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Grabowska K, Harwood E, Ciborowski P. HIV and Proteomics: What We Have Learned from High Throughput Studies. Proteomics Clin Appl 2021; 15:e2000040. [PMID: 32978881 PMCID: PMC7900993 DOI: 10.1002/prca.202000040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 09/04/2020] [Indexed: 12/17/2022]
Abstract
The accelerated development of technology over the last three decades has driven biological sciences to high-throughput profiling experiments, now broadly referred to as systems biology. The unprecedented improvement of analytical instrumentation has opened new avenues for more complex experimental designs and expands the knowledge in genomics, proteomics, and other omics fields. Despite the collective efforts of hundreds of researchers, gleaning all the expected information from omics experiments is still quite far. This paper summarizes what has been learned from high-throughput proteomics studies thus far, and what is believed should be done to reveal even more valuable information from such studies. It is drawn from the background in using proteomics to study human immunodeficiency virus 1 infection of macrophages and/or T cells, but it is believed that some conclusions will be more broadly applicable.
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Affiliation(s)
- Kinga Grabowska
- Laboratory of Virus Molecular BiologyIntercollegiate Faculty of BiotechnologyUniversity of GdanskGdansk80‐307Poland
- Department of Pharmacology and Experimental NeuroscienceCollege of MedicineUniversity of Nebraska Medical CenterOmahaNE68198‐5800USA
| | - Emma Harwood
- Department of Pharmacology and Experimental NeuroscienceCollege of MedicineUniversity of Nebraska Medical CenterOmahaNE68198‐5800USA
| | - Pawel Ciborowski
- Department of Pharmacology and Experimental NeuroscienceCollege of MedicineUniversity of Nebraska Medical CenterOmahaNE68198‐5800USA
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Ma J, Zhao F, Su W, Li Q, Li J, Ji J, Deng Y, Zhou Y, Wang X, Yang H, Saksena NK, Kristiansen K, Wang H, Liu Y. Zinc finger and interferon-stimulated genes play a vital role in TB-IRIS following HAART in AIDS. Per Med 2018; 15:251-269. [PMID: 29984631 DOI: 10.2217/pme-2017-0084] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
AIM Co-infection in HIV-1 patients with Mycobacterium tuberculosis poses considerable risk of developing the immune reconstitution inflammatory syndrome (IRIS), especially upon the initiation of antiretroviral therapy (ART). Methodology & results: For transcriptomic analysis, peripheral blood mononuclear cells' whole gene expression was used from three patient groups: HIV+ (H), HIV-TB+ (HT), HIV-TB+ with IRIS (HTI). Pathway enrichment and functional analysis was performed before and after highly active ART. Genes in the interferon-stimulating and ZNF families maintained tight functional interaction and tilted the balance in favor of TB-IRIS. DISCUSSION & CONCLUSION The functional impairment of interaction between ZNF genes and interferon-stimulated genes, along with higher expression of S100A8/S100A9 genes possibly forms the genomic basis of TB-IRIS in a subset of HIV patients while on highly active ART.
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Affiliation(s)
- Jinmin Ma
- BGI-Shenzhen, Shenzhen 518083, PR China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen 2100, Denmark.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, PR China
| | - Fang Zhao
- Shenzhen Third People's Hospital, Shenzhen 518112, PR China
| | - Wei Su
- BGI-Shenzhen, Shenzhen 518083, PR China
| | - Qiongfang Li
- BGI-Shenzhen, Shenzhen 518083, PR China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, PR China
| | - Jiandong Li
- BGI-Shenzhen, Shenzhen 518083, PR China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, PR China
| | - Jingkai Ji
- BGI-Shenzhen, Shenzhen 518083, PR China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, PR China
| | - Yong Deng
- Shenzhen Third People's Hospital, Shenzhen 518112, PR China
| | - Yang Zhou
- Shenzhen Third People's Hospital, Shenzhen 518112, PR China
| | - Xinfa Wang
- Shenzhen Third People's Hospital, Shenzhen 518112, PR China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen 518083, PR China.,James D. Watson Institute of Genome Science, Hangzhou 310007, PR China
| | - Nitin K Saksena
- BGI-Shenzhen, Shenzhen 518083, PR China.,IGO, 19a Boundary Street, Rushcutters Bay, Sydney, NSW, Australia
| | - Karsten Kristiansen
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen 2100, Denmark
| | - Hui Wang
- BGI-Shenzhen, Shenzhen 518083, PR China.,Department of Engineering Science, University of Oxford, Oxford OX3 7DQ, UK
| | - Yingxia Liu
- Shenzhen Third People's Hospital, Shenzhen 518112, PR China
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Lefterov I, Schug J, Mounier A, Nam KN, Fitz NF, Koldamova R. RNA-sequencing reveals transcriptional up-regulation of Trem2 in response to bexarotene treatment. Neurobiol Dis 2015; 82:132-140. [PMID: 26071899 DOI: 10.1016/j.nbd.2015.05.019] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 05/15/2015] [Accepted: 05/28/2015] [Indexed: 01/08/2023] Open
Abstract
We have recently demonstrated that short term bexarotene treatment of APP/PS1 mice significantly improves their cognitive performance. While there were no changes in plaque load, or insoluble Aβ levels in brain, biochemical analysis strongly suggested improved clearance of soluble Aβ, including Aβ oligomers. To get further insight into molecular mechanisms underlying this therapeutic effect, we explored genome-wide differential gene expression in brain of bexarotene and control treated APP/PS1 mice. We performed high throughput massively parallel sequencing on mRNA libraries generated from cortices of bexarotene or vehicle treated APP/PS1 mice and compared the expression profiles for differential gene expression. Gene Ontology (GO) Biological Process categories with the highest fold enrichment and lowest False Discovery Rate (FDR) are clustered in GO terms immune response, inflammatory response, oxidation-reduction and immunoglobulin mediated immune response. Chromatin immunoprecipitation (ChIP) followed by ChIP-QPCR, and RT-QPCR expression assays were used to validate select genes, including Trem2, Tyrobp, Apoe and Ttr, differentially expressed in response to Retinoid X Receptor (RXR) activation. We found that bexarotene significantly increased the phagocytosis of soluble and insoluble Aβ in BV2 cells. The results of our study demonstrate that in AD model mice expressing human APP, gene networks up-regulated in response to RXR activation by the specific, small molecule, ligand bexarotene may influence diverse regulatory pathways that are considered critical for cognitive performance, inflammatory response and Aβ clearance, and may provide an explanation of the bexarotene therapeutic effect at the molecular level. This study also confirms that unbiased massive parallel sequencing approaches are useful and highly informative for revealing brain molecular and cellular mechanisms underlying responses to activated nuclear hormone receptors in AD animal models.
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Affiliation(s)
- Iliya Lefterov
- Department of Environmental & Occupational Health, University of Pittsburgh, Pittsburgh, PA 15219, USA.
| | - Jonathan Schug
- Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania, Philadelphia, PA 19104, USA; Functional Genomics Core, Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Anais Mounier
- Department of Environmental & Occupational Health, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Kyong Nyon Nam
- Department of Environmental & Occupational Health, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Nicholas F Fitz
- Department of Environmental & Occupational Health, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Radosveta Koldamova
- Department of Environmental & Occupational Health, University of Pittsburgh, Pittsburgh, PA 15219, USA.
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