Paulo , Brazil
| | | | - Laís Anversa
- Núcleo de Ciências Químicas e Bromatológicas, Instituto Adolfo Lutz (IAL) , Bauru-SP , Brazil
| | | | - Marcos Ereno Auler
- Universidade Estadual do Centro-Oeste do Paraná , Guarapuava , Paraná , Brazil
| | | | - Luciana da Silva Ruiz
- Núcleo de Ciências Biomédicas, Instituto Adolfo Lutz (IAL) , CLR II, Bauru , São Paulo , Brazil
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Silva BCMD, Grassi MFR, Coutinho R, Mascarenhas REM, Olavarria VN, Coutinho-Borgo A, Kalil J, Cunha Neto E, Fonseca SG. Mycobacterium tuberculosis epitope-specific interferon-g production in healthy Brazilians reactive and non-reactive to tuberculin skin test. Mem Inst Oswaldo Cruz 2014; 109:999-1004. [PMID: 25494469 PMCID: PMC4325617 DOI: 10.1590/0074-0276140193] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 12/11/2014] [Indexed: 12/27/2022] Open
Abstract
The interferon (IFN)-γ response to peptides can be a useful diagnostic marker of
Mycobacterium tuberculosis (MTB) latent infection. We identified promiscuous and
potentially protective CD4+ T-cell epitopes from the most conserved
regions of MTB antigenic proteins by scanning the MTB antigenic proteins GroEL2,
phosphate-binding protein 1 precursor and 19 kDa antigen with the TEPITOPE algorithm.
Seven peptide sequences predicted to bind to multiple human leukocyte antigen
(HLA)-DR molecules were synthesised and tested with IFN-γ enzyme-linked immunospot
(ELISPOT) assays using peripheral blood mononuclear cells (PBMCs) from 16 Mantoux
tuberculin skin test (TST)-positive and 16 TST-negative healthy donors. Eighty-eight
percent of TST-positive donors responded to at least one of the peptides, compared to
25% of TST-negative donors. Each individual peptide induced IFN-γ production by PBMCs
from at least 31% of the TST-positive donors. The magnitude of the response against
all peptides was 182 ± 230 x 106 IFN-γ spot forming cells (SFC) among
TST-positive donors and 36 ± 62 x 106 SFC among TST-negative donors (p =
0.007). The response to GroEL2 (463-477) was only observed in the TST-positive group.
This combination of novel MTB CD4 T-cell epitopes should be tested in a larger cohort
of individuals with latent tuberculosis (TB) to evaluate its potential to diagnose
latent TB and it may be included in ELISPOT-based IFN-γ assays to identify
individuals with this condition.
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Affiliation(s)
| | | | - Raimundo Coutinho
- Laboratório Avançado de Saúde Pública, Fundação Oswaldo Cruz, Salvador, BA, Brasil
| | | | | | | | - Jorge Kalil
- Laboratório de Imunologia, Instituto do Coração, São Paulo, SP, Brasil
| | - Edecio Cunha Neto
- Laboratório de Imunologia, Instituto do Coração, São Paulo, SP, Brasil
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da Silva BCM, Paula CR, Auler ME, Ruiz LDS, Dos Santos JI, Yoshioka MCN, Fabris A, Castro LGM, Duarte AJDS, Gambale W. Dermatophytosis and immunovirological status of HIV-infected and AIDS patients from Sao Paulo city, Brazil. Mycoses 2014; 57:371-6. [PMID: 24417711 DOI: 10.1111/myc.12169] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Revised: 12/17/2013] [Accepted: 12/17/2013] [Indexed: 11/26/2022]
Abstract
Over the past decades, more people became infected with human immunodeficiency virus (HIV) and developed acquired immunodeficiency syndrome (AIDS). Because of that the incidence of fungal infections rose dramatically. It happened because this virus can modify the course of fungal diseases, leading to altered clinical pictures. The aim of this study was to evaluate epidemiological and biological aspects of dermatophytosis in HIV-positive and AIDS patients living in the city of São Paulo, Brazil. A total of 84 (44 HIV-positive and 40 AIDS) patients were enrolled in this study. The patients were tested for dermatophyte infections, as well as for the CD4(+) /CD8(+) and HIV viral load counts. Tinea unguium was most frequently observed in AIDS patients, whereas Tinea pedis was mostly observed in HIV-positive patients. The most frequent dermatophyte species was Trichophyton rubrum. CD4(+) counts and CD4(+) /CD8(+) ratios were not associated with a higher risk for dermatophytosis. On the other hand, viral load higher than 100 000 copies/ml was associated with a higher frequency of dermatophytosis. The results suggest to that although dermatophytosis is common in HIV-positive and AIDS patients, the degree of immunosuppression does not seems to correlate with increased risk of this fungal infection. In addition, high viral load as a predictive risk factor for dermatophyte infection should be subject of further evaluations.
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Affiliation(s)
- Bosco Christiano Maciel da Silva
- Laboratory of Mycology, Department of Microbiology, Biomedical Science Institute II (ICB II), University of São Paulo, São Paulo, Brazil; Laboratory of Medical Investigation in Dermatology and Immunodeficiency (LIM 56), Faculty of Medicine, University of São Paulo, São Paulo, Brazil
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