Biology subjects

Lewis, T.

Publications and source records attributed to Lewis, T..

18 recordsLinked to original sources

bioRxiv2026

5β-Dihydrotestosterone reveals a mutant androgen receptor vulnerability in prostate cancer

Bipolar androgen therapy (BAT) exploits the paradoxical vulnerability of castration-resistant prostate cancer (CRPC) cells to rapid cycling between castrate and supraphysiologic androgen concentrations, but clinical BAT uses testosterone, which can also activate wild-type androgen receptor (AR) in androgen-responsive tissues, causing systemic side effects. 5{beta}-dihydrotestosterone (5{beta}-DHT) is a naturally occurring testosterone metabolite generally considered androgenically inactive because it binds wild-type AR weakly, yet its activity against clinically relevant AR mutants has not been systematically evaluated. Here, we tested whether 5{beta}-DHT and related 5{beta}-reduced testosterone metabolites activate AR signaling and growth programs in prostate cancer models that carry AR mutations. In C4-2 cells, 5{beta}-DHT and 3{beta}-etiocholanediol (3{beta}-ecdiol) increased canonical AR target genes, including KLK3 and TMPRSS2, with weaker activity than testosterone, whereas other 5{beta} metabolites showed limited activity. In androgen-responsive LNCaP and C4-2 models, 5{beta}-DHT and 3{beta}-ecdiol promoted cell growth under androgen-depleted conditions, and this effect was suppressed by enzalutamide, supporting AR dependence. RNA-seq confirmed that 5{beta}-DHT and 3{beta}-ecdiol induced androgen-response gene sets substantially overlapping with testosterone, albeit at lower transcriptional magnitude. Further, we found that 5{beta}-DHT, but not 3{beta}-ecdiol, suppresses cell proliferation of LNCaP, C4-2, and PC-3 cells stably expressing the clinically relevant AR gain-of-function mutants W742C and H875Y through activating AR-induced senescence-like features after high-dose exposure, consistent with the therapeutic logic of BAT. These findings identify 5{beta}-DHT as an overlooked mutant-AR agonist capable of BAT-like tumor suppression and propose it as a testosterone surrogate in BAT with potentially reduced systemic androgenic side effects. HighlightsO_LI5{beta}-DHT and 3{beta}-ecdiol promote AR-dependent prostate cancer cell growth C_LIO_LIBoth are weaker AR agonists than testosterone by RNA-seq and qPCR C_LIO_LISupraphysiologic 5{beta}-DHT suppresses growth via AR-mediated senescence C_LIO_LIGrowth suppression extends to AR mutants W742C and H875Y C_LIO_LI5{beta}-DHT may be a lower-androgenicity testosterone surrogate for BAT C_LI

cancer biology↗

bioRxiv2026

Using iPALM to determine protein organisation in cardiac muscle Z-discs

Sarcomeres, the basic repeating unit of striated muscle, are joined together by crosslinked actin filaments found at the boundaries of muscle sarcomeres, termed Z-discs. Z-discs play a key role in cardiac signalling and disease, however, the arrangement and function of many of the proteins present in the Z-disc remain to be understood. Here, we determined the organisation of 3 key proteins, ZASP, [a]-Actinin-2 and the Z1Z2 epitope of titin, located within the Z-disc. We fluorescently labelled these proteins in cardiac myofibrils using Adhirons specific to each protein and used interferometric photoactivated localization microscopy (iPALM) to obtain the 3D position of these proteins to a high precision (<10nm in x,y,z). We then used PERPL (Pattern Extraction from Relative Positions of Localisations) to analyse patterns in the relative positions of the proteins and reveal their underlying organisation. This analysis revealed that ZASP and [a]-Actinin-2 have a similar repeating organisation, but that the organisation of Z1Z2 is different.

biophysics↗

bioRxiv2025

Maternal Influenza A Virus Infection Induces Antiviral and Immune Dysregulation in the Placenta and Fetus Without Vertical Transmission

Influenza A virus (IAV) infection during pregnancy is associated with stillbirth and preterm birth, but the degree to which IAV alters placental and fetal immunity is poorly understood. The objective of our study was to determine the immunologic impact of maternal IAV infection on the placenta and fetus in a pigtail macaque (Macaca nemestrina) model. Pregnant pigtail macaques were inoculated with 107 plaque forming units (PFU) of IAV [A/California/07/2009 (H1N1)] and underwent necropsy 5 days post-infection (N=11). Results were compared to uninfected historical controls (N=16). IAV inoculation induced maternal pneumonia in all cases. Stillbirth occurred in 18% (2/11) of IAV-infected pregnancies, but not in controls. While vertical transmission was not observed, low-level IAV viral RNA was detected in two placentas. In the placenta, maternal IAV infection was associated with increased IL-1{beta}, IL-18, and IFN-{beta} levels, and an upregulated type I interferon (IFN) transcriptional response. IAV infection was also associated with significantly higher frequencies of intermediate and non-classical monocytes, plasmacytoid dendritic cells, CD4 T cells, and NKT cells in the fetus (lung, lymph node, blood). Although placental immune and transcriptional perturbations were rarely correlated with maternal IAV disease indicators (e.g., maternal lung viral load/IFN-/IFN-{beta}/IL-6), there were consistent and significant correlations between these metrics and perturbed immune cell populations in the fetus (CD4+ and CD8+ T cells, plasmacytoid dendritic cells, monocyte sub-populations). Maternal IAV infection disrupted both placental and fetal immune environments, but only fetal immune alterations correlated with maternal lung disease severity. One Sentence SummaryMaternal influenza A virus infection in pregnant pigtail macaques dysregulates placental and fetal immunity, with disease severity correlating strongly with fetal, but not placental, immune perturbations.

systems biology↗

bioRxiv2025

Evaluating genotyping strategies for a small managed population with simulation

BackgroundCollecting genomic information is crucial to advance breeding for complex traits such as health, welfare, and behaviour in domesticated populations. For that purpose, different data collection scenarios can be envisioned based on the number of individuals, the number of markers, and the genotyping technology. This study developed a simulation framework, based on a service dog population, aiming to identify an optimal and cost-effective genotyping strategy that would support the implementation of genomic selection, investigation of the genetic architecture of traits of interest, and track loci of interest. MethodsWe simulated a population based on the existing pedigree, using the gene drop method in AlphaSimR. The existing pedigree was extended with additional progeny generations to evaluate the outcomes of different genotyping strategies in the future. We generated genotype data based on existing high-coverage whole-genome sequences (WGS) for the current breeding dogs and evaluated different scenarios for genotyping the progeny. The genotyping options considered SNP arrays of various densities and WGS callsets produced from different sequencing depths. We then phased and imputed the genotype data to high-coverage WGS using AlphaPeel. ResultsAll scenarios were compared based on individual imputation accuracy against the simulated true whole-genome genotype. Averaged over five generations of simulated progeny, low-pass sequencing (0.5 to 2X depth) achieved accuracies of 0.998 to 0.999. The accuracy of SNP array genotyping (25K to 710K markers) was lower, with means of 0.911 to 0.938. ConclusionsOur simulation was tailored to identify the most cost-effective and efficient strategy for downstream use in genomic selection and genetic research into traits and loci of interest. Low-pass sequencing outperformed SNP array genotyping in imputation accuracy of whole-genome genotypes as expected. Additionally, low-pass sequencing technology was the most affordable genotyping approach currently available for dogs. Thus, it appears to be the optimal choice for balancing the goals of regimented breeding programmes such as those that produce service dogs. This simulation framework could also be adapted to address other objectives for breeding organisations working with small populations.

genomics↗

bioRxiv2024

Impact of a transient neonatal visual deprivation on the development of the ventral occipito-temporal cortex in humans

How does experience shape the development of visual brain regions? We demonstrate that a transient period of visual deprivation early in life in humans leads to permanent alteration in the function of the early visual cortex (EVC), while leaving the categorical coding of downstream ventral occipito-temporal cortex (VOTC) mostly unaffected. We used fMRI to characterize the brain response to five categories (faces, bodies, objects, buildings and words) in a rare group of cataract-reversal individuals who experienced a transient period of blindness early in life, and in matched participants with typical visual development. We show that the encoding of low-level visual properties is impaired in EVC in cataract-reversal participants, while the categorical response in the VOTC is preserved. When altering the visual properties of our stimuli to mimic in controls the deficit of EVC response of the cataract, we observe a cascading alteration of the categorical coding from EVC to VOTC that is not observed in the cataract-reversal group. Our results show that a typical visual categorical organization develops in VOTC despite a period of visual deprivation early in life and in the presence of impaired processing in EVC. A deep neural network exposed to a visual diet that emulates the experience of our participants reproduced our brain observations within an artificial system. These findings emphasize how specific visual regions are differently affected by a period of visual deprivation early in life, with information encoded in EVC being permanently affected, while the categorical coding in VOTC shows resilience to deprivation.

neuroscience↗

bioRxiv2024

A Multiscale approach reveals the molecular architecture of the autoinhibited kinesin KIF5A.

Kinesin-1 is a microtubule motor that transports cellular cargo along microtubules. KIF5A is one of three kinesin-1 isoforms in humans, all of which are autoinhibited by an interaction between the motor and an IAK motif in the proximal region of the C-terminal tail. The C-terminal tail of KIF5A is [~]80 residues longer than the other two kinesin-1 isoforms (KIF5B and KIF5C) and it is unclear if it contributes to autoinhibition. Mutations in KIF5A cause neuronal diseases and could affect autoinhibition, as reported for a mutation that skips exon 27, altering its C-terminal sequence. Here, we combined negative-stain electron microscopy, crosslinking mass spectrometry (XL-MS) and AlphaFold2 structure prediction to determine the molecular architecture of the full-length autoinhibited KIF5A homodimer, in the absence of light chains. We show that KIF5A forms a compact, bent conformation, through a bend between coiled coils 2 and 3, around P687. XL-MS of WT KIF5A revealed extensive interactions between residues in the motor, between coiled-coil 1 and the motor, between coiled-coils 1 and 2, with coiled coils 3 and 4, and the proximal region of the C-terminal tail and the motor in the autoinhibited state, but not between the distal C-terminal region and the rest of the molecule. While negative stain electron microscopy of exon-27 KIF5A splice mutant showed the presence of autoinhibited molecules, XL-MS analysis suggested that its autoinhibited state is more labile. Our model offers a conceptual framework for understanding how mutations within the motor and stalk domain may affect motor activity.

cell biology↗

bioRxiv2023

High pathogenicity avian influenza (H5N1) in Northern Gannets: Global spread, clinical signs, and demographic consequences

During 2021-22 High Pathogenicity Avian Influenza (HPAI) killed thousands of wild birds across Europe and North America, suggesting a change in infection dynamics and a shift to new hosts, including seabirds. Northern Gannets (Morus bassanus) appeared especially severely impacted, but limited understanding of how the virus spread across the metapopulation, or the demographic consequences of mass mortality limit our understanding of its severity. Accordingly, we collate information on HPAIV outbreaks across most North Atlantic gannet colonies and for the largest colony (Bass Rock, UK), provide impacts on population size, breeding success, adult survival, and preliminary results on serology. Unusually high numbers of dead gannets were first noted in Iceland during April 2022. Outbreaks in May occurred in many Scottish colonies, followed by colonies in Canada, Germany and Norway. By the end of June, outbreaks had occurred in five Canadian colonies and in the Channel Islands. Outbreaks in 12 UK and Ireland colonies appeared to follow a clockwise pattern with the last infected colonies recorded in late August/September. Unusually high mortality was recorded at 40 colonies (75% of global total colonies). Dead birds testing positive for HPAIV H5N1 were associated with 58% of these colonies. At Bass Rock, the number of occupied sites decreased by at least 71%, breeding success declined by [~]66% compared to the long-term UK mean and adult survival between 2021 and 2022 was 42% lower than the preceding 10-year average. Serological investigation detected antibodies specific to H5 in apparently healthy birds indicating that some gannets recover from HPAIV infection. Further, most of these recovered birds had black irises, suggestive of a phenotypic indicator of previous infection. Untangling the impacts of HPAIV infection from other key pressures faced by seabirds is key to establishing effective conservation strategies for threatened seabird populations, HPAIV being a novel and pandemic threat.

ecology↗

bioRxiv2023

The role of airborne particles in the epidemiology of clade 2.3.4.4b H5N1 high pathogenicity avian influenza virus in commercial poultry production units

Since October 2021, Europe has experienced the largest avian influenza virus (AIV) epizootic, caused by clade 2.3.4.4b H5N1 high pathogenicity AIV (HPAIV), with over 320 poultry and captive bird infected premises (IPs) and 2480 dead H5N1 positive wild birds detected in Great Britain alone. Many IPs have been detected as geographical clusters, raising questions around potential lateral spread between premises by airborne particles. Airborne transmission over short distances has been reported for some AIVs strains. However, the risk of airborne spread of this strain remains to be elucidated. We conducted extensive sampling from IPs where clade 2.3.4.4b H5N1 HPAIVs was confirmed during the 2022/23 epizootic, each representing a major poultry species (ducks, turkeys, and chickens). A range of environmental samples were collected inside and outside houses, including deposited dust, feathers, and other potential fomites. Viral RNA (vRNA) and infectious virus were detected in air samples collected from inside and outside, but in close proximity, of infected houses, with vRNA alone being detected greater distances (>10m) outside. Some dust samples collected outside of the affected houses contained infectious virus, while feathers from the affected houses, located up to 60m away, only contained vRNA. Together, these data suggest that airborne particles harbouring infectious HPAIV can be translocated short distances (<10m) through the air, while particles containing vRNA might travel further (<50m). Therefore, the potential for airborne transmission of clade 2.3.4.4b H5N1 HPAIV between premises is considered low. Other factors, including indirect contact with wild birds, fomite spread and the efficiency of biosecurity represent greater importance in disease incursion. IMPORTANCEUnderstanding the routes of avian influenza virus incursion into poultry premises is critical to ensure the implementation of effective preventative measures, reducing the risk of spread of the virus. Extensive environmental sampling across three infected premises, representing the major global commercial poultry species, detected viral RNA and infectious virus in air samples, dust, and other fomites inside of the houses containing infected poultry, as well as within the immediate proximity of infected houses. This suggests that particles harbouring infectious virus may travel short distances outside of affected houses, which may potentially contribute to house-to-house transmission on the same premises, but not at distances likely to contribute to the transmission to another poultry premises. Consequently, control efforts should be focused on traditional, robust biosecurity measures at key barriers on poultry houses. Human behaviour in and around poultry houses as factors contributing to biosecurity risks should be considered.

microbiology↗

bioRxiv2023

Clade 2.3.4.4b H5N1 high pathogenicity avian influenza virus (HPAIV) from the 2021/22 epizootic is highly duck adapted and poorly adapted to chickens

The 2021/2022 epizootic of high pathogenicity avian influenza (HPAIV) remains one of the largest ever in the UK, being caused by a clade 2.3.4.4b H5N1 HPAIV. This epizootic affected more than 145 poultry premises, most likely through independent incursion from infected wild birds, supported by more than 1700 individual detections of H5N1 from wild bird mortalities. Here an H5N1 HPAIV, representative of this epizootic (H5N1-21), was used to investigate its virulence, pathogenesis and transmission in layer chickens and pekin ducks, two species of epidemiological importance. We inoculated both avian species with decreasing H5N1-21 doses. The virus was highly infectious in ducks, with high infection levels and accompanying shedding of viral RNA, even in ducks inoculated with the lowest dose, reflecting the strong waterfowl adaptation of the clade 2.3.4.4 HPAIVs. Duck-to-duck transmission was very efficient, coupled with high environmental contamination. H5N1-21 was frequently detected in water sources, serving as likely sources of infection for ducks, but inhalable dust and aerosols represented low transmission risks. In contrast, chickens inoculated with the highest dose exhibited lower rates of infection compared to ducks. There was no evidence for experimental H5N1-21 transmission to any naive chickens, in two stocking density scenarios, coupled with minimal and infrequent contamination being detected in the chicken environment. Systemic viral dissemination to multiple organs reflected the pathogenesis and high mortalities in both species. In summary, the H5N1-21 virus is highly infectious and transmissible in anseriformes, yet comparatively poorly adapted to galliformes, supporting strong host preferences for wild waterfowl. Key environmental matrices were also identified as being important in the epidemiological spread of this virus during the continuing epizootic.

microbiology↗

bioRxiv2022

Investigating the genetic diversity of H5 avian influenza in the UK 2020-2022

Since 2020, the UK and Europe, have experienced annual epizootics of high pathogenicity avian influenza virus (HPAIV). The first during autumn/winter 2020/21 involved the detected with six H5Nx subtypes although H5N8 HPAIV dominated in the UK. Whilst genetic assessment of the H5N8 HPAIVs within the UK demonstrated relative homogeneity, there was a background of other genotypes circulating at a lower degree with different neuraminidase and internal genes. Following a small number of summer detections of H5N1 in wild birds over the summer of 2021, autumn/winter 2021/22 saw another European H5 HPAIV epizootic, that has dwarfed the prior epizootic. This second epizootic was dominated almost exclusively by H5N1 HPAIV, although six distinct genotypes were defined. We have used genetic analysis to evaluate the emergence of different genotypes and proposed reassortment events that have been observed. The existing data suggests that the H5N1 circulating in Europe during late 2020, continued to circulate in wild birds throughout 2021, with minimal adaptation, but has then gone on to reassort with AIVs in the wild bird population. We have undertaken an in-depth genetic assessment of H5 HPAIVs detected in the UK, over the last two winter seasons and demonstrate the utility of in-depth genetic analyses in defining the diversity of H5 HPAIVs circulating in avian species, the potential for zoonotic risk and whether incidents of lateral spread can be defined over independent incursion of infection from wild birds. Key supporting data for mitigation activities. ImportanceHigh pathogenicity avian influenza virus (HPAIV) outbreaks devastate avian species across all sectors having both economic and ecological impacts through mortalities in poultry and wild birds, respectively. These viruses can also represent a significant zoonotic risk. Since 2020, the UK has experienced two successive outbreaks of H5 HPAIV. Whilst H5N8 HPAIV was predominant during the 2020/21 outbreak, other H5 subtypes were also detected. The following year there was a shift in subtype dominance to H5N1 HPAIV, but multiple H5N1 genotypes were detected. Through thorough utilisation of whole-genome sequencing, it was possible to track and characterise the genetic evolution of these H5 HPAIVs in UK poultry and wild birds. This has enabled us to assess the risk posed by these viruses at the poultry:wild bird and the avian:human interface and to investigate potential lateral spread between infected premises, a key factor in understanding threat to the commercial sector.

molecular biology↗

bioRxiv2022

Steric-free bioorthogonal profiling of cellular acetylation and glycosylation via a fluorine-selenol displacement reaction (FSeDR)

Global detection and identification of protein post-translational modification (PTM) is a major bottleneck due to its dynamic property and rather low abundance. Tremendous efforts have been since made to develop antibody-based immunoaffinity enrichment or bioorthogonal chemistry-based chemical reporter approach but both suffer from inherent limitations. Following our previously reported steric-free tagging strategy, we hereby report the invention of selenol as a new generation of fluorine-displacement probe. The fluorine-selenol based displacement reaction enabled us to efficiently label and image acetylation and glycosylation at cellular level. We further pursued FSeDR in tandem with SILAC based quantitative proteomics to globally profile acetylation substrate proteins in a representative prostate cancer cell line PC3. Our results unraveled the fluorine-based toolbox for powerful chemical biology probing and allow for the future study of PTMs in a systemic manner.

cell biology↗

bioRxiv2022

Genetic architecture and evolution of color variation in American black bears

Color variation is a frequent evolutionary substrate for camouflage in small mammals but the underlying genetics and evolutionary forces that drive color variation in natural populations of large mammals are mostly unexplained. The American black bear, Ursus americanus, exhibits a range of colors including the cinnamon morph which has a similar color to the brown bear, U. arctos, and is found at high frequency in the American southwest. Reflectance and chemical melanin measurements showed little distinction between U. arctos and cinnamon U. americanus individuals. We used a genome-wide association for hair color as a quantitative trait in 151 U. americanus individuals and identified a single major locus (P < 10-13). Additional genomic and functional studies identified a missense alteration (R153C) in Tyrosinase-related protein 1 (TYRP1) that impaired protein localization and decreased pigment production. Population genetic analyses and demographic modeling indicated that the R153C variant arose 9.36kya in a southwestern population where it likely provided a selective advantage, spreading both northwards and eastwards by gene flow. A different TYRP1 allele, R114C, contributes to the characteristic brown color of U. arctos, but is not fixed across the range. HIGHLIGHTSO_LIThe cinnamon morph of American black bears and brown bears have different missense mutations in TYRP1 that account for their similar coloration C_LIO_LITYRP1 variants in American black bears and brown bears are loss-of-function alleles associated with impaired protein localization to melanosomes C_LIO_LIIn American black bears, the variant causing the cinnamon morph arose 9,360 years ago in the western lineage where it provides an adaptive advantage, and has spread northwards and eastwards by migration C_LI

evolutionary biology↗

bioRxiv2021

COVID-19 and the abrupt shift to remote learning: Impact on grades and perceived learning for undergraduate biology students

Institutions across the world transitioned abruptly to remote learning in 2020 due to the COVID-19 pandemic. This rapid transition to remote learning has generally been predicted to negatively affect students, particularly those marginalized due to their race, socioeconomic class, or gender identity. In this study, we examined the impact of this transition in the Spring 2020 semester on the grades of students enrolled in the in-person biology program at a large university in Southwestern United States as compared to the grades earned by students in the fully online biology program at the same institution. We also surveyed in-person instructors to understand changes in assessment practices as a result of the transition to remote learning during the pandemic. Finally, we surveyed students in the in-person program to learn about their perceptions of the impacts of this transition. We found that both online and in-person students received a similar small increase in grades in Spring 2020 compared to Spring 2018 and 2019. We also found no evidence of disproportionately negative impacts on grades received by students marginalized due to their race, socioeconomic class, or gender in either modality. Focusing on in-person courses, we documented that instructors made changes to their courses when they transitioned to remote learning, which may have offset some of the potential negative impacts on course grades. However, despite receiving higher grades, in-person students reported negative impacts on their learning, interactions with peers and instructors, feeling part of the campus community, and career preparation. Women reported a more negative impact on their learning and career preparation compared to men. This work provides insights into students perceptions of how they were disadvantaged as a result of the transition to remote instruction and illuminates potential actions that instructors can take to create more inclusive education moving forward.

scientific communication and education↗

bioRxiv2021

An updated genome-scale metabolic network reconstruction of Pseudomonas aeruginosa PA14 to characterize mucin-driven shifts in bacterial metabolism

Mucins are present in mucosal membranes throughout the body and play a key role in the microbe clearance and infection prevention. Understanding the metabolic responses of pathogens to mucins will further enable the development of protective approaches against infections. We update the genome-scale metabolic network reconstruction (GENRE) of one such pathogen, Pseudomonas aeruginosa PA14, through metabolic coverage expansion, format update, extensive annotation addition, and literature-based curation to produce iPau21. We then validate iPau21 through MEMOTE, growth rate, carbon source utilization, and gene essentiality testing to demonstrate its improved quality and predictive capabilities. We then integrate the GENRE with transcriptomic data in order to generate context-specific models of P. aeruginosa metabolism. The contextualized models recapitulated known phenotypes of unaltered growth and a differential utilization of fumarate metabolism, while also revealing an increased utilization of propionate metabolism upon MUC5B exposure. This work serves to validate iPau21 and demonstrate its utility for providing biological insights.

systems biology↗

bioRxiv2020

Decadal changes in fire frequencies shift tree communities and functional traits

Global change has resulted in chronic shifts in fire regimes, increasing fire frequency in some regions and decreasing it in others. Predicting the response of ecosystems to changing fire frequencies is challenging because of the multi-decadal timescales over which fire effects emerge and the variability in environmental conditions, fire types, and plant composition across biomes. Here, we address these challenges using surveys of tree communities across 29 sites that experienced multi-decadal alterations in fire frequencies spanning ecosystems and environmental conditions. Relative to unburned plots, more frequently burned plots had lower tree basal area and stem densities that compounded over multiple decades: average fire frequencies reduced basal area by only 4% after 16 years but 57% after 64 years, relative to unburned plots. Fire frequency had the largest effects on basal area in savanna ecosystems and in sites with strong wet seasons. Analyses of tree functional-trait data across North American sites revealed that frequently burned plots had tree communities dominated by species with low biomass nitrogen and phosphorus content and with more efficient nitrogen acquisition through ectomycorrhizal symbioses (rising from 85% to nearly 100%). Our data elucidate the impact of long-term fire regimes on tree community structure and composition, with the magnitude of change depending on climate, vegetation type, and fire history. The effects of widespread changes in fire regimes underway today will manifest in decades to come and have long-term consequences for carbon storage and nutrient cycling.

ecology↗

bioRxiv2020

Single-dose replicating RNA vaccine induces neutralizing antibodies against SARS-CoV-2 in nonhuman primates

The ongoing COVID-19 pandemic, caused by infection with SARS-CoV-2, is having a dramatic and deleterious impact on health services and the global economy. Grim public health statistics highlight the need for vaccines that can rapidly confer protection after a single dose and be manufactured using components suitable for scale-up and efficient distribution. In response, we have rapidly developed repRNA-CoV2S, a stable and highly immunogenic vaccine candidate comprised of an RNA replicon formulated with a novel Lipid InOrganic Nanoparticle (LION) designed to enhance vaccine stability, delivery and immunogenicity. We show that intramuscular injection of LION/repRNA-CoV2S elicits robust anti-SARS-CoV-2 spike protein IgG antibody isotypes indicative of a Type 1 T helper response as well as potent T cell responses in mice. Importantly, a single-dose administration in nonhuman primates elicited antibody responses that potently neutralized SARS-CoV-2. These data support further development of LION/repRNA-CoV2S as a vaccine candidate for prophylactic protection from SARS-CoV-2 infection.

immunology↗

bioRxiv2018

Algorithmic improvements for discovery of germline copy number variants in next-generation sequencing data

Copy number variants (CNVs) play a significant role in human heredity and disease, however sensitive and specific characterization of CNVs from NGS data has remained challenging. Detection is especially problematic for hybridization-capture data in which read counts are the sole source of copy number information. We describe two algorithmic adaptations that improve CNV detection accuracy in a Hidden Markov Model (HMM) context. First, we present a method for com puting target- and copy number state-specific emission distributions. Second, we demonstrate that the Pointwise Maximum a posteriori (PMAP) HMM decoding procedure yields improved sensitivity for small CNV calls compared to the more common Viterbi HMM decoder. We develop a prototype implementation, called Cobalt, and compare it to other CNV detection tools using sets of simulated and previously detected CNVs with sizes spanning a single exon up to a full chromosome. In both the simulation and previously detected CNV studies Cobalt shows similar sensitivity but significantly improved positive predictive value (PPV) compared to other callers. Overall sensitivity is 80%-90% for deletion CNVs spanning 1-4 targets and 90%-100% for larger deletion events, while sensitivity is somewhat lower for small duplication CNVs. Cobalt demonstrates significantly improved positive predictive value (PPV) compared to other callers with similar sensitivity, typically making 5X fewer total calls overall.

bioinformatics↗

bioRxiv2018

Characterization of novel inhibition of indoleamine 2,3-dioxygenase by targeting its apo form.

Indoleamine-2,3-dioxygenase 1 (IDO1) is a heme-containing enzyme that catalyzes the rate-limiting step in the kynurenine pathway of tryptophan (TRP) metabolism. As an inflammation-induced immunoregulatory enzyme, pharmacological inhibition of IDO1 activity is currently being pursued as a potential therapeutic tool for the treatment of cancer and other disease states. As such, a detailed understanding of the mechanism of action of established and novel IDO1 inhibitors remains of great interest. Comparison of a newly-developed IDO1 inhibitor (GSK5628) to the existing best-in-class compound, epacadostat (Incyte), allows us to report on a unique inhibition mechanism for IDO1. Here, we demonstrate that GSK5628 inhibits IDO1 by competing with heme for binding to a heme-free conformation of the enzyme (apo-IDO1) while epacadostat coordinates its binding with the iron atom of the IDO1 heme cofactor. Comparison of these two compounds in cellular systems reveals a long-lasting inhibitory effect of GSK5628, undescribed for other known IDO1 inhibitors. Detailed characterization of this apo-binding mechanism for IDO1 inhibition may help design superior inhibitors or may confer a unique competitive advantage over other IDO1 inhibitors vis-a-vis specificity and pharmacokinetic parameters.

biochemistry↗