Biology subjects

Hamilton, C.

Publications and source records attributed to Hamilton, C..

10 recordsLinked to original sources

bioRxiv2026

FLIP is essential for oncogenic KRAS-driven lung cancer

Mutations in KRAS represent the most common oncogenic event in human cancer and occur in approximately 30% of lung adenocarcinomas. The mechanisms by which lung tumours evade apoptosis induced by oncogenic KRAS-driven stress remain incompletely understood. Here, we identify the anti-apoptotic regulator FLIP (CFLAR) as a critical dependency in KRAS-mutant lung cancers. We demonstrate that KRAS-mutant human lung cancer cell lines exhibit elevated FLIP expression and enhanced dependence on FLIP for survival compared to KRAS wild-type counterparts. Subsequently, using genetically engineered mouse models (GEMMs), we show that FLIP is essential for Kras-driven lung tumour development in vivo. In vitro, FLIP-deficient lung cancer cells display spontaneous, caspase-8- dependent apoptosis and hyper-sensitivity to the immune/inflammatory cytokines TNF and TRAIL. Strikingly, FLIP-null lung cancer cells fail to engraft even in highly immunodeficient orthotopic models that lack TRAIL-expressing immune cells but retain TNF-expressing monocytes. Moreover, silencing of TNFR1 or TNF but not TRAIL-R2 rescued constitutive caspase-8-dependent apoptosis in FLIP null lung cancer cells, implicating TNF/TNFR1 in mediating this apoptotic response. Mechanistically, we find that mutant KRAS sustains FLIP expression via ERK1/2 signalling, thereby protecting cells from caspase-8 activation. Notably, KRAS inhibition downregulates FLIP, sensitising cells to TNF- and TRAIL-induced apoptosis. These findings uncover a novel KRAS-ERK-FLIP axis that protects tumour cells from caspase-8-mediated apoptosis and reveal FLIP as a key survival factor co-opted by KRAS-mutant lung cancers. Beyond identifying FLIP as a promising therapeutic target in KRAS mutant lung cancer, our work also provides mechanistic insight into the pro-apoptotic effects of KRAS inhibitors and suggests that FLIP expression may serve as a predictive biomarker to enhance patient stratification and the therapeutic efficacy of these agents in lung cancer.

cancer biology↗

bioRxiv2026

Natural selection driven by escape from shifting antibody classes shapes SARS-CoV-2 evolution

The phenotypic fitness landscape defines the action of natural selection on pathogens, linking changes in their phenotypes to transmission and evolution. The rapidly changing nature of epidemic spread and antigenic landscapes pushes viruses to evolve on fitness seascapes. As a result, evolution of viruses such as SARS-CoV-2 proceeds in a neverending series of waves, driven by epistatic interactions and by the arms race between viral adaptation and human immunity. Phenotypic characterisation of these rapidly changing fitness seascapes is an open challenge. Using a Phenotypic Selection Inference framework that links phylogenetic estimates of mutation fitness effects with deep mutational scanning data, we traced how selective pressures on viral phenotypes have shifted throughout the COVID-19 pandemic. Natural selection has favoured enhanced ACE2 binding since the emergence of SARS-COV-2, with relatively constant selective pressure even for the most recent variants. The strength of selection for antibody escape was comparable to ACE2 binding during early evolution, but as population immunity rose, escape from class 3 and then class 2 antibodies became dominant. For variants circulating in 2024, natural selection shifted toward class 3 antibody escape, while those circulating in 2025 have experienced dynamic, rapidly changing pressures for escape from all antibody classes. These transitions reflect an ongoing arms race between viral adaptation and human immunity. Our findings reveal that SARS-CoV-2 antigenic evolution is governed by dynamic, class-specific immune pressures, and that selection for replication capacity has been continuously present during the pandemic, presumably to compensate for the effects of antigenic escape on viral replication. Our approach for the inference of phenotypic selection provides a framework to understand and anticipate the evolution of future variants.

evolutionary biology↗

bioRxiv2025

Immune stromal components impede biological effectiveness of carbon ion therapy in a preclinical model of pancreatic ductal adenocarcinoma

The tumor landscape of pancreatic ductal adenocarcinoma (PDAC) is refractory to conventional photon radiotherapy (RT) due to a fibrotic tumor microenvironment (TME) that promotes chronic hypoxia and reduced immune surveillance. The radiobiological factors unique to carbon ion radiotherapy (CIRT), such as high linear energy transfer (LET) and less dependence on oxygen, make it well-suited to overcome the PDAC TME. Here, we utilized clonal syngeneic KPC pancreatic tumor cell lines and tumors to examine this postulate and to identify underlying factors that impact the response of PDAC to CIRT. While KPC cell lines exhibited radiobiologic effectiveness (RBE) greater than 3, subcutaneous tumors in the mouse hind leg showed lower RBEs - 1.3 based on quintupling time - at a LET of 75 keV/m. Four days after CIRT, we observed widespread transcriptomic changes in the tumor immune microenvironment (TME), suggesting increased infiltration of anti-tumor immune cells, elevated expression of anti-tumor T cell cytokines, MHC class I molecules, and co-stimulatory signals. Fewer immunologic changes were observed following photon irradiation. By seven days after CIRT, tumor-supportive transcriptomic programs characterized by pro-tumor cytokines, M2 macrophages, and cancer-associated fibroblasts (CAFs) emerged, promoting resistance and limiting the durability of tumor growth delay. These findings suggest that CIRT may offer a favorable platform compared to conventional photon radiation therapy for combining with immunotherapies. Furthermore, these data highlight the risk of using in vitro survival data alone in treatment planning and indicate that underlying TME factors impact the response of PDAC in vivo.

cancer biology↗

bioRxiv2024

Order among chaos: high throughput MYCroplanters can distinguish interacting drivers of host infection in a highly stochastic system

While microbiomes provide diverse benefits for their host, they are notoriously variable in structure and function. As a result, substantial experimental replication and scalability are required to identify the contributions of and interactions between microbiota, the host and the environment. Here, we describe a novel high throughput plant growth system (MYCroplanters) to test how multiple host, microbiota, and pathogen variables predict host health. Using an Arabidopsis-Pseudomonas host-microbiome-pathogen model, we found that host genotype and order of arrival predict competition outcome between strains in the rhizosphere, but pathogen and microbiota dose can overwhelm these effects. Regardless of host or inoculation conditions, final microbial community structure emerged as a consistent predictor of host health. We demonstrate that high-throughput tools like MYCroplanters can isolate interacting drivers of host health. Increasing the scale at which we can screen components of microbiome-mediated host benefits will facilitate building microbiome engineering solutions for medicine and agricultural applications.

ecology↗

bioRxiv2020

Working Memory Capacities Neurally Dissociate: Evidence from Acute Stroke

Substantial behavioral evidence implies the existence of separable working memory (WM) components for maintaining phonological and semantic information. In contrast, only a few studies have addressed the neural basis of phonological vs. semantic WM using functional neuroimaging and none has used a lesion-symptom mapping (LSM) approach. Here we address this gap, reporting a multivariate LSM study of phonological and semantic WM for 94 individuals at the acute stage of left hemisphere stroke. Testing at the acute stage avoids issues of brain reorganization and the adoption of patient strategies for task performance. The LSM analyses for each WM component controlled for the other WM component and semantic and phonological knowledge at the single word level. For phonological WM, the regions uncovered included the supramarginal gyrus, argued to be the site of phonological storage, and several cortical and subcortical regions plausibly related to inner rehearsal. For semantic WM, inferior frontal regions and the angular gyrus were uncovered. The findings thus provide converging evidence for separable systems for phonological and semantic WM that are distinguished from the systems supporting long-term knowledge representations in those domains.

neuroscience↗

bioRxiv2020

Phosphatidylinositol Acyl Chains Configure TLR-Dependent Priming and Activation of the NLRP3 Inflammasome

Imbalance in lipid homeostasis is associated with discrepancies in immune signalling and is tightly linked to metabolic disorders. The diverse ways in which lipids impact immune signalling, however, remain ambiguous. The phospholipid phosphatidylinositol (PI), which is implicated in numerous immune disorders, is chiefly defined by its phosphorylation status. By contrast, the significance of the two fatty acid chains attached to the PI remains unknown. Here, by employing a mass-spectrometry-based assay, we demonstrate a role for PI acyl group chains in regulating both the priming and activation steps of the NLRP3 inflammasome in mouse macrophages. In response to NLRP3 stimuli, cells deficient in ABC transporter ABCB1, which effluxes lipid derivatives, revealed defective inflammasome activation. Mechanistically, Abcb1-deficiency shifted the total PI configuration exhibiting a reduced ratio of short-chain to long-chain PI-acyl lipids. Consequently, Abcb1-deficiency resulted in rapid degradation of TIRAP, the TLR adaptor protein which binds PI(4,5)-phosphate. Moreover, this accompanied increased NLRP3 phosphorylation at the Ser293 position and blunted inflammasome activation. Exogenously supplementing WT cells with linoleic acid, but not arachidonic acid, reconfigured PI acyl chains. Accordingly, linoleic acid supplementation increased TIRAP degradation, elevated NLRP3 phosphorylation, and abrogated inflammasome activation. Altogether, our study reveals a novel metabolic-inflammatory circuit which contributes to calibrating immune responses.

immunology↗

bioRxiv2019

Dissociation between Frontal and Temporal-Parietal Contributions to Connected Speech in Acute Stroke

Humans are uniquely able to retrieve and combine words into syntactic structure to produce connected speech. Previous identification of focal brain regions necessary for production focused primarily on associations with the content produced by speakers with chronic stroke, where function may have shifted to other regions after reorganization occurred. Here, we relate patterns of brain damage with deficits to the content and structure of spontaneous connected speech in 52 speakers during the acute stage of a left hemisphere stroke. Multivariate lesion behavior mapping demonstrated that damage to temporal-parietal regions impacted the ability to retrieve words and produce them within increasingly complex combinations. Damage primarily to inferior frontal cortex affected the production of syntactically accurate structure. In contrast to previous work, functional-anatomical dissociations did not depend on lesion size likely because acute lesions were smaller than typically found in chronic stroke. These results are consistent with predictions from theoretical models based primarily on evidence from language comprehension and highlight the importance of investigating individual differences in brain-language relationships in speakers with acute stroke.

neuroscience↗

bioRxiv2019

Staphylococcus aureus uses the bacilliredoxin (BrxAB)/bacillithiol disulfide reductase (YpdA) redox pathway to defend against oxidative stress under infections

Staphylococcus aureus is a major human pathogen and has to cope with reactive oxygen and chlorine species (ROS, RCS) during infections. The low molecular weight thiol bacillithiol (BSH) is an important defense mechanism of S. aureus for detoxification of ROS and HOCl stress to maintain the reduced state of the cytoplasm. Under HOCl stress, BSH forms mixed disulfides with proteins, termed as S-bacillithiolations, which are reduced by bacilliredoxins (BrxA and BrxB). The NADPH-dependent flavin disulfide reductase YpdA is phylogenetically associated with the BSH synthesis and BrxA/B enzymes and was proposed to function as BSSB reductase. Here, we investigated the role of the bacilliredoxin BrxAB/BSH/YpdA pathway in S. aureus COL under oxidative stress and macrophage infection conditions in vivo and in biochemical assays in vitro. Using HPLC thiol metabolomics, a strongly enhanced BSSB level and a decreased BSH/BSSB ratio were measured in the S. aureus COL ypdA deletion mutant under control and NaOCl stress. Monitoring the BSH redox potential (EBSH) using the Brx-roGFP2 biosensor revealed that YpdA is required for regeneration of the reduced EBSH upon recovery from oxidative stress. In addition, the ypdA mutant was impaired in H2O2 detoxification as measured with the novel H2O2-specific Tpx-roGFP2 biosensor. Phenotype analyses further showed that BrxA and YpdA are required for survival under NaOCl and H2O2 stress in vitro and inside murine J-774A.1 macrophages in infection assays in vivo. Finally, NADPH-coupled electron transfer assays provide evidence for the function of YpdA in BSSB reduction, which depends on the conserved Cys14 residue. YpdA acts together with BrxA and BSH in de-bacillithiolation of S-bacilithiolated GapDH. In conclusion, our results point to a major role of the BrxA/BSH/YpdA pathway in BSH redox homeostasis in S. aureus during recovery from oxidative stress and under infections.

microbiology↗

bioRxiv2019

The Dialysis Procedure Triggers Autonomic Imbalance and Cardiac Arrhythmias: Insights from Continuous 14-day ECG Monitoring

BackgroundIn end-stage kidney disease the dialytic cycle relates to the rate of sudden cardiac death. We hypothesized that circadian, dialytic cycles, paroxysmal arrhythmias, and cardiovascular risk factors are associated with periodic changes in heart rate and heart rate variability (HRV) in incident dialysis patients.\n\nMethodsWe conducted a prospective ancillary study of the Predictors of Arrhythmic and Cardiovascular Risk in End Stage Renal Disease cohort (n=28; age 54{+/-}13 y; 57% men; 96% black; 33% with a history of structural heart disease; left ventricular ejection fraction 70{+/-}9%). Continuous ECG monitoring was performed using an ECG patch (Zio Patch, iRhythm) and short-term HRV was measured for three minutes every hour. HRV was measured by root mean square of the successive normal-to-normal intervals (rMSSD), high and low frequency power, Poincare plot, and sample and Renyi entropy.\n\nResultsArrhythmias were detected in 46% (n=13). Non-sustained ventricular tachycardia (VT) was more frequent during dialysis or within 6 hours post-dialysis, as compared to pre-or between-dialysis (63% vs. 37%, P=0.015), whereas supraventricular tachycardia was more frequent pre-/ between-dialysis, as compared to during-/ post-dialysis (84% vs. 16%, P=0.015). In adjusted for cardiovascular disease and its risk factors autoregressive conditional heteroscedasticity panel (ARCH) model, VT events were associated with increased heart rate by 11.2 (95%CI 10.1-12.3) bpm (P<0.0001). During regular dialytic cycle, rMSSD demonstrated significant circadian pattern (Mesor 10.6(0.9-11.2) ms; Amplitude 1.5(1.0-3.1) ms; Peak at 02:01(20:22-03:16) am; P<0.0001), which was abolished on a second day interdialytic extension (adjusted ARCH trend for rMSSD -1.41(-1.67 to -1.15) ms per 24h; P<0.0001).\n\nConclusionCardiac arrhythmias associate with dialytic phase. Regular dialytic schedule preserves physiological circadian rhythm, but the second day without dialysis is characterized by parasympathetic withdrawal and a steady increase in sympathetic predominance.\n\nSubject TermsArrhythmias, Autonomic Nervous System, Electrocardiology (ECG), Treatment.

epidemiology↗

bioRxiv2019

Dynamic Predictive Accuracy of Electrocardiographic Biomarkers of Sudden Cardiac Death within a Survival Framework: The Atherosclerosis Risk in Communities (ARIC) study

BackgroundThe risk of sudden cardiac death (SCD) is known to be dynamic. However, an accuracy of a dynamic SCD prediction, and \"expiration date\" of ECG biomarkers is unknown. Our goal was to measure dynamic predictive accuracy of ECG biomarkers of SCD and competing outcomes.\n\nMethodsAtherosclerosis Risk In Community study participants with analyzable digital ECGs were included (n=15,768; 55% female, 73% white, age 54.2{+/-}5.8 y). ECGs of 5 follow-up visits were analyzed. Global electrical heterogeneity (GEH) and traditional ECG metrics were measured. Adjudicated SCD served as the primary outcome; non-sudden cardiac death served as competing outcome. Time-dependent area under the (receiver operating characteristic) curve (AUC) analysis was performed to assess prediction accuracy of a continuous biomarker in a period of 3,6,9 months, and 1,2,3,5,10, and 15 years, using survival analysis framework.\n\nResultsOver a median 24.4 y follow-up, there were 581 SCDs (incidence 1.77 (95%CI 1.63-1.92)/1,000 person-years), and 838 nonSCDs [2.55 (95%CI 2.39-2.73)]. Resting heart rate was the strongest (AUC 0.930) short-term (3-month) non-specific SCD predictor, whereas spatial peak QRS-T angle predicted specifically SCD 15 years after ECG recording (AUC 0.719). QRS duration (AUC 0.885) and QTc (AUC 0.711) short-term predicted advanced structural heart disease better than SCD. \"Expiration date\" for most ECG biomarkers was two years after ECG recording. GEH significantly improved reclassification of SCD risk beyond age, sex, race, diabetes, hypertension, coronary heart disease and stroke.\n\nConclusionShort-term predictors of SCD, nonSCD, and biomarkers of long-term SCD risk differed, reflecting differences in transient vs. persistent SCD substrates.

epidemiology↗