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Piatek P, Tarkowski M, Namiecinska M, Riva A, Wieczorek M, Michlewska S, Dulska J, Domowicz M, Kulińska-Michalska M, Lewkowicz N, Lewkowicz P. H3K4me3 Histone ChIP-Seq Analysis Reveals Molecular Mechanisms Responsible for Neutrophil Dysfunction in HIV-Infected Individuals. Front Immunol 2021; 12:682094. [PMID: 34335583 PMCID: PMC8320512 DOI: 10.3389/fimmu.2021.682094] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 05/25/2021] [Indexed: 01/15/2023] Open
Abstract
Peripheral neutrophils in HIV-infected individuals are characterized by impairment of chemotaxis, phagocytosis, bactericidal activity, and oxidative burst ability regardless of whether patients are receiving antiretroviral therapy or not. Neutrophil dysfunction leads not only to increased susceptibility to opportunistic infections but also to tissue damage through the release of reactive oxygen species (ROS), proteases, and other potentially harmful effector molecules contributing to AIDS progression. In this study, we demonstrated high levels of histone H3 lysine K4 trimethylated (H3K4me3) and dysregulation of DNA transcription in circulating neutrophils of HIV-infected subjects. This dysregulation was accompanied by a deficient response of neutrophils to LPS, impaired cytokine/chemokine/growth factor synthesis, and increased apoptosis. Chromatin immunoprecipitation sequencing (ChIPseq) H3K4me3 histone analysis revealed that the most spectacular abnormalities were observed in the exons, introns, and promoter-TSS regions. Bioinformatic analysis of Gene Ontology, including biological processes, molecular function, and cellular components, demonstrated that the main changes were related to the genes responsible for cell activation, cytokine production, adhesive molecule expression, histone remodeling via upregulation of methyltransferase process, and downregulation of NF-κB transcription factor in canonical pathways. Abnormalities within H3K4me3 implicated LPS-mediated NF-κB canonical activation pathway that was a result of low amounts of κB DNA sites within histone H3K4me3, low NF-κB (p65 RelA) and TLR4 mRNA expression, and reduced free NF-κB (p65 RelA) accumulation in the nucleus. Genome-wide survey of H3K4me3 provided evidence that chromatin modifications lead to an impairment within the canonical NF-κB cell activation pathway causing the neutrophil dysfunction observed in HIV-infected individuals.
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Affiliation(s)
- Paweł Piatek
- Department of Neurology, Laboratory of Neuroimmunology, Medical University of Lodz, Lodz, Poland
| | - Maciej Tarkowski
- Department of Biomedical and Clinical Sciences, 'Luigi Sacco', University of Milan, Milan, Italy
| | - Magdalena Namiecinska
- Department of Neurology, Laboratory of Neuroimmunology, Medical University of Lodz, Lodz, Poland
| | - Agostino Riva
- Department of Biomedical and Clinical Sciences, 'Luigi Sacco', University of Milan, Milan, Italy
| | - Marek Wieczorek
- Department of Neurobiology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Sylwia Michlewska
- Laboratory of Microscopic Imaging and Specialized Biological Techniques, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | | | - Małgorzata Domowicz
- Department of Neurology, Laboratory of Neuroimmunology, Medical University of Lodz, Lodz, Poland
| | | | - Natalia Lewkowicz
- Department of Periodontology and Oral Mucosal Diseases, Medical University of Lodz, Lodz, Poland
| | - Przemysław Lewkowicz
- Department of Neurology, Laboratory of Neuroimmunology, Medical University of Lodz, Lodz, Poland
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Rubio-Camarillo M, López-Fernández H, Gómez-López G, Carro Á, Fernández JM, Torre CF, Fdez-Riverola F, Glez-Peña D. RUbioSeq+: A multiplatform application that executes parallelized pipelines to analyse next-generation sequencing data. Comput Methods Programs Biomed 2017; 138:73-81. [PMID: 27886717 DOI: 10.1016/j.cmpb.2016.10.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 09/05/2016] [Accepted: 10/18/2016] [Indexed: 06/06/2023]
Abstract
BACKGROUND AND OBJECTIVE To facilitate routine analysis and to improve the reproducibility of the results, next-generation sequencing (NGS) analysis requires intuitive, efficient and integrated data processing pipelines. METHODS We have selected well-established software to construct a suite of automated and parallelized workflows to analyse NGS data for DNA-seq (single-nucleotide variants (SNVs) and indels), CNA-seq, bisulfite-seq and ChIP-seq experiments. RESULTS Here, we present RUbioSeq+, an updated and extended version of RUbioSeq, a multiplatform application that incorporates a suite of automated and parallelized workflows to analyse NGS data. This new version includes: (i) an interactive graphical user interface (GUI) that facilitates its use by both biomedical researchers and bioinformaticians, (ii) a new pipeline for ChIP-seq experiments, (iii) pair-wise comparisons (case-control analyses) for DNA-seq experiments, (iv) and improvements in the parallelized and multithreaded execution options. Results generated by our software have been experimentally validated and accepted for publication. CONCLUSIONS RUbioSeq+ is free and open to all users at http://rubioseq.bioinfo.cnio.es/.
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Affiliation(s)
- Miriam Rubio-Camarillo
- Bioinformatics Unit (UBio), Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Hugo López-Fernández
- Higher Technical School of Computer Engineering, University of Vigo, Ourense, Spain; Instituto de Investigación Biomédica de Vigo (IBIV), Vigo, Spain.
| | - Gonzalo Gómez-López
- Bioinformatics Unit (UBio), Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Ángel Carro
- Bioinformatics Unit (UBio), Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - José María Fernández
- Spanish National Bioinformatics Institute (INB), INB Node 2, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Coral Fustero Torre
- Bioinformatics Unit (UBio), Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Florentino Fdez-Riverola
- Higher Technical School of Computer Engineering, University of Vigo, Ourense, Spain; Instituto de Investigación Biomédica de Vigo (IBIV), Vigo, Spain
| | - Daniel Glez-Peña
- Higher Technical School of Computer Engineering, University of Vigo, Ourense, Spain; Instituto de Investigación Biomédica de Vigo (IBIV), Vigo, Spain
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