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Hannigan, B.

Publications and source records attributed to Hannigan, B..

3 recordsLinked to original sources

PAC: A novel translational concordance framework identifies preclinical seizure models with highest predictive validity for clinical focal onset seizures

ABSTRACT/SUMMARYO_ST_ABSObjectiveC_ST_ABSCentral to the development of novel antiseizure medications (ASMs) is testing of anticonvulsant activity in preclinical models. While various well-established models exist, their predictive validity across the spectrum of clinical epilepsies has been less clear. We sought to establish the translational concordance of commonly used preclinical models to define models with the highest predictive clinical validity for focal onset seizures (FOS). MethodsThe Praxis Analysis of Concordance (PAC) framework was implemented to assess the translational concordance between preclinical and clinical ASM response for 32 FDA-approved ASMs. Preclinical ASM responses in historically used seizure models were collected. Protective indices based on reported TD50 and ED50 values were calculated for each ASM in each preclinical model. A weighted scale representing relative anticonvulsant effect was used to grade preclinical ASM response for each seizure model. Data depth was further scored based on the number of evaluated ASMs with publicly available data. Established reports of clinical ASM use in patients with FOS were similarly evaluated and a weighted scale representing prescribing patterns and perceived efficacy used to grade clinical ASM response for each indication. To assess the predictive validity of preclinical models, a unified translational scoring matrix was developed to assign a concordance score spanning the spectrum of complete discordance (-1) to complete concordance (1) between preclinical and clinical ASM responses. Scores were summed and normalized to generate a global translational concordance score. ResultsThe preclinical models with the highest translational concordance and greatest data depth for FOS were rodent maximal electroshock seizure (MES), mouse audiogenic seizure, mouse 6 Hz (32mA) and rat amygdala kindling. SignificanceThe PAC-FOS framework highlights mouse MES, mouse audiogenic and mouse 6 Hz (32mA) as three acute seizure models consistently demonstrating high predictive validity for FOS. We provide a pragmatic decision tree approach to support efficient resource utilization for novel ASM discovery for FOS. KEY POINT BOXUsing a newly developed translational scoring matrix, we provide novel insights into the clinical validity of common preclinical seizure models for FOS. O_LIThe PAC-FOS Framework identifies mouse MES, audiogenic and 6-Hz 32 mA as three acute models with greatest predictive validity and versatility for FOS drug discovery. C_LIO_LIWe present a pragmatic approach and decision tree to support efficient use of drug discovery resources and in consideration of the 3Rs of animal ethics. C_LIO_LIThe work presented would allow for faster and more effective screening of ASMs, while potentially reducing future patient exposures to likely ineffective drugs. C_LI

pharmacology and toxicology↗

Functional and structural characterization of a combination of pan-sarbecovirus antibodies with potent antiviral activity

Sarbecoviruses, a subgenus of coronaviruses, include strains with zoonotic spillover risk as exemplified by recent outbreaks (SARS-CoV-1, SARS-CoV-2). Monoclonal antibodies targeting conserved spike protein regions (RBD class 4, S2 fusion machinery) exhibit broad sarbecovirus neutralization, but their utility has been impacted by immune selection leading to escape and suboptimal neutralization. Using structure-conditioned machine-learning protein design we optimized two broadly neutralizing sarbecovirus antibodies to rescue the activity of a class 4 anti-RBD antibody against Omicron variants and improve the neutralization profile of an anti-S2 stem antibody, resulting in the identification of the lead candidates PRO-37587 and GB-0669. Both antibodies displayed remarkable resilience to SARS-CoV-2 evolution. Structural analyses elucidated the mechanistic basis of their broad neutralization profiles. In combination, these antibodies exhibited improved SARS-CoV-2 neutralization in vitro and in vivo and a higher barrier to resistance. These findings support further evaluation of such antibody combination as countermeasure against current and emerging sarbecoviruses.

microbiology↗

How well can we create phased, diploid, human genomes?: An assessment of FALCON-Unzip phasing using a human trio

Long read sequencing technology has allowed researchers to create de novo assemblies with impressive continuity[1,2]. This advancement has dramatically increased the number of reference genomes available and hints at the possibility of a future where personal genomes are assembled rather than resequenced. In 2016 Pacific Biosciences released the FALCON-Unzip framework, which can provide long, phased haplotype contigs from de novo assemblies. This phased genome algorithm enhances the accuracy of highly heterozygous organisms and allows researchers to explore questions that require haplotype information such as allele-specific expression and regulation. However, validation of this technique has been limited to small genomes or inbred individuals[3].\n\nAs a roadmap to personal genome assembly and phasing, we assess the phasing accuracy of FALCON-Unzip in humans using publicly available data for the Ashkenazi trio from the Genome in a Bottle Consortium[4]. To assess the accuracy of the Unzip algorithm, we assembled the genome of the son using FALCON and FALCON Unzip, genotyped publicly available short read data for the mother and the father, and observed the inheritance pattern of the parental SNPs along the phased genome of the son. We found that 72.8% of haplotype contigs share SNPs with only one parent suggesting that these contigs are correctly phased. Most mis-phased SNPs are random but present in high frequency toward the end of haplotype contigs. Approximately 20.7% of mis-phased haplotype contigs contain clusters of mis-phased SNPs, suggesting that haplotypes were mis-joined by FALCON-Unzip. Mis-joined boundaries in those contigs are located in areas of low SNP density. This research demonstrates that the FALCON-Unzip algorithm can be used to create long and accurate haplotypes for humans and identifies problematic regions that could benefit in future improvement.

bioinformatics↗