Biology subjects

Keating, S. M.

Publications and source records attributed to Keating, S. M..

5 recordsLinked to original sources

bioRxiv2020

Capturing and Recreating Diverse Antibody Repertoires as Multivalent Recombinant Polyclonal Antibody Drugs

Plasma-derived polyclonal antibodies are polyvalent drugs used for many important clinical indications that require modulation of multiple drug targets simultaneously, including emerging infectious disease and transplantation. However, plasma-derived drugs suffer many problems, including low potency, impurities, constraints on supply, and batch-to-batch variation. In this study, we demonstrated proofs-of-concept for a technology that uses microfluidics and molecular genomics to capture diverse mammalian antibody repertoires as multivalent recombinant drugs. These "recombinant hyperimmune" drugs comprised thousands to tens of thousands of antibodies and were derived from convalescent human donors, or vaccinated human donors or immunized mice. Here we used our technology to build a highly potent recombinant hyperimmune for Severe Acute Respiratory Syndrome Coronavirus-2 (SARS CoV-2) in less than three months. We also validated a recombinant hyperimmune for Zika virus disease that abrogates antibody-dependent enhancement (ADE) through Fc engineering. For patients with primary immune deficiency (PID), we built high potency polyvalent recombinant hyperimmunes against pathogens that commonly cause serious lung infections. Finally, to address the limitations of rabbit-derived anti-thymocyte globulin (ATG), we generated a recombinant human version and demonstrated in vivo function against graft-versus-host disease (GVHD). Recombinant hyperimmunes are a novel class of drugs that could be used to target a wide variety of other clinical applications, including cancer and autoimmunity.

immunology↗

bioRxiv2019

Wikidata as a FAIR knowledge graph for the life sciences

Wikidata is a community-maintained knowledge base that epitomizes the FAIR principles of Findability, Accessibility, Interoperability, and Reusability. Here, we describe the breadth and depth of biomedical knowledge contained within Wikidata, assembled from primary knowledge repositories on genomics, proteomics, genetic variants, pathways, chemical compounds, and diseases. We built a collection of open-source tools that simplify the addition and synchronization of Wikidata with source databases. We furthermore demonstrate several use cases of how the continuously updated, crowd-contributed knowledge in Wikidata can be mined. These use cases cover a diverse cross section of biomedical analyses, from crowdsourced curation of biomedical ontologies, to phenotype-based diagnosis of disease, to drug repurposing.

bioinformatics↗

bioRxiv2019

Performance comparison of the Maxim and Sedia Limiting Antigen Avidity assays for incidence surveillance

BackgroundTwo manufacturers, Maxim Biomedical and Sedia Biosciences Corporation, supply US CDC-approved versions of the HIV-1 Limiting Antigen Avidity EIA (LAg assay) for detecting recent HIV infection in cross-sectional incidence estimation. This study assesses and compares the performance of the Maxim and Sedia LAg assays for incidence surveillance.\n\nMethodsWe ran both assays on a panel of 2,500 well-characterized HIV-1-infected specimens, most with estimated dates of (detectable) infection. We analysed concordance of assay results, assessed reproducibility using repeat testing and estimated the critical performance characteristics of a test for recent infection--mean duration of recent infection (MDRI) and false-recent rate (FRR)--for a range of normalized optical density (ODn) recency discrimination thresholds, alone and in combination with viral load thresholds. We further defined three hypothetical surveillance scenarios and evaluated overall performance for incidence surveillance, defined as the precision of incidence estimates, by estimating context-specific performance characteristics.\n\nResultsThe Maxim assay produced lower ODn values than the Sedia assay on average, largely as a result of higher calibrator readings (mean calibrator OD of 0.749 vs. 0.643). Correlation of non-normalized OD readings was greater (R2 = 0.938) than those of ODn readings (R2 = 0.908), and the slope was closer to unity (1.054 vs. 0.899). Reproducibility of repeat testing of three blinded control specimens (25 replicates each) was slightly better for the Maxim assay (CV 8.9% to 14.8% vs. 13.2% to 15.0%). The MDRI of a Maxim-based algorithm at the standard recency discrimination threshold in combination with viral load (ODn [≤]1.5 & VL >1,000) was 201 days (95% CI: 180,223) and for Sedia was 171 days (95% CI: 152,191). Commensurately, the Maxim algorithm had a higher FRR in treatment-naive subjects (1.7% vs. 1.1%). We observed statistically significant differences in MDRI using the ODn alone ([≤]1.5) and in combination with viral load (>1,000). Under three fully-specified hypothetical surveillance scenarios (comparable to South Africa, Kenya and a concentrated epidemic), recent infection testing algorithms based on the two assays produced similar precision of incidence estimates.\n\nConclusionsDifferences in ODn measurements between the Maxim and Sedia LAg assays on the same specimens largely resulted from differences in the reactivity of calibrators supplied by the manufacturers. Performance for surveillance purposes was extremely similar, although different ODn thresholds were optimal and different values of MDRI and FRR were appropriate for use in survey planning and incidence estimation.

epidemiology↗

bioRxiv2018

Assessing intra-lab precision and inter-lab repeatability of outgrowth assays of HIV-1 latent reservoir size

Quantitative viral outgrowth assays (QVOA) use limiting dilutions of CD4+ T cells to measure the size of the latent HIV-1 reservoir, a major obstacle to curing HIV-1. Efforts to reduce the reservoir require assays that can reliably quantify its size in blood and tissues. Although QVOA is regarded as a \"gold standard\" for reservoir measurement, little is known about its accuracy and precision or about how cell storage conditions or laboratory-specific practices affect results. Owing to this lack of knowledge, confidence intervals around reservoir size estimates - as well as judgments of the ability of therapeutic interventions to alter the size of the replication-competent but transcriptionally inactive latent reservoir - rely on theoretical statistical assumptions about dilution assays. To address this gap, we have carried out a Bayesian statistical analysis of QVOA reliability on 75 split samples of peripheral blood mononuclear cells (PBMC) from 5 antiretroviral therapy (ART)-suppressed participants, measured using four different QVOAs at separate labs, estimating assay precision and the effect of frozen cell storage on estimated reservoir size. We found that typical assay results are expected to differ from the true value by a factor of 1.6 to 1.9 up or down. Systematic assay differences comprised a 24-fold range between the assays with highest and lowest scales, likely reflecting differences in viral outgrowth readout and input cell stimulation protocols. We also found that controlled-rate freezing and storage of samples did not cause substantial differences in QVOA compared to use of fresh cells (95% probability of < 2-fold change), supporting continued use of frozen storage to allow transport and batched analysis of samples. Finally, we simulated an early-phase clinical trial to demonstrate that batched analysis of pre- and post-therapy samples may increase power to detect a three-fold reservoir reduction by 15 to 24 percentage points.\n\nAuthor summaryThe latent reservoir of resting CD4+ T cells is a major, if not the primary, obstacle to curing HIV. Quantitative viral outgrowth assays (QVOAs) are used to measure the latent reservoir in ART-suppressed HIV-infected people. Using QVOA is difficult, however, as the fraction of cells constituting the latent reservoir is typically about one in one million, far lower than other infectious disease biomarkers. To study reliability of these assays, we distributed 75 PBMC samples from five ART-suppressed HIV-infected participants among four labs, each conducting QVOA and following prespecified sample batching procedures. Using a Bayesian statistical method, we analyzed detailed assay output to understand how results varied within batches, between batches, and between labs. We found that, if batch variation can be controlled (i.e., a lab assays all samples in one batch), typical assay results are expected to differ from the true value by a factor of 1.6 to 1.9 up or down. We also found that freezing, storing, and thawing samples for later analysis caused no more than a 2-fold change in results. These outcomes, and the statistical methods developed to obtain them, should lead towards more precise and powerful assessments of HIV cure strategies.

microbiology↗

bioRxiv2017

Diagnostic, Infection Timing and Incidence Surveillance Applications of High Dynamic Range Chemiluminescent HIV Immuno-Assay Platforms

BackgroundCustom staging assays, including the Sedia HIV-1 Limiting Antigen Avidity EIA (LAg) and avidity modifications of the Ortho VITROS anti-HIV-1+2 and Abbott ARCHITECT HIV Ag/Ab Combo assays, are used to identify recent infections in clinical settings and for cross-sectional HIV incidence estimation. However, the high dynamic range of chemiluminescent platforms allows differentiating recent and longstanding infection on signal intensity, and this raises the prospect of using unmodified diagnostic assays for infection timing and surveillance applications.\n\nMethodsWe tested a panel of 2,500 well-characterised specimens with estimable duration of HIV infection with the three assays and the unmodified ARCHITECT. Regression models were used to estimate mean durations of recent infection (MDRI), context-specific false-recent rates (FRR) and correlation between signal intensity and LAg measurements. A hypothetical epidemiological scenario was constructed to evaluate utility in surveillance applications.\n\nResultsOver a range of MDRIs (reflecting recency discrimination thresholds), a diluted ARCHITECT-based RITA produced lower FRRs than the VITROS platform (FRR {approx} 0.5% and 1.5% respectively at MDRI of 200 days) and the unmodified diagnostic ARCHITECT produces incidence estimates with comparable precision to LAg (RSE {approx} 17.5% and 15% respectively at MDRI of 200 days). ARCHITECT S/CO measurements were highly correlated with LAg ODn measurements (r = 0.80) and values below 200 are strongly predictive of LAg recency and duration of infection less than one year.\n\nConclusionsLow quantitative measurements from the unmodified ARCHITECT obviate the need for additional recency testing and its use is feasible in clinical staging and incidence surveillance applications.

epidemiology↗