Browsing by Author "Denny, Thomas"
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Item Open Access A model for harmonizing flow cytometry in clinical trials.(Nat Immunol, 2010-11) Maecker, Holden T; McCoy, J Philip; FOCIS Human Immunophenotyping Consortium; Amos, Michael; Elliott, John; Gaigalas, Adolfas; Wang, Lili; Aranda, Richard; Banchereau, Jacques; Boshoff, Chris; Braun, Jonathan; Korin, Yael; Reed, Elaine; Cho, Judy; Hafler, David; Davis, Mark; Fathman, C Garrison; Robinson, William; Denny, Thomas; Weinhold, Kent; Desai, Bela; Diamond, Betty; Gregersen, Peter; Di Meglio, Paola; Nestle, Frank O; Peakman, Mark; Villanova, Federica; Ferbas, John; Field, Elizabeth; Kantor, Aaron; Kawabata, Thomas; Komocsar, Wendy; Lotze, Michael; Nepom, Jerry; Ochs, Hans; O'Lone, Raegan; Phippard, Deborah; Plevy, Scott; Rich, Stephen; Roederer, Mario; Rotrosen, Dan; Yeh, Jung-HuaComplexities in sample handling, instrument setup and data analysis are barriers to the effective use of flow cytometry to monitor immunological parameters in clinical trials. The novel use of a central laboratory may help mitigate these issues.Item Open Access Assessment of an Online Tool to Simulate the Effect of Pooled Testing for SARS-CoV-2 Detection in Asymptomatic and Symptomatic Populations.(JAMA network open, 2020-12) Polage, Christopher R; Lee, Mark J; Hubbard, Christopher; Rehder, Catherine; Cardona, Diana; Denny, Thomas; Datto, Michael BItem Open Access Concerning the article by de Carvalho Bittencourt et al.: Value of HIV patients with regular follow-up as in-house internal controls of flow cytometry measurement of lymphocyte subsets.(Cytometry B Clin Cytom, 2013-09) Marti, Gerald E; Mandy, Frank; Denny, Thomas; Preffer, Frederic IItem Open Access Early experience with universal preprocedural testing for SARS-CoV-2 in a relatively low-prevalence area.(Infection control and hospital epidemiology, 2020-08-03) Lewis, Sarah S; Smith, Becky A; Akinboyo, Ibukunoluwa C; Seidelman, Jessica; Wolfe, Cameron; Kirk, Allan B; Martin, Gavin; Denny, Thomas; Lobaugh, Bruce; Rehder, Catherine; Cardona, Diana; Lee, Mark J; Polage, Christopher R; Datto, Michael BWe implemented universal severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing of patients undergoing surgical procedures as a means to conserve personal protective equipment (PPE). The rate of asymptomatic coronavirus disease 2019 (COVID-19) was <0.5%, which suggests that early local public health interventions were successful. Although our protocol was resource intensive, it prevented exposures to healthcare team members.Item Open Access Establishment and maintenance of a PBMC repository for functional cellular studies in support of clinical vaccine trials.(J Immunol Methods, 2014-07) Sambor, Anna; Garcia, Ambrosia; Berrong, Mark; Pickeral, Joy; Brown, Sara; Rountree, Wes; Sanchez, Ana; Pollara, Justin; Frahm, Nicole; Keinonen, Sarah; Kijak, Gustavo H; Roederer, Mario; Levine, Gail; D'Souza, M Patricia; Jaimes, Maria; Koup, Richard; Denny, Thomas; Cox, Josephine; Ferrari, GuidoA large repository of cryopreserved peripheral blood mononuclear cells (PBMCs) samples was created to provide laboratories testing the specimens from human immunodeficiency virus-1 (HIV-1) vaccine clinical trials the material for assay development, optimization, and validation. One hundred thirty-one PBMC samples were collected using leukapheresis procedure between 2007 and 2013 by the Comprehensive T cell Vaccine Immune Monitoring Consortium core repository. The donors included 83 human immunodeficiency virus-1 (HIV-1) seronegative and 32 HIV-1 seropositive subjects. The samples were extensively characterized for the ability of T cell subsets to respond to recall viral antigens including cytomegalovirus, Epstein-Barr virus, influenza virus, and HIV-1 using Interferon-gamma (IFN-γ) enzyme linked immunospot (ELISpot) and IFN-γ/interleukin 2 (IL-2) intracellular cytokine staining (ICS) assays. A subset of samples was evaluated over time to determine the integrity of the cryopreserved samples in relation to recovery, viability, and functionality. The principal results of our study demonstrate that viable and functional cells were consistently recovered from the cryopreserved samples. Therefore, we determined that this repository of large size cryopreserved cellular samples constitutes a unique resource for laboratories that are involved in optimization and validation of assays to evaluate T, B, and NK cellular functions in the context of clinical trials.Item Open Access Evaluation and recommendations on good clinical laboratory practice guidelines for phase I-III clinical trials.(PLoS Med, 2009-05-26) Sarzotti-Kelsoe, Marcella; Cox, Josephine; Cleland, Naana; Denny, Thomas; Hural, John; Needham, Leila; Ozaki, Daniel; Rodriguez-Chavez, Isaac R; Stevens, Gwynneth; Stiles, Timothy; Tarragona-Fiol, Tony; Simkins, AnitaItem Open Access Evaluation of SARS-CoV-2 identification methods through surveillance of companion animals in SARS-CoV-2-positive homes in North Carolina, March to December 2020(PeerJ) Gin, Taylor E; Petzold, Elizabeth A; Uthappa, Diya M; Neighbors, Coralei E; Borough, Anna R; Gin, Craig; Lashnits, Erin; Sempowski, Gregory D; Denny, Thomas; Bienzle, Dorothee; Weese, J Scott; Callahan, Benjamin J; Woods, Christopher WWe collected oral and/or rectal swabs and serum from dogs and cats living in homes with SARS-CoV-2-PCR-positive persons for SARS-CoV-2 PCR and serology testing. Pre-COVID-19 serum samples from dogs and cats were used as negative controls, and samples were tested in duplicate at different timepoints. Raw ELISA results scrutinized relative to known negative samples suggested that cut-offs for IgG seropositivity may require adjustment relative to previously proposed values, while proposed cut-offs for IgM require more extensive validation. A small number of pet dogs (2/43, 4.7%) and one cat (1/21, 4.8%) were positive for SARS-CoV-2 RNA, and 28.6 and 37.5% of cats and dogs were positive for anti-SARS-CoV-2 IgG, respectively.Item Open Access External Quality Assessment Program for Next-Generation Sequencing-Based HIV Drug Resistance Testing: Logistical Considerations.(Viruses, 2020-05-18) Ji, Hezhao; Parkin, Neil; Gao, Feng; Denny, Thomas; Jennings, Cheryl; Sandstrom, Paul; Kantor, RamiNext-generation sequencing (NGS) is likely to become the new standard method for HIV drug resistance (HIVDR) genotyping. Despite the significant advances in the development of wet-lab protocols and bioinformatic data processing pipelines, one often-missing critical component of an NGS HIVDR assay for clinical use is external quality assessment (EQA). EQA is essential for ensuring assay consistency and laboratory competency in performing routine biomedical assays, and the rollout of NGS HIVDR tests in clinical practice will require an EQA. In September 2019, the 2nd International Symposium on NGS HIVDR was held in Winnipeg, Canada. It convened a multidisciplinary panel of experts, including research scientists, clinicians, bioinformaticians, laboratory biologists, biostatisticians, and EQA experts. A themed discussion was conducted on EQA strategies towards such assays during the symposium. This article describes the logistical challenges identified and summarizes the opinions and recommendations derived from these discussions, which may inform the development of an inaugural EQA program for NGS HIVDR in the near future.Item Open Access HIV-1 subtype C is significantly more infectious than other subtypes(JOURNAL OF THE INTERNATIONAL AIDS SOCIETY, 2015-07) Demarco, Todd; Rountree, Wes; Hora, Bhavna; Chen, Yue; Keinonen, Sarah; Racz, Laura; Daniell, Lily; Louzao, Raul; Sanchez, Ana; Busch, Michael; Denny, Thomas; Gao, FengItem Open Access Immunization with an SIV-based IDLV Expressing HIV-1 Env 1086 Clade C Elicits Durable Humoral and Cellular Responses in Rhesus Macaques(MOLECULAR THERAPY, 2016-11) Negri, Donatella; Blasi, Maria; LaBranche, Celia; Parks, Robert; Balachandran, Harikrishnan; Lifton, Michelle; Shen, Xiaoying; Denny, Thomas; Ferrari, Guido; Vescio, Maria Fenicia; Andersen, Hanne; Montefiori, David C; Tomaras, Georgia D; Liao, Hua-Xin; Santra, Sampa; Haynes, Barton F; Klotman, Mary E; Cara, AndreaItem Open Access Infectious virion capture by HIV-1 gp120-specific IgG from RV144 vaccinees.(J Virol, 2013-07) Liu, Pinghuang; Yates, Nicole L; Shen, Xiaoying; Bonsignori, Mattia; Moody, M Anthony; Liao, Hua-Xin; Fong, Youyi; Alam, S Munir; Overman, R Glenn; Denny, Thomas; Ferrari, Guido; Ochsenbauer, Christina; Kappes, John C; Polonis, Victoria R; Pitisuttithum, Punnee; Kaewkungwal, Jaranit; Nitayaphan, Sorachai; Rerks-Ngarm, Supachai; Montefiori, David C; Gilbert, Peter; Michael, Nelson L; Kim, Jerome H; Haynes, Barton F; Tomaras, Georgia DThe detailed examination of the antibody repertoire from RV144 provides a unique template for understanding potentially protective antibody functions. Some potential immune correlates of protection were untested in the correlates analyses due to inherent assay limitations, as well as the need to keep the correlates analysis focused on a limited number of endpoints to achieve statistical power. In an RV144 pilot study, we determined that RV144 vaccination elicited antibodies that could bind infectious virions (including the vaccine strains HIV-1 CM244 and HIV-1 MN and an HIV-1 strain expressing transmitted/founder Env, B.WITO.c). Among vaccinees with the highest IgG binding antibody profile, the majority (78%) captured the infectious vaccine strain virus (CM244), while a smaller proportion of vaccinees (26%) captured HIV-1 transmitted/founder Env virus. We demonstrated that vaccine-elicited HIV-1 gp120 antibodies of multiple specificities (V3, V2, conformational C1, and gp120 conformational) mediated capture of infectious virions. Although capture of infectious HIV-1 correlated with other humoral immune responses, the extent of variation between these humoral responses and virion capture indicates that virion capture antibodies occupy unique immunological space.Item Open Access RADx-UP Testing Core: Access to COVID-19 Diagnostics in Community-Engaged Research with Underserved Populations.(Journal of clinical microbiology, 2023-08) Narayanasamy, Shanti; Veldman, Timothy H; Lee, Mark J; Glover, William A; Tillekeratne, L Gayani; Neighbors, Coralei E; Harper, Barrie; Raghavan, Vidya; Kennedy, Scott W; Carper, Miranda; Denny, Thomas; Tsalik, Ephraim L; Reller, Megan E; Kibbe, Warren A; Corbie, Giselle; Cohen-Wolkowiez, Michael; Woods, Christopher W; Petti, Cathy AResearch on the COVID-19 pandemic revealed a disproportionate burden of COVID-19 infection and death among underserved populations and exposed low rates of SARS-CoV-2 testing in these communities. A landmark National Institutes of Health (NIH) funding initiative, the Rapid Acceleration of Diagnostics-Underserved Populations (RADx-UP) program, was developed to address the research gap in understanding the adoption of COVID-19 testing in underserved populations. This program is the single largest investment in health disparities and community-engaged research in the history of the NIH. The RADx-UP Testing Core (TC) provides community-based investigators with essential scientific expertise and guidance on COVID-19 diagnostics. This commentary describes the first 2 years of the TC's experience, highlighting the challenges faced and insights gained to safely and effectively deploy large-scale diagnostics for community-initiated research in underserved populations during a pandemic. The success of RADx-UP shows that community-based research to increase access and uptake of testing among underserved populations can be accomplished during a pandemic with tools, resources, and multidisciplinary expertise provided by a centralized testing-specific coordinating center. We developed adaptive tools to support individual testing strategies and frameworks for these diverse studies and ensured continuous monitoring of testing strategies and use of study data. In a rapidly evolving setting of tremendous uncertainty, the TC provided essential and real-time technical expertise to support safe, effective, and adaptive testing. The lessons learned go beyond this pandemic and can serve as a framework for rapid deployment of testing in response to future crises, especially when populations are affected inequitably.Item Open Access SARS-CoV-2 Viremia is Associated with COVID-19 Severity and Predicts Clinical Outcomes.(Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 2021-08-10) Jacobs, Jana L; Bain, William; Naqvi, Asma; Staines, Brittany; Castanha, Priscila MS; Yang, Haopu; Boltz, Valerie F; Barratt-Boyes, Simon; Marques, Ernesto TA; Mitchell, Stephanie L; Methé, Barbara; Olonisakin, Tolani F; Haidar, Ghady; Burke, Thomas W; Petzold, Elizabeth; Denny, Thomas; Woods, Chris W; McVerry, Bryan J; Lee, Janet S; Watkins, Simon C; St Croix, Claudette M; Morris, Alison; Kearney, Mary F; Ladinsky, Mark S; Bjorkman, Pamela J; Kitsios, Georgios D; Mellors, John WBackground
SARS-CoV-2 viral RNA (vRNA) is detected in the bloodstream of some patients with COVID-19 ("RNAemia") but it is not clear whether this RNAemia reflects viremia (i.e., virus particles) and how RNAemia/viremia is related to host immune responses and outcomes.Methods
SARS-CoV-2 vRNA was quantified by ultra-sensitive RT-PCR in plasma samples (0.5-1.0 ml) from observational cohorts of 51 COVID-19 patients including 9 outpatients, 19 hospitalized (non-ICU), and 23 ICU patients, and vRNA levels compared with cross-sectional indices of COVID-19 severity and prospective clinical outcomes. We used multiple imaging methods to visualize virions in pelleted plasma.Results
SARS-CoV-2 vRNA was detected in plasma of 100%, 52.6% and 11.1% of ICU, non-ICU, and outpatients respectively. Virions were detected in plasma pellets by electron tomography and immunostaining. Plasma vRNA levels were significantly higher in ICU > non-ICU > outpatients (p<0.0001); and for inpatient, plasma vRNA levels were strongly associated with higher WHO score at admission (p=0.01), maximum WHO score (p=0.002) and discharge disposition (p=0.004). A plasma vRNA level >6,000 copies/ml was strongly associated with mortality (HR: 10.7). Levels of vRNA were significantly associated with several inflammatory biomarkers (p<0.01) but not with plasma neutralizing antibody titers (p=0.8).Conclusions
Visualization of virus particles in plasma indicates that SARS-CoV-2 RNAemia is due, at least in part, to viremia. The levels of SARS-CoV-2 RNAemia quantified by ultrasensitive RT-PCR correlate strongly with disease severity, patient outcome and specific inflammatory biomarkers but not neutralizing antibody titers.Item Open Access Systematic review of the performance of HIV viral load technologies on plasma samples.(PLoS One, 2014) Sollis, Kimberly A; Smit, Pieter W; Fiscus, Susan; Ford, Nathan; Vitoria, Marco; Essajee, Shaffiq; Barnett, David; Cheng, Ben; Crowe, Suzanne M; Denny, Thomas; Landay, Alan; Stevens, Wendy; Habiyambere, Vincent; Perrins, Jos; Peeling, Rosanna WBACKGROUND: Viral load (VL) monitoring is the standard of care in developing country settings for detecting HIV treatment failure. Since 2010 the World Health Organization has recommended a phase-in approach to VL monitoring in resource-limited settings. We conducted a systematic review of the accuracy and precision of HIV VL technologies for treatment monitoring. METHODS AND FINDINGS: A search of Medline and Embase was conducted for studies evaluating the accuracy or reproducibility of commercially available HIV VL assays. 37 studies were included for review including evaluations of the Amplicor Monitor HIV-1 v1.5 (n = 25), Cobas TaqMan v2.0 (n = 11), Abbott RealTime HIV-1 (n = 23), Versant HIV-1 RNA bDNA 3.0 (n = 15), Versant HIV-1 RNA kPCR 1.0 (n = 2), ExaVir Load v3 (n = 2), and NucliSens EasyQ v2.0 (n = 1). All currently available HIV VL assays are of sufficient sensitivity to detect plasma virus levels at a lower detection limit of 1,000 copies/mL. Bias data comparing the Abbott RealTime HIV-1, TaqMan v2.0 to the Amplicor Monitor v1.5 showed a tendency of the Abbott RealTime HIV-1 to under-estimate results while the TaqMan v2.0 overestimated VL counts. Compared to the Amplicor Monitor v1.5, 2-26% and 9-70% of results from the Versant bDNA 3.0 and Abbott RealTime HIV-1 differed by greater than 0.5log10. The average intra and inter-assay variation of the Abbott RealTime HIV-1 were 2.95% (range 2.0-5.1%) and 5.44% (range 1.17-30.00%) across the range of VL counts (2log10-7log10). CONCLUSIONS: This review found that all currently available HIV VL assays are of sufficient sensitivity to detect plasma VL of 1,000 copies/mL as a threshold to initiate investigations of treatment adherence or possible treatment failure. Sources of variability between VL assays include differences in technology platform, plasma input volume, and ability to detect HIV-1 subtypes. Monitoring of individual patients should be performed on the same technology platform to ensure appropriate interpretation of changes in VL. Prospero registration # CD42013003603.Item Open Access Systematic review of the use of dried blood spots for monitoring HIV viral load and for early infant diagnosis.(PLoS One, 2014) Smit, Pieter W; Sollis, Kimberly A; Fiscus, Susan; Ford, Nathan; Vitoria, Marco; Essajee, Shaffiq; Barnett, David; Cheng, Ben; Crowe, Suzanne M; Denny, Thomas; Landay, Alan; Stevens, Wendy; Habiyambere, Vincent; Perriens, Joseph H; Peeling, Rosanna WBACKGROUND: Dried blood spots (DBS) have been used as alternative specimens to plasma to increase access to HIV viral load (VL) monitoring and early infant diagnosis (EID) in remote settings. We systematically reviewed evidence on the performance of DBS compared to plasma for VL monitoring and EID. METHODS AND FINDINGS: Thirteen peer reviewed HIV VL publications and five HIV EID papers were included. Depending on the technology and the viral load distribution in the study population, the percentage of DBS samples that are within 0.5 log of VL in plasma ranged from 52-100%. Because the input sample volume is much smaller in a blood spot, there is a risk of false negatives with DBS. Sensitivity of DBS VL was found to be 78-100% compared to plasma at VL below 1000 copies/ml, but this increased to 100% at a threshold of 5000 copies/ml. Unlike a plasma VL test which measures only cell free HIV RNA, a DBS VL also measures proviral DNA as well as cell-associated RNA, potentially leading to false positive results when using DBS. The systematic review showed that specificity was close to 100% at DBS VL above 5000 copies/ml, and this threshold would be the most reliable for predicting true virologic failure using DBS. For early infant diagnosis, DBS has a sensitivity of 100% compared to fresh whole blood or plasma in all studies. CONCLUSIONS: Although limited data are available for EID, DBS offer a highly sensitive and specific sampling strategy to make viral load monitoring and early infant diagnosis more accessible in remote settings. A standardized approach for sampling, storing, and processing DBS samples would be essential to allow successful implementation. TRIAL REGISTRATION: PROSPERO Registration #: CRD42013003621.Item Open Access The External Quality Assurance Oversight Laboratory (EQAPOL) proficiency program for IFN-gamma enzyme-linked immunospot (IFN-γ ELISpot) assay.(Journal of Immunological Methods, 2014-07) Sanchez, Ana M; Rountree, Wes; Berrong, Mark; Garcia, Ambrosia; Schuetz, Alexandra; Cox, Josephine; Frahm, Nicole; Manak, Mark; Sarzotti-Kelsoe, Marcella; D'Souza, M Patricia; Denny, Thomas; Ferrari, GuidoThe interferon-gamma enzyme-linked immunospot (IFN-γ ELISpot) assay has been developed and used as an end-point assay in clinical trials for infectious diseases and cancer to detect the magnitude of antigen-specific immune responses. The ability to compare data generated by different laboratories across organizations is pivotal to understand the relative potency of different therapeutic and vaccine strategies. We developed an external proficiency program for the IFN-γ ELISpot assay that evaluates laboratory performance based on five parameters: timeliness for data reporting; ability to handle cellular samples; detection of background (non-specific) responses; accuracy to consensus of the results; and precision of the measurements. Points are awarded for each criterion, and the sum of the points is used to determine a numeric and adjectival performance rating. Importantly, the evaluation of the accuracy to the consensus mean for the detection of antigen-specific responses using laboratory-specific procedures informs each laboratory and its sponsor on the degree of concordance of its results with those obtained by other laboratories. This study will ultimately provide the scientific community with information on how to organize and implement an external proficiency program to evaluate longitudinally the performance of the participating laboratories and, therefore, fulfill the requirements of the GCLP guidelines for laboratories performing end-point IFN-γ ELISpot assay for clinical trials.Item Open Access Vaccine-Induced Antibodies Mediate Higher Antibody-Dependent Cellular Cytotoxicity After Interleukin-15 Pretreatment of Natural Killer Effector Cells.(Frontiers in immunology, 2019-01) Fisher, Leigh; Zinter, Melissa; Stanfield-Oakley, Sherry; Carpp, Lindsay N; Edwards, R Whitney; Denny, Thomas; Moodie, Zoe; Laher, Fatima; Bekker, Linda-Gail; McElrath, M Juliana; Gilbert, Peter B; Corey, Lawrence; Tomaras, Georgia; Pollara, Justin; Ferrari, GuidoThe secondary analyses for correlates of risk of infection in the RV144 HIV-1 vaccine trial implicated vaccine-induced antibody-dependent cellular cytotoxicity (ADCC) responses in the observed protection, highlighting the importance of assessing such responses in ongoing and future HIV-1 vaccine trials. However, in vitro assays that detect ADCC activity in plasma from HIV-1 infected seropositive individuals are not always effective at detecting ADCC activity in plasma from HIV-1 vaccine recipients. In vivo, ADCC-mediating antibodies must operate at the site of infection, where effector cells are recruited and activated by a local milieu of chemokines and cytokines. Based on previous findings that interleukin 15 (IL-15) secretion increases during acute HIV-1 infection and enhances NK cell-mediated cytotoxicity, we hypothesized that IL-15 pretreatment of NK effector cells could be used to improve killing of infected cells by vaccine-induced antibodies capable of mediating ADCC. Using the HIV-1 infectious molecular clone (IMC)-infected target cell assay along with plasma samples from HIV-1 vaccine recipients, we found that IL-15 treatment of effector cells improved the ability of the vaccine-induced antibodies to recruit effector cells for ADCC. Through immunophenotyping experiments, we showed that this improved killing was likely due to IL-15 mediated activation of NK effector cells and higher intracellular levels of perforin and granzyme B in the IL-15 pretreated NK cells. We also found that using a 4-fold dilution series of plasma and subtraction of pre-vaccination responses resulted in lowest response rates among placebo recipients and significant separation between treatment groups. This represents the first attempt to utilize IL-15-treated effector cells and optimized analytical approaches to improve the detection of HIV-1 vaccine-induced ADCC responses and will inform analyses of future HIV vaccine clinical trials.