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Yero A, Goulet JP, Shi T, Costiniuk CT, Routy JP, Tremblay C, Mboumba Bouassa RS, Alexandrova Y, Pagliuzza A, Chomont N, Ancuta P, Jenabian MA. Altered memory CCR6 + Th17-polarised T-cell function and biology in people with HIV under successful antiretroviral therapy and HIV elite controllers. EBioMedicine 2024; 107:105274. [PMID: 39178742 PMCID: PMC11388266 DOI: 10.1016/j.ebiom.2024.105274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 07/17/2024] [Accepted: 07/27/2024] [Indexed: 08/26/2024] Open
Abstract
BACKGROUND Despite successful antiretroviral therapy (ART), frequencies and immunological functions of memory CCR6+ Th17-polarised CD4+ T-cells are not fully restored in people with HIV (PWH). Moreover, long-lived Th17 cells contribute to HIV persistence under ART. However, the molecular mechanisms underlying these observations remain understudied. METHODS mRNA-sequencing was performed using Illumina technology on freshly FACS-sorted memory CCR6+CD4+ T-cells from successfully ART-treated (ST), elite controllers (EC), and uninfected donors (HD). Gene expression validation was performed by RT-PCR, flow cytometry, and in vitro functional assays. FINDINGS Decreased Th17 cell frequencies in STs and ECs versus HDs coincided with reduced Th17-lineage cytokine production in vitro. Accordingly, the RORγt/RORC2 repressor NR1D1 was upregulated, while the RORγt/RORC2 inducer Semaphorin 4D was decreased in memory CCR6+ T-cells of STs and ECs versus HDs. The presence of HIV-DNA in memory CCR6+ T-cells of ST and EC corresponded with the downregulation of HIV restriction factors (SERINC3, KLF3, and RNF125) and HIV inhibitors (tetraspanins), along with increased expression of the HIV-dependency factor MRE11, indicative of higher susceptibility/permissiveness to HIV-1 infection. Furthermore, markers of DNA damage/modification were elevated in memory CCR6+ T-cells of STs and ECs versus HDs, in line with their increased activation (CD38/HLA-DR), senescence/exhaustion phenotype (CTLA-4/PD-1/CD57) and their decreased expression of proliferation marker Ki-67. INTERPRETATION These results reveal new molecular mechanisms of Th17 cell deficit in ST and EC PWH despite a successful control of HIV-1 replication. This knowledge points to potential therapeutic interventions to limit HIV-1 infection and restore frequencies, effector functions, and senescence/exhaustion in Th17 cells. FUNDING This study was funded by the Canadian Institutes of Health Research (CIHR, operating grant MOP 142294, and the Canadian HIV Cure Enterprise [CanCURE 2.0] Team Grant HB2 164064), and in part, by the Réseau SIDA et maladies infectieuses du Fonds de recherche du Québec-Santé (FRQ-S).
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Affiliation(s)
- Alexis Yero
- Department of Biological Sciences and CERMO-FC Research Centre, Université du Québec à Montréal (UQAM), Montreal, QC, Canada
| | | | - Tao Shi
- Department of Biological Sciences and CERMO-FC Research Centre, Université du Québec à Montréal (UQAM), Montreal, QC, Canada
| | - Cecilia T Costiniuk
- Chronic Viral Illness Service and Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Jean-Pierre Routy
- Chronic Viral Illness Service and Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Cecile Tremblay
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CR-CHUM), Montreal, QC, Canada; Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université de Montréal, Montreal, QC, Canada
| | - Ralph-Sydney Mboumba Bouassa
- Department of Biological Sciences and CERMO-FC Research Centre, Université du Québec à Montréal (UQAM), Montreal, QC, Canada
| | - Yulia Alexandrova
- Department of Biological Sciences and CERMO-FC Research Centre, Université du Québec à Montréal (UQAM), Montreal, QC, Canada
| | - Amélie Pagliuzza
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CR-CHUM), Montreal, QC, Canada
| | - Nicolas Chomont
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CR-CHUM), Montreal, QC, Canada; Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université de Montréal, Montreal, QC, Canada
| | - Petronela Ancuta
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CR-CHUM), Montreal, QC, Canada; Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université de Montréal, Montreal, QC, Canada
| | - Mohammad-Ali Jenabian
- Department of Biological Sciences and CERMO-FC Research Centre, Université du Québec à Montréal (UQAM), Montreal, QC, Canada; Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université de Montréal, Montreal, QC, Canada.
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Anwar S, Khawar MB, Ovais M, Afzal A, Zhang X. Gold nanocubes based optical detection of HIV-1 DNA via surface enhanced Raman spectroscopy. J Pharm Biomed Anal 2023; 226:115242. [PMID: 36638548 DOI: 10.1016/j.jpba.2023.115242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/16/2022] [Accepted: 01/09/2023] [Indexed: 01/11/2023]
Abstract
Optical detection of HIV-1 DNA with surface enhanced Raman spectroscopy (SERS) is a quick and versatile method, having great potential in screening and characterization of HIV-1 virus particle. We have synthesized and applied novel gold nanocubes (AuNCs) for signal enhancement of SERS to study HIV-1 DNA strands by taking into account the specific vibrational bands of functional groups. Raman peaks at 562 cm-1, 800 cm-1, 1094 cm-1 were observed in both Human Random Control DNA and HIV-1 DNA, while three new peaks were detected in infected DNA at 421 cm-1, 1069 cm-1 and 1254 cm-1. Raman bands in case of AuNCs coated HIV-1 DNA molecules were observed with enhanced intensity values as compared to the silver nanoparticles-based SERS substrate. In case of silver nanoparticles (AgNPs) conjugate DNA, we get all signatures of HIV-1 virus at almost the same position with peak distortions, peak alterations and intensities reductions. We overall molecularly observed HIV-1 infected DNA and Human Random Control DNA, with high sensitivity and selectivity using highly sensitive and stable AuNCs in SERS. This technique can be utilized to identify molecular structures and chemical identification of biomacromolecules which can further be investigated as biomarkers for the screening of whole-body HIV-1 virus particles.
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Affiliation(s)
- Shahzad Anwar
- Agri. & Biophotonics Division, National Institute of Lasers and Optronics College, Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad 45650, Pakistan; National Laboratory of Biomacromolecules, CAS Centre for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, PR China.
| | - Muhammad Babar Khawar
- Applied Molecular Biology and Biomedicine Lab, Department of Zoology, University of Narowal, Narowal, Pakistan.
| | - Muhammad Ovais
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, National Center for Nanoscience & Technology (NCNST), Beijing 100190, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Ali Afzal
- Molecular Medicine and Cancer Therapeutics Lab, Department of Zoology, Faculty of Sciences and Technology, University of Central Punjab, Lahore, Pakistan
| | - Xiang Zhang
- National Laboratory of Biomacromolecules, CAS Centre for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, PR China
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CAGE-seq reveals that HIV-1 latent infection does not trigger unique cellular responses in a Jurkat T cell model. J Virol 2021; 95:JVI.02394-20. [PMID: 33504604 PMCID: PMC8103700 DOI: 10.1128/jvi.02394-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The cure for HIV-1 is currently stalled by our inability to specifically identify and target latently infected cells. HIV-1 viral RNA/DNA or viral proteins are recognized by cellular mechanisms and induce interferon responses in virus producing cells, but changes in latently infected cells remain unknown. HIVGKO contains a GFP reporter under the HIV-1 promoter and an mKO2 reporter under the internal EF1α promoter. This viral construct enables direct identification of HIV-1 both productively and latently infected cells. In this study we aim to identify specific cellular transcriptional responses triggered by HIV-1 entry and integration using Cap Analysis of Gene Expression (CAGE).We deep sequenced CAGE tags in uninfected, latently and productively infected cells and compared their differentially expressed transcription start site (TSS) profiles. Virus producing cells had differentially expressed TSSs related to T-cell activation and apoptosis when compared to uninfected cells or latently infected cells. Surprisingly, latently infected cells had only 33 differentially expressed TSSs compared to uninfected cells. Among these, SPP1 and APOE were down-regulated in latently infected cells. SPP1 or APOE knockdown in Jurkat T cells increased susceptibility to HIVGKO infection, suggesting that they have anti-viral properties. Components of the PI3K/mTOR pathway, MLST8, 4EBP and RPS6, were significant TSSs in productively infected cells, and S6K phosphorylation was increased compared to latently infected cells, suggesting that mTOR pathway activity plays a role in establishing the latent reservoir. These findings indicate that HIV-1 entry and integration do not trigger unique transcriptional responses when infection becomes latent.Importance: Latent HIV-1 infection is established as early as the first viral exposure and remains the most important barrier in obtaining the cure for HIV-1 infection. Here, we used CAGE to compare the transcriptional landscape of latently infected cells with that of non-infected or productively infected cells. We found that latently infected cells and non-infected cells show quite similar transcriptional profiles. Our data suggest that T-cells cannot recognize incoming viral components nor the integrated HIV-1 genome when infection remains latent. These findings should guide future research into widening our approaches to identify and target latent HIV-1 infected cells.
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Zhao Z, Wu X, He F, Xiang C, Feng X, Bai X, Liu X, Zhao J, Takeda S, Qing Y. Critical roles of Rad54 in tolerance to apigenin-induced Top1-mediated DNA damage. Exp Ther Med 2021; 21:505. [PMID: 33791014 DOI: 10.3892/etm.2021.9936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 07/07/2020] [Indexed: 02/05/2023] Open
Abstract
Apigenin (APG), a flavone sub-class of flavonoids, possesses a diverse range of biological activities, including anti-cancer and anti-inflammatory effects. Previous studies identified the genotoxicity of APG in certain cancer cells, which may be associated with its anticancer effect. However, the DNA damage repair mechanism induced by APG has remained elusive. In order to clarify the molecular mechanisms, the present study determined the toxicity of APG to the wild-type (WT) DT40 chicken B-lymphocyte cell line, as well as to DT40 cells with deletions in various DNA repair genes, and their sensitivities were compared. It was demonstrated that cells deficient of Rad54, a critical homologous recombination gene, were particularly sensitive to APG. Cell-cycle analysis demonstrated that APG caused an increase in the G2/M-phase population of Rad54- / - cells that was greater than that in WT cells. Furthermore, it was demonstrated by immunofluorescence assay that Rad54- / - cells exhibited significantly increased numbers of γ-phosphorylated H2AX variant histone foci and chromosomal aberrations compared to the WT cells in response to APG. Of note, the in vitro complex of enzyme assay indicated that APG induced increased topoisomerase I (Top1) covalent protein DNA complex in Rad54- / - cells compared to WT cells. Finally, these results were verified using the TK6 human lymphoblastoid cell line and it was demonstrated that, as for DT40 cells, Rad54 deficiency sensitized TK6 cells to APG. The present study demonstrated that Rad54 was involved in the repair of APG-induced DNA damage, which was associated with Top1 inhibition.
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Affiliation(s)
- Zilu Zhao
- Department of Pharmacology, Key Laboratory of Drug-Targeting and Drug Delivery Systems of the Education Ministry, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Xiaohua Wu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Fang He
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Cuifang Xiang
- Department of Pharmacology, Key Laboratory of Drug-Targeting and Drug Delivery Systems of the Education Ministry, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Xiaoyu Feng
- Department of Pharmacology, Key Laboratory of Drug-Targeting and Drug Delivery Systems of the Education Ministry, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Xin Bai
- Department of Pharmacology, Key Laboratory of Drug-Targeting and Drug Delivery Systems of the Education Ministry, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Xin Liu
- Department of Pharmacology, Key Laboratory of Drug-Targeting and Drug Delivery Systems of the Education Ministry, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Jingxia Zhao
- Department of Pharmacology, Key Laboratory of Drug-Targeting and Drug Delivery Systems of the Education Ministry, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Shunichi Takeda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Yong Qing
- Department of Pharmacology, Key Laboratory of Drug-Targeting and Drug Delivery Systems of the Education Ministry, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan 610041, P.R. China
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Zhang F, Yuan W, Li Z, Zhang Y, Ye Y, Li K, Ding Z, Chen Y, Cheng T, Wu Q, Tang Y, Song D. RNA-Seq-Based Whole Transcriptome Analysis of IPEC-J2 Cells During Swine Acute Diarrhea Syndrome Coronavirus Infection. Front Vet Sci 2020; 7:492. [PMID: 32903570 PMCID: PMC7438718 DOI: 10.3389/fvets.2020.00492] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 06/30/2020] [Indexed: 12/13/2022] Open
Abstract
The new emergence of swine acute diarrhea syndrome coronavirus (SADS-CoV) has resulted in high mortality in suckling pigs in China. To date, the transcriptional expression of host cells during SADS-CoV infection has not been documented. In this study, by means of RNA-Seq technology, we investigated the whole genomic expression profiles of intestinal porcine epithelial cells (IPEC-J2) infected with a SADS-CoV strain SADS-CoV-CH-FJWT-2018. A total of 24,676 genes were identified: 23,677 were known genes, and 999 were novel genes. A total of 1,897 differentially expressed genes (DEGs) were identified between SADS-CoV-infected and uninfected cells at 6, 24, and 48 h post infection (hpi). Of these, 1,260 genes were upregulated and 637 downregulated. A Gene Ontology enrichment analysis revealed that DEGs in samples from 6, 24, and 48 hpi were enriched in 79, 383, and 233 GO terms, respectively, which were mainly involved in immune system process, response to stimulus, signal transduction, and cytokine-cytokine receptor interactions. The 1,897 DEGs were mapped to 109 KEGG Ontology (KO) pathways classified into four main categories. Most of the DEGs annotated in the KEGG pathways were related to the immune system, infectious viral disease, and signal transduction. The mRNA of porcine serum amyloid A-3 protein (SAA3), an acute phase response protein, was significantly upregulated during the infection. Over-expressed SAA3 in IPEC-J2 cells drastically inhibited the replication of SADS-CoV, while under-expressed SAA3 promoted virus replication. To our knowledge, this is the first report on the profiles of gene expression of IPEC-J2 cells infected by SADS-CoV by means of RNA-Seq technology. Our results indicate that SADS-CoV infection significantly modified the host cell gene expression patterns, and the host cells responded in highly specific manners, including immune response, signal and cytokine transduction, and antiviral response. The findings provide important insights into the transcriptome of IPEC-J2 in SADS-CoV infection.
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Affiliation(s)
- Fanfan Zhang
- Key Laboratory for Animal Health of Jiangxi Province, Jiangxi Agricultural University, Nanchang, China.,Department of Preventive Veterinary Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China.,Institute of Animal Husbandry and Veterinary Medicine, Jiangxi Academy of Agricultural Sciences, Nanchang, China
| | - Weifeng Yuan
- Key Laboratory for Animal Health of Jiangxi Province, Jiangxi Agricultural University, Nanchang, China.,Department of Preventive Veterinary Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Zhiquan Li
- Key Laboratory for Animal Health of Jiangxi Province, Jiangxi Agricultural University, Nanchang, China.,Department of Preventive Veterinary Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Yuhan Zhang
- Key Laboratory for Animal Health of Jiangxi Province, Jiangxi Agricultural University, Nanchang, China.,Department of Preventive Veterinary Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Yu Ye
- Key Laboratory for Animal Health of Jiangxi Province, Jiangxi Agricultural University, Nanchang, China.,Department of Preventive Veterinary Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Kai Li
- Key Laboratory for Animal Health of Jiangxi Province, Jiangxi Agricultural University, Nanchang, China.,Department of Preventive Veterinary Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Zhen Ding
- Key Laboratory for Animal Health of Jiangxi Province, Jiangxi Agricultural University, Nanchang, China.,Department of Preventive Veterinary Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Yunyan Chen
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Ting Cheng
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Qiong Wu
- Key Laboratory for Animal Health of Jiangxi Province, Jiangxi Agricultural University, Nanchang, China.,Department of Preventive Veterinary Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Yuxin Tang
- Key Laboratory for Animal Health of Jiangxi Province, Jiangxi Agricultural University, Nanchang, China.,Department of Preventive Veterinary Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Deping Song
- Key Laboratory for Animal Health of Jiangxi Province, Jiangxi Agricultural University, Nanchang, China.,Department of Preventive Veterinary Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
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