Biology subjects

Hall, S.

Publications and source records attributed to Hall, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Recombinant Echis disintegrins reveal distinct inhibitory profiles on platelet aggregation and endothelial cell migration

Disintegrins are snake venom toxins that bind integrins and modulate platelet aggregation and cell migration. Isolation from venom often yields insufficient quantities for comprehensive study, making recombinant expression essential for detailed toxin characterisation. Here, we produced and characterised four disintegrins from Echis coloratus and Echis ocellatus in Escherichia coli. These homologous proteins contain distinct integrin-binding motifs: EcDis_RGD, EoDis_RGD, EcDis_KGD, and EcDis_VGD. Functional activities were evaluated using human platelet aggregation and endothelial cell scratch wound-healing assays. RGD-containing disintegrins exhibited the strongest inhibition of platelet aggregation, with EcDis_RGD showing the highest potency. The EcDis_KGD disintegrin inhibited platelet aggregation less potently, whereas EcDis_VGD showed no detectable activity in our assays. In endothelial cells, EcDis_RGD disintegrin markedly impaired cell migration, while EoDis_RGD displayed weaker anti-migratory activity. Neither KGD- nor VGD-containing disintegrins significantly affected wound closure. EoDis_RGD exhibited similar antiplatelet activity to the native, venom-purified disintegrin ocellatusin, validating our recombinant expression strategy. However, the corresponding PII-SVMP preparation displayed reduced inhibitory activity, consistent with incomplete generation of fully mature disintegrins species. Our findings demonstrate the importance of both integrin-binding motif identity and surrounding sequence context in determining disintegrin function, and support further use of recombinant toxins in toxinology and as therapeutic lead molecules.

biochemistry↗

bioRxiv2026

Chemistry and Structure of Birch Bark Support Passive Radiative Cooling

White-barked birches extend to the northern limit of tree growth, and their bark is known to reduce solar damage during winter and early-spring by limiting solar heating and the incidence of harmful freeze-thaw events. The physical basis for this protection, however, has remained unclear. Here, we show that extracted betulin, the dominant triterpenoid responsible for the bark's whiteness, and Himalayan birch bark, both exhibit passive radiative cooling. Under low solar irradiance, bark and betulin-pellets reach temperatures below that of a shaded reference, and pellets cool more than bark. The cooling arises from high solar reflectance, which suppresses solar heating, and substantial mid-infrared emission, which drives radiative heat loss toward outer space. These findings help explain how bark-whiteness may contribute to protecting birch trees from solar-induced thermal stress.

plant biology↗

bioRxiv2026

Disintegrin-like and Cysteine-rich Domains Govern Enzymatic Activity and Substrate Recognition in Echis Snake Venom Metalloproteinases

Snake venom metalloproteinases (SVMPs) are major drivers of pathology following viper envenomation and represent important targets for the development of next-generation recombinant antivenoms. PIII SVMPs are among the most potent haemorrhagic toxins and contain disintegrin-like (Dis) and cysteine-rich (C-rich) accessory domains. Despite their biomedical importance, the mechanistic roles of these accessory domains in substrate recognition and catalysis remain poorly understood. We produced recombinant full-length and domain-deletion variants of two functionally distinct PIII SVMPs: the broadly proteolytic, cytotoxic cPIII and the highly specific prothrombin activator Ecarin. Proteins were expressed as latent zymogens in insect cells, auto-activated by Zn2+, and analysed using enzymatic, blood clotting, and cell-based assays. Progressive removal of the C-rich and Dis domains reduced zymogen auto-activation and markedly diminished catalytic activity in both toxins. In cPIII, domain deletion caused a stepwise loss of proteolytic and cytotoxic activity without altering substrate preference. In Ecarin, removal of the accessory domains strongly impaired prothrombin activation, and thus plasma clotting, demonstrating a critical role in substrate recognition. Conversely, deletion of the C-rich domain increased fibrinogenolytic activity, revealing a substrate-dependent gatekeeping function. Deglycosylation showed that N-linked glycans modulate SVMP activity in a construct-dependent manner. Recombinant Ecarin closely recapitulated the biochemical properties of the native venom-derived toxin. Our data support a model in which PIII SVMP accessory domains enhance substrate positioning and catalytic efficiency while selectively restricting access to non-cognate substrates. These findings establish accessory-domain-mediated substrate recognition as a key determinant of SVMP function, informing rational antivenom design.

biochemistry↗

bioRxiv2026

Nitric oxide inhibits platelet adhesion to platelet-microparticles through reducing integrin αIIbβ3 activation

Increased platelet microparticle (PMP) levels in individuals with risk factors for cardiovascular disease correlate with clinical outcomes in these patient groups. PMPs promote thrombosis through enhancing platelet aggregation and binding to the sub-endothelial matrix following vascular injury. Thus, PMPs behave as soluble ligands and adhesive substrates for platelets, and may drive cardiovascular disease progression. Nitric oxide (NO) is released continually from the endothelium as a potent regulator of platelet activation that is crucial to the balance between haemostasis and thrombosis. However, it is unknown if NO regulates PMP-induced platelet activation. In this study we isolated platelets and PMPs from whole blood and measured their interactions in adhesion assays and by flow cytometry. Platelet activation was analysed by ELISA for ADP and thromboxane-B2; both secondary platelet agonists released by activated platelets which enhance thrombosis. The affinity upregulation of the principal platelet integrin receptor responsible for platelet aggregation, integrin IIb{beta}3, was measured using the antibody PAC-1. Our data show that PMP induced platelet adhesion was associated with, and partially dependent upon, platelet ADP release, TxA2 production and IIb{beta}3 upregulation. Crucially, NO dose-dependently reduced these events through cGMP dependent signalling. This is the first report that NO signalling can regulate PMP induced platelet activation and may open an avenue of exploration for clinically targeting PMP driven cardiovascular disease processes.

cell biology↗

bioRxiv2026

Inhibition of p65 NF-κB enhances production of galactose-deficient IgA1 through suppression of C1GALT1 and SP1 in plasmablast-like cell subpopulations

IgA nephropathy (IgAN) is a common primary glomerulonephritis characterized by glomerular immune-complex deposits with (co)dominant IgA. These deposits are enriched for IgA1 glycoforms with some O-glycans deficient in galactose (Gd-IgA1). Circulating Gd-IgA1 is bound by IgG autoantibodies to form immune complexes, some of which deposit in glomeruli. Genomic and immunologic studies indicate involvement of pro-inflammatory signaling pathways in the production of Gd-IgA1 in IgAN. Genomic studies identified multiple genetic loci associated with IgAN and suggested a convergence on the NF-{kappa}B pathway, including RELA, the gene encoding the NF-{kappa}B subunit p65. However, the mechanisms by which NF-{kappa}B pathways may affect O-glycosylation in IgA1-producing cells are unknown. Using EBV-immortalized B cells derived from peripheral-blood mononuclear cells of IgAN patients and healthy controls that have constitutively activated NF-{kappa}B, we report that inhibition of NF-{kappa}B/p65 by a selective IKK{beta} inhibitor TPCA-1 reduced phosphorylation of NF-{kappa}B/p65 at S536 and decreased production of IgA1 and, conversely, increased Gd-IgA1 production. This was likely related to reduced expression of C1GALT1 gene that encodes the enzyme responsible for galactosylation of IgA1 O-glycans. Flow-cytometry imaging revealed changes in nuclear translocation and co-localization of the NF-{kappa}B/p65 with co-transcriptional factor SP1, a transcriptional activator of C1GALT1, suggesting that NF-{kappa}B pathway affects IgA1 O-glycosylation via SP1 transcriptional control of C1GALT1 expression. Furthermore, prolonged IKK{beta} inhibition altered B cell subpopulations, enhancing generation of cells with a plasmablast-like phenotype, characterized by high SSC MFI and CD138 expression. Together, these findings provide functional evidence for involvement of NF-{kappa}B/p65 and its transcriptional partners in IgA1 O-glycosylation. HighlightsO_LIIKK{beta} inhibition reduced C1GALT1 expression and thereby increased galactose-deficient IgA1 (Gd-IgA1) production in immortalized human B cells. C_LIO_LISP1+ subpopulations, a transcriptional activator of C1GALT1, declined after sustained NF-{kappa}B inhibition. C_LIO_LINF-{kappa}B inhibition shifted a subpopulation of B cells into a plasmablast-like phenotype. C_LIO_LIThis study links NF-{kappa}B signaling with the GWAS-identified RELA susceptibility locus and IgA1 O-glycosylation. C_LI

immunology↗

bioRxiv2026

PREFERENTIAL INVASION OF DIFFERENTIATED BLADDER CARCINOMA CELLS BY FLAGELLATED GROUP B2 ESCHERICHIA COLI

Phylogenetic group B2 Escherichia coli is associated with urinary tract infections and other pathologies, but the basis for this phylogenetic skew is not understood. One aspect of urinary tract infections is binding to and entering uroepithelial cells. To test whether a phylogenetic skew exists for cell invasion, we examined invasion of 10 E. coli strains from three phylogenetic groups into CRL2169 and HTB-9 cells, which are derived from grade 1 and grade 2 bladder carcinomas, respectively. The top four strains that invaded CRL2169 were from group B2: three of these strains had more flagella gene transcripts than the other seven strains. The seven strains that invaded HTB-9 were from different phylogenetic groups. For the model uropathogenic group B2 strain UTI89, which expresses pili over flagella, loss of flagella or pili impacted invasion into CRL2169 to similar extents, but loss of pili had a greater effect on invasion into HTB-9 and a murine infection model than loss of flagella. A hyperflagellated variant of a group A strain did not invade either cell line better than the parental strain. Reported transcript differences, which were confirmed experimentally, showed that CRL2169 was more differentiated. The endocytosis stimulator tanshinone enhanced invasion into HTB-9, but not into CRL2169, which suggests differences in endocytic pathways and is consistent with differences in differentiation states. If the initial or recurring event in urinary tract infection is invasion into differentiated urothelial cells, as opposed to tight junctions, then the role of flagella may have been underestimated.

molecular biology↗

bioRxiv2026

Chronic nicotine reduces nigral dopaminergic activity and remodels pedunculopontine cholinergic subpopulations

Chronic nicotine is linked to neuroprotective effects and reduced Parkinsons disease (PD) risk, yet its physiological effects on vulnerable substantia nigra pars compacta (SNc) dopaminergic and pedunculopontine nucleus (PPN) cholinergic neurons are not fully understood. These populations exhibit specialized properties such as spontaneous pacemaking and elevated dendritic calcium influx that contribute to their selective neurodegeneration in PD. Here, we used whole-cell patch-clamp, two-photon calcium imaging, and morphological reconstruction in acute brain slices from adult mice of both sexes following 8-10 weeks of oral nicotine. Chronic nicotine reduced spontaneous pacemaking, burst propensity, and rebound firing in SNc dopaminergic neurons, while decoupling tonic firing rate from proximal dendritic calcium levels. The changes in the SNc occurred without altering L-type channel contributions, dendritic arborization, or excitatory synaptic drive. In PPN cholinergic neurons, chronic nicotine induced subregion-specific plasticity. Rostral PPN neurons showed depolarized membrane potentials, broadened action potentials, and dendritic pruning, whereas caudal PPN neurons showed reduced spike frequency adaptation and accelerated excitatory postsynaptic current kinetics. These findings reveal potential cellular and circuit mechanisms by which nicotine may contribute to resilience against PD. Significant StatementEpidemiological studies have revealed nicotines surprising protective effect in Parkinsons disease (PD). Interestingly, this protection appears only preventative, as nicotine shows no therapeutic benefits after PD diagnosis. Here, we evaluated the effects of chronic nicotine on two brainstem populations known to selectively degenerate in PD: substantia nigra pars compacta (SNc) dopaminergic neurons and pedunculopontine (PPN) cholinergic neurons. Chronic nicotine decreases activity levels of SNc neurons, depolarizes rostral PPN neurons, and enhances sustained firing capability in caudal PPN neurons. Notably, this is the first study to assess whether chronic nicotine alters the physiology and dendritic morphology of these vulnerable subpopulations. These cellular insights uncover potential mechanisms for promoting neuronal resilience in neurodegenerative diseases.

neuroscience↗

bioRxiv2025

Myelin Basic Protein Binding Is Modulated by Leaflet Asymmetry and Lipid Composition

Compositional asymmetry between lipid bilayer leaflets is a defining feature of biological membranes, yet its role in modulating protein binding remains largely unexplored. Here, we investigate how leaflet-specific composition affects the interaction between Myelin Basic Protein and biomimetic myelin membranes using neutron reflectometry. Asymmetric supported myelin bilayers containing deuterated cholesterol in the cytoplasmic leaflet enabled resolution of structural asymmetry. Neutron reflectometry measurements show that Myelin Basic Protein binds preferentially to asymmetric supported bilayers mimicking native myelin, whereas Experimental Autoimmune Encephalomyelitis-modified compositions exhibit weaker binding and more pronounced protein insertion. Disruption of asymmetry--either by thermal-induced lipid redistribution or by using symmetric cytoplasmic myelin--leads to a marked reduction in Myelin Basic Protein binding, despite increased membrane charge. Following vesicle adsorption and formation of a second bilayer, the protein layer narrows to near in vivo thickness in both systems, with the diseased condition exhibiting a wider inter-bilayer spacing. These results underscore the relevance of lipid asymmetry and composition in governing protein - membrane interactions, with implications for the molecular basis of myelin stability and demyelination.

biophysics↗

bioRxiv2025

Procrustean pseudo-landmark methods in Python to measure massive quantities of leaf shape data

PremiseWhen examining leaf shapes that are different from one another, it can be difficult to compare both the overall leaf shape and points along the leaf margin in biologically and statistically meaningful ways. MethodTo address this problem, we present a simple and user-friendly leaf shape analysis in Jupyter Notebook and Python that uses pseudo-landmarks and Generalized Procrustes Analysis to measure and compare the shape of any leaf. To demonstrate our analysis, we created a repository of real leaves gathered from eight experimental datasets. ResultsUsing our leaf repository, we explain how we can use pseudo-landmarks to compare all leaf shapes both within and between species using dimension reduction techniques like Principal Component Analysis and can predict leaf shapes using pseudo-landmarks through Linear Discriminant Analysis. Our leaf shape analysis also maps differences in shape as leaves grew around a rosette, showing the transition of shape across development (phyllotaxy). Finally, we showed how we can investigate the relationship between leaf shape variation and genetic diversity by combining shape with genetic data. DiscussionThrough the use of Generalized Procrustes Analysis and pseudo-landmarks, our leaf shape analysis presents a powerful tool for examining the shape of any leaf across multiple biological, ecological, evolutionary, and developmental scales.

plant biology↗

bioRxiv2025

Efficient Recombinant Production and Functional Characterisation of Cytotoxic and Haemotoxic Snake Venom Metalloproteinases

Snake venoms contain diverse mixtures of toxins that evolved to incapacitate prey, but in humans they cause extensive pathology following snakebite envenomation. In viper venom, some of the most potent toxins are the haemorrhagic and coagulopathic snake venom metalloproteinases (SVMPs). Because venoms contain a SVMP cocktail, and due to their cytotoxicity, SVMP characterizations have been hampered by the lack of purified enzymes. By incorporating their prodomain, which blocks the active SVMP site, we overcame their cytotoxicity and enabled recombinant production of zymogens from all three structurally variable SVMP classes (PI, PII and PIII) using our baculovirus/insect cell expression system. Zymogens were auto-activated by incubation with Zn2+ ions, resulting in prodomain cleavage, PII disintegrin cleavage and PIII prodomain proteolysis. Auto-activated SVMPs were characterized using protein substrate degradation, platelet aggregation and blood coagulation assays, benchmarked to native venom-purified SVMP. Our recombinant zymogen production protocol is generically applicable for the expression of SVMPs, unlocking biomedical use in haematology, and discovery of novel snakebite therapeutics.

pharmacology and toxicology↗

bioRxiv2024

Control of pili synthesis and putrescine homeostasis in Escherichia coli

Polyamines are biologically ubiquitous cations that bind to nucleic acids, ribosomes, and phospholipids and, thereby, modulate numerous processes, including surface motility in Escherichia coli. We characterized the metabolic pathways that contribute to polyamine-dependent control of surface motility in the commonly used strain W3110 and the transcriptome of a mutant lacking a putrescine synthetic pathway that was required for surface motility. Genetic analysis showed that surface motility required type 1 pili, the simultaneous presence of two independent putrescine anabolic pathways, and modulation by putrescine transport and catabolism. An immunological assay for FimA--the major pili subunit, reverse transcription quantitative PCR of fimA, and transmission electron microscopy confirmed that pili synthesis required putrescine. Comparative RNAseq analysis of a wild type and {Delta}speB mutant which exhibits impaired pili synthesis showed that the latter had fewer transcripts for pili structural genes and for fimB which codes for the phase variation recombinase that orients the fim operon promoter in the ON phase, although loss of speB did not affect the promoter orientation. Results from the RNAseq analysis also suggested (a) changes in transcripts for several transcription factor genes that affect fim operon expression, (b) compensatory mechanisms for low putrescine which implies a putrescine homeostatic network, and (c) decreased transcripts of genes for oxidative energy metabolism and iron transport which a previous genetic analysis suggests may be sufficient to account for the pili defect in putrescine synthesis mutants. We conclude that pili synthesis requires putrescine and putrescine concentration is controlled by a complex homeostatic network that includes the genes of oxidative energy metabolism.

microbiology↗

bioRxiv2024

Cellular and molecular characterization of peripheral glia in the lung and other organs

Peripheral glia are important regulators of diverse physiologic functions yet their molecular distinctions and locations in almost all visceral organs are not well-understood. We performed a systematic analysis of peripheral glia, focusing on the lung and leveraging single cell RNA sequencing (scRNA-seq) analysis to characterize their cellular and molecular features. Using in vivo lineage studies, we characterized the anatomic, cellular, and molecular features of the Sox10+ glial lineage of the mouse lung. Using high-resolution imaging, we quantified the distribution and cellular morphologies of myelinating, non-myelinating, satellite, and terminal glial cells with their intricate extensions along peripheral nerves, including terminals at specialized neurosensory structures within the lung. Spatial analysis of selectively expressed myelinating (periaxin/Prx, claudin 19/Cldn) or non-myelinating (sodium channel/Scn7a) glial cell genes identified by scRNA-seq analysis revealed molecularly distinct populations surrounding myelinated nerve fibers in the lung. To extend this analysis to primates and other organs, we extracted rare peripheral glial cells in whole organism scRNA-seq atlases of mouse lemur and human. Our cross-species data analysis and integration of scRNA-seq data of [~]700 peripheral glial cells from mouse, mouse lemur, and human glial cells identified conserved gene expression of molecularly distinct peripheral glial cell populations. This foundational knowledge facilitates subsequent functional studies targeting molecularly distinct subsets of peripheral glia and integrating them into organ-specific disorders of autonomic dysregulation. In addition, our cross-species analysis identifying conserved gene expression patterns and glial networks in extrapulmonary organs provides a valuable resource for studying the functional role of peripheral glia in multiorgan human diseases.

cell biology↗

bioRxiv2024

Discovery of active mouse, plant and fungal cytochrome P450s in endogenous proteomes and upon expression in planta.

Eukaryotes produce a large number of cytochrome P450s that mediate the synthesis and degradation of diverse endogenous and exogenous metabolites. Yet, most of these P450s are uncharacterized and global tools to study these challenging, membrane-resident enzymes remain to be exploited. Here, we applied activity profiling of plant, mouse and fungal P450s with chemical probes that become reactive when oxidized by P450 enzymes. Identification by mass spectrometry revealed labeling of a wide range of active P450s, including six plant P450s, 40 mouse P450s and 13 P450s of the fungal wheat pathogen Zymoseptoria tritici. We next used transient expression of GFP-tagged P450s by agroinfiltration to show ER-targeting and NADPH-dependent, activity-based labeling of plant, mouse and fungal P450s. Both global profiling and transient expression can be used to detect a broad range of active P450s to study e.g. their regulation and discover selective inhibitors.

plant biology↗

bioRxiv2023

Antibodies generated in vitro and in vivo elucidate design of a thermostable ADDomer COVID-19 nasal nanoparticle vaccine

COVID-19 continues to damage populations, communities and economies worldwide. Vaccines have reduced COVID-19-related hospitalisations and deaths, primarily in developed countries. Persisting infection rates, and highly transmissible SARS-CoV-2 Variants of Concern (VOCs) causing repeat and breakthrough infections, underscore the ongoing need for new treatments to achieve a global solution. Based on ADDomer, a self-assembling protein nanoparticle scaffold, we created ADDoCoV, a thermostable COVID-19 candidate vaccine displaying multiple copies of a SARS-CoV-2 receptor binding motif (RBM)-derived epitope. In vitro generated neutralising nanobodies combined with molecular dynamics (MD) simulations and electron cryo-microscopy (cryo-EM) established authenticity and accessibility of the epitopes displayed. A Gigabody comprising multimerized nanobodies prevented SARS-CoV-2 virion attachment with picomolar EC50. Antibodies generated by immunising mice cross-reacted with VOCs including Delta and Omicron. Our study elucidates nasal administration of ADDomer-based nanoparticles for active and passive immunisation against SARS-CoV-2 and provides a blueprint for designing nanoparticle reagents to combat respiratory viral infections.

biochemistry↗

bioRxiv2023

Vascular Smooth Muscle Cell Mechanotransduction Through Serum and Glucocorticoid Inducible Kinase-1 Promotes Interleukin-6 Production and Macrophage Accumulation in Murine Hypertension

ObjectiveThe objective of this investigation was to demonstrate that in vivo induction of hypertension (HTN) and in vitro cyclic stretch of aortic VSMCs can cause SGK-1-dependent production of cytokines to promote macrophage accumulation as agents of vascular remodeling. MethodsHTN was induced in C57Bl/6 mice with AngiotensinII (AngII) infusion (1.46mg/kg/day x 21 days) with or without systemic infusion of EMD638683 (2.5mg/kg/day x 21 days), a selective SGK-1 inhibitor. Systolic blood pressure (SBP) was recorded on days 0 and 21. At terminal study, abdominal aortas were harvested to quantify SGK-1 activity (pSGK-1:SGK-1) by immunoblot. Additional replicates were digested and analyzed by flow cytometry for abundance of CD11b+/F4-80+ cells (macrophages). Plasma was analyzed by ELISA to quantify IL-6 and MCP-1. Aortic VSMCs from wild-type (WT) mice were subjected to 12% biaxial cyclic stretch for 3 or 12 hours +/- EMD638683 (10M) and +/- SGK-1siRNA with subsequent QPCR for IL-6 and MCP-1 expression. Culture media was analyzed by ELISA for IL-6 and MCP-1. Aortic VSMCs from SGK-1flox+/+ mice were transfected with Cre-Adenovirus to knockout SGK-1 (SGK-1KO VSMCs) and underwent parallel tension experimentation. Computational modeling was employed to simulate VSMC signaling due to mechanical strain and AngII. Statistical analysis included ANOVA with significance at p<0.05. ResultsSGK-1 activity (pSGK-1:SGK-1) was upregulated in the abdominal aorta of mice with HTN and significantly reduced by treatment with EMD638683. Concurrently, increased CD11b+/F4-80+ cells and plasma IL-6 levels in the HTN group and reduction with EMD638683 was observed. This mirrored the increased abundance of IL-6 in media from Stretch WT VSMCs, and attenuation of the effect with EMD638683. Treating WT VSMCs with SGK-1siRNA likewise inhibited IL-6 expression. MCP-1 also demonstrated increased expression and secretion into the media in WT VSMCs with Stretch. Further supporting the integral role of mechanical signaling through SGK-1, target gene expression and cytokine secretion was unchanged in SGK-1KO VSMCs with Stretch, and computer modeling confirmed SGK-1 as an intersecting node of signaling due to mechanical strain and AngII. In summation, this data suggests a biomechanical link between aortic VSMC mechanotransduction and cytokine production to promote macrophage accumulation, mediated in-part by SGK-1 activation. ConclusionMechanotransduction through SGK-1 is instrumental in pro-inflammatory cytokine production and aortic macrophage accumulation in systemic HTN, therefore further investigation into targeting this kinase may present opportunities to modulate hypertensive vascular remodeling.

physiology↗

bioRxiv2023

Hemoxygenase-1 as a key mediator of acute radiation pneumonitis revealed in a human lung alveolus-on-a-chip

Exposure to gamma radiation either due to environmental disasters or cancer radiotherapy can result in development of acute radiation syndrome (ARS), characterized by pneumonitis and lung fibrosis. We leveraged a microfluidic organ-on-a-chip lined by human lung alveolar epithelium interfaced with pulmonary endothelium to model acute radiation-induced lung injury in vitro. Both lung epithelium and endothelium exhibited DNA damage, cellular hypertrophy, upregulation of inflammatory cytokines, and loss of barrier function within 6 h of radiation exposure, although greater damage was observed in the endothelium. Transcriptomic analysis revealed increased expression of the cytoprotective gene, hemoxygenase-1 (HMOX-1) and gene network analysis identified it as a central mediator of radiation-induced injury. Pharmacological stimulation of HMOX-1 activity also significantly reduced acute radiation-induced lung injury, although it enhanced damage at later times. Thus, this human lung chip offers a new platform to study ARS and these results suggest that HMOX-1 may be mechanistically involved in this injury response.

bioengineering↗

bioRxiv2023

Utility of long-read sequencing for All of Us

The All of Us (AoU) initiative aims to sequence the genomes of over one million Americans from diverse ethnic backgrounds to improve personalized medical care. In a recent technical pilot, we compared the performance of traditional short-read sequencing with long-read sequencing in a small cohort of samples from the HapMap project and two AoU control samples representing eight datasets. Our analysis revealed substantial differences in the ability of these technologies to accurately sequence complex medically relevant genes, particularly in terms of gene coverage and pathogenic variant identification. We also considered the advantages and challenges of using low coverage sequencing to increase sample numbers in large cohort analysis. Our results show that HiFi reads produced the most accurate results for both small and large variants. Further, we present a cloud-based pipeline to optimize SNV, indel and SV calling at scale for long-reads analysis. These results will lead to widespread improvements across AoU.

bioinformatics↗

bioRxiv2022

The potentiative cytotoxic effect of IGF1R and EGFR inhibition on the Head and Neck Cancer Proteome

Head and neck cancers are the sixth most common cancer worldwide. Combinatorial targeted therapy has the potential to reduce drug resistance and increase cytotoxicity to head and neck squamous cell carcinoma (HNSCC). Using drug combinations is especially important when targeting the epidermal growth factor receptor (EGFR) since we previously demonstrated that activation of the insulin-like growth factor 1 receptor (IGF1R) is a mechanism for resistance against EGFR inhibition and that a combination of an IGF1R inhibitor, BMS754807, and an EGFR inhibitor, BMS599626, robustly inhibited the growth of HNSCC cell lines in vitro. To examine the mechanism of cytotoxicity, we performed protein pathway activation mapping via reverse phase protein array (RPPA) analysis of 145 proteins and phosphoproteins in five HNSCC cell lines to map key proteins and phosphoproteins important in tumorigenesis. By performing principal component analysis, calculating log fold changes, and constructing protein networks, we were able to provide evidence to support the hypothesis that the combination of IGF1R and EGFR inhibitors has a potentiative effect on inhibiting receptor tyrosine kinase signaling. The effects of the individual drugs are amplified, demonstrating that the combination more robustly inhibits the pathways of both receptors.

cancer biology↗