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Multi-level functional genomics reveals molecular and cellular oncogenicity of patient-based 3' untranslated region mutations. Cell Rep 2023; 42:112840. [PMID: 37516102 PMCID: PMC10540565 DOI: 10.1016/j.celrep.2023.112840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 06/05/2023] [Accepted: 07/05/2023] [Indexed: 07/31/2023] Open
Abstract
3' untranslated region (3' UTR) somatic mutations represent a largely unexplored avenue of alternative oncogenic gene dysregulation. To determine the significance of 3' UTR mutations in disease, we identify 3' UTR somatic variants across 185 advanced prostate tumors, discovering 14,497 single-nucleotide mutations enriched in oncogenic pathways and 3' UTR regulatory elements. By developing two complementary massively parallel reporter assays, we measure how thousands of patient-based mutations affect mRNA translation and stability and identify hundreds of functional variants that allow us to define determinants of mutation significance. We demonstrate the clinical relevance of these mutations, observing that CRISPR-Cas9 endogenous editing of distinct variants increases cellular stress resistance and that patients harboring oncogenic 3' UTR mutations have a particularly poor prognosis. This work represents an expansive view of the extent to which disease-relevant 3' UTR mutations affect mRNA stability, translation, and cancer progression, uncovering principles of regulatory functionality and potential therapeutic targets in previously unexplored regulatory regions.
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Sustained Virological Response Rates following Hepatitis C treatment with Direct-Acting Antivirals in patients. IRISH MEDICAL JOURNAL 2023; 116:813. [PMID: 37606261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
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A second riboswitch class for the enzyme cofactor NAD . RNA (NEW YORK, N.Y.) 2021; 27:99-105. [PMID: 33087526 PMCID: PMC7749635 DOI: 10.1261/rna.077891.120] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 10/19/2020] [Indexed: 06/01/2023]
Abstract
A bacterial noncoding RNA motif almost exclusively associated with pnuC genes was uncovered using comparative sequence analysis. Some PnuC proteins are known to transport nicotinamide riboside (NR), which is a component of the ubiquitous and abundant enzyme cofactor nicotinamide adenine dinucleotide (NAD+). Thus, we speculated that the newly found "pnuC motif" RNAs might function as aptamers for a novel class of NAD+-sensing riboswitches. RNA constructs that encompass the conserved nucleotides and secondary structure features that define the motif indeed selectively bind NAD+, nicotinamide mononucleotide (NMN), and NR. Mutations that disrupt strictly conserved nucleotides of the aptamer also disrupt ligand binding. These bioinformatic and biochemical findings indicate that pnuC motif RNAs are likely members of a second riboswitch class that regulates gene expression in response to NAD+ binding.
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Bacillus halodurans OapB forms a high-affinity complex with the P13 region of the noncoding RNA OLE. J Biol Chem 2020; 295:9326-9334. [PMID: 32376692 DOI: 10.1074/jbc.ra120.012676] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 04/28/2020] [Indexed: 11/06/2022] Open
Abstract
Noncoding RNAs (ncRNAs) longer than 200 nucleotides are rare in bacteria, likely because bacterial genomes are under strong evolutionary pressures to maintain a small genome size. Of the long ncRNAs unique to bacteria, the OLE (ornate, large, extremophilic) RNA class is among the largest and most structurally complex. OLE RNAs form a ribonucleoprotein (RNP) complex by partnering with at least two proteins, OapA and OapB, that directly bind OLE RNA. The biochemical functions of the OLE RNP complex remain unknown, but are required for proper adaptation to certain environmental stresses, such as cold temperatures, short chain alcohols, and high magnesium concentrations. In the current study, we used electrophoretic mobility shift assays to examine the binding of OLE RNA fragments by OapB and found that OapB recognizes a small subregion of OLE RNA, including stem P13, with a dissociation constant (KD ) of ∼700 pm Analyses with mutated RNA constructs, and the application of in vitro selection, revealed that strong binding of OLE RNA by OapB requires a stem containing a precisely located single-nucleotide bulge and a GNRA tetraloop. Although the vast majority of bacteria with the ole gene also have the oapB gene, there are many whose genomes contain oapB but lack ole, suggesting that OapB has other RNA partners in some species that might exhibit similar structural features.
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Development of anti-PD-1 chimeric antigen receptor T cells to target a PD-1+ CD4 T cell population enriched in HIV provirus. J Virus Erad 2019. [DOI: 10.1016/s2055-6640(20)30228-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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In situ multiplex RNA fluorescence imaging of SHIV1157ipd3N4 and anti-HIV CAR T cells to study CAR T cell trafficking to sites of viral reservoir in macaque lymphoid tissues. J Virus Erad 2017. [DOI: 10.1016/s2055-6640(20)30670-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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β-Caryophyllene protects against alcoholic steatohepatitis by attenuating inflammation and metabolic dysregulation in mice. Br J Pharmacol 2017; 175:320-334. [PMID: 28107775 DOI: 10.1111/bph.13722] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 01/05/2017] [Accepted: 01/13/2017] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND AND AIMS β-Caryophyllene (BCP) is a plant-derived FDA approved food additive with anti-inflammatory properties. Some of its beneficial effects in vivo are reported to involve activation of cannabinoid CB2 receptors that are predominantly expressed in immune cells. Here, we evaluated the translational potential of BCP using a well-established model of chronic and binge alcohol-induced liver injury. METHODS In this study, we investigated the effects of BCP on liver injury induced by chronic plus binge alcohol feeding in mice in vivo by using biochemical assays, real-time PCR and histology analyses. Serum and hepatic BCP levels were also determined by GC/MS. RESULTS Chronic treatment with BCP alleviated the chronic and binge alcohol-induced liver injury and inflammation by attenuating the pro-inflammatory phenotypic `M1` switch of Kupffer cells and by decreasing the expression of vascular adhesion molecules intercellular adhesion molecule 1, E-Selectin and P-Selectin, as well as the neutrophil infiltration. It also beneficially influenced hepatic metabolic dysregulation (steatosis, protein hyperacetylation and PPAR-α signalling). These protective effects of BCP against alcohol-induced liver injury were attenuated in CB2 receptor knockout mice, indicating that the beneficial effects of this natural product in liver injury involve activation of these receptors. Following acute or chronic administration, BCP was detectable both in the serum and liver tissue homogenates but not in the brain. CONCLUSIONS Given the safety of BCP in humans, this food additive has a high translational potential in treating or preventing hepatic injury associated with oxidative stress, inflammation and steatosis. LINKED ARTICLES This article is part of a themed section on Inventing New Therapies Without Reinventing the Wheel: The Power of Drug Repurposing. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v175.2/issuetoc.
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Interrogation of HHV-8 transcriptome in KS tumors and association with KS presentation and outcomes in Uganda. Ann Glob Health 2015. [DOI: 10.1016/j.aogh.2015.02.732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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Role of Intestinal Microbiota in Shaping the B Cell Repertoire in HIV Infection and Env Vaccination. AIDS Res Hum Retroviruses 2014. [DOI: 10.1089/aid.2014.5023a.abstract] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Are there benefits to starting antiretroviral therapy during primary HIV infection? Conclusions from the Seattle Primary Infection Cohort vary by control group. Int J STD AIDS 2012; 23:201-6. [PMID: 22581875 DOI: 10.1258/ijsa.2011.011178] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
It is controversial whether starting combination antiretroviral therapy (cART) during primary HIV infection (PHI) is beneficial. Subjects in this observational cohort began cART <30 days (group 1: acute treatment, n = 40), 31-180 days (group 2: early treatment, n = 82) or >180 days (group 3: delayed treatment, n = 35) after HIV infection, and were compared with 27 historical and 60 contemporary controls. Time to HIV-related diagnoses did not differ for group 1 (adjusted hazard ratio [aHR] 1.44, P = 0.3) or group 2 (aHR 1.17, P = 0.5) compared with contemporary controls, but it was delayed for both treated groups (aHR 0.38 for group 1, P = 0.01; and aHR 0.28 for group 2, P < 0.0001) compared with historical controls. Although rates of HIV-related diagnoses were similar in acutely treated subjects and contemporary controls, results were confounded by associations between higher CD4 counts, lower HIV RNA levels and delayed disease progression as reasons for deferring treatment. Randomized trials are needed to address benefits of cART during PHI.
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Multiple antibody specificities (gp41, V1V2, and V3) elicited in the phase II multiclade (A, B, C) HIV-1 DNA prime, rAd5 boost vaccine trial. Retrovirology 2012. [PMCID: PMC3441791 DOI: 10.1186/1742-4690-9-s2-o55] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Safety and pharmacokinetics of aciclovir in women following release from a silicone elastomer vaginal ring. J Antimicrob Chemother 2012; 67:2005-12. [PMID: 22556381 DOI: 10.1093/jac/dks151] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
OBJECTIVES Systemic aciclovir and its prodrug valaciclovir are effective in treating and reducing recurrences of genital herpes simplex virus (HSV) and reducing transmission. Local aciclovir delivery, if it can achieve and maintain comparable intracellular genital tract levels, may be equally effective in the treatment and suppression of genital HSV. Intravaginal ring (IVR) delivery of aciclovir may provide pre-exposure prophylaxis against HSV acquisition. METHODS Tolerability and pharmacokinetics were evaluated in six HIV-negative women with recurrent genital HSV who switched their daily oral valaciclovir suppression to an aciclovir IVR for 7 days (n = 3) or 14 days (n = 3). Blood and cervicovaginal lavage (CVL) were collected after oral and IVR dosing to measure aciclovir concentrations and genital swabs were obtained to quantify HSV shedding by PCR. RESULTS The rings were well tolerated. Median plasma aciclovir concentrations were 110.2 ng/mL (IQR, 85.9-233.5) 12-18 h after oral valaciclovir. Little or no drug was detected in plasma following IVR dosing. Median (IQR) CVL aciclovir levels were 127.3 ng/mL (21-660.8) 2 h after oral valaciclovir, 154.4 ng/mL (60.7-327.5) 12-18 h after oral valaciclovir and 438 ng/mL (178.5-618.5) after 7 days and 393 ng/mL (31.6-1615) after 14 days of aciclovir ring use. Median CVL aciclovir levels 2 h after oral dosing were similar to levels observed 7 (P = 0.99) and 14 (P = 0.75) days after ring use. HSV DNA was not detected in genital swabs and there was no significant change in inflammatory mediators. CONCLUSIONS This first-in-human study demonstrated that an IVR could safely deliver mucosal levels of aciclovir similar to oral valaciclovir without systemic absorption. More intensive site-specific pharmacokinetic studies are needed to determine whether higher local concentrations are needed to achieve optimal drug distribution within the genital tract.
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O3-S5.03 High-dose valacyclovir decreases plasma HIV-1 levels more than standard dose acyclovir in HIV-1, HSV-2 positive persons: a randomised, crossover trial. Sex Transm Infect 2011. [DOI: 10.1136/sextrans-2011-050109.129] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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O3-S5.02 Frequent breakthrough genital HSV-2 shedding on standard and high dose valacyclovir. Sex Transm Infect 2011. [DOI: 10.1136/sextrans-2011-050109.128] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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O3-S5.01 Impact of AIC316, a novel antiviral helicase-primase inhibitor, on genital HSV shedding: randomised, double-blind, placebo-controlled trial. Sex Transm Infect 2011. [DOI: 10.1136/sextrans-2011-050109.127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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P3-S2.04 Clinical evaluation of the BD HSV2 Qx assay for the direct qualitative testing of HSV2 as compared to viral culture and a laboratory-based PCR assay using male and female external anogenital lesions. Br J Vener Dis 2011. [DOI: 10.1136/sextrans-2011-050108.448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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LBO-1.1 Acyclovir achieves lower concentration in African HIV-, HSV-2+ women compared to non-African populations, possibly explaining lower herpes suppression. Br J Vener Dis 2011. [DOI: 10.1136/sextrans-2011-050119.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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P3-S2.03 Clinical evaluation of the BD HSV1 Qx assay for the direct qualitative testing of HSV1 as compared to viral culture and a laboratory-based PCR assay using male and female external anogenital lesions. Br J Vener Dis 2011. [DOI: 10.1136/sextrans-2011-050108.447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Evaluation of a Novel Viral Load Based Surveillance Strategy for Prevention of Cytomegalovirus (CMV) Disease in Hematopoietic Cell Transplantation. Biol Blood Marrow Transplant 2011. [DOI: 10.1016/j.bbmt.2010.12.376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Early emergence of an H275Y mutation in a hematopoietic cell transplant recipient treated with intravenous peramivir. Transpl Infect Dis 2010; 12:513-7. [PMID: 21062390 PMCID: PMC3024056 DOI: 10.1111/j.1399-3062.2010.00582.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Oseltamivir resistance in pandemic 2009 influenza A/H1N1 is caused by the neuraminidase mutation H275Y. This mutation has also been associated with in vitro resistance to peramivir, but few clinical cases have been described to date. Using allele-specific real-time reverse transcriptase polymerase chain reaction assay for the H275Y mutation, we were able to identify resistant H1N1 in a hematopoietic cell transplant recipient receiving intravenous peramivir therapy, and through serial testing we determined the molecular evolution of resistance. This case demonstrates that an H275Y mutant population can emerge early and replicate in vivo under peramivir antiviral pressure to become the major viral population.
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Abstract
BACKGROUND Most persons who are infected with human immunodeficiency virus type 1 (HIV-1) are also infected with herpes simplex virus type 2 (HSV-2), which is frequently reactivated and is associated with increased plasma and genital levels of HIV-1. Therapy to suppress HSV-2 reduces the frequency of reactivation of HSV-2 as well as HIV-1 levels, suggesting that suppression of HSV-2 may reduce the risk of transmission of HIV-1. METHODS We conducted a randomized, placebo-controlled trial of suppressive therapy for HSV-2 (acyclovir at a dose of 400 mg orally twice daily) in couples in which only one of the partners was seropositive for HIV-1 (CD4 count, > or = 250 cells per cubic millimeter) and that partner was also infected with HSV-2 and was not taking antiretroviral therapy at the time of enrollment. The primary end point was transmission of HIV-1 to the partner who was not initially infected with HIV-1; linkage of transmissions was assessed by means of genetic sequencing of viruses. RESULTS A total of 3408 couples were enrolled at 14 sites in Africa. Of the partners who were infected with HIV-1, 68% were women, and the baseline median CD4 count was 462 cells per cubic millimeter. Of 132 HIV-1 seroconversions that occurred after randomization (an incidence of 2.7 per 100 person-years), 84 were linked within couples by viral sequencing: 41 in the acyclovir group and 43 in the placebo group (hazard ratio with acyclovir, 0.92, 95% confidence interval [CI], 0.60 to 1.41; P=0.69). Suppression with acyclovir reduced the mean plasma concentration of HIV-1 by 0.25 log(10) copies per milliliter (95% CI, 0.22 to 0.29; P<0.001) and the occurrence of HSV-2-positive genital ulcers by 73% (risk ratio, 0.27; 95% CI, 0.20 to 0.36; P<0.001). A total of 92% of the partners infected with HIV-1 and 84% of the partners not infected with HIV-1 remained in the study for 24 months. The level of adherence to the dispensed study drug was 96%. No serious adverse events related to acyclovir were observed. CONCLUSIONS Daily acyclovir therapy did not reduce the risk of transmission of HIV-1, despite a reduction in plasma HIV-1 RNA of 0.25 log(10) copies per milliliter and a 73% reduction in the occurrence of genital ulcers due to HSV-2. (ClinicalTrials.gov number, NCT00194519.)
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OA06-06 LB. Evidence of vaccine-induced changes in breakthrough HIV-1 strains from the Step trial. Retrovirology 2009. [PMCID: PMC2767565 DOI: 10.1186/1742-4690-6-s3-o42] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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P17-25. A model for coverage of T-cell HIV vaccines: where are we and where do we need to be? Retrovirology 2009. [PMCID: PMC2767812 DOI: 10.1186/1742-4690-6-s3-p307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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P14-07. Offering new prevention modalities in HIV vaccine trials: experience with male circumcision in the Phambili trial. Retrovirology 2009. [PMCID: PMC2767687 DOI: 10.1186/1742-4690-6-s3-p195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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P11-17. Intermittent rectal shedding of multiple human adenovirus serotypes among HIV-positive MSM. Retrovirology 2009. [PMCID: PMC2767651 DOI: 10.1186/1742-4690-6-s3-p162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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OA01-06 LB. HIV-1 plasma RNA and risk of HIV-1 transmission. Retrovirology 2009. [PMCID: PMC2767532 DOI: 10.1186/1742-4690-6-s3-o12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Functional properties and epitope characteristics of T-cells recognizing natural HIV-1 variants. Vaccine 2009; 27:6678-87. [PMID: 19747576 DOI: 10.1016/j.vaccine.2009.08.093] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2009] [Revised: 08/17/2009] [Accepted: 08/26/2009] [Indexed: 11/18/2022]
Abstract
To understand how broad recognition of HIV-1 variants may be achieved we examined T-cell reactivity in newly infected persons as well as vaccine recipients to a broad spectrum of potential T-cell epitope (PTE) variants containing conservative, semi-conservative and non-conservative amino acid substitutions. Among early infected persons T-cells recognized epitope variants with one substitution at a significantly higher frequency versus those with two (P=0.0098) and three (P=0.0125) substitutions. Furthermore T-cells recognized variants containing conservative substitutions at a higher frequency versus those containing semi-conservative (P=0.0029) and non-conservative (P<0.0001) substitutions. Similar effects were observed on recognition of variants by vaccine-induced T-cells. Moreover even when variants were recognized, the IFN-gamma and granzyme B responses as well as T-cell proliferation were of lower magnitude. Finally, we show that epitope distribution is strongly influenced by both processing preferences and amino acid entropy. We conclude that induction of broad immunity is likely to require immunogen sequences that encompass multiple variants. However, cost-effective design of peptide and sequence based vaccine immunogens that provide maximal coverage of circulating sequences may be achieved through emphasis on virus domains likely to be T-cell targets.
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AIDS-associated Kaposi sarcoma in Uganda: response to treatment with highly active antiretroviral therapy and chemotherapy. Infect Agent Cancer 2009. [PMCID: PMC4261744 DOI: 10.1186/1750-9378-4-s2-o5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Comparison of conventional and molecular detection of respiratory viruses in hematopoietic cell transplant recipients. Transpl Infect Dis 2009; 11:298-303. [PMID: 19453994 DOI: 10.1111/j.1399-3062.2009.00400.x] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
BACKGROUND Sensitive detection of respiratory viruses is important for early diagnosis of infection in patients following hematopoietic cell transplantation (HCT). To evaluate the relative sensitivity of respiratory virus detection in specimens from HCT recipients, we compared the results of conventional and quantitative molecular methods. METHODS We tested 688 nasal wash samples collected prospectively from 131 patients during the first 100 days after HCT by viral culture, fluorescent antibody staining (FA), and real-time quantitative reverse transcription-polymerase chain reaction (PCR) assay for detection of respiratory syncytial virus (RSV), influenza virus types A (FluA) and B (FluB), and parainfluenza virus types 1 (PIV1) and 3 (PIV3). Testing for human metapneumovirus (MPV) was performed only by PCR. Data regarding 10 respiratory symptoms were collected with each sample. RESULTS By any method 37 specimens were positive for a respiratory virus; 34 were positive by PCR, 15 by culture, and 6 by FA. Four specimens were positive by all 3 methods (3 RSV, 1 FluA). One specimen was positive for PIV1, and 2 were positive for rhinovirus by culture alone. Specimens positive by PCR alone included 2 RSV, 2 PIV1, 8 PIV3, and 8 MPV. In 10 specimens positive for RSV, PIV, or influenza virus collected from patients reporting no respiratory symptoms, 9, 4, and 1 specimen were positive by PCR, culture, and FA, respectively. Overall, specimens positive only by PCR had significantly fewer viral copies/mL (mean log(10)=4.32) than specimens positive by both PCR and culture (mean log(10)=5.75; P=0.002) or PCR and FA (mean log(10)=6.83; P<0.001). CONCLUSIONS FA testing alone did not detect a significant proportion of respiratory virus-positive samples in HCT recipients, especially in patients with no respiratory symptoms and patients with PIV detection. PCR increased the yield of positive specimens 2 times relative to culture and more than 4 times relative to FA. Detection of respiratory viruses by PCR alone was associated with lower virus quantities and with fewer reported respiratory symptoms compared with concomitant detection by both PCR and conventional methods, indicating that PCR may be important to detect asymptomatic or mildly symptomatic stages of respiratory viral infections.
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Use of predictive markers of HIV disease progression in vaccine trials. Vaccine 2009; 27:1997-2015. [DOI: 10.1016/j.vaccine.2009.01.039] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2008] [Revised: 12/19/2008] [Accepted: 01/08/2009] [Indexed: 10/21/2022]
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Human Coronavirus (HCOV) and Rhinovirus (HRHV) Infection among Hematopoietic Stem Cell Transplantation (HCT) Recipients. Biol Blood Marrow Transplant 2009. [PMCID: PMC7129590 DOI: 10.1016/j.bbmt.2008.12.275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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75: Prevention of Late CMV Disease After HCT: A Randomized Double-Blind Multicenter Trial of Valganciclovir (VGCV) Prophylaxis Versus PCR-guided GCV/VGCV Preemptive Therapy. Biol Blood Marrow Transplant 2008. [DOI: 10.1016/j.bbmt.2007.12.083] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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80: Primary CMV Infection in CMV Seronegative Recipients of a Stem Cell Product from a Seropositive Donor (D+/R-): Frequency of and Risk Factors for Transmission. Biol Blood Marrow Transplant 2008. [DOI: 10.1016/j.bbmt.2007.12.088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Invasive Pseudomonas aeruginosa infections: high rate of recurrence and mortality after hematopoietic cell transplantation. Bone Marrow Transplant 2007; 39:687-93. [PMID: 17401395 DOI: 10.1038/sj.bmt.1705653] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Limited data exist regarding the incidence and factors associated with outcome of invasive Pseudomonal infections in hematopoietic cell transplant (HCT). A retrospective analysis of cases of invasive Pseudomonas aeruginosa infection and factors associated with outcome was performed. P. aeruginosa invasive infection occurred in 95 of 5772 patients (1.65%) a median of 63 days after HCT (range 5-1435). Only 28% of infections occurred during periods of neutropenia (absolute neutrophil count<500 cells/mm(3)). Infection-attributable mortality during the initial episode of infection was 35.8%. Factors associated with initial mortality included the presence of a copathogen and high-dose steroid use. Ten (16.4%) of those who survived the initial infection experienced a recurrence of P. aeruginosa infection at a median of 9 days (range 3-17) after stopping antibiotics and 60% of those died as a result of recurrent infection a median of 1 day (range 1-7) after onset of recurrence. Grade 3-4 graft-versus-host disease was associated with a higher risk of recurrent infection. The risk of recurrence was not influenced by the presence of copathogens. Thus, invasive P. aeruginosa infections are associated with high recurrence rates and mortality in this immunocompromised population. Aggressive attempts to reduce immunosuppression and to treat copathogens may help during the initial infection.
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OSELTAMIVIR PROPHYLAXIIS IN HEMATOPOIETIC STEM CELL TRANSPLANTATION RECIPIENTS: A CASE-CONTROL STUDY. J Investig Med 2007. [DOI: 10.1097/00042871-200701010-00024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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HIV serodiscordant sex partners and the prevalence of human herpesvirus 8 infection among HIV negative men who have sex with men: baseline data from the EXPLORE Study. Sex Transm Infect 2006; 82:229-35. [PMID: 16731675 PMCID: PMC2564745 DOI: 10.1136/sti.2005.016568] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
OBJECTIVES Human herpesvirus 8 (HHV-8) infection is common among men who have sex with men (MSM), especially those infected with HIV, and is frequently detected in saliva. We sought to determine whether oral or anogenital contact with HIV discordant, or unknown serostatus sexual partners is associated with HHV-8 seroprevalence among HIV negative MSM. METHODS HIV negative MSM participating in a behavioural intervention trial for the prevention of HIV infection (the EXPLORE study) were recruited from the Seattle and Denver areas for participation in this cross sectional study. Participants completed detailed questionnaires regarding sexual behaviour, focusing on activities with possible exposure to the oropharynx. Serum samples from study enrollment were tested for the presence of HHV-8 antibodies using whole virus enzyme immunoassay and immunofluorescence assay to latent and lytic proteins. RESULTS 198/819 MSM (24.3%) were HHV-8 antibody positive. Exposure to saliva with HIV positive and HIV unknown serostatus sex partners was reported by 83% and 90% of all men, respectively. In a multivariate model, reporting more than the median number of lifetime sex partners (OR 2.2, p = 0.03) or lifetime sex partners of unknown HIV status (OR 1.7, p = 0.03), and the performance of oro-anal sex ("rimming") on partners whose HIV status is unknown (OR 2.7, p = 0.04) were independently associated with HHV-8 infection. CONCLUSIONS The oropharynx may be an important anatomical site in HHV-8 acquisition, and contact with HIV serodiscordant or unknown sex partners is associated with higher HHV-8 seroprevalence among HIV negative MSM.
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Impact of neutralizing antibody to respiratory syncytial virus (RSV) on respiratory disease progression in hematopoietic stem cell transplant recipients (HCT). Biol Blood Marrow Transplant 2006. [DOI: 10.1016/j.bbmt.2005.11.428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Long term suppressive acyclovir (ACV) reduces VZV disease and ACV-resistant HSV after HCT. Biol Blood Marrow Transplant 2006. [DOI: 10.1016/j.bbmt.2005.11.430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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56 Changing patterns in the risk for Cytomegalovirus infection and disease and treatment-related outcomes in the Era of preemptive antiviral therapy. Int J Infect Dis 2006. [DOI: 10.1016/s1201-9712(06)80054-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Abstract
Genital herpes, caused by either herpes simplex virus type 1 or 2 (HSV-1 and HSV-2), is a significant public health problem worldwide. It increases the risk of infection with HIV, upregulates HIV after infection and can be associated with serious morbidity and mortality. It is now known that clinical and subclinical viral reactivation with resultant shedding from anogenital mucosa occurs frequently, resulting in transmission during sexual contact. Sexual transmission of HSV infection is common, even between monogamous individuals. Antiviral therapy reduces the frequency and degree of viral shedding and lowers the transmission rate in discordant monogamous couples, although transmission can still occur in people prescribed antiviral therapy. These encouraging data raise important questions for the management of genital HSV infection, particularly with regard to the prevention of transmission. Although the quantity of virus present is clearly important in transmission of some viruses, it is not clear whether this is the case for HSV transmission. Ideally, a surrogate marker needs to be able to identify individuals with detectable amounts of virus, and differentiate them from individuals with detectable amounts of virus that are transmissible. The aim of this supplement is to explore the issues surrounding the validation of surrogate markers of transmission of HSV, using examples from other human viral diseases, and to review the available evidence. In the future, exploration of these issues may shed light on management and prevention strategies. In particular, the results may clarify what evidence is required to warrant prescribing a drug for reducing HSV transmission, and for which patient populations this strategy is appropriate.
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Abstract
Viral shedding of HSV occurs frequently in infected individuals. HSV is shed asymptomatically from multiple anatomical sites and shedding, like exposure, is a significant risk for transmission. However, the relationship between shedding frequency, viral titer and transmission is unknown. HSV-2 shedding is affected by the site and time since acquisition of infection. The advent of sensitive PCR techniques has shown that the magnitude and frequency of viral shedding is higher than shown previously with viral culture techniques. It has also clearly demonstrated that suppressive (daily) antiviral therapy reduces clinical and subclinical reactivation rates, and has been successfully used in the prevention of recurrent oral and genital HSV infections. A recent study has demonstrated that daily antiviral therapy with valaciclovir can significantly reduce transmission of HSV-2 between discordant heterosexual couples in monogamous relationships.
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Abstract
A number of important risk factors for the acquisition of HSV-2 have been established including female gender, black or Hispanic ethnic origin, HIV infection, age, and increased number of sexual partners. Transmission is influenced by a number of biological factors such as sexual behavior, use of condoms, duration of relationships, and knowledge of a partner's serologic status. Vertical transmission (transmission of HSV from mother to neonate) is potentially life-threatening; neonatal HSV infection is associated with significant morbidity and mortality. The valaciclovir transmission study provides evidence that an antiviral agent can interrupt the transmission of a viral sexually transmitted disease between serologically discordant sexual partners. This review explores the importance of the cofactors that affect transmission, and makes recommendations on considerations for the prophylactic use of antiviral agents for the prevention of transmission in other patient populations.
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Abstract
Surrogate markers are an important component in the process of investigating management and prevention strategies, and for increasing understanding of viral diseases. The importance of surrogate markers and applied statistical models is particularly true for HIV. For HIV infection, the development of such methods provides new approaches for evaluation of HIV therapies and vaccines, and for the study of HIV transmission and its pathogenesis. The complex natural history of hepatitis B infection demonstrates that viral load is not the only predictor of transmission of this virus; for hepatitis C infection, viral load per se is not a prognostic factor for disease progression, but cumulative viral load may affect the outcome, and therapy is aimed at eliminating active viral replication.
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Abstract
OBJECTIVES Herpes simplex virus (HSV) 1 and HSV-2 reactivate preferentially in the oral and genital area, respectively. We aimed to define frequency and characteristics associated with oral shedding of HSV-2. METHODS Demographic, clinical and laboratory data of patients with documented HSV-2 infection and at least one oral viral culture obtained were selected from the University of Washington Virology Research Clinic database. RESULTS Of 1388 people meeting the entry criteria, 44 (3.2%) had HSV-2 isolated at least once from their mouths. In comparison with the 1344 people who did not have HSV-2 isolated from their mouth, participants with oral HSV-2 were more likely to be male (OR = 1.9, 95% CI 1.0 to 3.7), HIV positive (OR = 2.9, 95% CI 1.4 to 6.0), and homosexual (OR = 2.2, 95% CI 1.1 to 4.2), and to have collected a larger number of oral specimens (median 32 v 4, p<0.001). Of the 58 days with oral HSV-2 isolation, 15 (25%) occurred during newly acquired HSV-2 infection, 12 (21%) during a recurrence with genital lesions, three (5%) during a recurrence with oral lesions, and three (5%) during a recurrence with oral and genital lesions; 25 (43%) occurred during asymptomatic shedding. Oral HSV-2 was found less frequently than oral HSV-1 (0.06% v 1%, p<0.001) in people with HSV-1 and HSV-2 antibody, and less frequently than genital HSV-2 (0.09% v 7%, p<0.001). CONCLUSIONS Oral reactivation of HSV-2 as defined by viral isolation is uncommon and usually occurs in the setting of first episode of genital HSV-2 or during genital recurrence of HSV-2.
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Abstract
Oral therapy for chronic hepatitis B remains suboptimal. Mathematical modelling of viral decay kinetics to rapidly assess potential antiviral regimens has proved valuable for human immunodeficiency virus and cytomegalovirus. We defined the kinetics of viral replication in 10 chronic hepatitis B patients randomized to lamivudine 100 mg vs 600 mg for 48 weeks. Viral decay kinetics conformed to a biphasic pattern in nine of 10 subjects. Persons receiving 600 mg daily of lamivudine exhibited a 1.6-fold faster decay rate in the infected cell compartment (0.028/day vs 0.017/day, P = 0.06) and a greater overall change in serum viral load when compared with those receiving 100 mg (4.06 vs 1.52 log(10) copies/mL, P = 0.08). More potent therapy appeared to result in more rapid decrease in the infected cell population. Studies using mathematical modelling of viral decay may be a useful method to evaluate single or combination therapy for HBV infection in vivo.
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282 HERPES SIMPLEX VIRUS-INFECTED CELLS INACTIVATE CYTOTOXIC T LYMPHOCYTES: INSIGHT INTO A NOVEL IMMUNE EVASION MECHANISM. J Investig Med 2004. [DOI: 10.1136/jim-52-suppl1-282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Herpes simplex virus type 1 infection: a sexually transmitted infection of adolescence? Sex Transm Infect 2002; 78:346-8. [PMID: 12407237 PMCID: PMC1744523 DOI: 10.1136/sti.78.5.346] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
OBJECTIVES To examine the factors associated with antibodies to herpes simplex virus type 1 (HSV-1). DESIGN Cross sectional study with HSV-1 antibody testing performed by University of Washington western blot assay. SETTING Central London STD clinic (1990-1) and central London blood donation centre (1992). PARTICIPANTS Representative sample of 869 new and rebooked GUM clinic attenders and 1494 consecutive blood donors. RESULTS The prevalence of HSV-1 antibody among clinic attenders was 60.4% (95% CI 57.0 to 63.7) and among donors was 46.1% (95% CI 43.5 to 48.7). HSV-1 antibody was independently associated with increasing age in both populations (p<0.001). Among clinic attenders, HSV-1 was less common among heterosexual men than women and homosexual men (p<0.005), and was more common among black people (p=0.001) and those of lower socioeconomic status (p=0.05). Among blood donors, being single rather than married was independently associated with HSV-1 infection (p=0.03). Early age at first intercourse was strongly associated with presence of HSV-1 in both populations. The adjusted odds of HSV-1 among GUM clinic attenders was 0.37 (95% CI 0.21 to 0.65) for someone aged 20 at first intercourse compared with someone aged <or=15. Among blood donors, those aged 20 had an adjusted odds of 0.64 (95% CI 0.39 to 1.05) compared with someone aged 15. HSV-1 was not associated with increasing number of lifetime partners after adjustment for other factors. CONCLUSIONS Genital herpes due to HSV-1 antibody is increasing in the United Kingdom, particularly among young people. In this study we found that HSV-1 was strongly associated with early age of first sexual intercourse, which may reflect the sexual practices of people initiating sex in this age group.
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