Biology subjects

Murphy, C. L.

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

8 recordsLinked to original sources

bioRxiv2026

A rationally designed neuraminidase immunogen elicits humoral responses to a conserved viral site

Efforts to develop a universal influenza vaccine have primarily focused on the surface-exposed viral hemagglutinin (HA), but neuraminidase (NA) is an additional target for cross-reactive, protective responses. Here, we used hyperglycosylation as an immunogen design approach to reshape anti-NA humoral immunity toward conserved antigenic regions. Iterative design produced a hyperglycosylated NA immunogen that retained enzymatic activity and reactivity to a conformation-specific antibody recognizing the conserved catalytic site. In mice, the hyperglycosylated immunogen elicited serum antibody responses of comparable magnitude to those elicited by the wild-type NA immunogen. However, serum antibodies elicited by the hyperglycosylated immunogen had increased breadth, recognizing N2 NAs from H2N2 and H3N2 viruses spanning nearly 65 years of antigenic drift, as well as a heterosubtypic N9 NA. Single B cell analyses identified a monoclonal antibody that competed with a component of the serum antibody response elicited by the hyperglycosylated immunogen, and structural characterization showed that it recognizes a previously undefined, conserved epitope at the NA tetramer interface. Passive transfer of this interface-directed antibody partially protected mice against lethal heterologous influenza challenge. Collectively, these data show that glycan shielding can reshape and enrich humoral responses toward a conserved antigenic region on NA. The immunogen and hyperglycosylation design strategy described here provide a template for developing next- generation NA-based influenza vaccines. ONE SENTENCE SUMMARYA hyperglycosylated influenza neuraminidase immunogen reshapes humoral immunity and elicits antibodies targeting a conserved tetramer-interface epitope.

immunology↗

bioRxiv2026

ARID5B drives an inflammatory-to-destructive shift in pathologic fibroblast behavior

During inflammatory diseases such as rheumatoid arthritis, fibroblasts prominently drive chronic inflammation and the subsequent destruction of cartilage and bone. The mechanism by which an activated, inflammatory fibroblast acquires tissue destructive behaviors is unknown. Here, we describe ARID5B as a transcription factor that directs inflammatory fibroblasts to become migratory and invasive. Upon upregulation in inflammatory fibroblasts, ARID5B binds to histone editors and localizes to both inflammatory and invasive gene loci, epigenetically repressing pro-inflammatory genes while enhancing expression of pro-invasive genes. Likewise, fibroblast-specific ARID5B overexpression in vivo drives an inflammatory-to-erosive shift in arthritis pathology. Our findings highlight ARID5B as a maladaptive brake on inflammatory fibroblast activation that endows fibroblasts with pathologic invasive properties, thus mechanistically linking fibroblast-driven tissue inflammation to tissue damage. These insights into the regulation of inflammatory and invasive fibroblast pathology may inform successful therapeutic targeting of fibroblasts in inflammatory diseases.

immunology↗

bioRxiv2026

Egyptian rousette bat humoral immunity to H9 influenza hemagglutinin

In mammals, antibodies are central to antiviral defense, but they can also impose selective pressure that drives viral evolution. The interplay between viral antigenic variation and host antibody diversification constitutes a molecular arms race that influences pathogenicity, transmission, and spillover risk. Bats are reservoirs for zoonotic viruses with pandemic potential yet they appear to tolerate infection without overt disease. Although distinctive features of bat innate immunity have been described, the role of adaptive immunity--particularly antibody-mediated responses--remains largely undefined. Moreover, how antibody evolutionary pressure operates in bats is unknown, in part because tools to interrogate bat B cell responses at the monoclonal level are limited. Here, we developed a yeast surface display library of bat antibodies derived from splenic RNA of wild-caught Egyptian rousette bats to interrogate humoral responses to the bat-derived H9 influenza hemagglutinin. We isolated monoclonal antibodies recognizing the hemagglutinin (HA) antigen and defined their gene usage, somatic hypermutation frequency, binding affinities, and breadth. We then used cryo-EM to structurally characterize three bat antibodies in complex with HA engaging distinct antigenic sites. Together, these data enable direct comparison with human anti-influenza antibodies highlighting similarities in humoral immunity across mammals and provides a tool to examine bat antibody responses to other potential zoonotic viruses.

immunology↗

bioRxiv2025

Wnt signaling drives stromal inflammation in inflammatory arthritis

The concept that fibroblasts are critical mediators of inflammation is an emerging paradigm. In rheumatoid arthritis (RA), they are the main producers of IL-6 as well as a host of other cytokines and chemokines. Their pathologic activation also directly causes cartilage and bone degradation. Yet, therapeutic agents specifically targeting fibroblasts are not available. Here, we find that Wnt receptors and modulators are predominantly expressed in stromal populations in the synovium. Importantly, non-canonical Wnt activation induces robust inflammatory gene expression including an abundance of cytokines and chemokines in synovial fibroblasts in vitro. Strikingly, the addition of Wnt ligands or inhibition of Wnt secretion exacerbates or reduces arthritis severity, respectively, in vivo in a murine model of inflammatory arthritis. These observations are relevant in human disease, as Wnt activation signatures are enhanced in fibroblasts derived from inflamed RA synovial tissue as well as fibroblasts across other inflammatory diseases. Together, these findings implicate Wnt signaling as a major driver of fibroblast-mediated inflammation and joint pathology. They further suggest that targeting the Wnt pathway is a therapeutically relevant approach to rheumatoid arthritis, particularly in patients who do not respond to conventional treatments and who often express fibroblast-predominant synovial phenotypes.

immunology↗

bioRxiv2023

Pandemic preparedness through genomic surveillance: Overview of mutations in SARS-CoV-2 over the course of COVID-19 outbreak

Genomic surveillance is a vital strategy for preparedness against the spread of infectious diseases and to aid in development of new treatments. In an unprecedented effort, millions of samples from COVID-19 patients have been sequenced worldwide for SARS-CoV-2. Using more than 8 million sequences that are currently available in GenBanks SARS-CoV-2 database, we report a comprehensive overview of mutations in all 26 proteins and open reading frames (ORFs) from the virus. The results indicate that the spike protein, NSP6, nucleocapsid protein, envelope protein and ORF7b have shown the highest mutational propensities so far (in that order). In particular, the spike protein has shown rapid acceleration in mutations in the post-vaccination period. Monitoring the rate of non-synonymous mutations (Ka) provides a fairly reliable signal for genomic surveillance, successfully predicting surges in 2022. Further, the external proteins (spike, membrane, envelope, and nucleocapsid proteins) show a significant number of mutations compared to the NSPs. Interestingly, these four proteins showed significant changes in Ka typically 2 to 4 weeks before the increase in number of human infections ("surges"). Therefore, our analysis provides real time surveillance of mutations of SARS-CoV-2, accessible through the project website http://pandemics.okstate.edu/covid19/. Based on ongoing mutation trends of the virus, predictions of what proteins are likely to mutate next are also made possible by our approach. The proposed framework is general and is thus applicable to other pathogens. The approach is fully automated and provides the needed genomic surveillance to address a fast-moving pandemic such as COVID-19.

genomics↗

bioRxiv2021

Genomic characterization of three novel Desulfobacterota classes expand the metabolic and phylogenetic diversity of the Phylum

An overwhelming majority of bacterial life remains uncharacterized. Recent efforts to assemble genomes from metagenomes have provided invaluable insights into these yet-uncultured bacterial lineages. We report on the characterization of 30 genomes belonging to three novel classes within the phylum Desulfobacterota. One class (proposed name Candidatus "Anaeroferrophillalia") was characterized by the capacity for heterotrophic growth, either fermentatively or utilizing polysulfide, tetrathionate and thiosulfate as electron acceptors. Autotrophic growth using the Wood Ljungdahl pathway and hydrogen or Fe(II) as an electron donor could also occur in absence of organic carbon sources. The second class (proposed name Candidatus "Anaeropigmentia") was characterized by its capacity for fermentative or aerobic growth at low oxygen thresholds using a broad range of sugars and amino acids, and the capacity to synthesize the methyl/alkyl carrier CoM, an ability that is prevalent in the archaeal but rare in the bacterial domain. Pigmentation is inferred from the capacity for carotenoids (lycopene) production, as well as the occurrence of the majority of genes involved in bacteriochlorophyll a biosynthesis. The third class (proposed name Candidatus "Zymogenia") was characterized by the capacity for heterotrophic growth fermentatively using broad sugars and amino acids as carbon sources, and the adaptation of some of its members to hypersaline habitats. Analysis of the distribution pattern of all three classes showed their occurrence as rare community members in multiple habitats, with preferences for anaerobic terrestrial (e.g. hydrocarbon contaminated environments, wetlands, bioreactors), freshwater (e.g. ground water and gas-saturated temperate lakes), and marine (e.g. hydrothermal vents, marine sediments, and coastal sediments) environments, over oxygenated (e.g. pelagic ocean and agricultural land) settings. Special preference for some members of the class Candidatus "Zymogenia" to hypersaline environments, e.g. hypersaline microbial mats and lagoons was observed. ImportanceCulture-independent diversity surveys conducted in the last three decades have clearly demonstrated that the scope of microbial diversity is much broader than that inferred from isolation efforts. Multiple reasons have been put forth to explain the refractiveness of a wide range of the earths microbiome to isolation efforts. Documenting the scope of high-rank phylogenetic diversity on earth, as well as deciphering and documenting the metabolic capacities, physiological preferences, and putative ecological roles of these yet-uncultured lineages represents one of the central goals in current microbial ecology research. Recent efforts to assemble genomes from metagenomes have provided invaluable insights into these yet-uncultured lineages. This study expands our knowledge of the phylum Desulfobacterota through the characterization of 30 genomes belonging to three novel classes. The analyzed genomes were either recovered from Zodletone Spring in southwestern Oklahoma in this study, or recently binned from public metagenomes as part of the Global Earth Microbiome initiative. Our results expand the high-rank diversity within the bacterial tree of life by describing three novel classes within the phylum Desulfobacterota, document the utilization of multiple metabolic processes, e.g. iron-oxidation, aromatic hydrocarbon degradation, reduction of sulfur-cycling intermediates, and features, e.g. coenzyme M biosynthesis, and pigmentation, as salient characteristics in these novel Desulfobacterota classes.

microbiology↗

bioRxiv2020

Methylotrophy, alkane-degradation, and pigment production as defining features of the globally distributed yet-uncultured phylum Binatota

The recent leveraging of genome-resolved metagenomics has opened a treasure trove of genomes from novel uncultured microbial lineages, yet left many clades undescribed. We here present a global analysis of genomes belonging to the Binatota (UBP10), a globally distributed, yet-uncharacterized bacterial phylum. All orders in the Binatota encoded the capacity for aerobic methylotrophy using methanol, methylamine, sulfomethanes, chloromethanes, and potentially methane as substrates. Methylotrophy in the Binatota was characterized by order-specific substrate degradation preferences, as well as extensive metabolic versatility, i.e. the utilization of diverse sets of genes, pathways and combinations to achieve a specific metabolic goal. The genomes also encoded an arsenal of alkane hydroxylases and monooxygenases, potentially enabling growth on a wide range of alkanes and fatty acids. Pigmentation is inferred from a complete pathway for carotenoids (lycopene, {beta} and {gamma} carotenes, xanthins, chlorobactenes, and spheroidenes) production. Further, the majority of genes involved in bacteriochlorophyll a, c, and d biosynthesis were identified; although absence of key genes and failure to identify a photosynthetic reaction center precludes proposing phototrophic capacities. Analysis of 16S rRNA databases showed Binatotas preferences to terrestrial and freshwater ecosystems, hydrocarbon-rich habitats, and sponges supporting their suggested potential role in mitigating methanol and methane emissions, alkanes degradation, and nutritional symbiosis with sponges. Our results expand the lists of methylotrophic, aerobic alkane degrading, and pigment-producing lineages. We also highlight the consistent encountering of incomplete biosynthetic pathways and gene shrapnel in microbial genomes, a phenomenon necessitating careful assessment when assigning putative functions based on a set-threshold of pathway completion.

microbiology↗

bioRxiv2018

MEF2C is a new regulator of the human articular chondrocyte phenotype

MEF2C plays a role in diverse tissues, most notably heart, brain, eyes and developing bones. Here we report for the first time that MEF2C is present and active in the permanent articular cartilage in humans which lines and protects our joints throughout life. We show that MEF2C directly targets cartilage master regulator gene SOX9, and SOX9, in turn, regulates MEF2C in a novel positive feedback loop maintaining high expression levels of both transcription factors, and consequently stabilising the articular chondrocyte phenotype and helping prevent hypertrophy and subsequent calcification and vascularisation. We propose that MEF2C and SOX9 may show similar cooperative activity in other tissues, and across a range of adult murine tissues we found co-expression of both transcription factors in cartilage, trachea, brain, eyes and heart. Strikingly, all of these tissues are prone to calcification and further study of MEF2C/SOX9 cooperativity in these organs will be revealing.

cell biology↗