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O'Meara, T. R.

Publications and source records attributed to O'Meara, T. R..

15 recordsLinked to original sources

Bacterial metabolites induce cell wall remodeling, antifungal resistance, and immune recognition of commensal fungi

The fungus Candida albicans commensally colonizes mucosal surfaces in healthy individuals but can cause both superficial mucosal and life-threatening disseminated infections. The balance between commensalism and pathogenicity is complex and depends on factors including host and fungal genetic background, the host environment, and fungal interactions with local microbes. The major interaction interface of C. albicans with the host is its multilayered cell wall, which is dynamic and highly responsive to the surrounding environment. Therefore, factors that influence the fungal cell wall will directly impact C. albicans-host interactions. Our work demonstrates that multiple physiologically-relevant gastrointestinal bacteria influence fungal cell wall composition during co-culture with C. albicans, including as complex communities derived from the gut. Using Escherichia coli as a model, we show that bacterial-induced fungal cell wall remodeling occurs rapidly and is mediated by secreted bacterial metabolite(s). Fungal mutant analysis revealed that the high osmolarity glycerol (HOG) pathway, which is critical for responding to environmental stresses, has an important role in regulating this cell wall remodeling phenotype through the Sln1 histidine kinase. Importantly, bacterial-mediated fungal cell wall remodeling increases C. albicans resistance to the echinocandins, increases recognition by both dectin-1 and dectin-2, and decreases recognition by human IgA. Overall, this work comprehensively characterizes an interaction between C. albicans and common gastrointestinal bacteria that has important implications for fungal biology and host interactions.

microbiology↗

Growth phase influences virulence in Candida auris systemic infection models

Candidozyma auris is a growing public health concern, capable of causing long-term contamination of healthcare settings, skin colonization, and life-threatening bloodstream infections. However, C. auris pathogenesis is not well understood, which is exacerbated by limitations and discrepancies in existing animal infection models. Further, the effects of C. auris growth phase on virulence have not been examined, despite growth phase being linked to virulence in many bacterial species. To address this question, and to develop an immunocompetent murine model of infection, we directly compared log and stationary phase C. auris systemic infection in immunocompetent C57BL/6J mice at high and low doses of infection. Systemic infection with high dose log phase C. auris results in rapid mortality between 2 hours and 1 day post infection, whereas stationary phase C. auris results in significantly extended survival. However, at low doses of infection, there was no difference in mortality kinetics between log and stationary phase cells. We observed that C. auris initially colonizes multiple organs but is rapidly cleared from the lungs and spleen, while kidney fungal burdens remain stable. Mice infected with high dose log phase C. auris had Fibrin-associated blood clotting in multiple organs and decreased serum Fibrinogen levels, suggesting that coagulation may drive rapid mortality. This was associated with increased {beta}-glucan exposure and mannan abundance in log phase C. auris. These results will inform the development of a more standardized animal model of systemic C. auris infection, which can be used to reveal key aspects of C. auris pathogenesis. ImportanceDespite its growing medical importance, there is limited understanding of Candidozyma auris pathogenesis, due in part to limitations of existing laboratory models of infection. To develop a more complete understanding of factors that contribute to C. auris pathogenesis, it will be necessary to establish consistent parameters for animal models of infection. To address this need, we directly compared log and stationary growth phases on C. auris pathogenesis in immunocompetent C57BL/6J mice using a single virulent Clade I isolate. At a high dose of infection, host survival was dramatically different between log or stationary phase C. auris, suggesting that growth phase can affect C. auris pathogenesis. These differences correlated with increased exposure of pathogen-associated molecular patterns in the C. auris cell wall in log phase cells. These results will be instrumental in the future development of standardized animal models to study C. auris pathogenesis.

microbiology↗

Deep homology and design of proteasome chaperone proteins in Candida auris

A central tenet of biology is that protein structure mediates the sequence-function relationship. Recently, there has been excitement about the promise of advances in protein structure modeling to generate hypotheses about sequence-structure-function relationships based on successes with controlled benchmarks. Here, we leverage structural similarity to identify rapidly evolving proteasome assembly chaperones and characterize their function in the emerging fungal pathogen Candida auris. Despite the large sequence divergence, we demonstrate conservation of structure and function across hundreds of millions of years of evolution, representing a case of rapid neutral evolution. Using the functional constraints on structure from these naturally evolved sequences, we prospectively designed de novo chaperones and demonstrate that these artificial proteins can rescue complex biological processes in the context of the whole cell.

evolutionary biology↗

Candida auris skin colonization is mediated by Als4112 and interactions with host extracellular matrix proteins

Candida auris is an often multidrug-resistant fungal pathogen notorious for persistent skin colonization and transmission in healthcare settings. However, the mechanisms driving its adherence to skin remain poorly understood. Here, we developed in vitro systems to allow for detailed analysis of early skin colonization events and identified critical host and pathogen mediators of attachment. Across multiple strains and clades of C. auris, we identified that Als4112, a conserved adhesin, is required for skin colonization via keratinocyte attachment and direct interactions with host extracellular matrix (ECM) proteins, especially basement membrane proteins such as laminin. In a murine epicutaneous infection and human skin explants, deletion of ALS4112 significantly reduced skin colonization, underscoring its essential role in establishing cutaneous persistence. Als4112 also contributes to systemic infection, highlighting the connection between adherence and pathogenicity in this organism. Finally, coating plastic and catheter surfaces with collagen I or III markedly inhibited C. auris attachment and biofilm formation, offering an approach to curb nosocomial transmission. Our study highlights the critical role of Als4112 in C. auris colonization and virulence in vivo, making it an attractive target for future vaccine development. This study also explores the potential of specific collagen coatings as a novel strategy to prevent C. auris adherence to abiotic surfaces, offering new therapeutic avenues to control the spread of C. auris in healthcare settings.

microbiology↗

Type I interferon governs immunometabolic checkpoints that coordinate inflammation during Staphylococcal infection

Fine-tuned inflammation during infection enables pathogen clearance while minimizing host damage. Inflammation regulation depends on macrophage metabolic plasticity, yet coordination of metabolic and inflammatory programs is underappreciated. Here we show that type I interferon (IFN) temporally guides metabolic control of inflammation during methicillin-resistant Staphylococcus aureus (MRSA) infection. In macrophages, staggered Toll-like receptor and type I IFN signaling permitted a transient respiratory burst followed by inducible nitric oxide synthase (iNOS)-mediated OXPHOS disruption. OXPHOS disruption promoted type I IFN, suppressing other pro-inflammatory cytokines, notably IL-{beta}. iNOS expression peaked at 24h post-infection, followed by lactate-driven iNOS repression via histone lactylation. In contrast, type I IFN pre-conditioning sustained infection-induced iNOS expression and amplified type I IFN. Cutaneous MRSA infection in mice constitutively expressing epidermal type I IFN led to elevated iNOS levels, impaired wound healing, vasculopathy, and lung infection. Thus, kinetically regulated type I IFN signaling coordinates immunometabolic checkpoints that control infection-induced inflammation. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=101 SRC="FIGDIR/small/575104v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@977b1eorg.highwire.dtl.DTLVardef@1142c6corg.highwire.dtl.DTLVardef@170776borg.highwire.dtl.DTLVardef@b02c2f_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

Non-canonical activation of IRE1α during Candida albicans infection enhances macrophage fungicidal activity

While the canonical function of IRE1 is to detect misfolded proteins and activate the unfolded protein response (UPR) to maintain cellular homeostasis, microbial pathogens can also activate IRE1, which modulates innate immunity and infection outcomes. However, how infection activates IRE1 and its associated inflammatory functions have not been fully elucidated. Recognition of microbe-associated molecular patterns can activate IRE1, but it is unclear whether this depends on protein misfolding. Here, we report that a common and deadly fungal pathogen, Candida albicans, activates macrophage IRE1 through C-type lectin receptor signaling, reinforcing a role for IRE1 as a central regulator of host responses to infection by a broad range of pathogens. This activation did not depend on protein misfolding in response to C. albicans infection. Moreover, lipopolysaccharide treatment was also able to activate IRE1 prior to protein misfolding, suggesting that pathogen-mediated activation of IRE1 occurs through non-canonical mechanisms. During C. albicans infection, we observed that IRE1 activity promotes phagolysosomal fusion that supports the fungicidal activity of macrophages. Consequently, macrophages lacking IRE1 activity displayed inefficient phagosome maturation, enabling C. albicans to lyse the phagosome, evade fungal killing, and drive aberrant inflammatory cytokine production. Mechanistically, we show that IRE1 activity supports phagosomal calcium flux after phagocytosis of C. albicans, which is crucial for phagosome maturation. Importantly, deletion of IRE1 activity decreased the fungicidal activity of phagocytes in vivo during systemic C. albicans infection. Together, these data provide mechanistic insight for the non-canonical activation of IRE1 during infection, and reveal central roles for IRE1 in macrophage antifungal responses.

molecular biology↗

CryptoCEN: A Co-Expression Network for Cryptococcus neoformans reveals novel proteins involved in DNA damage repair

Elucidating gene function is a major goal in biology, especially among non-model organisms. However, doing so is complicated by the fact that molecular conservation does not always mirror functional conservation, and that complex relationships among genes are responsible for encoding pathways and higher-order biological processes. Co-expression, a promising approach for predicting gene function, relies on the general principal that genes with similar expression patterns across multiple conditions will likely be involved in the same biological process. For Cryptococcus neoformans, a prevalent human fungal pathogen greatly diverged from model yeasts, approximately 60% of the predicted genes in the genome lack functional annotations. Here, we leveraged a large amount of publicly available transcriptomic data to generate a C. neoformans Co-Expression Network (CryptoCEN), successfully recapitulating known protein networks, predicting gene function, and enabling insights into the principles influencing co-expression. With 100% predictive accuracy, we used CryptoCEN to identify 13 new DNA damage response genes, underscoring the utility of guilt-by-association for determining gene function. Overall, co-expression is a powerful tool for uncovering gene function, and decreases the experimental tests needed to identify functions for currently under-annotated genes.

genetics↗

Imaging-based screening identifies modulators of the eIF3 translation initiation factor complex in Candida albicans

Fungal pathogens like Candida albicans can cause devastating human disease. Treatment of candidemia is complicated by the high rate of resistance to common antifungal therapies. Additionally, there is host toxicity associated with many antifungal compounds due to the conservation between essential mammalian and fungal proteins. An attractive new approach for antimicrobial development is to target virulence factors: non-essential processes that are required for the organism to cause disease in human hosts. This approach expands the potential target space while reducing the selective pressure towards resistance, as these targets are not essential for viability. In C. albicans, a key virulence factor is the ability to transition to hyphal morphology. We developed a high-throughput image analysis pipeline to distinguish between yeast and filamentous growth in C. albicans at the single cell level. Based on this phenotypic assay, we screened the FDA drug repurposing library of 2,017 compounds for their ability to inhibit filamentation and identified 33 compounds that block the hyphal transition in C. albicans with IC50 values ranging from 0.2 to 150 {micro}M. Multiple compounds showed a phenyl vinyl sulfone chemotype, prompting further analysis. Of these phenyl vinyl sulfones, NSC 697923 displayed the most efficacy, and by selecting for resistant mutants, we identified eIF3 as the target of NSC 697923 in C. albicans.

microbiology↗

Reduced SARS-CoV-2 mRNA vaccine immunogenicity and protection in mice with diet-induced obesity and insulin resistance.

BackgroundObesity and Type 2 Diabetes Mellitus (T2DM) are associated with an increased risk of severe outcomes from infectious diseases, including COVID-19. These conditions are also associated with distinct responses to immunization, including an impaired response to widely used SARS-CoV-2 mRNA vaccines. ObjectiveTo establish a connection between reduced immunization efficacy via modeling the effects of metabolic diseases on vaccine immunogenicity that is essential for the development of more effective vaccines for this distinct vulnerable population. MethodsWe utilized a murine model of diet-induced obesity and insulin resistance to model the effects of comorbid T2DM and obesity on vaccine immunogenicity and protection. ResultsMice fed a high-fat diet (HFD) developed obesity, hyperinsulinemia, and glucose intolerance. Relative to mice fed a normal diet (ND), HFD mice vaccinated with a SARS-CoV-2 mRNA vaccine exhibited significantly lower anti-spike IgG titers, predominantly in the IgG2c subclass, associated with a lower type 1 response, along with a 3.83-fold decrease in neutralizing titers. Furthermore, enhanced vaccine-induced spike-specific CD8+ T cell activation and protection from lung infection against SARS-CoV-2 challenge were seen only in ND mice but not in HFD mice. ConclusionWe demonstrate impaired immunity following SARS-CoV-2 mRNA immunization in a murine model of comorbid T2DM and obesity, supporting the need for further research into the basis for impaired anti-SARS-CoV-2 immunity in T2DM and investigation of novel approaches to enhance vaccine immunogenicity among those with metabolic diseases. Capsule summaryObesity and type 2 diabetes impair SARS-CoV-2 mRNA vaccine efficacy in a murine model.

immunology↗

Adjuvant Discovery via a High Throughput Screen using Human Primary Mononuclear Cells

We describe a methodology utilizing high-throughput and high-content screening for novel adjuvant candidates that was used to screen a library of [~]2,500 small molecules via a 384-well quantitative combined cytokine and flow cytometry immunoassay in primary human peripheral blood mononuclear cells (PBMCs) from 4 healthy adult study participants. Hits were identified based on their induction of soluble cytokine (TNF, IFN{gamma} and IL-10) secretion and PBMC maturation (CD 80/86, Ox40, and HLA-DR) in at least two of the four donors screened. From an initial set of 197 compounds identified using these biomarkers--an 8.6% hit rate--we downselected to five scaffolds that demonstrated robust efficacy and potency in vitro and evaluated the top hit, vinblastine sulfate, for adjuvanticity in vivo. Vinblastine sulfate significantly enhanced murine humoral responses to recombinant SARS-CoV-2 spike protein, including a four-fold enhancement of IgG titer production when compared to treatment with the spike antigen alone. Overall, we outline a methodology for discovering immunomodulators with adjuvant potential via high-throughput screening of PBMCs in vitro that yielded a lead compound with in vivo adjuvanticity. MotivationVaccines are a key biomedical intervention to prevent the spread of infectious diseases, but their efficacy can be limited by insufficient immunogenicity and nonuniform reactogenic profiles. Adjuvants are molecules that potentiate vaccine responses by inducing innate immune activation. However, there are a limited number of adjuvants in approved vaccines, and current approaches for preclinical adjuvant discovery and development are inefficient. To enhance adjuvant identification, we developed a protocol based on in vitro screening of human primary leukocytes.

immunology↗

Alum:CpG adjuvant enables SARS-CoV-2 RBD-induced protection in aged mice and synergistic activation of human elder type 1 immunity

Global deployment of vaccines that can provide protection across several age groups is still urgently needed to end the COVID-19 pandemic especially for low- and middle-income countries. While vaccines against SARS-CoV-2 based on mRNA and adenoviral-vector technologies have been rapidly developed, additional practical and scalable SARS-CoV-2 vaccines are needed to meet global demand. In this context, protein subunit vaccines formulated with appropriate adjuvants represent a promising approach to address this urgent need. Receptor-binding domain (RBD) is a key target of neutralizing antibodies (Abs) but is poorly immunogenic. We therefore compared pattern recognition receptor (PRR) agonists, including those activating STING, TLR3, TLR4 and TLR9, alone or formulated with aluminum hydroxide (AH), and benchmarked them to AS01B and AS03-like emulsion-based adjuvants for their potential to enhance RBD immunogenicity in young and aged mice. We found that the AH and CpG adjuvant formulation (AH:CpG) demonstrated the highest enhancement of anti-RBD neutralizing Ab titers in both age groups ([~]80-fold over AH), and protected aged mice from the SARS-CoV-2 challenge. Notably, AH:CpG-adjuvanted RBD vaccine elicited neutralizing Abs against both wild-type SARS-CoV-2 and B.1.351 variant at serum concentrations comparable to those induced by the authorized mRNA BNT162b2 vaccine. AH:CpG induced similar cytokine and chemokine gene enrichment patterns in the draining lymph nodes of both young adult and aged mice and synergistically enhanced cytokine and chemokine production in human young adult and elderly mononuclear cells. These data support further development of AH:CpG-adjuvanted RBD as an affordable vaccine that may be effective across multiple age groups. One Sentence SummaryAlum and CpG enhance SARS-CoV-2 RBD protective immunity, variant neutralization in aged mice and Th1-polarizing cytokine production by human elder leukocytes.

immunology↗

Forward and Reverse Genetic Dissection of Morphogenesis Identifies Filament-Competent Candida auris Strains

Candida auris is an emerging healthcare-associated pathogen of global concern. Although this organism does not display the same morphological plasticity as the related fungal pathogen Candida albicans, recent reports have identified numerous C. auris isolates that grow in cellular aggregates or filaments. However, the genetic circuitry governing C. auris morphology remains largely uncharacterized. Here, we developed an Agrobacterium-mediated transformation system to generate mutants exhibiting aggregating or filamentous cell morphologies. Aggregating strains were associated with disruption of homologs of Saccharomyces cerevisiae chitinase and chitin synthase regulatory proteins, including components of the Regulation of ACE2 Morphogenesis (RAM) pathway, while disruption of a homolog of the S. cerevisiae ELM1 gene resulted in a novel filamentous strain of C. auris. To facilitate targeted genetic manipulation, we developed a transiently expressed Cas9 and sgRNA expression system for use in C. auris. Transformation using this system significantly increased the efficiency of homologous recombination and targeted integration of a reporter cassette in all four clades of C. auris. Using this system, we generated targeted deletion mutants to confirm the roles of RAM and Elm1 proteins in regulating C. auris morphogenesis. Overall, our findings provide novel insights into the genetic regulation of aggregating and filamentous morphogenesis in C. auris. Furthermore, the genetic manipulation tools described here will allow for inexpensive and efficient manipulation of the C. auris genome. ImportanceCandida auris is an emerging and often multi-drug resistant fungal pathogen responsible for outbreaks globally. Current difficulties in performing genetic manipulation in this organism remain a barrier to understanding C. auris biology. Homologous recombination approaches can result in less than 1% targeted integration of a reporter cassette, emphasizing the need for new genetic tools specific for manipulating C. auris. Here, we adapted Agrobacterium-mediated transformation and a transient Cas9 and sgRNA expression system for use in forward and reverse genetic manipulation of C. auris. We demonstrated the efficacy of each system by uncovering genes underlying cellular morphogenesis in C. auris. We identified a novel filamentous mutant of C. auris, demonstrating that this organism has maintained the capacity for filamentous growth. Our findings provide additional options for improving the genetic tractability of C. auris, which will allow for further characterization of this emerging pathogen.

microbiology↗

DeORFanizing Candida albicans Genes using Co-Expression

Functional characterization of open reading frames in non-model organisms, such as the common opportunistic fungal pathogen Candida albicans, can be labor intensive. To meet this challenge, we built a comprehensive and unbiased co-expression network for C. albicans, which we call CalCEN, from data collected from 853 RNA sequencing runs from 18 large scale studies deposited in the NCBI Sequence Read Archive. Retrospectively, CalCEN is highly predictive of known gene function annotations and can be synergistically combined with sequence similarity and interaction networks in Saccharomyces cerevisiae through orthology for additional accuracy in gene function prediction. To prospectively demonstrate the utility of the co-expression network in C. albicans, we predicted the function of under-annotated open reading frames (ORF)s and identified CCJ1 as a novel cell cycle regulator in C. albicans. This study provides a tool for future systems biology analyses of gene function in C. albicans. We provide a computational pipeline for building and analyzing the co-expression network and CalCEN itself at (http://github.com/momeara/CalCEN). ImportanceCandida albicans is a common and deadly fungal pathogen of humans, yet the genome of this organism contains many genes of unknown function. By determining gene function, we can help identify essential genes, new virulence factors, or new regulators of drug resistance, and thereby give new targets for antifungal development. Here, we use information from large scale RNAseq studies and generate a C. albicans co-expression network (CalCEN) that is robust and able to predict gene function. We demonstrate the utility of this network in both retrospective and prospective testing, and use CalCEN to predict a role for C4_06590W/CCJ1 in cell cycle. This tool will allow for a better characterization of under-annotated genes in pathogenic yeasts.

microbiology↗

Morphological Cell Profiling of SARS-CoV-2 Infection Identifies Drug Repurposing Candidates for COVID-19

The global spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and the associated disease COVID-19, requires therapeutic interventions that can be rapidly identified and translated to clinical care. Traditional drug discovery methods have a >90% failure rate and can take 10-15 years from target identification to clinical use. In contrast, drug repurposing can significantly accelerate translation. We developed a quantitative high-throughput screen to identify efficacious agents against SARS-CoV-2. From a library of 1,425 FDA-approved compounds and clinical candidates, we identified 17 dose-responsive compounds with in vitro antiviral efficacy in human liver Huh7 cells and confirmed antiviral efficacy in human colon carcinoma Caco-2, human prostate adenocarcinoma LNCaP, and in a physiologic relevant model of alveolar epithelial type 2 cells (iAEC2s). Additionally, we found that inhibitors of the Ras/Raf/MEK/ERK signaling pathway exacerbate SARS-CoV-2 infection in vitro. Notably, we discovered that lactoferrin, a glycoprotein classically found in secretory fluids, including mammalian milk, inhibits SARS-CoV-2 infection in the nanomolar range in all cell models with multiple modes of action, including blockage of virus attachment to cellular heparan sulfate and enhancement of interferon responses. Given its safety profile, lactoferrin is a readily translatable therapeutic option for the management of COVID-19. IMPORTANCESince its emergence in China in December 2019, SARS-CoV-2 has caused a global pandemic. Repurposing of FDA-approved drugs is a promising strategy for identifying rapidly deployable treatments for COVID-19. Herein, we developed a pipeline for quantitative high-throughput image-based screening of SARS-CoV-2 infection in human cells that led to the identification of several FDA-approved drugs and clinical candidates with in vitro antiviral activity.

cell biology↗

Selective protein O-GlcNAcylation in cells by a proximity-directed O-GlcNAc transferase

O-Linked N-acetylglucosamine (O-GlcNAc) is a monosaccharide that plays an essential role in cellular signaling throughout the nucleocytoplasmic proteome of eukaryotic cells. Yet, the study of post-translational modifications like O-GlcNAc has been limited by the lack of strategies to induce O-GlcNAcylation on a target protein in cells. Here, we report a generalizable genetic strategy to induce O-GlcNAc to specific target proteins in cells using a nanobody as a proximity-directing agent fused to O-GlcNAc transferase (OGT). Fusion of a nanobody that recognizes GFP (nGFP) or a nanobody that recognizes the four-amino acid sequence EPEA (nEPEA) to OGT(4), a truncated form of OGT, yielded a nanobody-OGT(4) construct that selectively delivered O-GlcNAc to the target protein (e.g., JunB, cJun, Nup62) and reduced alteration of global O-GlcNAc levels in the cell. Quantitative chemical proteomics confirmed the selective increase in O-GlcNAc to the target protein by nanobody-OGT(4). Glycoproteomics revealed that nanobody-OGT(4) or full-length OGT produced a similar glycosite profile on the target protein. Finally, we demonstrate the ability to selectively target endogenous -synuclein for glycosylation in HEK293T cells. Thus, the use of nanobodies to redirect OGT substrate selection is a versatile strategy to induce glycosylation of desired target proteins in cells that will facilitate discovery of O-GlcNAc functions and provide a mechanism to engineer O-GlcNAc signaling. The proximity-directed OGT approach for protein-selective O-GlcNAcylation is readily translated to additional protein targets and nanobodies that may constitute a generalizable strategy to control post-translational modifications in cells.\n\nSignificance StatementNature uses post-translational modifications (PTMs) like glycosylation as a mechanism to alter protein signaling and function. However, the study of these modified proteins in cells is confined to loss-of-function strategies, such as mutagenic elimination of the modification site. Here, we report a generalizable strategy for induction of O-GlcNAc to a protein target in cells. The O-GlcNAc modification is installed by O-GlcNAc transferase (OGT) to thousands of nucleocytoplasmic proteins. Fusion of a nanobody to OGT enables the selective increase of O-GlcNAc levels on a series of target proteins. The described approach will facilitate direct studies of O-GlcNAc and its regulatory enzymes and drive new approaches to engineer protein signaling via a strategy that may be conceptually translatable to additional PTMs.

biochemistry↗