Biology subjects

Bradley, J. R.

Publications and source records attributed to Bradley, J. R..

4 recordsLinked to original sources

bioRxiv2024

A Zero-Inflated Hierarchical Generalized Transformation Model to Address Non-Normality in Spatially-Informed Cell-Type Deconvolution

Oral squamous cell carcinomas (OSCC), the predominant head and neck cancer, pose significant challenges due to late-stage diagnoses and low five-year survival rates. Spatial transcriptomics offers a promising avenue to decipher the genetic intricacies of OSCC tumor microenvironments. In spatial transcriptomics, Cell-type deconvolution is a crucial inferential goal; however, current methods fail to consider the high zero-inflation present in OSCC data. To address this, we develop a novel zero-inflated version of the hierarchical generalized transformation model (ZI-HGT) and apply it to the Conditional AutoRegressive Deconvolution (CARD) for cell-type deconvolution. The ZI-HGT serves as an auxiliary Bayesian technique for CARD, reconciling the highly zero-inflated OSCC spatial transcriptomics data with CARDs normality assumption. The combined ZI-HGT + CARD framework achieves enhanced cell-type deconvolution accuracy and quantifies uncertainty in the estimated cell-type proportions. We demonstrate the superior performance through simulations and analysis of the OSCC data. Furthermore, our approach enables the determination of the locations of the diverse fibroblast population in the tumor microenvironment, critical for understanding tumor growth and immunosuppression in OSCC.

genomics↗

bioRxiv2023

Microfluidic antibody profiling after repeated SARS-CoV-2 vaccination links antibody affinity and concentration to impaired immunity and variant escape in patients on anti-CD-20 therapy

BackgroundPatients with autoimmune/inflammatory conditions on anti-CD20 therapies, such as Rituximab, have suboptimal humoral responses to vaccination and are vulnerable to poorer clinical outcomes following SARS-CoV-2 infection. We aimed to examine how the fundamental parameters of antibody responses, namely affinity and concentration, shape the quality of humoral immunity after vaccination in these patients. MethodsWe performed in depth antibody characterisation in sera collected four to six weeks after each of three vaccine doses to wild-type (WT) SARS-CoV-2 in Rituximab-treated primary vasculitis patients (n=14) using Luminex and pseudovirus neutralisation assays, whereas a novel microfluidic-based immunoassay was used to quantify polyclonal antibody affinity and concentration against both WT and Omicron (B.1.1.529) variants. Comparative antibody profiling was performed at equivalent time points in healthy individuals after three antigenic exposures to WT SARS-CoV-2 (one infection and two vaccinations; n=15) and in convalescent patients after WT SARS-CoV-2 infection (n=30). ResultsRituximab-treated patients had lower antibody levels and neutralisation titres against both WT and Omicron SARS-CoV-2 variants compared to healthy individuals. Neutralisation capacity was weaker against Omicron versus WT both in Rituximab-treated patients and in healthy individuals. In the Rituximab cohort, this was driven by lower antibody affinity against Omicron versus WT (median [range] KD: 21.6 [9.7-38.8] nM vs 4.6 [2.3-44.8] nM, p=0.0004). By contrast, healthy individuals with hybrid immunity produced a broader antibody response, a subset of which recognised Omicron with higher affinity than antibodies in Rituximab-treated patients (median [range] KD: 1.05 [0.45-1.84] nM vs 20.25 [13.2-38.8] nM, p=0.0002), underpinning the stronger serum neutralisation capacity against Omicron in the former group. Rituximab-treated patients had similar anti-WT antibody levels and neutralisation titres to unvaccinated convalescent individuals, despite two more exposures to SARS-CoV-2 antigen. Temporal profiling of the antibody response showed evidence of affinity maturation in healthy convalescent patients after a single SARS-CoV-2 infection which was not observed in Rituximab-treated patients, despite repeated vaccination. DiscussionOur results enrich previous observations of impaired humoral immune responses to SARS-CoV-2 in Rituximab-treated patients and highlight the significance of quantitative assessment of serum antibody affinity and concentration in monitoring anti-viral immunity, viral escape, and the evolution of the humoral response.

immunology↗

bioRxiv2023

Hierarchical Bayesian modeling identifies key considerations in the development of quantitative loop-mediated isothermal amplification assays

MotivationLoop-mediated isothermal amplification (LAMP) is a rapidly growing, fast, and cost-effective technique for detection of DNA/RNA in point-of-care biomedical applications. However, it remains unclear what factors affect LAMPs quantitative resolution, and experimental optimization of primers presents a major bottleneck in assay design. A lack of model-based frameworks to characterize LAMP data and address these questions presents an unmet need for LAMP assay development. ResultsWe present hierarchical Bayesian models of LAMP amplification based on Gompertz functions, and use these models to infer the effect of RNA variation and other factors on LAMP amplification curves derived from 80 blood samples of patients with suspected acute infection. Our analysis uncovers associations between LAMP assay resolution and characteristics such as primer sequence composition and thermodynamic properties. In addition to correlations between RNA input abundance and time shift of the the LAMP amplification curve, we also detect RNA-dependent assocations with amplification rate. We further investigate associations between primer/target properties and quantitative performance of the assay by generating a set of synthetic RNA samples with systematically varied primer sequences and applying our framework. We find evidence that the associations observed are driven by across-target rather than within-target variation, an important observation for study design. Our findings represent important first steps towards guided development of quantitative LAMP assays. Availability and ImplementationAnalysis and modeling code is available upon reasonable request.

bioinformatics↗

bioRxiv2017

Consequences Of Natural Perturbations In The Human Plasma Proteome

Proteins are the primary functional units of biology and the direct targets of most drugs, yet there is limited knowledge of the genetic factors determining inter-individual variation in protein levels. Here we reveal the genetic architecture of the human plasma proteome, testing 10.6 million DNA variants against levels of 2,994 proteins in 3,301 individuals. We identify 1,927 genetic associations with 1,478 proteins, a 4-fold increase on existing knowledge, including trans associations for 1,104 proteins. To understand consequences of perturbations in plasma protein levels, we introduce an approach that links naturally occurring genetic variation with biological, disease, and drug databases. We provide insights into pathogenesis by uncovering the molecular effects of disease-associated variants. We identify causal roles for protein biomarkers in disease through Mendelian randomization analysis. Our results reveal new drug targets, opportunities for matching existing drugs with new disease indications, and potential safety concerns for drugs under development.

genomics↗