Biology subjects

Butler, K.

Publications and source records attributed to Butler, K..

7 recordsLinked to original sources

bioRxiv2026

APOBEC3G expression marks a TMB-high, T cell-inflamed tumor state and is associated with response to immune checkpoint blockade in multiple cancer cohorts

Immune checkpoint therapies have transformed clinical practice; however, reliable biomarkers to predict response remain limited. Tumor mutational burden (TMB) has emerged as an important biomarker because it is thought to reflect neoantigen load, yet its predictive utility has been inconsistent. This limitation may partly arise because TMB primarily captures tumor-intrinsic immunogenicity, which is heterogeneous and does not fully reflect the state of antitumor immunity. To identify transcriptomic surrogates that capture both high mutational burden and antitumor immune activation, we investigated whether mRNA expression of mutagenic APOBEC3 family members could serve as surrogates for high TMB and T cell-rich tumors. Using a pan-cancer computational framework, we evaluated the association of four APOBEC3 genes with mutational burden, neoantigen load, immune infiltration, and immune checkpoint blockade response. Among APOBEC3A, APOBEC3B, APOBEC3G, and APOBEC3H, APOBEC3G emerged as the strongest and most consistent marker of a TMBhighCD8high and NeoantigenhighCD8high tumor phenotypes. Single-cell analyses further demonstrated that APOBEC3G is enriched in both malignant cells and T cells compared with other APOBEC3 family members, with APOBEC3G-positive CD8+ T cells exhibiting elevated activation markers including GZMB and IFNG. Importantly, retrospective analyses of 50 immune checkpoint blockade cohorts showed that APOBEC3G had the most consistent association among APOBEC3 family members with treatment response and clinical outcomes. Together, these findings identify APOBEC3G as a candidate transcriptomic marker of a TMB-associated, T cell-inflamed tumor state linked to immune-checkpoint blockade benefit, warranting further prospective validation.

genomics↗

bioRxiv2026

APOBEC3-driven neoantigen-rich cancers co-opt 1q23.3 amplification for tumor-intrinsic immune cloaking

Hypermutational processes, including those driven by the APOBEC3 family of cytidine deaminases, generate abundant neoantigens yet give rise to tumors that evade immune recognition. Here, using multi-omics analyses followed by functional validation, we identified a tumor-intrinsic immune-cloaking mechanism in neoantigen-rich epithelial cancers, characterized by coordinated suppression of antigen presentation, immune-recruiting cytokines and immune-checkpoint programs. In bladder cancer, genome-wide copy-number analysis identified recurrent 1q23.3 amplification as a genomic feature of a neoantigen-high/CD8-low tumor state. Within this locus, NECTIN4 emerged as the dominant candidate effector, outperforming extrachromosomal DNA status as a predictor of immune-neoantigen discordance. Similar associations were observed across breast and lung cancers. Functional studies demonstrated that NECTIN4 was sufficient to establish a T-cell-poor tumor microenvironment and confer resistance to PD-1 blockade in immunocompetent mice. Mechanistically, NECTIN4 engaged a DDR1-SHP2 axis that suppressed STAT1 phosphorylation, silencing tumor-cell immune-engagement programs. NECTIN4 blockade restored STAT1 activity and reduced tumor growth, indicating that the cloaked state is pharmacologically reversible. Mutational signature, breakpoint motif, timing and clonality analyses, together with APOBEC3B expression and germline genetic evidence, linked APOBEC3-mediated mutagenesis to recurrent 1q23.3 amplification encompassing NECTIN4. These findings reveal how neoantigen-generating mutational processes can be coupled to structural genome evolution to enable tumor-intrinsic immune cloaking through a therapeutically targetable NECTIN4-DDR1-SHP2 axis.

cancer biology↗

bioRxiv2025

An application-specific approach to modelling the probability of unsuccessful initial attack on wildfires in Victoria, Australia

BackgroundInitial attack refers to the first firefighting actions undertaken at a newly reported fire, with the intention to control the fires spread. When multiple ignitions are reported and resources constrained, decisions need to be made about triaging fires for an escalated response. AimsWe developed empirical initial attack models for grass and forest fires for the specific purpose of triaging fires, and evaluated the models relative to their intended application. MethodsWe used a recently developed dataset of spreading fires and tested three statistical modelling techniques to model the probability of unsuccessful initial attack. Model performance was evaluated with case studies, including major fire episodes. Key resultsThe models showed limited skill overall. The best performance was observed for lightning-ignited forest fires in remote areas, but performance was not adequate to support implementation on days with extreme fire behaviour. ConclusionsOur approach did not yield suitable models for operational triage of fires, because there are many on-the-ground factors that influence the success of initial attack, and they are difficult to capture as data. ImplicationsThis study shows the importance of developing and testing empirical models relative to their intended application. It also demonstrates the significance of unmeasured bottlenecks in wildfire suppression on initial attack outcome. Summary text for Table of ContentsThis study develops models to aid operational staff in triaging fires for an escalated response. We determined that model performance was not suitable for this use case. We found that using both modelling visualisations and case studies were fundamental in assessing the models applicability for operations.

ecology↗

bioRxiv2024

Engineered Cardiac Microtissue Biomanufacturing Using Human Induced Pluripotent Stem Cell-Derived Epicardial Cells

Epicardial cells are a crucial component in constructing in vitro 3D tissue models of the human heart, contributing to the ECM environment and the resident mesenchymal cell population. Studying the human epicardium and its development from the proepicardial organ is difficult, but induced pluripotent stem cells can provide a source of human epicardial cells for developmental modeling and for biomanufacturing heterotypic cardiac tissues. This study shows that a robust population of epicardial cells (approx. 87.7% WT1+) can be obtained by small molecule modulation of the Wnt signaling pathway. The population maintains WT1 expression and characteristic epithelial morphology over successive passaging, but increases in size and decreases in cell number, suggesting a limit to their expandability in vitro. Further, low passage number epicardial cells formed into more robust 3D microtissues compared to their higher passage counterparts, suggesting that the ideal time frame for use of these epicardial cells for tissue engineering and modeling purposes is early on in their differentiated state. Additionally, the differentiated epicardial cells displayed two distinct morphologic sub populations with a subset of larger, more migratory cells which led expansion of the epicardial cells across various extracellular matrix environments. When incorporated into a mixed 3D co-culture with cardiomyocytes, epicardial cells promoted greater remodeling and migration without impairing cardiomyocyte function. This study provides an important characterization of stem cell-derived epicardial cells, identifying key characteristics that influence their ability to fabricate consistent engineered cardiac tissues.

bioengineering↗

bioRxiv2022

Type-specific EV-D68 real-time RT-PCR assay for the detection of all extant enterovirus D68 strains

Enterovirus D68 (EV-D68) has caused recurring respiratory disease outbreaks in the United States since 2014. The dominant circulating EV-D68 strain has evolved from clade B1 to the more recent B2 and B3 clades. As recurrent outbreaks and continued virus evolution are expected for EV-D68, a robust real-time PCR assay that detects known strains as well as potential emerging strains is critical for national surveillance and clinical diagnostics. We describe a type-specific EV-D68 real-time RT-PCR (rRT-PCR) assay termed CDC2022, which targets sequences encoding conserved amino acid regions of all extant EV-D68 strains. We targeted three motifs conserved among all strains in the last 60 years. The assay achieved 100% (270/270) sensitivity and 100% (344/344) specificity when tested with a collection of 613 respiratory specimens, compared to the gold-standard EV semi-nested VP1 PCR and sequencing assay (snPCR/Seq). CDC2022 gave negative results with 289/289 non-target viruses, including 104 EV A-D isolates, 165 rhinovirus (RV) isolates or clinical specimens, and 14 other common respiratory viruses. The assay can detect as few as 0.28 CCID50 per reaction. An in silico "phylo-primer-mismatch" analysis was performed to visualize primer/probe mismatches and to compare CDC2022 with other EV-D68 rRT-PCR assays, including the previous CDC assay (CDC2015) developed in 2014 for clade B1 strains. It showed that CDC2022 has the fewest primer/probe mismatches among all assays analyzed and is suitable for all clades. We additionally tested 11 EV-D68-positive clinical specimens from 2022 that were confirmed by snPCR/Seq, and all were detected. CDC2022 assay could provide a critical tool for molecular surveillance of EV-D68.

microbiology↗

bioRxiv2021

Particle-associated and free-living microbial assemblages are distinct in a permanently redox-stratified freshwater lake

Microbial assemblages associated with biogenic particles are phylogenetically distinct from free-living counterparts, yet biogeochemically coupled. Compositions may vary with organic carbon and inorganic substrate availability and with redox conditions, which determine reductant and oxidant availability. To explore microbial assemblage compositional responses to steep oxygen and redox gradients and seasonal variability in particle and substrate availability, we analyzed taxonomic compositions of particle-associated (PA) and free-living (FL) bacteria and archaea in permanently redox-stratified Fayetteville Green Lake. PA and FL assemblages (> 2.7 {micro}m and 0.2 - 2.7 {micro}m) were surveyed at the peak (July) and end (October) of concurrent cyanobacteria, purple and green sulfur bacteria blooms that result in substantial vertical fluxes of particulate organic carbon. Assemblage compositions varied significantly among redox conditions and size fractions (PA or FL). Temporal differences were only apparent among samples from the mixolimnion and oxycline, coinciding with seasonal hydrographic changes. PA assemblages of the mixolimnion and oxycline shifted from aerobic heterotrophs in July to fermenters, iron-reducers, and denitrifiers in October, likely reflecting seasonal variability in photoautotroph biomass and inorganic nitrogen. Within a light-scattering layer spanning the lower oxycline and upper monimolimnion, photoautotrophs were more abundant in July than in October, when Desulfocapsa, a sulfate-reducing and sulfur-disproportionating bacterium, and Chlorophyte chloroplasts were abundant in PA assemblages. In this layer, microbial activity and cell concentrations were also highest. Below, the most abundant resident taxa were sulfate-reducing bacteria and anaerobic respirers. Results suggest PA and FL assemblage niche partitioning interconnects multiple elemental cycles that involve particulate and dissolved phases.

microbiology↗

bioRxiv2019

Complete blood count with differential: An effective diagnostic for IBS subtype in the context of BMI?

The Complete Blood Count with Differential hematological assay is a mainstay diagnostic for point-of-care clinical diagnoses for a spectrum of diseases including infection, inflammation, anemia, and leukemia, and CBC-D profiles are under investigation as early prognostic biomarkers for leukemias and other diseases. Chronic abdominal pain (CAP) and irritable bowel syndrome (IBS) are prevalent gastrointestinal disorders in the United States, with obesity among the most common comorbidities. Often, IBS-like gastrointestinal (GI) symptoms persist after resolution of known inflammation and/or enteropathogenic infection, and current literature contains significant discussion of the extent to which IBS is within the biological spectrum of inflammatory disease. Obesity is also associated with generalized signatures of inflammation and may confound accurate diagnoses. We performed ANOVA, multiple means comparisons, statistical analyses of CBC data from our \"Brain-Gut Natural History\" (BGNH) clinical cohort, with additional ELISA assays for lipopolysaccharide binding protein (LBP), IL-10, cortisol, and ACTH, signatures of immune-inflammatory response and Hypothalamic-Pituitary-Adrenal (HPA) axis activity, respectively. BGNH cohort includes healthy and overweight individuals diagnosed with IBS diarrhea-(IBS-D) and constipation-predominant (IBS-C) subtypes. We identified several potentially significant markers for IBS-D and IBS-C, notably IL-10, mean platelet volume (MPV), with LBP and monocyte percent also showing some statistical significance. Weight also showed significant results for overweight vs. normal weight, regardless of IBS subtype, particularly for Cortisol. CBC-D predictive profiles for IBS subtype and weight were identified using discriminant functions analysis and show that predictivity of marker profiles have poor performance relative to their normal weight subsets. Further refinement of this analysis will be performed utilizing increased sample size, additional molecular profiles, and enhanced statistical analysis.

immunology↗