Biology subjects

Murphy, S. C.

Publications and source records attributed to Murphy, S. C..

4 recordsLinked to original sources

bioRxiv2025

Systemic trafficking of mRNA lipid nanoparticle vaccine following intramuscular injection generates potent tissue-specific T cell response

The mRNA lipid nanoparticles (LNPs) represent a new generation of vaccine carriers designed to elicit potent immune responses against infectious diseases and cancer. Despite the clinical success and rapid advancements in mRNA LNP technologies, the trafficking patterns of LNPs after intramuscular (i.m.) administration and the subsequent tissue-specific immunological effects have not been systematically characterized. Here, we report that trafficking of mRNA LNPs to different organs following i.m. injection is crucial for the induction of tissue-specific immunity beyond systemic immune response, particularly in tissue-resident CD8+ T cell generation, which is important for localized defense. By fine-tuning the composition of mRNA LNPs, trafficking patterns to systemic organs can be modulated, which can alter the resulting tissue-specific immune response. Formulations with a greater ability to enter the bloodstream can preferentially localize and transfect cells in specific organs like the liver, elicit stronger tissue-specific CD8+ T cell immune responses, and achieve enhanced efficacy in a liver tumor model. These findings highlight the potential to tailor mRNA LNP compositions to modulate trafficking following i.m. injection, thereby providing novel strategies for designing tissue-specific vaccines. Such strategies are particularly valuable for organ-specific diseases like cancer and infectious diseases, where tissue targeting and long-lasting immunity are essential for therapeutic success.

bioengineering↗

bioRxiv2025

Distinguishing new from persistent infections at the strain level using longitudinal genotyping data

MotivationLongitudinal pathogen genotyping data from individual hosts can uncover strain-specific infection dynamics and their relationships to disease and intervention, especially in the malaria field. An important use case involves distinguishing newly incident from pre-existing (persistent) strains, but implementation faces statistical challenges relating to individual samples containing multiple strains, strains sharing alleles, and markers dropping out stochastically during the genotyping process. Current approaches to distinguish new versus persistent strains therefore rely primarily on simple rules that consider only the time since alleles were last observed. ResultsWe developed DINEMITES (Distinguishing New Malaria Infections in Time Series), a set of statistical methods to estimate, from longitudinal genotyping data, the probability each sequenced allele represents a new infection harboring that allele, the total molecular force of infection (molFOI, the cumulative number of newly acquired strains over time) for each individual, and the total number of new infection events for each individual. DINEMITES can handle time points with missing sequencing data, incorporate treatment history and covariates affecting the rate of new or persistent infections, and can scale to studies with thousands of samples sequenced across multiple loci containing hundreds of possible alleles. In synthetic evaluations, the DINEMITES Bayesian model, which generally outperformed an alternative clustering-based model also developed in this work, accurately estimated key clinical parameters such as molFOI (bias 2.5, compared to -12.2 for a typical simple rule). When applied to three real longitudinal genotyping datasets, the model detected 33%, 112%, and 359% more average infections per participant than would have been detected by applying a typical simple rule to the equivalent datasets without sequencing. Availability and implementationDINEMITES is freely available as an R package, along with documentation, tutorials, and example data, at https://github.com/WillNickols/dinemites.

genomics↗

bioRxiv2023

Accelerated prime-and-trap vaccine regimen in mice using repRNA-based CSP malaria vaccine

Malaria, caused by Plasmodium parasites, remains one of the most devastating infectious diseases worldwide, despite control efforts that have lowered morbidity and mortality. The only P. falciparum vaccine candidates to show field efficacy are those targeting the asymptomatic pre-erythrocytic (PE) stages of infection. The subunit (SU) RTS,S/AS01 vaccine, the only licensed malaria vaccine to date, is only modestly effective against clinical malaria. Both RTS,S/AS01 and the SU R21 vaccine candidate target the PE sporozoite (spz) circumsporozoite (CS) protein. These candidates elicit high-titer antibodies that provide short-term protection from disease, but do not induce the liver-resident memory CD8+ T cells (Trm) that confer strong PE immunity and long-term protection. In contrast, whole-organism (WO) vaccines, employing for example radiation-attenuated spz (RAS), elicit both high antibody titers and Trm, and have achieved high levels of sterilizing protection. However, they require multiple intravenous (IV) doses, which must be administered at intervals of several weeks, complicating mass administration in the field. Moreover, the quantities of spz required present production difficulties. To reduce reliance on WO while maintaining protection via both antibodies and Trm responses, we have developed an accelerated vaccination regimen that combines two distinct agents in a prime-and-trap strategy. While the priming dose is a self-replicating RNA encoding P. yoelii CS protein, delivered via an advanced cationic nanocarrier (LIONTM), the trapping dose consists of WO RAS. This accelerated regime confers sterile protection in the P. yoelii mouse model of malaria. Our approach presents a clear path to late-stage preclinical and clinical testing of dose-sparing, same-day regimens that can confer sterilizing protection against malaria.

immunology↗

bioRxiv2022

A conserved Plasmodium protein that localizes to liver stage nuclei is critical for late liver stage development.

Malaria, the disease caused by Plasmodium parasites, causes significant mortality and morbidity. Whole parasite vaccination with pre-erythrocytic parasite stages, attenuated through sporozoite irradiation or chemo-attenuation, confers sterilizing immunity against subsequent parasite infection. This provides a rationale for the creation of whole parasite vaccines that are attenuated using gene editing. Here, we report on the creation of a novel genetically attenuated parasite (GAP) by the deletion of Plasmodium LINUP, encoding a liver stage nuclear protein. Epitope-tagging of LINUP in the rodent malaria parasite Plasmodium yoelii showed LINUP expression exclusively in liver stage nuclei after the onset of exo-erythrocytic schizogony. P. yoelii parasites with a gene deletion of LINUP (linup --) suffered an exclusive liver stage phenotype with developmental arrested late in exo-erythrocytic schizogony. Liver stages showed incomplete segregation of nuclei and, mitochondria and apicoplast. These cellular perturbations caused a defect in exo-erythrocytic merozoite formation and a concomitant severe attenuation of liver stage-to-blood stage transition. LINUP gene deletion in Plasmodium falciparum also caused a severe defect in late liver stage differentiation. Importantly, P. falciparum linup -- liver stages showed a severe defect in parasite transitioning from liver stage to viable blood stage infection. These results suggest that P. falciparum LINUPis a useful target for late liver stage attenuation and an additional gene deletion that can be incorporated into a late liver stage-arresting replication competent whole parasite vaccine.

cell biology↗