Biology subjects

Davis, D.

Publications and source records attributed to Davis, D..

At least 19 recordsLinked to original sources

bioRxiv2026

Vaccination targeting the novel endogenous tumor-associated antigen Gpr149 induces protective immunity against checkpoint inhibitor-refractory SB28 glioblastoma

Background: Glioblastoma is a lethal brain tumor notable for its limited spontaneous induction of CD8+ T cell responses. Vaccination may overcome this limitation by generating tumor-specific CD8+ T cells capable of mediating anti-tumor immunity in the brain. However, preclinical vaccine development is constrained by a lack of immunologically stringent glioblastoma models with defined endogenous antigens. We therefore sought to identify endogenous, vaccine-targetable antigens expressed by the immune checkpoint-refractory SB28 syngeneic mouse glioblastoma model and to evaluate their targetability using a heterologous prime-boost regimen with the chimpanzee adenovirus ChAdOx1 and the modified vaccinia Ankara (MVA) viral vector-based vaccines. Methods: RNA sequencing and whole-exome sequencing were used to identify candidate tumor-associated antigens (TAAs) and neoantigens, and tumor-specific expression was validated by RT-qPCR. ChAdOx1 and MVA vectors encoding candidate antigens were generated and evaluated for immunogenicity and anti-tumor efficacy. Antigen-specific CD8+ T cell responses and minimal epitopes were characterized by ex vivo restimulation, MHC-I binding assays, tetramer staining, and tumor cytotoxicity assays. Results: We identified five candidate TAAs (Gpr149, Cdh6, Fbn2, Igf2bp1, and Shox2) but no suitable neoantigen targets in SB28. Vaccination induced CD8+ T cell responses against the candidate TAAs, and immunogenic minimal epitopes were identified for each. Among the candidates, Gpr149 elicited the strongest vaccine-induced CD8+ T cell responses. In mice challenged intracranially with SB28, Gpr149-targeted ChAdOx1/MVA vaccination combined with immune checkpoint blockade significantly prolonged median survival and resulted in long-term survival in 50% of mice, whereas vaccination targeting the other TAAs did not improve survival. CD8+ T cells recognizing the immunodominant Gpr149128-135 epitope (VCYNFYTM) specifically recognized and lysed wild-type SB28 cells, but not Gpr149-knockout SB28 cells, confirming endogenous processing and presentation of the targeted epitope. Conclusions: Gpr149 is an endogenous SB28 tumor antigen that can be effectively targeted by ChAdOx1/MVA vaccination to generate protective anti-tumor immunity against intracranial glioblastoma. Protection was associated with a dominant CD8+ T cell response to the Gpr149128-135 epitope VCYNFYTM. These findings establish endogenously expressed Gpr149 in SB28 as a physiologically relevant model for evaluating antigen-targeted immunotherapies and provide a systematic approach for identifying endogenous vaccine targets in other preclinical models.

immunology↗

bioRxiv2026

Systemic viral vector vaccination induces brain resident memory T cells to drive anti-glioblastoma immunity

Glioblastoma is a lethal brain tumor that is unresponsive to current cancer immunotherapeutic approaches, including immune checkpoint blockade (ICB). This suggests that initial priming of T cells, rather than their expansion and licensing as effectors, is a restricting feature in this tumor setting. To overcome the limited initiation of CD8+ T cell responses, we employed a strong heterologous prime-boost vaccination with the simian adenovirus ChAdOx1 and poxvirus modified vaccinia Ankara (MVA). Vaccination conferred therapeutic efficacy against orthotopic, immune checkpoint-blockade (ICB)-refractory SB28 murine glioblastoma. Vaccination was effective against both the murine tumor antigen, P1A, and a newly identified glioblastoma-associated antigen, Gpr149. Additional treatment with ICB provided no additional benefit. Systemic ChAdOx1/MVA vaccination induced robust infiltration of antigen-specific T cells in tumor-challenged brains, the majority of which exhibited a CD103+CD69+CD8+ tissue-resident memory (TRM)-like phenotype. These cells were polyfunctional, durable in brains with sustained tumor control, and mediated tissue-specific immunological memory. Moreover, intracranial adoptive transfer of glioblastoma-derived antigen-specific TRM-like cells was sufficient to protect naive recipients from subsequent orthotopic tumor challenge. Together, these findings establish that viral vector vaccination can generate tumor-specific TRM-like cells that mediate effective anti-glioblastoma immunity, providing a rationale for clinical evaluation of ChAdOx1/MVA-based strategies in glioblastoma.

immunology↗

bioRxiv2026

SCD1 inhibition synergizes with TMZ to improve IDH1 MUT glioma survival of mice via lipotoxic stress

Mutations in the isocitrate dehydrogenase enzyme (IDH1) are prevalent in low-grade gliomas, such as oligodendrogliomas. Other than surgery, radiation, and chemotherapy, few options for treatment exist. The standard of care for patients currently consists of maximal safe resection, as well as the potential use of radiation and chemotherapy, typically followed by radiographic surveillance. Although significant advances have been achieved, these have not translated into meaningful improvements in overall survival, warranting the development of novel therapies. Herein, we demonstrate that the inhibition of SCD1 in vitro leads to decreased colony formation and is more specific to IDH1MUT glioma than the IDH1WT cells, We further identified MF-438 as an active inhibitor of this enzyme and showed that this inhibitor is linked with iron transport and ferroptosis. MF438 depleted oleic (C18:1) and palmitoleic acid (C16:1) levels, driving saturated phosphatidylcholine (PC) accumulation and ER stress (INSIG1, SEL1L upregulation). TS603 exhibited selective polyunsaturated phosphatidylcholine reduction with downregulation of GPX4, FTH1, and KEAP1, and upregulation of NCOA4, SLC11A2, ALDH7A1, and DPP4, consistent with ferroptosis priming via ferritinophagy-driven expansion of the labile iron pool, as confirmed by FerroOrange flow cytometry. Neutral lipid metabolism genes (LPIN1, LDLR, PNPLA3, ACSL1), intracellular lipid transport genes (TMEM41B, OSBP, STARD4), and lipid droplet organization genes (SQLE, CHKA, AUP1) were coordinately upregulated in TS603 after treatment with MF-438. MF438+TMZ activated the integrated stress response (ATF3, DDIT3, IRF1, CDKN1A, GADD45B) and synergistically suppressed TS603 neurosphere growth (p=0.0326). In vivo combination between MF-438 and TMZ showed improved survival versus the TMZ-alone group, in an IDH1-mutant oligodendroglioma model. Tissue analyses showed significant reduced Ki67 expression, a marker of cellular proliferation, in the combination treatment. Collectively, these findings suggest that targeting lipid metabolism may enhance the efficacy of standard-of-care therapy in IDH1-mutant oligodendroglioma.

Cancer Biology↗

bioRxiv2025

New insights into the extinction and recovery of marine vertebrates across the Permian-Triassic mass extinction event in the Dolomites, Southern Alps, Italy

The impact of the Permian-Triassic mass extinction on marine vertebrates is poorly known due to their scarce fossil record. Here, we report Acrodus sp. [Chondrichthyes], Bobasatrania aff. ladina [Osteichthyes] and an indeterminate actinopterygian from the Changhsingian Bellerophon Formation, and a saurosphargid reptile from the lower Spathian Val Badia Member of the Werfen Formation in the Dolomites, Italy. The saurosphargid is represented by a single vertebra, whose relatively tall neural spine indicates that it might belong to a new species. This is one of the oldest Sauropterygomorpha records worldwide and the first unambiguous occurrence of Saurosphargidae in the western Paleo-Tethys during the Early Triassic. These new findings suggest fishes were more diverse in this paleo-tropical shallow shelf community of the western Paleo-Tethys in the latest Permian than during the Early Triassic. The evolution of the new apex predator niche (Saurosphargidae) relatively shortly after the mass extinction event coincides with the reappearance of predatory cephalopods and precedes the full ecological and taxonomic recovery of benthic groups in the Dolomites community. This contrasts with previous hypotheses about the delayed recovery of higher trophic groups. Furthermore, we dated a surface sample with actinopterygian scales found at a Permian-Triassic boundary outcrop. The U-Pb indicates 248+/-1 Ma as a maximum depositional age, and radiolarian biostratigraphy indicates an Anisian age. This suggests age assignments to surface samples require caution. U-Pb dating further reveals an age discrepancy in the scales and the host rock, likely due to 206Pb enrichment in scales during diagenesis.

paleontology↗

bioRxiv2025

Mapping of genotype-by-environment interaction loci for Metabolic Syndrome-like traits using the multi-parent Drosophila Synthetic Population Resource determines that main genetic effects are distinct from environment dependent plastic loci

Metabolic Syndrome (MetS) risk, driven by genotype-environment interactions like diet, is rising globally. Due to its genetic and environmental complexity, the genetic architecture and interconnected traits underlying MetS is poorly understood. In Drosophila, genotype-by-diet interactions significantly influence MetS-like traits. This study used the Drosophila Synthetic Population Resource to dissect the genetic architecture of both genotypic and genotype-by-diet interaction effects underlying trait variation. The study hypotheses were: 1) Loci responsible for metabolic phenotypic variation should be shared across traits. 2) Genetic loci responsible for plasticity and epistatic interactions for metabolic traits should also be the loci responsible for the main effects. 3) Genes responsible for variation in metabolic traits should share common functions. Using a round-robin crossing scheme and novel analyses, we mapped additive, dominance, and epistatic loci--some diet-specific, others diet-independent. Main-effect and plastic loci were largely distinct, as were epistatic loci from main-effect loci, highlighting that main genetic effects alone will not explain how genetic variants interact with the environment or the genome to influence disease risk. gene-by-diet or gene-by-gene interactions influencing MetS risk. Further, tremendous cryptic genetic variation for metabolic traits is lurking in natural populations. We explored the function of candidate genes from our study empirically and with bioinformatics. While some of the candidate genes might have been expected, most would not have been identified a priori, thus with this study we have identified many new candidate mechanisms contributing to the genetic and genotype-by-diet interaction effects on MetS variance.

genetics↗

bioRxiv2025

Novel Gain of Function Mouse Model of KCNT1-Related Epilepsy

KCNT1-related epilepsy is an autosomal dominant neurodevelopmental disorder with at least 64 known human variants, each with unique electrophysiological and epileptic characteristics. A multi-disciplinary collaboration generated a novel mouse model (C57BL/6-Kcnt1em1Bryd) carrying the G269S variant, corresponding to human G288S, located within the coding region of the channel pore. Network excitability of cultured cortical neurons from Kcnt1+/G269S exhibited sustained hyperexcitability and hypersynchronous bursting while Kcnt1G269S/G269S neurons showed early excessive bursting followed by network collapse, suggesting excitotoxicity. Kcnt1+/G269S displayed poor motor coordination, erratic breathing, and increased apneas. Critically, Kcnt1+/G269S were more susceptible to thermal-induced seizures in early life. In summary, these data: (i) provide a novel mouse model of KCNT1-related epilepsy, (ii) provide strong in vitro evidence of neuronal hyperexcitability, (iii) illustrate early-life seizures as a functional outcome measure, and (iv) lay the groundwork for future analysis of neural activity in vivo and modeling circuit level dynamics in vitro and in silico. Significance StatementGain-of-function mutations in the sodium-gated potassium channel KCNT1 have been linked to pediatric epilepsy of varying severity. The human KCNT1 variant G288S (G269S in mice) is linked to Autosomal Dominant Nocturnal Frontal Lobe Epilepsy (ADNFLE), Epilepsy of Infancy with Migrating Focal Seizures (EIMFS), and other severe developmental epileptic encephalopathies. There are currently no therapeutics to prevent the progression of KCNT1-related epilepsy, therefore, the scientific community requires a novel mouse model that is well characterized, in vitro and in vivo, to screen and assess targeted therapeutics. Herein, we engineered a novel mouse to assess developmental and adult phenotypes resulting from the G288S/G269S variant, in vitro and in vivo, to advance translation toward therapeutic testing for individuals with KCNT1-related epilepsy.

neuroscience↗

bioRxiv2025

Germline-targeting HIV Envelope SOSIP immunization more frequently elicits broadly-neutralizing antibody precursor responses in infant compared to juvenile rhesus macaques

A vaccine capable of inducing broadly neutralizing antibodies (bnAbs) is essential for effective prevention against HIV in children and adolescents. Germline-targeting vaccine strategies aim to stimulate bnAb precursor B cells through carefully designed immunogens, such as the stabilized SOSIP trimers, which mimic native HIV envelope (Env) proteins while presenting key neutralizing epitopes to germline B cell receptors. Given the ability of children living with HIV to develop bnAbs earlier and at a higher frequency than adults, we compared the immunogenicity of a CD4 binding site (CD4bs) bnAb germline-targeting SOSIP trimer immunization strategy in infant (n = 5) and juvenile (n = 4) rhesus macaques (RMs). Animals received 3 doses of the germline-targeting BG505 GT1.1 immunogen, followed by 3 boosts of wild-type BG505 SOSIP, each adjuvanted with the TLR7/8 agonist, 3M-052-SE. After 1.5 years, the RMs were further boosted with a mixed clade B Env trimer nanoparticle to enhance heterologous virus neutralization responses. This germline-targeting strategy induced equivalent titers of neutralizing antibodies in both groups of RMs, yet the infants exhibited a higher magnitude of vaccine-specific IgG binding. Notably, after 3 doses of BG505 GT1.1 SOSIP, infants had higher BG505 GT1.1-specific IgD- B cells. Upon completion of the vaccine regimen, 4 of 5 infants developed a CD4bs bnAb precursor response detectable in serum compared to only 1 of 4 juveniles. Finally, administration of the mixed clade B nanoparticle was able to increase the breadth of antibody responses in 3 of 5 infants and 2 of 4 juveniles. These results suggest that immunization in early-life may enhance bnAb induction and highlight the potential for future pediatric HIV-1 vaccine strategies. Author SummaryVaccines that can generate antibody responses that have breadth and potency in neutralization can protect children and adolescents from acquiring multi-strain viruses like HIV. Increasingly, vaccine strategies have become better tailored to elicit these broadly neutralizing antibodies (bnAbs), such as the germline-targeting HIV envelope antigens, which have shown great promise. To determine if we could elicit protective antibody responses against HIV in early life, we immunized infant and juvenile monkeys using the same vaccine strategy. In this study, we found that while both infants and juveniles developed similar levels of antibodies that could neutralize HIV, the infants showed stronger antibody responses in several key areas. Moreso, infants developed the type of early antibody response that researchers believe is needed to eventually evolve into broadly neutralizing antibodies. These findings suggest that initiating HIV vaccination earlier in life may offer a better chance at generating the bnAbs needed to protect against various HIV strains. Our work highlights the potential benefits of initiating an HIV vaccine regimen in childhood.

immunology↗

bioRxiv2025

Caspase Cleavage of Kaposi Sarcoma-Associated Herpesvirus Proteins: A role for K5 in Preventing Caspase-Mediated Cell Death during Lytic Replication

We previously reported that Kaposi sarcoma-associated herpesvirus (KSHV) latency-associated nuclear antigen (LANA) acts as a pseudo-substrate for caspases-1 and 3, thereby interfering with their inflammatory and apoptotic activity, respectively. To determine if other KSHV proteins undergo caspase cleavage, we screened the KSHV proteome for potential caspase cleavage sites. Using SitePrediction (SP), 30 KSHV proteins with potential caspase-cleavage sites were identified. Among those with highest SP score was an early lytic protein, K5. Treatment of BJAB K5-FLAG cells with Fas, an apoptotic stimulus, led to caspase-processing of full length K5-FLAG and generation of a C-terminal peptide fragment. Using mass spectrometry, we determined that K5-FLAG undergoes caspase cleavage at D222. K5 was also cleaved by caspases in KSHV infected cells induced to lytic replication. Importantly, the expression of K5-FLAG significantly inhibited Fas-induced caspase-mediated cell death. To determine if K5 plays a protective role in KSHV infected cells, iSLKK cells infected with wild type or K5 knockout BAC16 virus were induce to lytic replication to activate caspases. Although lytic induction showed little effect on the viability of WT infected cells, the viability of K5-knockout cells decreased by 25%. Thus, K5 may protect KSHV-infected cells from caspase-mediated cell death during lytic replication. Interestingly, cleavage of K5 by caspases did not affect its ability to downregulate MHC-1 surface expression. Overall, these data suggest that K5 not only downregulates immunologic surface marker expression to avoid immune recognition but may also play an additional role in mitigating caspase-mediated cell death during KSHV lytic replication.

biochemistry↗

bioRxiv2024

Rapid Detection of Active Coronavirus Infection by Lateral Flow Test Strips: A New Approach to Distinguish Replicating Viruses from Non-Replicating Viruses

This manuscript describes the development of an alternative method to detect active coronavirus infection, which targets negative-sense RNA, a product of active viral replication. Few diagnostic methods are capable of discriminating between replicating and non-replicating viruses, complicating decisions related to quarantine and therapeutic interventions. We propose strand-specific nucleic acid diagnostics as a means of distinguishing between active and inactive RNA virus infections and prototype a CRISPR-based lateral flow assay that specifically detects replicating coronaviruses. Such a paradigm in diagnostics could guide more effective public health measures to curb the spread of SARS-CoV-2 and other single-stranded viruses.

microbiology↗

bioRxiv2024

Targeting the sphingolipid rheostat in IDH1mut glioma alters cholesterol homeostasis and triggers apoptosis via membrane degradation

The cross-regulation of metabolism and trafficking is not well understood for the vital sphingolipids and cholesterol constituents of cellular compartments. While reports are starting to surface on how sphingolipids like sphingomyelin (SM) dysregulate cholesterol levels in different cellular compartments (Jiang et al., 2022), limited research is available on the mechanisms driving the relationship between sphingolipids and cholesterol homeostasis, or its biological implications. Previously, we have identified sphingolipid metabolism as a unique vulnerability for IDH1mut gliomas via a rational drug design. Herein, we show how modulating sphingolipid levels affects cholesterol homeostasis in brain tumors. However, we unexpectedly discovered for the first time that C17 sphingosine and NDMS addition to cancer cells alters cholesterol homeostasis by impacting its cellular synthesis, uptake, and efflux leading to a net decrease in cholesterol levels and inducing apoptosis. Our results reflect a reverse correlation between the levels of sphingosines, NDMS, and unesterified, free cholesterol in the cells. We show that increasing sphingosine and NDMS (a sphingosine analog) levels alter not only the trafficking of cholesterol between membranes but also the efflux and synthesis of cholesterol. We also demonstrate that despite the effort to remove free cholesterol by ABCA1-mediated efflux or by suppressing machinery for the influx (LDLR) and biosynthetic pathway (HMGCR), apoptosis is inevitable for IDH1mut glioma cells. This is the first study that shows how altering sphingosine levels directly affects cholesterol homeostasis in cancer cells and can be used to manipulate this relationship to induce apoptosis in IDH1mut gliomas.

cancer biology↗

bioRxiv2023

Germline-targeting SOSIP trimer immunization elicits precursor CD4 binding-site targeting broadly neutralizing antibodies in infant macaques.

A vaccine that can achieve protective immunity prior to sexual debut is critical to prevent the estimated 410,000 new HIV infections that occur yearly in adolescents. As children living with HIV can make broadly neutralizing antibody (bnAb) responses in plasma at a faster rate than adults, early childhood is an opportune window for implementation of a multi-dose HIV immunization strategy to elicit protective immunity prior to adolescence. Therefore, the goal of our study was to assess the ability of a B cell lineage-designed HIV envelope SOSIP to induce bnAbs in early life. Infant rhesus macaques (RMs) received either BG505 SOSIP or the germline-targeting BG505 GT1.1 SOSIP (n=5/group) with the 3M-052-SE adjuvant at 0, 6, and 12 weeks of age. All infant RMs were then boosted with the BG505 SOSIP at weeks 26, 52 and 78, mimicking a pediatric immunization schedule of multiple vaccine boosts within the first two years of life. Both immunization strategies induced durable, high magnitude binding antibodies and plasma autologous virus neutralization that primarily targeted the CD4-binding site (CD4bs) or C3/465 epitope. Notably, three BG505 GT1.1-immunized infants exhibited a plasma HIV neutralization signature reflective of VRC01-like CD4bs bnAb precursor development and heterologous virus neutralization. Finally, infant RMs developed precursor bnAb responses at a similar frequency to that of adult RMs receiving a similar immunization strategy. Thus, a multi-dose immunization regimen with bnAb lineage designed SOSIPs is a promising strategy for inducing protective HIV bnAb responses in childhood prior to adolescence when sexual HIV exposure risk begins.

immunology↗

bioRxiv2023

Exploiting the therapeutic vulnerability of IDH-mutant gliomas with zotiraciclib

Isocitrate dehydrogenase (IDH)-mutant gliomas have distinctive metabolic and biological traits that may render them susceptible to targeted treatments. Here, by conducting a high-throughput drug screen, we pinpointed a specific susceptibility of IDH-mutant gliomas to zotiraciclib (ZTR). ZTR exhibited selective growth inhibition across multiple IDH-mutant glioma in vitro and in vivo models. Mechanistically, ZTR at low doses suppressed CDK9 and RNA Pol II phosphorylation in IDH-mutant cells, disrupting mitochondrial function and NAD+ production, causing oxidative stress. Integrated biochemical profiling of ZTR kinase targets and transcriptomics unveiled that ZTR-induced bioenergetic failure was linked to the suppression of PIM kinase activity. We posit that the combination of mitochondrial dysfunction and an inability to adapt to oxidative stress resulted in significant cell death upon ZTR treatment, ultimately increasing the therapeutic vulnerability of IDH-mutant gliomas. These findings prompted a clinical trial evaluating ZTR in IDH-mutant gliomas towards precision medicine (NCT05588141). HighlightsO_LIZotiraciclib (ZTR), a CDK9 inhibitor, hinders IDH-mutant glioma growth in vitro and in vivo. C_LIO_LIZTR halts cell cycle, disrupts respiration, and induces oxidative stress in IDH-mutant cells. C_LIO_LIZTR unexpectedly inhibits PIM kinases, impacting mitochondria and causing bioenergetic failure. C_LIO_LIThese findings led to the clinical trial NCT 05588141, evaluating ZTR for IDH-mutant gliomas. C_LI

cancer biology↗

bioRxiv2023

A novel method to accurately estimate pathway activity in single cells for clustering and differential analysis

Inferring which and how biological pathways and gene sets are changing is a key question in many studies that utilize single-cell RNA sequencing. Typically, these questions are addressed by quantifying the enrichment of known gene sets in lists of genes derived from global analysis. Here we offer SiPSiC, a new method to infer pathway activity in each cell. This allows more sensitive differential analysis and utilizing pathway scores to cluster cells and compute UMAP or other similar projections. We apply our method on datasets of COVID-19, lung adenocarcinoma and glioma, and demonstrate its utility. SiPSiC analysis is consistent with findings reported by previous analyses in many cases, but also reveals the differential activity of novel pathways, enabling us to suggest new mechanisms underlying the pathophysiology of these diseases and demonstrating SiPSiCs high accuracy and sensitivity in detecting biological function and traits. In addition, we demonstrate how it can be used to better classify cells based on activity of biological pathways instead of single genes and its ability to overcome patient specific artifacts.

bioinformatics↗

bioRxiv2023

Shift from a Simplified to Complex Gut Microbiota Reduces Adenoma Burden in a Preclinical Rat Model of Colon Cancer

Specific bacterial taxa in the gastrointestinal tract have been strongly associated with cases of colorectal cancer (CRC) cancer in familial adenomatous polyposis and spontaneous disease cases in humans. This has been recapitulated in animal models of CRC with positive correlations with many commensals and pathogens. However, many of these studies are performed either in germ-free animals or employ an antibiotic regime, overlooking the complex interactions of the commensals within the colon. To simplify the challenges associated with the complexity of the microbiota in the GI tract we established the Pirc rat model of colon cancer on an Altered Schaedler Flora (ASF) gut microbiota (GM), maintained in a barrier room. To elucidate the role of the simplified (ASF) and conventional GMs on disease susceptibility, We conventionalized ASF Pirc littermates. We found that the conventionalized F1 rats had increased microbial diversity and decreased colonic adenoma multiplicity. Our findings show that the complexity and the interactions of the GM community and not a Firmicutes to Bacteroidetes ratio are an important factor affecting disease susceptibility.

microbiology↗

bioRxiv2023

A New Approach for Active Coronavirus Infection Identification by Targeting the Negative RNA Strand- A Replacement for the Current Positive RNA-based qPCR Detection Method

This manuscript describes the development of an alternative method to detect active coronavirus infection, in light of the current COVID-19 pandemic caused by the SARS-CoV-2 virus. The pandemic, which was first identified in Wuhan, China in December 2019, has had a significant impact on global health as well as on the economy and daily life in the world. The current positive RNA-based detection systems are unable to discriminate between replicating and non-replicating viruses, complicating decisions related to quarantine and therapeutic interventions. The proposed method targets the negative strand of the virus and has the potential to effectively distinguish between active and inactive infections, which could provide a more accurate means of determining the spread of the virus and guide more effective public health measures during the current pandemic.

microbiology↗

bioRxiv2022

Gene amplification mutations originate prior to selective stress in Acinetobacter baylyi

The controversial theory of adaptive amplification states gene amplification mutations are induced by selective environments where they are enriched due to the stress caused by growth restriction on unadapted cells. We tested this theory with three independent assays using an Acinetobacter baylyi model system that exclusively selects for cat gene amplification mutants. Our results demonstrate all cat gene amplification mutant colonies arise through a multistep process. While the late steps occur during selection exposure, these mutants derive from low-level amplification mutant cells that form before growth-inhibiting selection is imposed. During selection, these partial mutants undergo multiple secondary steps generating higher amplification over several days to multiple weeks to eventually form visible high-copy amplification colonies. Based on these findings, amplification in this Acinetobacter system can be explained by a natural selection process that does not require a stress response. These findings have fundamental implications to understanding the role of growth-limiting selective environments on cancer development.

genetics↗

bioRxiv2021

Design and proof-of-concept for targeted phage-based COVID-19 vaccination strategies with a streamlined cold-free supply chain

Development of effective vaccines against Coronavirus Disease 2019 (COVID-19) is a global imperative. Rapid immunization of the world human population against a widespread, continually evolving, and highly pathogenic virus is an unprecedented challenge, and many different vaccine approaches are being pursued to meet this task. Engineered filamentous bacteriophage (phage) have unique potential in vaccine development due to their inherent immunogenicity, genetic plasticity, stability, cost-effectiveness for large-scale production, and proven safety profile in humans. Herein we report the design, development, and initial evaluation of targeted phage-based vaccination approaches against Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) by using dual ligand peptide-targeted phage and adeno-associated virus/phage (AAVP) particles. Towards a unique phage- and AAVP-based dual-display candidate approach, we first performed structure-guided antigen design to select six solvent-exposed epitopes of the SARS-CoV-2 spike (S) protein for display on the recombinant major capsid coat protein pVIII. Targeted phage particles carrying one of these epitopes induced a strong and specific humoral response. In an initial experimental approach, when these targeted phage particles were further genetically engineered to simultaneously display a ligand peptide (CAKSMGDIVC) on the minor capsid protein pIII, which enables receptor-mediated transport of phage particles from the lung epithelium into the systemic circulation (termed "dual-display"), they enhanced a systemic and specific spike (S) protein-specific antibody response upon aerosolization into the lungs of mice. In a second line of investigation, we engineered targeted AAVP particles to deliver the entire S protein gene under the control of a constitutive cytomegalovirus (CMV) promoter, which induced tissue-specific transgene expression stimulating a systemic S protein-specific antibody response. As proof-of-concept preclinical experiments, we show that targeted phage- and AAVP-based particles serve as robust yet versatile enabling platforms for ligand-directed immunization and promptly yield COVID-19 vaccine prototypes for further translational development. SignificanceThe ongoing COVID-19 global pandemic has accounted for over 2.5 million deaths and an unprecedented impact on the health of mankind worldwide. Over the past several months, while a few COVID-19 vaccines have received Emergency Use Authorization and are currently being administered to the entire human population, the demand for prompt global immunization has created enormous logistical challenges--including but not limited to supply, access, and distribution--that justify and reinforce the research for additional strategic alternatives. Phage are viruses that only infect bacteria and have been safely administered to humans as antibiotics for decades. As experimental proof-of-concept, we demonstrated that aerosol pulmonary vaccination with lung-targeted phage particles that display short epitopes of the S protein on the capsid as well as preclinical vaccination with targeted AAVP particles carrying the S protein gene elicit a systemic and specific immune response against SARS-CoV-2 in immunocompetent mice. Given that targeted phage- and AAVP-based viral particles are sturdy yet simple to genetically engineer, cost-effective for rapid large-scale production in clinical grade, and relatively stable at room temperature, such unique attributes might perhaps become additional tools towards COVID-19 vaccine design and development for immediate and future unmet needs.

microbiology↗

bioRxiv2019

Data Resource Profile:The Dementias Platform UK (DPUK) Data Portal

The Dementias Platform UK (DPUK) Data Portal is a data repository facilitating access to data for 3 370 929 individuals in 42 cohorts. The Data Portal is an end-to-end data management solution providing a secure, fully auditable, remote access environment for the analysis of cohort data. All projects utilising the data are by default collaborations with the cohort research teams generating the data. The Data Portal uses UK Secure eResearch Platform (UKSeRP) infrastructure to provide three core utilities: data discovery, access, and analysis. These are delivered using a 7 layered architecture comprising: data ingestion, data curation, platform interoperability, data discovery, access brokerage, data analysis and knowledge preservation. Automated, streamlined, and standardised procedures reduce the administrative burden for all stakeholders, particularly for requests involving multiple independent datasets, where a single request may be forwarded to multiple data controllers. Researchers are provided with their own secure lab using VMware which is accessed using two factor authentication. Over the last 2 years, 160 project proposals involving 579 individual cohort data access requests were received. These were received from 268 applicants spanning 72 institutions (56 academic, 13 commercial, 3 government) in 16 countries with 84 requests involving multiple cohorts. Project are varied including multi-modal, machine learning, and Mendelian randomisation analyses. Data access is usually free at point of use although a small number of cohorts require a data access fee.

neuroscience↗