Biology subjects

Conway, J. M.

Publications and source records attributed to Conway, J. M..

At least 19 recordsLinked to original sources

bioRxiv2026

Development of a CRISPR-Cas9 genome editing system for the extremely thermophilic bacterium Anaerocellum bescii

Anaerocellum (f. Caldicellulosiruptor) bescii is an extremely thermophilic (Topt 75-78 {degrees}C) anaerobic bacterium and is also a highly efficient degrader of lignocellulose, making it a promising platform for metabolic engineering. To date, chromosomal genetic manipulations in A. bescii have required multistep procedures involving homologous recombination with integrating vectors and counterselection. Here, we demonstrate the first implementation of CRISPR-Cas9 genome editing in A. bescii facilitated by a thermostable Cas9 enzyme from Geobacillus stearothermophilus (GeoCas9). Delivery of heterologous CRISPR machinery via a replicating vector enabled us to individually and sequentially delete genes for lactate dehydrogenase (ldh) and pyrE in A. bescii. We then deployed this system to delete a novel target, tryptophan synthase (trpBA), generating a tryptophan auxotrophic strain of A. bescii. Using this strain, we show trpBA complementation enables selection and maintenance of a replicating vector expressing a heterologous enzymatic reporter gene.

microbiology↗

bioRxiv2026

Genetic determinants of Brevundimonas-mediated attenuation of plant pattern-triggered immunity

Root-associated commensal bacteria from diverse taxonomic groups can attenuate plant pattern-triggered immunity (PTI), yet the bacterial mechanisms underlying immune attenuation remain poorly understood. Brevundimonas sp. MF374 is a root-associated Alphaproteobacterium previously identified as a strong attenuator of flg22-triggered immunity. Here, to identify the genetic determinants underlying this phenotype, we conducted transposon mutagenesis and screened 4,032 MF374 mutants for defects in immune attenuation. Deletion and complementation of candidate loci identified tonB1 (BLR19_RS15045) as the strongest determinant of immune attenuation, with ppiD (BLR19_RS02880) making a weaker contribution. A panel of GUS reporter assays designed to distinguish among different mechanisms of attenuation showed that intact MF374 cells directly reduced the immune-eliciting activity of flg22 in a tonB1-dependent manner. TonB1 also contributed to attenuation of responses triggered by a distinct flg22 sequence and the endogenous plant elicitor AtPEP1. Together, these findings implicate TonB-dependent transport in attenuation of flg22-induced immunity by MF374 and reveal a previously uncharacterized mechanism of immune attenuation by a root-associated commensal.

microbiology↗

bioRxiv2025

Structural insights into xyloglucan recognition by an ABC transporter from a Gram-positive, thermophilic bacterium

Xyloglucan (an -1,6-xylosyl-substituted {beta}-1,4-glucan) is a major hemicellulose of the primary cell wall of many plants and an important growth substrate for biomass-degrading bacteria in diverse ecological niches, including the gut microbiome and hot springs. In Gram-positive bacteria, xyloglucan is deconstructed into soluble oligosaccharides in the extracytoplasmic space before import by ATP-Binding Cassette (ABC) transporters, but the structural basis for this process remains poorly understood. Here, we identified an ABC transporter for xyloglucan uptake (Athe_2052-2054) in the Gram-positive, plant biomass-degrading thermophile Anaerocellum bescii, which is conserved across the Anaerocellum genus. We solved the apo crystal structure of its extracellular substrate-binding protein (SBP), Athe_2052, revealing a unique tertiary fold found only in a small subset of SBPs that bind complex oligosaccharides. This structure represents the first ABC SBP known to bind xyloglucan oligosaccharides. Biophysical analysis showed that while Athe_2052 binds unsubstituted {beta}-glucan chains, recognition of xyloglucan side chains in the binding pocket markedly increases affinity (Kd = 14 nM) for xyloglucan heptasaccharide (XXXG), the principal oligosaccharide released during xyloglucan deconstruction. Molecular modeling revealed that xyloglucan heptasaccharide, owing to its branched substitutions, is bound in a distinct conformation compared to unsubstituted {beta}-glucans. This represents a unique mode of xyloglucan recognition driven by -linked side-chain interactions rather than {beta}-glucan backbone recognition alone. Together, these findings provide the first structural basis for xyloglucan oligosaccharide recognition by an ABC transporter in Gram-positive bacteria.

molecular biology↗

bioRxiv2025

The TEAIV model: Extending the standard TEIV model to account for viral budding ramp up

Understanding how viruses replicate and spread within a host is fundamental to predicting disease progression, timing, and dosage of effective therapeutic and prophylactic interventions. A target-cell limited approach is often used to model within-host viral kinetics to characterize disease infection dynamics. The standard target-cell limited model, the TEIV model, has been instrumental for understanding SARS-CoV-2 within-host viral kinetics, however, its core assumptions of instantaneous viral budding and exponentially distributed cell lifetimes oversimplify fundamental biological processes, potentially limiting predictive power. In this work, we consider a novel model approach, the TEAIV model: an extension to the TEIV model that considers an infected partially-productive cell state that ramps up through n stages to a fully productive state. We fit the TEAIV model to various SARS-CoV-2 viral load datasets, separated by hospitalized (severe infection) and non-hospitalized (mild infection) individual data, consider multiple different ramping functions, and compare to standard TEIV model fits. We further compare TEAIV and TEIV model fits with and without infected cell death incorporated in the eclipse (E) and partially infected (A) compartments and investigate best-fit frameworks up to 10 A states. We find that linear budding ramp-up dynamics minimizes the BIC (with {Delta}BIC > 2) across all model formulations when the total number of eclipse and budding compartments exceeds three. Furthermore, we find that the inclusion or exclusion of cell death applied to eclipse or ramping compartments does not substantially affect this result. Finally, we analytically consider the most general TEAIV model and discuss future modelling considerations. Our results demonstrate that accounting for non-instantaneous viral budding provides a better fit to SARS-CoV-2 viral load data and establishes a foundation for more mechanistically informed within-host models.

systems biology↗

bioRxiv2025

Engineering auxin degradation into root-associated bacteria promotes plant growth

Overproduction of indole-3-acetic acid (IAA) by rhizosphere bacteria disrupts plant auxin homeostasis and induces root growth inhibition (RGI). Variovorax reverses this effect by degrading IAA, but the underlying pathway remains incompletely resolved. Here, using genetics, metabolomics, and isotope tracing, we define a nine-gene region (iadCDEFGHIJK2) required for IAA catabolism in Variovorax paradoxus CL014, identify a previously uncharacterized intermediate (CHNO), and revise the early oxidative steps of the pathway. Although IadDE adopts a Rieske-type oxygenase architecture, our data are consistent with the IadCDE complex functioning as a monooxygenase during IAA degradation. Using these insights, we introduce iad genes into two rhizobacterial chassis, Polaromonas MF047 and Paraburkholderia MF376. These engineered strains degrade IAA and alleviate RGI induced by exogenous IAA, an auxin-producing strain, and a synthetic bacterial community. Engineered Paraburkholderia MF376 delivers the strongest performance, improving plant growth in natural soil. Together, these results establish a framework for engineering auxin-balancing root commensals.

microbiology↗

bioRxiv2025

A General Analytic Approach to Predicting the Best Antibiotic Dosing Regimen

Determining optimal antibiotic dosing strategies is complex. Clinically, some antibiotics work best in continuous low doses, while others require high repeated pulses. However, a rational understanding of the best approach depending on the specific pairing of antibiotic and bacterial species remains unclear. Using mathematical models, we analyze bacterial populations under two strategies - constant concentration and repeated dosing - given fixed pharmacodynamic and pharmacokinetic properties. Our results reveal that the shape of the dose-response curve, which measures bacterial net growth rate against antibiotic concentration, is crucial. Specifically, its concavity determines the best strategy. In cases where the curve exhibits multiple concavities, additional factors such as tolerable dosing range influence the regimen. These findings challenge the universal application of "hit hard and hit early," as some recommended schedules include lower, constant doses. This work contributes to the literature on rational antibiotic prescription, aiming to minimize antibiotic use and combat antimicrobial resistance.

pharmacology and toxicology↗

bioRxiv2025

A Straightforward and Robust Enzymatic Reporter System for Anaerobic Thermophiles

Thermophilic anaerobic organisms, particularly species that can naturally degrade lignocellulosic biomass, show great promise for next generation bioprocessing. This has led to the development of nascent genetic systems to metabolically engineer these non-model organisms. However, a major challenge remains a lack of reliable reporter systems compatible with the combination of thermophilic and anaerobic growth conditions. Additionally, native glycoside hydrolases in these organisms limit the usefulness of traditional glycosidic enzyme reporters (e.g. LacZ) because of the native background activity present on para-nitrophenyl glucoside substrates. Here we describe the development of a straightforward and robust enzymatic reporter system that overcomes these challenges in Anaerocellum (f. Caldicellulosiruptor) bescii, an anaerobic, extremely thermophilic (Topt [~]78 {degrees}C), lignocellulolytic bacterium. Our method is based on heterologous expression of hyperthermophilic archaeal galactosidases: an -galactosidase from Pyroccous furiosus (Pfgal), and a {beta}-galactosidase from Caldivirga maquilingensis (Cm{beta}gal). We show that these reporters produce strong, orthogonal signals on colorimetric substrates at high temperatures ([≥]90{degrees}C) that eliminate background activity from endogenous galactosidases. We then demonstrate the capability of Cm{beta}gal, the stronger of the two reporters, to distinguish differences in levels of expression between A. bescii promoter sequences, which we verify through qRT-PCR. With its high signal to noise ratio and ease of use, this reporter system offers a reliable method for assessing protein expression in anaerobic thermophilic organisms, opening doors to improved genetic tools and metabolic engineering applications for industrial biotechnology.

synthetic biology↗

bioRxiv2025

Functional and structural characterization of AtAbf43C: An exo-1,5-α-L-arabinofuranosidase from Acetivibrio thermocellus DSM1313

The Acetivibrio thermocellus DSM1313 genome codes for seven predicted glycoside hydrolase family 43 (GH43) enzymes, four of which remain uncharacterized. This study describes the function and structure of one such enzyme, AtAbf43C, from GH43 subfamily 26 (GH43_26) which acts as an -L-arabinofuranosidase (EC 3.2.1.55). AtAbf43C is active on para-nitrophenol--L-arabinofuranoside (pNPAra), with optimal activity observed at pH 5.5 and 65 . Multiple crystal structures of AtAbf43C were obtained, in which an N-terminal carbohydrate binding module family 42 (CBM42) domain displays a {beta}-trefoil type fold and the C-terminal GH43 domain displays a canonical 5-bladed {beta}-propeller motif. One structure, which was solved with two L-arabinofuranose molecules bound to {beta}- and {gamma}-subdomains of the CBM42, builds upon previous literature suggesting the -binding pocket of the AtAbf43C CBM42 is non-functional. Furthermore, structural alignment with the substrate bound structure of a closely homologous GH43_26 exo--1,5-arabinofuranosidase, SaAraf43A from Streptomyces avermitilis (PDB 3AKH), allowed for identification of the conserved catalytic triad via site-directed mutagenesis in AtAbf43C, as well as insight into the deep-narrow topology of the AtAbf43C binding pocket that suggested it would be active on similar arabino-oligosaccharide (AOS) substrates as SaAraf43A. Subsequent liquid chromatography-mass spectrometry (LC-MS) analysis of polysaccharides and oligosaccharides hydrolyzed by AtAbf43C provides experimental evidence confirming this enzyme acts in an exo manner primarily towards -1,5 linked arabino-oligosaccharides.

molecular biology↗

bioRxiv2025

Machine Learning Reveals Distinct Immunogenic Signatures of Th1 Imprinting in ART-Treated Individuals with HIV Following Repeated SARS-CoV-2 Vaccination

The human immune system is intrinsically variable and remarkably diverse across a population. The immune response to antigens is driven by a complex interplay of time-dependent interdependencies across components of the immune system. After repeated vaccination, the humoral and cellular arms of the immune response display highly heterogeneous dynamics, further complicating the attribution of a phenotypic outcome to specific immune system components. We employ a random forest (RF) approach to classify informative differences in immunogenicity between older people living with HIV (PLWH) on ART and an age-matched control group who received up to five SARS-CoV-2 vaccinations over 104 weeks. RFs identify immunological variables of importance, interpreted as evidence for Th1 imprinting, and suggest novel distinguishing immune features, such as saliva-based antibody screening, as promising diagnostic features towards classifying responses (whereas serum IgG is not). Additionally, we implement supervised and unsupervised Machine Learning methods to produce physiologically accurate synthetic datasets that conform to the statistical distribution of the original immunological data, thus enabling further data-driven hypothesis testing and model validation. Our results highlight the effectiveness of RFs in utilizing informative immune feature interdependencies for classification tasks and suggests broad impacts of ML applications for personalized vaccination strategies among high-risk populations.

immunology↗

bioRxiv2025

A Highly Conserved ABC Transporter Mediates Cello-Oligosaccharide Uptake in the Extremely Thermophilic, Lignocellulolytic Bacterium Anaerocellum (f. Caldicellulosiruptor) bescii

Cellulose deconstruction and utilization are key to unlocking renewable fuel and chemical production. Anaerocellum bescii (formerly Caldicellulosiruptor bescii) is an extremely thermophilic cellulolytic bacterium, among the most effective at degrading lignocellulosic biomass due to its arsenal of multi-domain cellulases and hemicellulases. However, little is known about how it transports the assorted sugars released from lignocellulose degradation into the cell for catabolism. Among its twenty-three ATP-Binding Cassette (ABC) sugar transporters, the mechanism for uptake of cello-oligosaccharides released from cellulose degradation remains unclear. Here, we identify an ABC transporter locus (Athe_0595 -- 0598), highly conserved in the genus with two extracellular binding proteins, Athe_0597 and Athe_0598. Biophysical analyses, including Differential Scanning Calorimetry (DSC) and Isothermal Titration Calorimetry (ITC), reveal that Athe_0597, binds cello-oligosaccharides of varying lengths (G2-5), while Athe_0598 is specific to cellobiose (G2). Computational modeling of ligand docking supports these findings and sheds light on the subsite configuration of the substrate binding proteins. To assess its physiological importance, we genetically deleted this transporter locus in A. bescii strain HTAB187, which does not grow on cellulose and grows poorly on cellobiose. Comparison of growth with a msmK deletion strain that cannot consume oligosaccharides shows that HTAB187 can grow on non-cello-oligosaccharides (e.g. maltose) or monosaccharides. Taken together, this study integrates biophysical characterization, structural modeling, and genetic perturbation to elucidate how A. bescii transports cello-oligosaccharides release from cellulose, opening doors for its future use in applied bioprocessing contexts. ImportanceAnaerocellum bescii is the most thermophilic cellulolytic bacterium known, and holds potential for bioprocessing lignocellulosic biomass into renewable fuels. Its diverse ATP-Binding Cassette (ABC) sugar transporters make it a valuable model for studying thermophilic sugar uptake. Here, we identify a single ABC transporter with two substrate binding proteins (Athe_0597 and Athe_0598) responsible for cello-oligosaccharide uptake. Genetic deletion of this transporter impaired growth on cellobiose and eliminated growth on cellulose. This is the first genetic manipulation in A. bescii to modulate transport of a specific sugar. We also characterize the substrate specificity of the substrate binding proteins associated with the locus; one binds various cellodextrins (G2-5), while the other specifically binds cellobiose (G2). Computational modeling reveals how each sugar docks within the binding pocket of these proteins. Understanding the mechanism of cello-oligosaccharide uptake by A. bescii expands opportunities for its metabolic engineering and furthers our understanding of thermophilic sugar transport.

microbiology↗

bioRxiv2024

Maltodextrin Transport in the Extremely Thermophilic, Lignocellulose Degrading Bacterium Anaerocellum bescii (f. Caldicellulosiruptor bescii)

Sugar transport into microbial cells is a critical, yet understudied step in the conversion of lignocellulosic biomass to metabolic products. Anaerocellum bescii (formerly Caldicellulosiruptor bescii) is an extremely thermophilic, anaerobic bacterium that readily degrades the cellulose and hemicellulose components of lignocellulosic biomass into a diversity of oligosaccharide substrates. Despite significant understanding of how this microorganism degrades lignocellulose, the mechanisms underlying its highly efficient transport of the resulting oligosaccharides into the cell are comparatively underexplored. Here, we identify and characterize the ATP-Binding Cassette (ABC) transporters in A. bescii governing maltodextrin transport. Utilizing past transcriptomic studies on Anaerocellum and Caldicellulosiruptor species, we identify two maltodextrin transporters in A. bescii and express and purify their substrate-binding proteins (Athe_2310 and Athe_2574) for characterization. Using differential scanning calorimetry and isothermal titration calorimetry, we show that Athe_2310 strongly interacts with shorter maltodextrins such as maltose and trehalose with dissociation constants in the micromolar range, while Athe_2574 binds longer maltodextrins, with dissociation constants in the sub-micro molar range. Using a sequence-structure-function comparison approach combined with molecular modeling we provide context for the specificity of each of these substrate-binding proteins. We propose that A. bescii utilizes orthogonal ABC transporters to uptake malto-oligosaccharides of different lengths to maximize transport efficiency. ImportanceHere, we reveal the biophysical and structural basis for oligosaccharide transport by two maltodextrin ABC transporters in A. bescii. This is the first biophysical characterization of carbohydrate uptake in this organism and establishes a workflow for characterizing other oligosaccharide transporters in A. bescii and similar lignocellulosic thermophiles of interest for lignocellulosic bioprocessing. By deciphering the mechanisms underlying high affinity sugar uptake in A. bescii, we shed light on an underexplored step between extracellular lignocellulose degradation and intracellular conversion of sugars to metabolic products. This understanding will expand opportunities for harnessing sugar transport in thermophiles to reshape lignocellulose bioprocessing as part of a renewable bioeconomy.

biophysics↗

bioRxiv2024

A Mechanistic Approach to Optimize Combination Antibiotic Therapy

Antimicrobial resistance is one of the most significant healthcare challenges of our times. Multidrug or combination therapies are sometimes required to treat severe infections; for example, the current protocols to treat pulmonary tuberculosis combine four antibiotics. However, combination therapy is usually based on lengthy empirical trials and it is difficult to predict its efficacy. We propose a new tool to identify antibiotic synergy or antagonism and optimize combination therapies. Our model explicitly incorporates the mechanisms of individual drug action and estimates their combined effect using a mechanistic approach. By quantifying the impact on growth and death of a bacterial population, we can identify optimal combinations of multiple drugs. Our approach also allows for the investigation of the drugs actions and the testing of theoretical hypotheses. We demonstrate the utility of this tool with in vitro Escherichia coli data using a combination of ampicillin and ciprofloxacin. In contrast to previous interpretations, our model finds a slight synergy between the antibiotics. Our mechanistic model allows investigating possible causes of the synergy.

pharmacology and toxicology↗

bioRxiv2024

Assessing the impact of autologous neutralizing antibodies on rebound dynamics in postnatally SHIV-infected ART-treated infant Rhesus macaques

AO_SCPLOWBSTRACTC_SCPLOWThe presence of antibodies against HIV in infected children is associated with a greater capacity to control viremia in the absence of therapy. While the benefits of early antiretroviral treatment (ART) in infants are well documented, early ART may interfere with the development of antibody responses. In contrast to adults, early treated children lack detectable HIV-specific antibodies, suggesting a fundamental difference in HIV pathogenesis. Despite this potential adverse effect, early ART may decrease the size of the latent reservoir established early in infection in infants, which can be beneficial in viral control. Understanding the virologic and immunologic aspects of pediatric HIV is crucial to inform innovative targeted strategies for treating children living with HIV. In this study, we investigate how ART initiation time sets the stage for trade-offs in the latent reservoir establishment and the development of humoral immunity and how these, in turn, affect post-treatment dynamics. We also elucidate the biological function of antibodies in pediatric HIV. We employ mathematical modeling coupled with experimental data from an infant nonhuman primate Simian/Human Immunodeficiency Virus (SHIV) infection model. Infant Rhesus macaques (RMs) were orally challenged with SHIV.C.CH505 375H dCT four weeks after birth and started treatment at different times after infection. In addition to viral load measurements, antibody responses and latent reservoir sizes were measured. We estimate model parameters by fitting viral load measurements to the standard HIV viral dynamics model within a nonlinear fixed effects framework. This approach allows us to capture differences between rhesus macaques (RMs) that develop antibody responses or exhibit high latent reservoir sizes compared to those that do not. We find that neutralizing antibody responses are associated with increased viral clearance and decreased viral infectivity but decreased death rate of infected cells. In addition, the presence of detectable latent reservoir is associated with less robust immune responses. These results demonstrate that both immune response and latent reservoir dynamics are needed to understand post-rebound dynamics and point to the necessity of a comprehensive approach in tailoring personalized medical interventions.

immunology↗

bioRxiv2024

Comparative Analysis of Within-Host Dynamics of Acute Infection and Viral Rebound Dynamics in Postnatally SHIV-Infected ART-Treated Infant Rhesus Macaques

Viral dynamics of acute HIV infection and HIV rebound following suspension of antiretroviral therapy may be qualitatively similar but must differ given, for one, development of adaptive immune responses. Understanding the differences of acute HIV infection and viral rebound dynamics in pediatric populations may provide insights into the mechanisms of viral control with potential implications for vaccine design and the development of effective targeted therapeutics for infants and children. Mathematical models have been a crucial tool to elucidate the complex processes driving viral infections within the host. Traditionally, acute HIV infection has been modeled with a standard model of viral dynamics initially developed to explore viral decay during treatment, while viral rebound has necessitated extensions of that standard model to incorporate explicit immune responses. Previous efforts to fit these models to viral load data have underscored differences between the two infection stages, such as increased viral clearance rate and increased death rate of infected cells during rebound. However, these findings have been predicated on viral load measurements from disparate adult individuals. In this study, we aim to bridge this gap, in infants, by comparing the dynamics of acute infection and viral rebound within the same individuals by leveraging an infant nonhuman primate Simian/Human Immunodeficiency Virus (SHIV) infection model. Ten infant Rhesus macaques (RMs) orally challenged with SHIV.C.CH505 375H dCT and given ART at 8 weeks post-infection. These infants were then monitored for up to 60 months post-infection with serial viral load and immune measurements. We use the HIV standard viral dynamics model fitted to viral load measurements in a nonlinear mixed effects framework. We find that the primary difference between acute infection and rebound is the increased death rate of infected cells during rebound. We use these findings to generate hypotheses on the effects of adaptive immune responses. We leverage these findings to formulate hypotheses to elucidate the observed results and provide arguments to support the notion that delayed viral rebound is characterized by a stronger CD8+ T cell response.

immunology↗

bioRxiv2024

A type II secreted subtilase from commensal rhizobacteria disarms the immune elicitor peptide flg22

Plant roots grow in association with a community of microorganisms collectively known as the rhizosphere microbiome. Immune activation in response to elicitors like the flagellin-derived epitope flg22 restricts bacteria on plant roots but also inhibits plant growth. Some commensal root-associated bacteria are capable of suppressing the plant immune response to elicitors. In this study, we investigated the ability of 165 root-associated bacteria to suppress flg22-induced immune activation and growth restriction. We demonstrate that a type II secreted subtilase, which we term Immunosuppressive Subtilase A (IssA), from Dyella japonica strain MF79 cleaves the immune eliciting peptide flg22 and contributes to immune suppression. IssA homologs are found in other plant-associated commensals, with particularly high conservation in the order Xanthomonadales. This represents a novel mechanism by which commensal microbes modulate flg22-induced immunity in the rhizosphere microbiome.

microbiology↗

bioRxiv2024

Understanding early HIV-1 rebound dynamics following antiretroviral therapy interruption: The importance of effector cell expansion

Most people living with HIV-1 experience rapid viral rebound once antiretroviral therapy is interrupted; however, a small fraction remain in viral remission for an extended duration. Understanding the factors that determine whether viral rebound is likely after treatment interruption can enable the development of optimal treatment regimens and therapeutic interventions to potentially achieve a functional cure for HIV-1. We built upon the theoretical framework proposed by Conway and Perelson to construct dynamic models of virus-immune interactions to study factors that influence viral rebound dynamics. We evaluated these models using viral load data from 24 individuals following antiretroviral therapy interruption. The best-performing model accurately captures the heterogeneity of viral dynamics and highlights the importance of the effector cell expansion rate. Our results show that post-treatment controllers and non-controllers can be distinguished based on the effector cell expansion rate in our models. Furthermore, these results demonstrate the potential of using dynamic models incorporating an effector cell response to understand early viral rebound dynamics post-antiretroviral therapy interruption.

immunology↗

bioRxiv2023

Somatic structural variants driving distinct modes of oncogenesis in melanoma

The diversity of structural variants (SVs) in melanoma and how they impact oncogenesis are incompletely known. We performed harmonized analysis of SVs across melanoma histological and genomic subtypes, and we identified distinct global properties between subtypes. These included the frequency and size of SVs and SV classes, their relation to chromothripsis events, and the role of topologically associated domain (TAD) boundary altering SVs on cancer-related genes. Following our prior identification of double-stranded break repair deficiency in a subset of triple wild-type cutaneous melanoma, we identified MRE11 and NBN loss-of-function SVs in melanomas with this mutational signature. Experimental knockouts of MRE11 and NBN, followed by olaparib cell viability assays in melanoma cells, indicated that dysregulation of each of these genes may cause sensitivity to PARPi in cutaneous melanomas. Broadly, harmonized analysis of melanoma SVs revealed distinct global genomic properties and molecular drivers, which may have biological and therapeutic impact. Statement of SignificanceThe diversity of SVs in melanoma, and how they directly or indirectly impact oncogenesis, are incompletely known. Here we present analysis of melanoma SVs that reveal distinct global genomic properties and molecular drivers, some of which point to opportunities for further biological and therapeutic investigation.

cancer biology↗

bioRxiv2023

Assessing the effect of antibody responses on viral rebound dynamics in postnatally SHIV-infected infant Rhesus macaques

AO_SCPLOWBSTRACTC_SCPLOWWhile the benefits of early antiretroviral therapy (ART) initiation in perinatally infected infants are well documented, early ART initiation is not always possible in postnatal pediatric HIV infections, which account for the majority of pediatric HIV cases worldwide. The timing of onset of ART initiation is likely to affect the size of the latent viral reservoir established, as well as the development of adaptive immune responses, such as the generation of neutralizing antibody responses against the virus. How these parameters impact the ability of infants to control viremia and the time to viral rebound after ART interruption is unclear. To gain insight into the dynamics, we utilized mathematical models to investigate the effect of time of ART initiation via latent reservoir size and autologous virus neutralizing antibody responses in delaying viral rebound when treatment is interrupted. We used an infant nonhuman primate Simian/Human Immunodeficiency Virus (SHIV) infection model that mimics breast milk HIV transmission in human infants. Infant Rhesus macaques (RMs) were orally challenged with SHIV.C.CH505 375H dCT and either given ART at 4-7 days post-infection (early ART condition), at 2 weeks post-infection (intermediate ART condition), or at 8 weeks post-infection (late ART condition). These infants were then monitored for up to 60 months post-infection with serial viral load and immune measurements. We develop a stochastic mathematical model to investigate the joint effect of latent reservoir size, the autologous neutralizing antibody potency, and CD4+ T cell levels on the time to viral rebound and control of post-rebound viral loads. We find that the latent reservoir size is an important determinant in explaining time to viral rebound by affecting the growth rate of the virus. The presence of neutralizing antibodies also can delay rebound, but we find this effect for high potency antibody responses only.

immunology↗