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Chattopadhyay P, Mehta P, Soni J, Tardalkar K, Joshi M, Pandey R. Cell-specific housekeeping role of lncRNAs in COVID-19-infected and recovered patients. NAR Genom Bioinform 2024; 6:lqae023. [PMID: 38426128 PMCID: PMC10903533 DOI: 10.1093/nargab/lqae023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 02/06/2024] [Accepted: 02/16/2024] [Indexed: 03/02/2024] Open
Abstract
A plethora of studies have demonstrated the roles of lncRNAs in modulating disease severity and outcomes during infection. However, the spatio-temporal expression of these lncRNAs is poorly understood. In this study, we used single-cell RNA-seq to understand the spatio-temporal expression dynamics of lncRNAs across healthy, SARS-CoV-2-infected, and recovered individuals and their functional role in modulating the disease and recovery. We identified 203 differentially expressed lncRNAs, including cell type-specific ones like MALAT1, NEAT1, ZFAS1, SNHG7, SNHG8, and SNHG25 modulating immune function in classical monocyte, NK T, proliferating NK, plasmablast, naive, and activated B/T cells. Interestingly, we found invariant lncRNAs (no significant change in expression across conditions) regulating essential housekeeping functions (for example, HOTAIR, NRAV, SNHG27, SNHG28, and UCA1) in infected and recovered individuals. Despite similar repeat element abundance, variant lncRNAs displayed higher Alu content, suggesting increased interactions with proximal and distal genes, crucial for immune response modulation. The comparable repeat abundance but distinct expression levels of variant and invariant lncRNAs highlight the significance of investigating the regulatory mechanisms of invariant lncRNAs. Overall, this study offers new insights into the spatio-temporal expression patterns and functional roles of lncRNAs in SARS-CoV-2-infected and recovered individuals while highlighting the importance of invariant lncRNAs in the disease context.
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Affiliation(s)
- Partha Chattopadhyay
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi-110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Priyanka Mehta
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi-110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Jyoti Soni
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi-110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Kishore Tardalkar
- Department of Stem Cells & Regenerative Medicine, D.Y. Patil Education Society, Kadamwadi, Kolhapur-416003,Maharashtra, India
| | - Meghnad Joshi
- Department of Stem Cells & Regenerative Medicine, D.Y. Patil Education Society, Kadamwadi, Kolhapur-416003,Maharashtra, India
| | - Rajesh Pandey
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi-110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
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Buck AM, Deveau TM, Henrich TJ, Deitchman AN. Challenges in HIV-1 Latent Reservoir and Target Cell Quantification in CAR-T Cell and Other Lentiviral Gene Modifying HIV Cure Strategies. Viruses 2023; 15:1126. [PMID: 37243212 PMCID: PMC10222761 DOI: 10.3390/v15051126] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/03/2023] [Accepted: 05/06/2023] [Indexed: 05/28/2023] Open
Abstract
Gene-modification therapies are at the forefront of HIV-1 cure strategies. Chimeric antigen receptor (CAR)-T cells pose a potential approach to target infected cells during antiretroviral therapy or following analytical treatment interruption (ATI). However, there are technical challenges in the quantification of HIV-1-infected and CAR-T cells in the setting of lentiviral CAR gene delivery and also in the identification of cells expressing target antigens. First, there is a lack of validated techniques to identify and characterize cells expressing the hypervariable HIV gp120 in both ART-suppressed and viremic individuals. Second, close sequence homology between lentiviral-based CAR-T gene modification vectors and conserved regions of HIV-1 creates quantification challenges of HIV-1 and lentiviral vector levels. Consideration needs to be taken into standardizing HIV-1 DNA/RNA assays in the setting of CAR-T cell and other lentiviral vector-based therapies to avoid these confounding interactions. Lastly, with the introduction of HIV-1 resistance genes in CAR-T cells, there is a need for assays with single-cell resolution to determine the competence of the gene inserts to prevent CAR-T cells from becoming infected in vivo. As novel therapies continue to arise in the HIV-1 cure field, resolving these challenges in CAR-T-cell therapy will be crucial.
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Affiliation(s)
- Amanda M. Buck
- Division of Experimental Medicine, University of California San Francisco, San Francisco, CA 94110, USA
| | - Tyler-Marie Deveau
- Division of Experimental Medicine, University of California San Francisco, San Francisco, CA 94110, USA
| | - Timothy J. Henrich
- Division of Experimental Medicine, University of California San Francisco, San Francisco, CA 94110, USA
| | - Amelia N. Deitchman
- Department of Clinical Pharmacy, University of California San Francisco, San Francisco, CA 94110, USA
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Blackard JT, Davies SM, Laskin BL. BK polyomavirus diversity-Why viral variation matters. Rev Med Virol 2020; 30:e2102. [PMID: 32128960 DOI: 10.1002/rmv.2102] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 02/12/2020] [Accepted: 02/13/2020] [Indexed: 02/06/2023]
Abstract
BK polyomavirus (BKPyV or BKV) is a non-enveloped, circular double-stranded DNA virus that may exceed 80% seroprevalence in adults. BKV infection typically occurs during childhood, and the majority of adults are latently infected. While BKV infection is rarely associated with clinical disease in most individuals, in immunosuppressed individuals, reactivation may cause kidney (BK-associated nephropathy) or bladder (hemorrhagic cystitis and ureteral stenosis) injury. No antiviral therapies have been approved for the treatment of BKV infection. Reducing immunosuppression is the most effective therapy, although this is not feasible in many patients. Thus, a robust understanding of viral pathogenesis and viral diversity remains important for the development of future therapeutic strategies. Studies of BKV diversity are quite sparse compared to other common viral infections; thus, much of our understanding of BVK variability and evolution relies heavily analogous studies of other viruses such as HIV or viral hepatitis. We provide a comprehensive review of BKV diversity at the population and individual level with careful consideration of how viral variability may impact viral replication, pathogenesis, tropism, and protein function. We also discuss a number of outstanding questions related to BK virus diversity that should be explored rigorously in future studies.
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Affiliation(s)
- Jason T Blackard
- Division of Digestive Diseases, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Stella M Davies
- Division of Bone Marrow Transplantation and Immune Deficiency, Cincinnati Children's Hospital Medical Center and the Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Benjamin L Laskin
- Division of Nephrology, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
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Liu Y, Nonnemacher MR, Alexaki A, Pirrone V, Banerjee A, Li L, Kilareski E, Wigdahl B. Functional Studies of CCAAT/Enhancer Binding Protein Site Located Downstream of the Transcriptional Start Site. Clin Med Insights Pathol 2017; 10:1179555717694556. [PMID: 29162980 PMCID: PMC5692137 DOI: 10.1177/1179555717694556] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 09/20/2016] [Indexed: 12/13/2022] Open
Abstract
Previous studies have identified a CCAAT/enhancer binding protein (C/EBP) site located downstream of the transcriptional start site (DS3). The role of the DS3 element with respect to HIV-1 transactivation by Tat and viral replication has not been characterized. We have demonstrated that DS3 was a functional C/EBPβ binding site and mutation of this site to the C/EBP knockout DS3-9C variant showed lower HIV-1 long terminal repeat (LTR) transactivation by C/EBPβ. However, it was able to exhibit similar or even higher transcription levels by Tat compared to the parental LTR. C/EBPβ and Tat together further enhanced the transcription level of the parental LAI-LTR and DS3-9C LTR, with higher levels in the DS3-9C LTR. HIV molecular clone viruses carrying the DS3-9C variant LTR demonstrated a decreased replication capacity and delayed rate of replication. These results suggest that DS3 plays a role in virus transcriptional initiation and provides new insight into C/EBP regulation of HIV-1.
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Affiliation(s)
- Yujie Liu
- Department of Microbiology and Immunology, Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Michael R Nonnemacher
- Department of Microbiology and Immunology, Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Aikaterini Alexaki
- Department of Microbiology and Immunology, Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Vanessa Pirrone
- Department of Microbiology and Immunology, Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Anupam Banerjee
- Department of Microbiology and Immunology, Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Luna Li
- Department of Microbiology and Immunology, Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Evelyn Kilareski
- Department of Microbiology and Immunology, Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Brian Wigdahl
- Department of Microbiology and Immunology, Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, USA.,Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
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Hyun JC, Choi J, Jung YG, Yang S. Microfluidic cell concentrator with a reduced-deviation-flow herringbone structure. BIOMICROFLUIDICS 2017; 11:054108. [PMID: 29034052 PMCID: PMC5617731 DOI: 10.1063/1.5005612] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 09/19/2017] [Indexed: 05/11/2023]
Abstract
In this study, a microfluidic cell concentrator with a reduced-deviation-flow herringbone structure is proposed. The reduced-deviation-flow herringbone structure reduces the magnitude of deviation flow by a factor of 3.3 compared to the original herringbone structure. This structure shows higher recovery efficiency compared to the original herringbone structure for various particle sizes at high flow rate conditions. Using the reduced-deviation-flow herringbone structure, the experimental results show a recovery efficiency of 98.5% and a concentration factor of 3.4× at a flow rate of 100 ml/h for all particle sizes. An iterative concentration process is performed to achieve a higher concentration factor for 10.2-μm particles and Jurkat cells. With two stages of the concentration process, we were able to achieve over 98% recovery efficiency and a concentration factor of 10-11×. Cell viability was found to be above 96% after iterative concentration. We believe that this device could be used to concentrate cells as a preparatory step for studying low-abundance cells.
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Affiliation(s)
- Ji-Chul Hyun
- School of Mechanical Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 500-712, South Korea
| | - Jongchan Choi
- School of Mechanical Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 500-712, South Korea
| | - Yu-Gyung Jung
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 500-712, South Korea
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Weber J, Gibson RM, Sácká L, Strunin D, Hodek J, Weberová J, Pávová M, Alouani DJ, Asaad R, Rodriguez B, Lederman MM, Quiñones-Mateu ME. Impaired human immunodeficiency virus type 1 replicative fitness in atypical viremic non-progressor individuals. AIDS Res Ther 2017; 14:15. [PMID: 28331526 PMCID: PMC5359922 DOI: 10.1186/s12981-017-0144-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 03/15/2017] [Indexed: 01/15/2023] Open
Abstract
Background Progression rates from initial HIV-1 infection to advanced AIDS vary significantly among infected individuals. A distinct subgroup of HIV-1-infected individuals—termed viremic non-progressors (VNP) or controllers—do not seem to progress to AIDS, maintaining high CD4+ T cell counts despite high levels of viremia for many years. Several studies have evaluated multiple host factors, including immune activation, trying to elucidate the atypical HIV-1 disease progression in these patients; however, limited work has been done to characterize viral factors in viremic controllers. Methods We analyzed HIV-1 isolates from three VNP individuals and compared the replicative fitness, near full-length HIV-1 genomes and intra-patient HIV-1 genetic diversity with viruses from three typical (TP) and one rapid (RP) progressor individuals. Results Viremic non-progressors and typical patients were infected for >10 years (range 10–17 years), with a mean CD4+ T-cell count of 472 cells/mm3 (442–529) and 400 cells/mm3 (126–789), respectively. VNP individuals had a less marked decline in CD4+ cells (mean −0.56, range −0.4 to −0.7 CD4+/month) than TP patients (mean −10.3, −8.2 to −13.1 CD4+/month). Interestingly, VNP individuals carried viruses with impaired replicative fitness, compared to HIV-1 isolates from the TP and RP patients (p < 0.05, 95% CI). Although analyses of the near full-length HIV-1 genomes showed no clear patterns of single-nucleotide polymorphisms (SNP) that could explain the decrease in replicative fitness, both the number of SNPs and HIV-1 population diversity correlated inversely with the replication capacity of the viruses (r = −0.956 and r = −0.878, p < 0.01, respectively). Conclusion It is likely that complex multifactorial parameters govern HIV-1 disease progression in each individual, starting with the infecting virus (phenotype, load, and quasispecies diversity) and the intrinsic ability of the host to respond to the infection. Here we analyzed a subset of viremic controller patients and demonstrated that similar to the phenomenon observed in patients with a discordant response to antiretroviral therapy (i.e., high CD4+ cell counts with detectable plasma HIV-1 RNA load), reduced viral replicative fitness seems to be linked to slow disease progression in these antiretroviral-naïve individuals. Electronic supplementary material The online version of this article (doi:10.1186/s12981-017-0144-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jan Weber
- 0000 0001 1015 3316grid.418095.1Institute of Organic Chemistry and Biochemistry v.v.i., Academy of Sciences of the Czech Republic, Flemingovo n. 2, 166 10 Prague 6, Czech Republic
| | - Richard M Gibson
- 0000 0000 9149 4843grid.443867.aUniversity Hospital Translational Laboratory, University Hospitals Cleveland Medical Center, Cleveland, OH USA
| | - Lenka Sácká
- 0000 0001 1015 3316grid.418095.1Institute of Organic Chemistry and Biochemistry v.v.i., Academy of Sciences of the Czech Republic, Flemingovo n. 2, 166 10 Prague 6, Czech Republic
| | - Dmytro Strunin
- 0000 0001 1015 3316grid.418095.1Institute of Organic Chemistry and Biochemistry v.v.i., Academy of Sciences of the Czech Republic, Flemingovo n. 2, 166 10 Prague 6, Czech Republic
| | - Jan Hodek
- 0000 0001 1015 3316grid.418095.1Institute of Organic Chemistry and Biochemistry v.v.i., Academy of Sciences of the Czech Republic, Flemingovo n. 2, 166 10 Prague 6, Czech Republic
| | - Jitka Weberová
- 0000 0001 1015 3316grid.418095.1Institute of Organic Chemistry and Biochemistry v.v.i., Academy of Sciences of the Czech Republic, Flemingovo n. 2, 166 10 Prague 6, Czech Republic
| | - Marcela Pávová
- 0000 0001 1015 3316grid.418095.1Institute of Organic Chemistry and Biochemistry v.v.i., Academy of Sciences of the Czech Republic, Flemingovo n. 2, 166 10 Prague 6, Czech Republic
| | - David J Alouani
- 0000 0000 9149 4843grid.443867.aUniversity Hospital Translational Laboratory, University Hospitals Cleveland Medical Center, Cleveland, OH USA
| | - Robert Asaad
- 0000 0001 2164 3847grid.67105.35Department of Medicine, Case Western Reserve University/University Hospitals Cleveland Medical Center, 10900 Euclid Avenue, Cleveland, OH 44106-7288 USA
| | - Benigno Rodriguez
- 0000 0001 2164 3847grid.67105.35Department of Medicine, Case Western Reserve University/University Hospitals Cleveland Medical Center, 10900 Euclid Avenue, Cleveland, OH 44106-7288 USA
| | - Michael M Lederman
- 0000 0001 2164 3847grid.67105.35Department of Medicine, Case Western Reserve University/University Hospitals Cleveland Medical Center, 10900 Euclid Avenue, Cleveland, OH 44106-7288 USA
| | - Miguel E Quiñones-Mateu
- 0000 0000 9149 4843grid.443867.aUniversity Hospital Translational Laboratory, University Hospitals Cleveland Medical Center, Cleveland, OH USA ; 0000 0001 2164 3847grid.67105.35Department of Medicine, Case Western Reserve University/University Hospitals Cleveland Medical Center, 10900 Euclid Avenue, Cleveland, OH 44106-7288 USA ; 0000 0001 2164 3847grid.67105.35Department of Pathology, Case Western Reserve University, Cleveland, OH USA
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Yu X, He R, Li S, Cai B, Zhao L, Liao L, Liu W, Zeng Q, Wang H, Guo SS, Zhao XZ. Magneto-controllable capture and release of cancer cells by using a micropillar device decorated with graphite oxide-coated magnetic nanoparticles. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2013; 9:3895-3901. [PMID: 23650272 DOI: 10.1002/smll.201300169] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Revised: 03/05/2013] [Indexed: 06/02/2023]
Abstract
Aiming to highly efficient capture and analysis of circulating tumor cells, a micropillar device decorated with graphite oxide-coated magnetic nanoparticles is developed for magneto-controllable capture and release of cancer cells. Graphite oxide-coated, Fe3 O4 magnetic nanoparticles (MNPs) are synthesized by solution mixing and functionalized with a specific antibody, following by the immobilization of such modified MNPs on our designed micropillar device. For the proof-of-concept study, a HCT116 colorectal cancer cell line is employed to exam the capture efficiency. Under magnetic field manipulation, the high density packing of antibody-modified MNPs on the micropillars increases the local concentration of antibody, as well as the topographic interactions between cancer cells and micropillar surfaces. The flow rate and the micropillar geometry are optimized by studying their effects on capture efficiency. Then, a different number of HCT116 cells spiked in two kinds of cell suspension are investigated, yielding capture efficiency >70% in culture medium and >40% in blood sample, respectively. Moreover, the captured HCT116 cells are able to be released from the micropillars with a saturated efficiency of 92.9% upon the removal of applied magnetic field and it is found that 78% of the released cancer cells are viable, making them suitable for subsequent biological analysis.
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Affiliation(s)
- Xiaolei Yu
- Key Laboratory of Artificial Micro- and Nano-Structures of the Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, Hubei, China
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Wang J, Lv H, Xu L, Yang J, Yang Z, Wu N. Generation of Human Immunodeficiency Virus–1 Long Terminal Repeat Reporter Genes by Rapid Polymerase Chain Reaction–Mediated Mutagenesis. Lab Med 2013. [DOI: 10.1309/lmb66mq8jixdccqj] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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Ferraro GA, Monteiro-Cunha JP, Fernandes FM, Mota-Miranda AC, Brites C, Alcantara LC, Galvão-Castro B, Morgado MG. Molecular characterization of long terminal repeat sequences from Brazilian human immunodeficiency virus type 1 isolates. AIDS Res Hum Retroviruses 2013; 29:837-41. [PMID: 23153102 DOI: 10.1089/aid.2012.0326] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
HIV-1 provirus activation is under control of the long terminal repeat (LTR)-5' viral promoter region, which presents remarkable genetic variation among HIV-1 subtypes. It is possible that molecular features of the LTR contribute to the unusual profile of the subtype C epidemic in the Brazilian Southern region. To characterize the LTR of Brazilian HIV isolates, we analyzed sequences from 21 infected individuals from Porto Alegre and Salvador cities. Sequences were compared with subtype B and C reference strains from different countries. Phylogenetic analysis showed that 17 (81%) samples were subtype B and four (19%) were subtype C. Common patterns of transcription factor binding sites (TFBS) in subtypes B and C sequences were confirmed and other potential TFBS specific for subtype C were found. Brazilian subtype C sequences contained an additional NF-κB biding site, as previously described for the majority of subtype C isolates. The high level of LTR polymorphisms identified in this study might be important for viral fitness.
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Affiliation(s)
- Geraldo A. Ferraro
- Laboratório Avançado de Saúde Pública (LASP), Centro de Pesquisa Gonçalo Moniz (CPqGM), Fundação Oswaldo Cruz (FIOCRUZ), Salvador, Bahia, Brazil
- Fundação Bahiana para o Desenvolvimento das Ciências (FBDC), Escola Bahiana de Medicina e Saúde Pública (EBMSP), Salvador, Bahia, Brazil
| | - Joana P. Monteiro-Cunha
- Laboratório Avançado de Saúde Pública (LASP), Centro de Pesquisa Gonçalo Moniz (CPqGM), Fundação Oswaldo Cruz (FIOCRUZ), Salvador, Bahia, Brazil
- Fundação Bahiana para o Desenvolvimento das Ciências (FBDC), Escola Bahiana de Medicina e Saúde Pública (EBMSP), Salvador, Bahia, Brazil
- Universidade Federal da Bahia, Salvador, Bahia, Brazil
| | - Flora M.C. Fernandes
- Laboratório Avançado de Saúde Pública (LASP), Centro de Pesquisa Gonçalo Moniz (CPqGM), Fundação Oswaldo Cruz (FIOCRUZ), Salvador, Bahia, Brazil
- Fundação Bahiana para o Desenvolvimento das Ciências (FBDC), Escola Bahiana de Medicina e Saúde Pública (EBMSP), Salvador, Bahia, Brazil
- Universidade Federal da Bahia, Salvador, Bahia, Brazil
| | - Aline C.A. Mota-Miranda
- Laboratório Avançado de Saúde Pública (LASP), Centro de Pesquisa Gonçalo Moniz (CPqGM), Fundação Oswaldo Cruz (FIOCRUZ), Salvador, Bahia, Brazil
- Fundação Bahiana para o Desenvolvimento das Ciências (FBDC), Escola Bahiana de Medicina e Saúde Pública (EBMSP), Salvador, Bahia, Brazil
- Universidade Federal da Bahia, Salvador, Bahia, Brazil
| | - Carlos Brites
- Universidade Federal da Bahia, Salvador, Bahia, Brazil
| | - Luiz C.J. Alcantara
- Laboratório Avançado de Saúde Pública (LASP), Centro de Pesquisa Gonçalo Moniz (CPqGM), Fundação Oswaldo Cruz (FIOCRUZ), Salvador, Bahia, Brazil
- Fundação Bahiana para o Desenvolvimento das Ciências (FBDC), Escola Bahiana de Medicina e Saúde Pública (EBMSP), Salvador, Bahia, Brazil
| | - Bernardo Galvão-Castro
- Laboratório Avançado de Saúde Pública (LASP), Centro de Pesquisa Gonçalo Moniz (CPqGM), Fundação Oswaldo Cruz (FIOCRUZ), Salvador, Bahia, Brazil
- Fundação Bahiana para o Desenvolvimento das Ciências (FBDC), Escola Bahiana de Medicina e Saúde Pública (EBMSP), Salvador, Bahia, Brazil
| | - Mariza G. Morgado
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz/FIOCRUZ, Rio de Janeiro, RJ, Brazil
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Liu Y, Nonnemacher MR, Stauff DL, Li L, Banerjee A, Irish B, Kilareski E, Rajagopalan N, Suchitra JB, Khan ZK, Ranga U, Wigdahl B. Structural and functional studies of CCAAT/enhancer binding sites within the human immunodeficiency virus type 1 subtype C LTR. Biomed Pharmacother 2010; 64:672-80. [PMID: 20970301 DOI: 10.1016/j.biopha.2010.09.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2010] [Accepted: 09/05/2010] [Indexed: 11/17/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) subtype C, which is most predominant in sub-Saharan Africa as well as in Asia and India, is the most prevalent subtype worldwide. A large number of transcription factor families have been shown to be involved in regulating HIV-1 gene expression in T lymphocytes and cells of the monocyte-macrophage lineage. Among these, proteins of the CCAAT/enhancer binding protein (C/EBP) family are of particular importance in regulating HIV-1 gene expression within cells of the monocytic lineage during the course of hematologic development and cellular activation. Few studies have examined the role of C/EBPs in long terminal repeat (LTR)-directed viral gene expression of HIV-1 subtypes other than subtype B. Within subtype B viruses, two functional C/EBP sites located upstream of the TATA box are required for efficient viral replication in cells of the monocyte-macrophage lineage. We report the identification of three putative subtype C C/EBP sites, upstream site 1 and 2 (C-US1 and C-US2) and downstream site 1 (C-DS1). C-US1 and C-DS1 were shown to form specific DNA-protein complexes with members of the C/EBP family (C/EBPα, β, and δ). Functionally, within the U-937 monocytic cell line, subtype B and C LTRs were shown to be equally responsive to C/EBPβ-2, although the basal activity of subtype C LTRs appeared to be higher. Furthermore, the synergistic interaction between C/EBPβ-2 and Tat with the subtype C LTR was also observed in U-937 cells as previously demonstrated with the subtype B LTR.
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Affiliation(s)
- Yujie Liu
- Department of Microbiology and Immunology, Drexel University College of Medicine, 2900 Queen Lane, Philadelphia, Pennsylvania 19129, USA
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Dharmasiri U, Witek MA, Adams AA, Soper SA. Microsystems for the capture of low-abundance cells. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2010; 3:409-31. [PMID: 20636049 DOI: 10.1146/annurev.anchem.111808.073610] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Efficient selection and enumeration of low-abundance biological cells are highly important in a variety of applications. For example, the clinical utility of circulating tumor cells (CTCs) in peripheral blood is recognized as a viable biomarker for the management of various cancers, in which the clinically relevant number of CTCs per 7.5 ml of blood is two to five. Although there are several methods for isolating rare cells from a variety of heterogeneous samples, such as immunomagnetic-assisted cell sorting and fluorescence-activated cell sorting, they are fraught with challenges. Microsystem-based technologies are providing new opportunities for selecting and isolating rare cells from complex, heterogeneous samples. Such approaches involve reductions in target-cell loss, process automation, and minimization of contamination issues. In this review, we introduce different application areas requiring rare cell analysis, conventional techniques for their selection, and finally microsystem approaches for low-abundance-cell isolation and enumeration.
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Affiliation(s)
- Udara Dharmasiri
- Departments of Chemistry, Louisiana State University, Baton Rouge, 70803, USA.
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A sequence similar to tRNA 3 Lys gene is embedded in HIV-1 U3-R and promotes minus-strand transfer. Nat Struct Mol Biol 2009; 17:83-9. [PMID: 19966801 PMCID: PMC2802660 DOI: 10.1038/nsmb.1687] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2009] [Accepted: 09/04/2009] [Indexed: 11/21/2022]
Abstract
We identified a sequence embedded in the U3/R region of HIV-1 RNA that is highly complementary to human tRNA3Lys. The free energy of annealing to tRNA3Lys is significantly lower for this sequence and the primer-binding site than for other similar length viral sequences. The only interruption in complementarity is a 29-nucleotide segment inserted where a tRNA intron would be expected. The insert contains the TATA box for viral RNA transcription. The embedded sequence includes a nine-nucleotide segment previously reported to aid minus strand transfer by binding the primer tRNA3Lys. Reconstituting transfer in vitro, we show that including segments from the embedded sequence in the acceptor template, beyond the nine nucleotides, further increases transfer efficiency. We propose that a tRNA3Lys gene was incorporated during HIV-1 evolution and retained largely intact because of its roles in transcription and strand transfer.
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Rouet F, Ménan H, Viljoen J, Ngo-Giang-Huong N, Mandaliya K, Valéa D, Lien TX, Danaviah S, Rousset D, Ganon A, Nerrienet E. In-house HIV-1 RNA real-time RT-PCR assays: principle, available tests and usefulness in developing countries. Expert Rev Mol Diagn 2009; 8:635-50. [PMID: 18785811 DOI: 10.1586/14737159.8.5.635] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The principle of currently available licensed HIV-1 RNA assays is based on real-time technologies that continuously monitor the fluorescence emitted by the amplification products. Besides these assays, in-house quantitative (q) real-time reverse transcription (RT)-PCR (RT-qPCR) tests have been developed and evaluated particularly in developing countries, for two main reasons. First, affordable and generalized access to HIV-1 RNA viral load is urgently needed in the context of expected universal access to prevention and antiretroviral treatment programs in these settings. Second, since many non-B subtypes, circulating recombinant forms and unique recombinant forms circulate in these areas, in-house HIV-1 RNA RT-qPCR assays are ideal academic tools to thoroughly evaluate the impact of HIV-1 genetic diversity on the accuracy of HIV-1 RNA quantification, as compared with licensed techniques. To date, at least 15 distinct in-house assays have been designed. They differ by their chemistry and the HIV-1 target sequence (located in gag, Pol-IN or LTR gene). Analytical performances of the tests that have been extensively evaluated appear at least as good as (or even better than) those of approved assays, with regard to HIV-1 strain diversity. Their clinical usefulness has been clearly demonstrated for early diagnosis of pediatric HIV-1 infection and monitoring of highly active antiretroviral therapy efficacy. The LTR-based HIV-1 RNA RT-qPCR assay has been evaluated by several groups under the auspices of the Agence Nationale de Recherches sur le SIDA et les hépatites virales B et C. It exists now as a complete standardized commercial test.
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Affiliation(s)
- François Rouet
- Laboratoire de Virologie, Centre Muraz, BP390 Bobo-Dioulasso 01, Burkina Faso.
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Rodriguez MA, Shen C, Ratner D, Paranjape RS, Kulkarni SS, Chatterjee R, Gupta P. Genetic and functional characterization of the LTR of HIV-1 subtypes A and C circulating in India. AIDS Res Hum Retroviruses 2007; 23:1428-33. [PMID: 18184086 DOI: 10.1089/aid.2007.0152] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Genetic analysis of HIV-1 sequences circulating in different parts of India have shown that the predominant proportion of HIV-1 subtypes circulating in India is type C and a small fraction are subtypes A, B, E, and CRFs. We sequenced the HIV-1 LTR promoter region of seven subtype C and five subtype A isolates obtained from two major cities in India. Sequence analysis of the complete promoter and TAR regions revealed conserved subtype-specific variability in several major binding sites. Three NF-kappaB sites were present in all subtype C isolates and two isolates contained an insertion in the MFNLP. The transcriptional activity of one of these isolates may have been hindered due to this insertion. Despite the apparent variability between the LTRs we did not observe any significant difference in the transcriptional activity between subtype C and subtype A. To our knowledge, this is the first study characterizing the genetic structure and functional attributes of subtype A LTRs from India.
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Affiliation(s)
- Milka A. Rodriguez
- Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania 15261
| | - Chengli Shen
- Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania 15261
| | - Deena Ratner
- Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania 15261
| | | | | | - Ramdas Chatterjee
- Department of Virology, Chittaranjan Cancer Research Institute, Calcutta, India
| | - Phalguni Gupta
- Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania 15261
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