1
|
Determination of HIV Tropism in Patients with Antiretroviral Therapy Failure in Arkhangelsk Region. PROBLEMS OF PARTICULARLY DANGEROUS INFECTIONS 2022. [DOI: 10.21055/0370-1069-2022-3-120-128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The aim of the study was to determine the tropism of the human immunodeficiency virus in patients with virological failure of antiretroviral therapy (ART) from the Arkhangelsk Region based on the analysis of the env gene V3 loop nucleotide sequence.Materials and methods. We used blood plasma samples obtained from 76 HIV-infected persons from the Arkhangelsk Region with virological failure of antiretroviral therapy. The nucleotide sequences of the HIV env gene C2-V3-C3 region were studied by PCR followed by sequencing. The genotype of the studied strains was determined based on the analysis of their phylogenetic relations with reference sequences from the international GenBank database, as well as using specialized programs. To predict viral tropism, the Garrido rule and the online bioinformatic tool Geno2Pheno[coreceptor] were used. The Geno2Pheno[coreceptor] algorithm, determines the false positive rate (FPR) based on the analysis of the env gene V3 loop nucleotide sequence. Results and discussion. Significantly lower representation of R5X4/X4-tropic HIV variants in long-term infected persons with subsubtype A6 virus compared to subtype B virus has been shown. For all FPR cut-off algorithms, a significant correlation between subtype and HIV tropism was observed (p=0.0014 and p=0.013 for FPR 10 % and FPR 20 %, respectively). While among subtype B strains, at least 57 % were identified as R5X4/X4-tropic variants (for an FPR of 10 %), including two strains classified as X4-tropic; among HIV subsubtype A6 even at an FPR of 20 %, the frequency of R5X4/X4-tropic samples only slightly exceeded 22 %. It can be assumed that the dynamics of changes in HIV tropism depends on the virus subtype. Significant differences in the distribution of amino acid residues of the V3 region sequences in the examined group between R5-tropic and R5X4/X4-tropic strains of subsubtype A6 for positions 18 (χ2=7.616, p=0.0058), 21 (χ2=7.281, p=0.007), 24 (χ2=5.587, p=0.0181), and 34 (χ2=5.144, p=0.0233) have been demonstrated. Among the R5X4/X4-tropic strains of the A6 subsubtype, amino acid substitutions were registered at positions 6, 19, 21, 26, 29, 30, which were not found in the R5-tropic A6 strains. The high occurrence frequency of a number of mutations previously described as presumably associated with resistance to maraviroc and similar drugs may indicate a natural polymorphism characteristic of the A6 subsubtype, which does not correlate with resistance to CCR5 co-receptor antagonists.
Collapse
|
2
|
Jadhav S, Yenorkar N, Bondre R, Karemore M, Bali N. Nanomedicines encountering HIV dementia: A guiding star for neurotherapeutics. J Drug Deliv Sci Technol 2022. [DOI: 10.1016/j.jddst.2022.103315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
3
|
Lewis ME, Simpson P, Mori J, Jubb B, Sullivan J, McFadyen L, van der Ryst E, Craig C, Robertson DL, Westby M. V3-Loop genotypes do not predict maraviroc susceptibility of CCR5-tropic virus or clinical response through week 48 in HIV-1-infected, treatment-experienced persons receiving optimized background regimens. Antivir Chem Chemother 2021; 29:20402066211030380. [PMID: 34343443 PMCID: PMC8369958 DOI: 10.1177/20402066211030380] [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: 11/16/2022] Open
Abstract
Viruses from 15 of 35 maraviroc-treated participants with virologic failure and CCR5-tropic (R5) virus in the MOTIVATE studies at Week 24 had reduced maraviroc susceptibility. On-treatment amino acid changes were observed in the viral envelope glycoprotein 120 third variable (V3)-loop stems and tips and differed between viruses. No amino acid change reliably predicted reduced susceptibility, indicating that resistance was genetic context-dependent. Through Week 24, poor adherence was associated with maraviroc-susceptible virologic failure, whereas reduced maraviroc susceptibility was associated with suboptimal background regimen activity, highlighting the importance of overall regimen activity and good adherence. Predictive values of pretreatment V3-loop sequences containing these Week 24 mutations or other variants present at >3% in pretreatment viruses of participants with virologic failure at Week 48 were retrospectively assessed. Week 48 clinical outcomes were evaluated for correlates with pretreatment V3-loop CCR5-tropic sequences from 704 participants (366 responders; 338 virologic failures [83 with R5 virus with maraviroc susceptibility assessment]). Seventy-five amino acid variants with >3% prevalence were identified among 23 V3-loop residues. Previously identified variants associated with resistance in individual isolates were represented, but none were associated reliably with virologic failure alone or in combination. Univariate analysis showed virologic-failure associations with variants 4L, 11R, and 19S (P < 0.05). However, 11R is a marker for CXCR4 tropism, whereas neither 4L nor 19S was reliably associated with reduced maraviroc susceptibility in R5 failure. These findings from a large study of V3-loop sequences confirm lack of correlation between V3-loop genotype and clinical outcome in participants treated with maraviroc.Clinical trial registration numbers (ClinicalTrials.gov): NCT00098306 and NCT00098722.
Collapse
Affiliation(s)
- M E Lewis
- Pfizer Global Research and Development, Sandwich Labs, Sandwich, Kent, UK.,The Research Network Ltd, Sandwich, Kent, UK
| | - P Simpson
- Pfizer Global Research and Development, Sandwich Labs, Sandwich, Kent, UK.,AstraZeneca, Cambridge, UK
| | - J Mori
- Pfizer Global Research and Development, Sandwich Labs, Sandwich, Kent, UK.,hVIVO, Queen Mary BioEnterprise Innovation Centre, London, UK
| | - B Jubb
- Pfizer Global Research and Development, Sandwich Labs, Sandwich, Kent, UK
| | - J Sullivan
- Pfizer Global Research and Development, Sandwich Labs, Sandwich, Kent, UK.,Cytel, London, UK
| | - L McFadyen
- Pfizer Inc, Pharmacometrics, Sandwich, UK
| | - E van der Ryst
- Pfizer Global Research and Development, Sandwich Labs, Sandwich, Kent, UK.,The Research Network Ltd, Sandwich, Kent, UK
| | - C Craig
- Pfizer Global Research and Development, Sandwich Labs, Sandwich, Kent, UK.,The Research Network Ltd, Sandwich, Kent, UK
| | - D L Robertson
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - M Westby
- Pfizer Global Research and Development, Sandwich Labs, Sandwich, Kent, UK.,Centauri Therapeutics Limited, Discovery Park, Kent, UK
| |
Collapse
|
4
|
The Evolution of Dendritic Cell Immunotherapy against HIV-1 Infection: Improvements and Outlook. J Immunol Res 2020; 2020:9470102. [PMID: 32537473 PMCID: PMC7267878 DOI: 10.1155/2020/9470102] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 04/28/2020] [Indexed: 12/18/2022] Open
Abstract
Dendritic cells (DC) are key phagocytic cells that play crucial roles in both the innate and adaptive immune responses against the human immunodeficiency virus type 1 (HIV-1). By processing and presenting pathogen-derived antigens, dendritic cells initiate a directed response against infected cells. They activate the adaptive immune system upon recognition of pathogen-associated molecular patterns (PAMPs) on infected cells. During the course of HIV-1 infection, a successful adaptive (cytotoxic CD8+ T-cell) response is necessary for preventing the progression and spread of infection in a variety of cells. Dendritic cells have thus been recognized as a valuable tool in the development of immunotherapeutic approaches and vaccines effective against HIV-1. The advancements in dendritic cell vaccines in cancers have paved the way for applications of this form of immunotherapy to HIV-1 infection. Clinical trials with patients infected with HIV-1 who are well-suppressed by antiretroviral therapy (ART) were recently performed to assess the efficacy of DC vaccines, with the goal of mounting an HIV-1 antigen-specific T-cell response, ideally to clear infection and eliminate the need for long-term ART. This review summarizes and compares methods and efficacies of a number of DC vaccine trials utilizing autologous dendritic cells loaded with HIV-1 antigens. The potential for advancement and novel strategies of improving efficacy of this type of immunotherapy is also discussed.
Collapse
|
5
|
Abstract
Human immunodeficiency virus (HIV)-associated neurocognitive disorders (HAND) remain a common end-organ manifestation of viral infection. Subclinical and mild symptoms lead to neurocognitive and behavioral abnormalities. These are associated, in part, with viral penetrance and persistence in the central nervous system. Infections of peripheral blood monocytes, macrophages, and microglia are the primary drivers of neuroinflammation and neuronal impairments. While current antiretroviral therapy (ART) has reduced the incidence of HIV-associated dementia, milder forms of HAND continue. Depression, comorbid conditions such as infectious liver disease, drugs of abuse, antiretroviral drugs themselves, age-related neurodegenerative diseases, gastrointestinal maladies, and concurrent social and economic issues can make accurate diagnosis of HAND challenging. Increased life expectancy as a result of ART clearly creates this variety of comorbid conditions that often blur the link between the virus and disease. With the discovery of novel biomarkers, neuropsychologic testing, and imaging techniques to better diagnose HAND, the emergence of brain-penetrant ART, adjunctive therapies, longer life expectancy, and better understanding of disease pathogenesis, disease elimination is perhaps a realistic possibility. This review focuses on HIV-associated disease pathobiology with an eye towards changing trends in the face of widespread availability of ART.
Collapse
|
6
|
Sojane K, Kangethe RT, Chang CC, Moosa MYS, Lewin SR, French MA, Ndung'u T. Individuals with HIV-1 Subtype C Infection and Cryptococcal Meningitis Exhibit Viral Genetic Intermixing of HIV-1 Between Plasma and Cerebrospinal Fluid and a High Prevalence of CXCR4-Using Variants. AIDS Res Hum Retroviruses 2018; 34:607-620. [PMID: 29658309 DOI: 10.1089/aid.2017.0209] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The genotypic properties of human immunodeficiency virus type 1 (HIV-1) subtype C in individuals presenting with cryptococcal meningitis (CM) are not well established. Employing single-genome amplification as well as bulk PCR, cloning and sequencing strategies, we evaluated the genetic properties of HIV-1 subtype C env in 16 antiretroviral therapy-naive study participants with CM. Eleven of the 16 participants had matched blood plasma and cerebrospinal fluid (CSF) evaluated, with the rest having either a plasma or CSF sample evaluated. Before antiretroviral therapy initiation, matched plasma and CSF-derived env sequences of all 11 participants displayed genetic intermixing between the two compartments. Overall, 7 of the 16 (∼43.8%) participants harbored CXCR4-using variants in plasma and/or CSF, according to coreceptor usage prediction algorithms. This study suggests that HIV-1 subtype C genetic intermixing between peripheral blood and the central nervous system is common in individuals presenting with CM, and that CXCR4 usage is present in one or both compartments in approximately 44% of individuals.
Collapse
Affiliation(s)
- Katlego Sojane
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Richard T. Kangethe
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Christina C. Chang
- Department of Infectious Diseases, Alfred Hospital and Monash University, Melbourne, Australia
| | - Mahomed-Yunus S. Moosa
- Department of Infectious Diseases, King Edward VIII Hospital, University of KwaZulu-Natal, Durban, South Africa
| | - Sharon R. Lewin
- Department of Infectious Diseases, Alfred Hospital and Monash University, Melbourne, Australia
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, Melbourne, Australia
| | - Martyn A. French
- Medical School and School of Biomedical Sciences, University of Western Australia, Perth, Australia
- Department of Clinical Immunology, Royal Perth Hospital and PathWest Laboratory Medicine, Perth, Australia
| | - Thumbi Ndung'u
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Africa Health Research Institute, Durban, South Africa
- Ragon Institute of MGH, MIT and Harvard University, Cambridge, Massachusetts
- Max Planck Institute for Infection Biology, Berlin, Germany
| |
Collapse
|
7
|
Eckstrand CD, Sparger EE, Murphy BG. Central and peripheral reservoirs of feline immunodeficiency virus in cats: a review. J Gen Virol 2017; 98:1985-1996. [DOI: 10.1099/jgv.0.000866] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- Chrissy D. Eckstrand
- Veterinary Microbiology and Pathology, College of Veterinary Medicine, 4003 Animal Disease Biotechnology Facility, Washington State University, Pullman, WA 99163, USA
| | - Ellen E. Sparger
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, 3115 Tupper Hall, Davis, CA 95616, USA
| | - Brian G. Murphy
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, 4206 Vet Med 3A, University of California, Davis, CA 95616, USA
| |
Collapse
|
8
|
Evidence of Divergent Amino Acid Usage in Comparative Analyses of R5- and X4-Associated HIV-1 Vpr Sequences. Int J Genomics 2017; 2017:4081585. [PMID: 28620613 PMCID: PMC5460428 DOI: 10.1155/2017/4081585] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 03/20/2017] [Indexed: 11/25/2022] Open
Abstract
Vpr is an HIV-1 accessory protein that plays numerous roles during viral replication, and some of which are cell type dependent. To test the hypothesis that HIV-1 tropism extends beyond the envelope into the vpr gene, studies were performed to identify the associations between coreceptor usage and Vpr variation in HIV-1-infected patients. Colinear HIV-1 Env-V3 and Vpr amino acid sequences were obtained from the LANL HIV-1 sequence database and from well-suppressed patients in the Drexel/Temple Medicine CNS AIDS Research and Eradication Study (CARES) Cohort. Genotypic classification of Env-V3 sequences as X4 (CXCR4-utilizing) or R5 (CCR5-utilizing) was used to group colinear Vpr sequences. To reveal the sequences associated with a specific coreceptor usage genotype, Vpr amino acid sequences were assessed for amino acid diversity and Jensen-Shannon divergence between the two groups. Five amino acid alphabets were used to comprehensively examine the impact of amino acid substitutions involving side chains with similar physiochemical properties. Positions 36, 37, 41, 89, and 96 of Vpr were characterized by statistically significant divergence across multiple alphabets when X4 and R5 sequence groups were compared. In addition, consensus amino acid switches were found at positions 37 and 41 in comparisons of the R5 and X4 sequence populations. These results suggest an evolutionary link between Vpr and gp120 in HIV-1-infected patients.
Collapse
|
9
|
Maubert ME, Wigdahl B, Nonnemacher MR. Opinion: Inhibition of Blood-Brain Barrier Repair as a Mechanism in HIV-1 Disease. Front Neurosci 2017; 11:228. [PMID: 28491017 PMCID: PMC5405129 DOI: 10.3389/fnins.2017.00228] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 04/05/2017] [Indexed: 12/22/2022] Open
Affiliation(s)
- Monique E Maubert
- Department of Microbiology and Immunology, and Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of MedicinePhiladelphia, PA, USA
| | - Brian Wigdahl
- Department of Microbiology and Immunology, and Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of MedicinePhiladelphia, PA, USA.,Sidney Kimmel Cancer Center, Thomas Jefferson UniversityPhiladelphia, PA, USA
| | - Michael R Nonnemacher
- Department of Microbiology and Immunology, and Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of MedicinePhiladelphia, PA, USA
| |
Collapse
|
10
|
Wei XM, Xu HF, Cheng XD, Bu N, Zhou HZ. Position 22 of the V3 loop is associated with HIV infectivity. Arch Virol 2016; 162:637-643. [PMID: 27815696 DOI: 10.1007/s00705-016-3138-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 10/28/2016] [Indexed: 11/29/2022]
Abstract
Human immunodeficiency virus subtype 1B (HIV-1B) binds to the CD4 receptor and co-receptor CCR5 or CXCR4 to enter T lymphocytes. The amino acid sequence of the HIV envelope glycoprotein V3 region determines the co-receptor tropism, thereby influencing the infectivity of the virus. Our research group previously found that the amino acid at position 22 of the V3 region may affect the infectivity of the virus, and in this study, we tested this hypothesis. We constructed pseudoviruses by changing the amino acids at position 22 of the V3 region in CCR5-tropic and CXCR4-tropic viruses and tested their infectivity. When the amino acid at V3 position 22 was altered in the CCR5- and CXCR4-tropic viruses, their ability to infect cells decreased to 20.6% and 17.14%, respectively. Therefore, we propose that residue 22 in the V3 region of subtype HIV-1B significantly influences the infectivity of the virus.
Collapse
Affiliation(s)
- Xue-Mei Wei
- Department of Laboratory Diagnosis, the First Affiliated Hospital of Harbin Medical University, 23 Youzheng Street, Nangang District, Harbin, Heilongjiang, 150001, People's Republic of China
| | - Hua-Feng Xu
- Department of Laboratory Diagnosis, Heilongjiang Provincial Hospital, Harbin, Heilongjiang, 150081, People's Republic of China
| | - Xue-Di Cheng
- Department of Laboratory Diagnosis, the First Affiliated Hospital of Harbin Medical University, 23 Youzheng Street, Nangang District, Harbin, Heilongjiang, 150001, People's Republic of China
| | - Nan Bu
- Department of Digestive Medicine, Jiamusi Central Hospital, Jiamusi, Heilongjiang, 154002, People's Republic of China
| | - Hai-Zhou Zhou
- Department of Laboratory Diagnosis, the First Affiliated Hospital of Harbin Medical University, 23 Youzheng Street, Nangang District, Harbin, Heilongjiang, 150001, People's Republic of China.
| |
Collapse
|
11
|
Dampier W, Antell GC, Aiamkitsumrit B, Nonnemacher MR, Jacobson JM, Pirrone V, Zhong W, Kercher K, Passic S, Williams JW, James T, Devlin KN, Giovannetti T, Libon DJ, Szep Z, Ehrlich GD, Wigdahl B, Krebs FC. Specific amino acids in HIV-1 Vpr are significantly associated with differences in patient neurocognitive status. J Neurovirol 2016; 23:113-124. [PMID: 27400931 DOI: 10.1007/s13365-016-0462-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 06/05/2016] [Accepted: 06/09/2016] [Indexed: 11/26/2022]
Abstract
Even in the era of combination antiretroviral therapies used to combat human immunodeficiency virus type 1 (HIV-1) infection, up to 50 % of well-suppressed HIV-1-infected patients are still diagnosed with mild neurological deficits referred to as HIV-associated neurocognitive disorders (HAND). The multifactorial nature of HAND likely involves the HIV-1 accessory protein viral protein R (Vpr) as an agent of neuropathogenesis. To investigate the effect of naturally occurring variations in Vpr on HAND in well-suppressed HIV-1-infected patients, bioinformatic analyses were used to correlate peripheral blood-derived Vpr sequences with patient neurocognitive performance, as measured by comprehensive neuropsychological assessment and the resulting Global Deficit Score (GDS). Our studies revealed unique associations between GDS and the presence of specific amino acid changes in peripheral blood-derived Vpr sequences [neuropsychological impairment Vpr (niVpr) variants]. Amino acids N41 and A55 in the Vpr sequence were associated with more pronounced neurocognitive deficits (higher GDS). In contrast, amino acids I37 and S41 were connected to measurably lower GDS. All niVpr variants were also detected in DNA isolated from HIV-1-infected brain tissues. The implication of these results is that niVpr variants alter the genesis and/or progression of HAND through differences in Vpr-mediated effects in the peripheral blood and/or the brain.
Collapse
Affiliation(s)
- Will Dampier
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, USA
- School of Biomedical Engineering, Science, and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Gregory C Antell
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, USA
- School of Biomedical Engineering, Science, and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Benjamas Aiamkitsumrit
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
- 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, Drexel University College of Medicine, Philadelphia, PA, USA
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Jeffrey M Jacobson
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
- Department of Medicine, Division of Infectious Diseases and HIV Medicine, Drexel University College of Medicine, Philadelphia, PA, USA
- Center for Clinical and Translational Medicine, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, USA
- Department of Medicine, Section of Infectious Disease, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA
| | - Vanessa Pirrone
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Wen Zhong
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Katherine Kercher
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Shendra Passic
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Jean W Williams
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Tony James
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Kathryn N Devlin
- Department of Psychology, Temple University, Philadelphia, PA, USA
| | | | - David J Libon
- Department of Geriatrics and Gerontology, New Jersey Institute for Successful Aging, School of Osteopathic Medicine, Rowan University, Stratford, NJ, USA
| | - Zsofia Szep
- Department of Medicine, Division of Infectious Diseases and HIV Medicine, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Garth D Ehrlich
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, USA
- Center for Advanced Microbial Processing, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Brian Wigdahl
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
- 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
| | - Fred C Krebs
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA.
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, USA.
| |
Collapse
|
12
|
Dimonte S. Different HIV-1 env frames: gp120 and ASP (antisense protein) biosynthesis, and theirs co-variation tropic amino acid signatures in X4- and R5-viruses. J Med Virol 2016; 89:112-122. [PMID: 27328810 DOI: 10.1002/jmv.24611] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/20/2016] [Indexed: 11/07/2022]
Abstract
Antisense protein (ASP) is the new actor of viral life of Human Immunodeficiency Virus type 1 (HIV-1) although proposed above 20 years ago. The asp ORF is into complementary strand of the gp120/gp41 junction of env gene. The ASP biological role remains little known. Knowing the Env markers of viral tropism, a dataset of sequences (660 strains) was used to analyze the hypothetical ASP involvement in CCR5 (R5) and/or CXCR4 (X4) co-receptor interaction. Preliminarily, prevalence of ASP and gp120V3 mutations was performed; following association among mutations were elaborate. The classical V3 tropic-signatures were confirmed, and 36 R5- and 22 X4-tropic ASP mutations were found. Moreover, by analyzing the ASP sequences, 36 out of 179 amino acid positions significantly associated with different co-receptor usage were found. Several statistically significant associations between gp120V3 and ASP mutations were observed. The dendrogram showed the existence of a cluster associated with R5-usage and a large cluster associated with X4-usage. These results show that gp120V3 and specific amino acid changes in ASP are associated together with CXCR4 and/or CCR5-usage. These findings implement previous observations on unclear ASP functions. J. Med. Virol. 89:112-122, 2017. © 2016 Wiley Periodicals, Inc.
Collapse
|
13
|
Dampier W, Nonnemacher MR, Mell J, Earl J, Ehrlich GD, Pirrone V, Aiamkitsumrit B, Zhong W, Kercher K, Passic S, Williams JW, Jacobson JM, Wigdahl B. HIV-1 Genetic Variation Resulting in the Development of New Quasispecies Continues to Be Encountered in the Peripheral Blood of Well-Suppressed Patients. PLoS One 2016; 11:e0155382. [PMID: 27195985 PMCID: PMC4873138 DOI: 10.1371/journal.pone.0155382] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 04/27/2016] [Indexed: 12/04/2022] Open
Abstract
As a result of antiretroviral therapeutic strategies, human immunodeficiency virus type 1 (HIV-1) infection has become a long-term clinically manageable chronic disease for many infected individuals. However, despite this progress in therapeutic control, including undetectable viral loads and CD4+ T-cell counts in the normal range, viral mutations continue to accumulate in the peripheral blood compartment over time, indicating either low level reactivation and/or replication. Using patients from the Drexel Medicine CNS AIDS Research and Eradication Study (CARES) Cohort, whom have been sampled longitudinally for more than 7 years, genetic change was modeled against to the dominant integrated proviral quasispecies with respect to selection pressures such as therapeutic interventions, AIDS defining illnesses, and other factors. Phylogenetic methods based on the sequences of the LTR and tat exon 1 of the HIV-1 proviral DNA quasispecies were used to obtain an estimate of an average mutation rate of 5.3 nucleotides (nt)/kilobasepair (kb)/year (yr) prior to initiation of antiretroviral therapy (ART). Following ART the baseline mutation rate was reduced to an average of 1.02 nt/kb/yr. The post-ART baseline rate of genetic change, however, appears to be unique for each patient. These studies represent our initial steps in quantifying rates of genetic change among HIV-1 quasispecies using longitudinally sampled sequences from patients at different stages of disease both before and after initiation of combination ART. Notably, while long-term ART reduced the estimated mutation rates in the vast majority of patients studied, there was still measurable HIV-1 mutation even in patients with no detectable virus by standard quantitative assays. Determining the factors that affect HIV-1 mutation rates in the peripheral blood may lead to elucidation of the mechanisms associated with changes in HIV-1 disease severity.
Collapse
Affiliation(s)
- Will Dampier
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
- School of Biomedical Engineering, Science, and Health Systems, Drexel University, Philadelphia, Pennsylvania, United States of America
| | - Michael R. Nonnemacher
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Joshua Mell
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Joshua Earl
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Garth D. Ehrlich
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
- Center for Advanced Microbial Processing, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Vanessa Pirrone
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Benjamas Aiamkitsumrit
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Wen Zhong
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Katherine Kercher
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Shendra Passic
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Jean W. Williams
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Jeffrey M. Jacobson
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
- Department of Medicine, Division of Infectious Diseases and HIV Medicine, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
- Center for Clinical and Translational Medicine, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Brian Wigdahl
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, United States of America
- * E-mail:
| |
Collapse
|
14
|
Antell GC, Dampier W, Aiamkitsumrit B, Nonnemacher MR, Jacobson JM, Pirrone V, Zhong W, Kercher K, Passic S, Williams JW, Schwartz G, Hershberg U, Krebs FC, Wigdahl B. Utilization of HIV-1 envelope V3 to identify X4- and R5-specific Tat and LTR sequence signatures. Retrovirology 2016; 13:32. [PMID: 27143130 PMCID: PMC4855882 DOI: 10.1186/s12977-016-0266-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 04/20/2016] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND HIV-1 entry is a receptor-mediated process directed by the interaction of the viral envelope with the host cell CD4 molecule and one of two co-receptors, CCR5 or CXCR4. The amino acid sequence of the third variable (V3) loop of the HIV-1 envelope is highly predictive of co-receptor utilization preference during entry, and machine learning predictive algorithms have been developed to characterize sequences as CCR5-utilizing (R5) or CXCR4-utilizing (X4). It was hypothesized that while the V3 loop is predominantly responsible for determining co-receptor binding, additional components of the HIV-1 genome may contribute to overall viral tropism and display sequence signatures associated with co-receptor utilization. RESULTS The accessory protein Tat and the HlV-1 long terminal repeat (LTR) were analyzed with respect to genetic diversity and compared by Jensen-Shannon divergence which resulted in a correlation with both mean genetic diversity as well as the absolute difference in genetic diversity between R5- and X4-genome specific trends. As expected, the V3 domain of the gp120 protein was enriched with statistically divergent positions. Statistically divergent positions were also identified in Tat amino acid sequences within the transactivation and TAR-binding domains, and in nucleotide positions throughout the LTR. We further analyzed LTR sequences for putative transcription factor binding sites using the JASPAR transcription factor binding profile database and found several putative differences in transcription factor binding sites between R5 and X4 HIV-1 genomes, specifically identifying the C/EBP sites I and II, and Sp site III to differ with respect to sequence configuration for R5 and X4 LTRs. CONCLUSION These observations support the hypothesis that co-receptor utilization coincides with specific genetic signatures in HIV-1 Tat and the LTR, likely due to differing transcriptional regulatory mechanisms and selective pressures applied within specific cellular targets during the course of productive HIV-1 infection.
Collapse
Affiliation(s)
- Gregory C Antell
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA.,Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, USA.,School of Biomedical Engineering, Science, and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Will Dampier
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA.,Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, USA.,School of Biomedical Engineering, Science, and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Benjamas Aiamkitsumrit
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA.,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, Drexel University College of Medicine, Philadelphia, PA, USA.,Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Jeffrey M Jacobson
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA.,Division of Infectious Diseases and HIV Medicine, Department of Medicine, Drexel University College of Medicine, Philadelphia, PA, USA.,Center for Clinical and Translational Medicine, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Vanessa Pirrone
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA.,Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Wen Zhong
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA.,Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Katherine Kercher
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA.,Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Shendra Passic
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA.,Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Jean W Williams
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA.,Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Gregory Schwartz
- School of Biomedical Engineering, Science, and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Uri Hershberg
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA.,School of Biomedical Engineering, Science, and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Fred C Krebs
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA.,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, Drexel University College of Medicine, Philadelphia, PA, USA. .,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.
| |
Collapse
|
15
|
Pacheco-Martínez E, Figueroa-Medina E, Villarreal C, Cocho G, Medina-Franco JL, Méndez-Lucio O, Huerta L. Statistical correlation of nonconservative substitutions of HIV gp41 variable amino acid residues with the R5X4 HIV-1 phenotype. Virol J 2016; 13:28. [PMID: 26879054 PMCID: PMC4754869 DOI: 10.1186/s12985-016-0486-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 02/09/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The interaction of the envelope glycoprotein of HIV-1 (gp120/gp41) with coreceptor molecules has important implications for specific cellular targeting and pathogenesis. Experimental and theoretical evidences have shown a role for gp41 in coreceptor tropism, although there is no consensus about the positions involved. Here we analyze the association of physicochemical properties of gp41 amino acid residues with viral tropism (X4, R5, and R5X4) using a large set of HIV-1 sequences. Under the assumption that conserved regions define the complex structural features essential for protein function, we focused our search only on amino acids in the gp41 variable regions. METHODS Gp41 amino acid sequences of 2823 HIV-1 strains from all clades with known coreceptor tropism were retrieved from Los Alamos HIV Database. Consensus sequences were constructed for homologous sequences (those obtained from the same patient and having the same tropism) in order to avoid bias due to sequence overrepresentation, and the variability (entropy) per site was determined. Comparisons of hydropathy index (HI) and charge (Q) of amino acid residues at highly variable positions between coreceptor groups were performed using two non-parametrical tests and Benjamini-Hochberg correction. Pearson's correlation analysis was performed to determine covariance of HI and Q values. RESULTS Calculation of variability per site rendered 58 highly variable amino acid positions. Of these, statistical analysis rendered significantly different HI or Q only for the R5 vs. R5X4 comparison at twelve positions: 535, 602, 619, 636, 640, 641, 658, 662, 667, 723, 756 and 841. The largest differences in particular amino acid frequencies between coreceptor groups were found at 619, 636, 640, 641, 662, 723 and 756. A hydrophobic tendency of residues 619, 640, 641, 723 and 756, along with a hydrophilic/charged tendency at residues 636 and 662 was observed in R5X4 with respect to R5 sequences. HI of position 640 covariated with that of 602, 619, 636, 662, and 756. CONCLUSIONS Variability and significant correlations of physicochemical properties with viral phenotype suggest that substitutions at residues in the loop (602 and 619), the HR2 (636, 640, 641, 662), and the C-terminal tail (723, 756) of gp41 may contribute to phenotype of R5X4 strains.
Collapse
Affiliation(s)
- Elena Pacheco-Martínez
- Programa de Maestría y Doctorado en Ciencias Bioquímicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Distrito Federal, 04510, México
| | - Evangelina Figueroa-Medina
- Unidad de Radio Oncología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Secretaría de Salud, Avenida Vasco de Quiroga No.15, ᅟDistrito Federal, 14080, México
| | - Carlos Villarreal
- Departmento de Física Teórica, Instituto de Física, Universidad Nacional Autónoma de México, Ciudad Universitaria, ᅟDistrito Federal, 04510, México.,Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Ciudad Univesitaria, ᅟDistrito Federal, 04510, México
| | - Germinal Cocho
- Departmento de Sistemas Complejos, Instituto de Física, Universidad Nacional Autónoma de México, Ciudad Universitaria, ᅟDistrito Federal, 04510, México.,Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Ciudad Univesitaria, ᅟDistrito Federal, 04510, México
| | - José L Medina-Franco
- Departmento de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, ᅟDistrito Federal, 04510, México
| | - Oscar Méndez-Lucio
- Departmento de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, ᅟDistrito Federal, 04510, México
| | - Leonor Huerta
- Departmento de Immunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Distrito Federal, México.
| |
Collapse
|
16
|
Kieslich CA, Tamamis P, Guzman YA, Onel M, Floudas CA. Highly Accurate Structure-Based Prediction of HIV-1 Coreceptor Usage Suggests Intermolecular Interactions Driving Tropism. PLoS One 2016; 11:e0148974. [PMID: 26859389 PMCID: PMC4747591 DOI: 10.1371/journal.pone.0148974] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 01/26/2016] [Indexed: 01/21/2023] Open
Abstract
HIV-1 entry into host cells is mediated by interactions between the V3-loop of viral glycoprotein gp120 and chemokine receptor CCR5 or CXCR4, collectively known as HIV-1 coreceptors. Accurate genotypic prediction of coreceptor usage is of significant clinical interest and determination of the factors driving tropism has been the focus of extensive study. We have developed a method based on nonlinear support vector machines to elucidate the interacting residue pairs driving coreceptor usage and provide highly accurate coreceptor usage predictions. Our models utilize centroid-centroid interaction energies from computationally derived structures of the V3-loop:coreceptor complexes as primary features, while additional features based on established rules regarding V3-loop sequences are also investigated. We tested our method on 2455 V3-loop sequences of various lengths and subtypes, and produce a median area under the receiver operator curve of 0.977 based on 500 runs of 10-fold cross validation. Our study is the first to elucidate a small set of specific interacting residue pairs between the V3-loop and coreceptors capable of predicting coreceptor usage with high accuracy across major HIV-1 subtypes. The developed method has been implemented as a web tool named CRUSH, CoReceptor USage prediction for HIV-1, which is available at http://ares.tamu.edu/CRUSH/.
Collapse
Affiliation(s)
- Chris A Kieslich
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, United States of America.,Texas A&M Energy Institute, Texas A&M University, College Station, TX, United States of America
| | - Phanourios Tamamis
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, United States of America.,Texas A&M Energy Institute, Texas A&M University, College Station, TX, United States of America
| | - Yannis A Guzman
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, United States of America.,Texas A&M Energy Institute, Texas A&M University, College Station, TX, United States of America.,Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, United States of America
| | - Melis Onel
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, United States of America.,Texas A&M Energy Institute, Texas A&M University, College Station, TX, United States of America
| | - Christodoulos A Floudas
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, United States of America.,Texas A&M Energy Institute, Texas A&M University, College Station, TX, United States of America
| |
Collapse
|
17
|
Jin Q, Chen H, Wang X, Zhao L, Xu Q, Wang H, Li G, Yang X, Ma H, Wu H, Ji X. The Effects of the Recombinant CCR5 T4 Lysozyme Fusion Protein on HIV-1 Infection. PLoS One 2015; 10:e0131894. [PMID: 26154172 PMCID: PMC4496087 DOI: 10.1371/journal.pone.0131894] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2014] [Accepted: 06/08/2015] [Indexed: 12/03/2022] Open
Abstract
Background Insertion of T4 lysozyme (T4L) into the GPCR successfully enhanced GPCR protein stability and solubilization. However, the biological functions of the recombinant GPCR protein have not been analyzed. Methods We engineered the CCR5-T4L mutant and expressed and purified the soluble recombinant protein using an E.coli expression system. The antiviral effects of this recombinant protein in THP-1 cell lines, primary human macrophages, and PBMCs from different donors were investigated. We also explored the possible mechanisms underlying the observed antiviral effects. Results Our data showed the biphasic inhibitory and promotion effects of different concentrations of soluble recombinant CCR5-T4L protein on R5 tropic human immunodeficiency virus-1 (HIV-1) infection in THP-1 cell lines, human macrophages, and PBMCs from clinical isolates. We demonstrated that soluble recombinant CCR5-T4L acts as a HIV-1 co-receptor, interacts with wild type CCR5, down-regulates the surface CCR5 expression in human macrophages, and interacts with CCL5 to inhibit macrophage migration. Using binding assays, we further determined that recombinant CCR5-T4L and [125I]-CCL5 compete for the same binding site on wild type CCR5. Conclusions Our results suggest that recombinant CCR5-T4L protein marginally promotes HIV-1 infection at low concentrations and markedly inhibits infection at higher concentrations. This recombinant protein may be helpful in the future development of anti-HIV-1 therapeutic agents.
Collapse
Affiliation(s)
- Qingwen Jin
- Department of Microbiology and Immunology, Nanjing Medical University, 140 Hanzhong Road, Nanjing, Jiangsu Province, China
- Department of Neurology, The People’s Hospital of Jiangsu Province, 300 Guangzhou Road, Nanjing, Jiangsu Province, China
- Department of Neurology, Nanjing First Hospital, 68 Changle Road, Nanjing, Jiangsu Province, China
| | - Hong Chen
- Department of Neurology, The People’s Hospital of Jiangsu Province, 300 Guangzhou Road, Nanjing, Jiangsu Province, China
| | - Xingxia Wang
- Department of Neurology, The People’s Hospital of Jiangsu Province, 300 Guangzhou Road, Nanjing, Jiangsu Province, China
| | - Liandong Zhao
- Department of Neurology, The Second Hospital of Huaian, 62 Huaihai South Road, Huaian, Jiangsu Province, China
| | - Qingchen Xu
- Department of Neurology, Nanjing First Hospital, 68 Changle Road, Nanjing, Jiangsu Province, China
| | - Huijuan Wang
- Department of Microbiology and Immunology, Nanjing Medical University, 140 Hanzhong Road, Nanjing, Jiangsu Province, China
| | - Guanyu Li
- Department of Neurology, Mingji Hospital of Nanjing, Jiangsu Province, 71 Riverside West Road, Nanjing, Jiangsu Province, China
| | - Xiaofan Yang
- Department of Microbiology and Immunology, Nanjing Medical University, 140 Hanzhong Road, Nanjing, Jiangsu Province, China
| | - Hongming Ma
- Department of Biomedical Sciences, Texas Tech University Health Sciences Center, 5001 El Paso Drive, El Paso, Texas, United States of America
| | - Haoquan Wu
- Department of Biomedical Sciences, Texas Tech University Health Sciences Center, 5001 El Paso Drive, El Paso, Texas, United States of America
| | - Xiaohui Ji
- Department of Microbiology and Immunology, Nanjing Medical University, 140 Hanzhong Road, Nanjing, Jiangsu Province, China
- * E-mail:
| |
Collapse
|
18
|
Aiamkitsumrit B, Sullivan NT, Nonnemacher MR, Pirrone V, Wigdahl B. Human Immunodeficiency Virus Type 1 Cellular Entry and Exit in the T Lymphocytic and Monocytic Compartments: Mechanisms and Target Opportunities During Viral Disease. Adv Virus Res 2015; 93:257-311. [PMID: 26111588 DOI: 10.1016/bs.aivir.2015.04.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
During the course of human immunodeficiency virus type 1 infection, a number of cell types throughout the body are infected, with the majority of cells representing CD4+ T cells and cells of the monocyte-macrophage lineage. Both types of cells express, to varying levels, the primary receptor molecule, CD4, as well as one or both of the coreceptors, CXCR4 and CCR5. Viral tropism is determined by both the coreceptor utilized for entry and the cell type infected. Although a single virus may have the capacity to infect both a CD4+ T cell and a cell of the monocyte-macrophage lineage, the mechanisms involved in both the entry of the virus into the cell and the viral egress from the cell during budding and viral release differ depending on the cell type. These host-virus interactions and processes can result in the differential targeting of different cell types by selected viral quasispecies and the overall amount of infectious virus released into the extracellular environment or by direct cell-to-cell spread of viral infectivity. This review covers the major steps of virus entry and egress with emphasis on the parts of the replication process that lead to differences in how the virus enters, replicates, and buds from different cellular compartments, such as CD4+ T cells and cells of the monocyte-macrophage lineage.
Collapse
Affiliation(s)
- Benjamas Aiamkitsumrit
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA; Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
| | - Neil T Sullivan
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA; Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
| | - Michael R Nonnemacher
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA; Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
| | - Vanessa Pirrone
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA; Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
| | - Brian Wigdahl
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA; Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA.
| |
Collapse
|