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Khadka, S.

Publications and source records attributed to Khadka, S..

At least 19 recordsLinked to original sources

Lipopolysaccharide and Wzi retain capsular polysaccharide at the Klebsiella pneumoniae cell surface and promote bloodstream infection fitness

Bacterial capsules are formed by individual capsular polysaccharide (CPS) polymers and are the outermost extracellular layers of many Gram-positive and Gram-negative bacteria. Capsules affect several aspects of bacterial biology, including resistance to host immune factors, survival in unfavorable environments and antimicrobial resistance. Research on CPS biology has largely focused on its synthesis and the pathogenic consequences of its presence or absence. Beyond synthesis, our understanding of its retention (attachment) on the cell surface is limited. Klebsiella pneumoniae is an important Gram-negative pathogen and expresses more than 80 capsular serotypes using the common Wzy-dependent CPS biosynthesis system and phenotypically manifests in various forms, making this species an attractive bacterial model to study the underexplored aspects of CPS biology. Here, we identified and characterized bacterial components involved in CPS retention in K. pneumoniae and assessed the importance of CPS retention on bloodstream fitness. Our examination revealed that lipopolysaccharide (LPS) and the outer-membrane protein, Wzi, collectively retain K. pneumoniae CPS on the bacterial surface. We demonstrate that the core-oligosaccharide domain of LPS and the extracellular surface of Wzi likely provide anchoring sites for CPS on the bacterial surface. Furthermore, CPS retention depends on divalent cation availability. Importantly, CPS retention on the bacterial surface is important for survival in serum and bacterial fitness at secondary infection sites in a murine bacteremia model. Together, our findings demonstrate that the functional importance of CPS to bacteria extends beyond synthesis and its overall abundance. Bacterial control over other CPS properties, like cell surface retention, are also important for K. pneumoniae fitness during bacteremia.

microbiology↗

V-SWITCH: A single-vector OFF-to-ON fluorescent reporter of live RNA virus infections

Fluorescent reporters of viral infection are powerful tools for studying viral pathogenesis and host-pathogen interactions. Here, we present V-SWITCH, a highly modular, single-vector, cell-based OFF-to-ON fluorescent reporter that enables robust detection of viral infection in living cells. V-SWITCH is based on a split mNeonGreen (mNG) system employing a release-and-capture mechanism. In the "OFF" state, the mNG3A(1-10) fragment is anchored to the endoplasmic reticulum via a Sec61 transmembrane domain, while the mNG(11) fragment, fused to BFP, is constitutively expressed in the nucleus. Upon infection, the viral protease cleaves a protease cleavage site (PCS) adjacent to the mNG3A(1-10) fragment, liberating it for translocation into the nucleus. There, it complements mNG(11) to reconstitute fluorescence. The constitutive BFP serves as both an expression control and a nuclear segmentation marker for image analysis. Each module in this dual-cassette design is flanked by unique restriction sites allowing rapid swapping of virus-specific PCS, split fluorophores, membrane anchors, and promoters. We demonstrate the versatility of the V-SWITCH reporter for several viruses (Dengue virus, Zika virus, West Nile virus and Human Coronavirus OC43) in several cell lines (A549, BJ-5 fibroblasts, HEK293T and HeLa). Reporter activation enables clear discrimination of infected and uninfected cells by flow cytometry and reveals time-dependent and heterogeneous infection dynamics by live-cell imaging at single-cell resolution. Importantly, we demonstrate the potential of V-SWITCH to support both rapid functional screening for host factor dependencies, as well as high-throughput compound screening to enable antiviral discovery and comparative evaluation of therapeutic strategies across multiple viruses and cell types.

microbiology↗

Sugar Import Suppresses Klebsiella pneumoniae Mucoidy in cAMP-CRP-dependent Manner

Klebsiella pneumoniae causes over 700,000 global deaths annually and this number continues to rise due to increasing antimicrobial resistance. Hypervirulent K. pneumoniae (hvKp) often causes severe invasive infections in community and hospital settings, typically originating from gut colonization. Capsular polysaccharide (CPS) and the associated features are a key hvKp virulence factor. Altering CPS properties, such as mucoidy, in response to environmental cues enhances K. pneumoniae fitness. Although several physical and nutrient cues influence mucoidy, the molecular mechanisms by which host-relevant signals, such as sugars, regulate this key CPS property remain undefined. Here, we show that sugar import, not catabolism, broadly suppresses hvKp mucoidy via cAMP-CRP signaling. Sugars suppress mucoidy by decreasing rmpADC promoter activity and the expression of the mucoidy regulator, rmpD. Moreover, this sugar-dependent regulation is conserved across multiple hvKp strains. hvKp associates with gut mucin and gut epithelial cells at a greater frequency when in a non-mucoid state. Together, our results suggest that sugar import broadly suppresses hvKp mucoidy and increases bacterial association to host cells.

microbiology↗

Connections between Klebsiella pneumoniae Bloodstream Dynamics and Serotype-Independent Capsule Properties

Klebsiella pneumoniae bacteremia is a significant public health burden with a 26% mortality rate, which increases when the infecting isolate is multi-drug resistant. An important virulence factor of K. pneumoniae is the capsule, the protective polysaccharide coat which surrounds the outer membrane and is made up of individual capsular polysaccharide (CPS) chains. Capsule can differ in abundance, attachment, and length of the individual CPS chains. Long, uniform CPS chains are associated with a high level of mucoidy. Typically, mucoid CPS is produced by the hypervirulent K. pneumoniae (hvKp) pathotype, which is associated with invasive community-acquired infections. In contrast, the classical K. pneumoniae (cKp) pathotype tends to be non-mucoid and is associated with nosocomial infections and multi-drug resistance. There are over 80 serotypes of K. pneumoniae capsule. Capsule swap experiments have begun to reveal the effect of serotype on virulence and immune interactions. Clinically, the K2 capsule serotype is a common serotype associated with neonatal sepsis cases. Both cKp and hvKp can produce K2 capsule, but how K2-encoding cKp and hvKp strains differ in a bloodstream infection remains unknown. To fill this gap in knowledge, we characterized the surface properties of K2 serotype cKp and hvKp bloodstream infection isolates, then tested the fitness of these strains in bloodstream infection-related in vitro and in vivo assays. Understanding how K2 cKp and hvKp strains differ in pathogenic potential provides further insight into how K. pneumoniae capsule properties influence bloodstream infection pathogenesis. IMPORTANCEMany studies have compared the pathogenesis of the two Klebsiella pneumoniae pathotypes, but did not control for differences in capsule serotype. In this study, we control for the K2 capsule serotype in classical and hypervirulent pathotypes. Our studies reveal that despite the two pathotypes exhibiting similar human serum survival, they display different tissue tropism in a murine bloodstream infection model. Additionally, although these pathotypes produce similar amounts of capsule, the hypervirulent strains are significantly more mucoid. Our study has provided more evidence on how capsule characteristics impact K. pneumoniae bacteremia pathogenesis and the importance of capsule serotype.

microbiology↗

Androgen Signaling in Type 2 Innate Lymphoid Cells Drives Sex Differences in Helicobacter-Induced Gastric Inflammation and Atrophy

Background & AimsGastric cancer is the fifth most common cancer worldwide. Men are disproportionately affected by gastric cancer, which ranks as the fourth most common cancer in men compared to eighth in women worldwide. Chronic inflammation driven by Helicobacter pylori infection remains the leading gastric cancer risk factor. Emerging evidence suggests that sex hormones modulate immune responses, contributing to sex differences in infection outcomes and cancer susceptibility. This study investigates how androgens influence the gastric inflammatory response to Helicobacter infection and contribute to sex disparities in disease progression. MethodsMale and female C57BL/6 mice were colonized with Helicobacter felis to investigate sex differences in gastric inflammation. Androgen levels were manipulated by bilateral castration in males and dihydrotestosterone (DHT) treatment in females. Single-cell RNA sequencing was used to identify androgen-responsive leukocyte populations and to establish cell communication networks between leukocyte clusters. The functional roles of these cells were further defined using ILC2- and T cell-deficient mouse models. ResultsInfected female mice developed significantly more severe gastric inflammation, atrophy, and metaplasia infection compared to males. Androgen depletion by castration increased gastric inflammation and accelerated preneoplastic lesion development, while these pathological features were reduced by DHT treatment. Androgen-responsive type 2 innate lymphoid cells (ILC2s) were key initiators of gastric inflammation and ILC2 depletion abolished the sex differences in H. felis pathogenesis. ConclusionsThis study reveals that androgens suppress Helicobacter-induced gastric inflammation by modulating ILC2 activation. We found that androgens are protective, as androgen depletion exacerbated gastric inflammation and accelerated preneoplastic lesion development. These findings provide mechanistic insight into the age-related increase in male gastric cancer incidence, coinciding with declining androgen levels. Our results suggest that circulating androgen concentrations may serve as a prognostic biomarker for gastric cancer risk in men. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=120 HEIGHT=200 SRC="FIGDIR/small/643321v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@6cf3c3org.highwire.dtl.DTLVardef@f797d6org.highwire.dtl.DTLVardef@1118c21org.highwire.dtl.DTLVardef@106e2ab_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

Defects in nephrogenesis result in an expansion of the Foxd1+ stromal progenitor population

Reciprocal signaling interactions coordinate multiple aspects of kidney development. While signals from the stroma have been shown to regulate nephron progenitor cell (NPC) differentiation, much less is known about regulation of the stromal progenitor population. Here, we demonstrate that disruption of the NPC lineage via loss of Wt1 (i.e., Six2cre;Wt1c/c) results in an expansion of Foxd1+ stromal progenitor cells. Analyses of the developing stroma in two additional models, including Wnt4-null mutants (which fail to form nephron structures similar to Six2cre;Wt1c/c kidneys) and NPC ablation via diphtheria toxin (i.e., Six2cre;RosaDTAc/+), both phenocopy Six2cre;Wt1c/c mutants, thus further confirming that defects in the NPC lineage result in abnormal development of the stromal progenitor population. Furthermore, we identify a subcluster of the Foxd1+ stroma that appears expanded in the three mutant mouse models and conserved in human fetal kidneys. Overall, the findings from this study suggest that loss of differentiating nephron structures may result in possible over proliferation of the stromal progenitor population and/or a block in stromal differentiation and further highlight how crosstalk amongst the progenitor cell lineages coordinates multiple aspects of kidney development. KEY POINTSO_LIMutant mouse models targeting the nephron lineage (i.e., Six2cre;Wt1c/c and Wnt4-null mutants which fail to form early nephron structures) suggest that a block in NPC differentiation results in an abnormal expansion of the Foxd1+ stromal progenitor population. C_LIO_LIMutant kidneys with NPC ablation (i.e., Six2cre;RosaDTAc/+) show maintenance of stromal progenitors independent of signals from adjacent nephron progenitors and ureteric bud. C_LIO_LISingle nuclei RNA-seq identifies three subclusters of the Foxd1+ stromal progenitor population at E15.5, including one cluster of proliferating cells and a distinct Fap+, Igf1+, Gria1+, Gdnf- subcluster which appears expanded in Six2cre;Wt1c/c, Wnt4-null, and Six2cre;RosaDTAc/+ mutant kidneys and conserved in human fetal kidneys. C_LI

developmental biology↗

Arginine Regulates the Mucoid Phenotype of Hypervirulent Klebsiella pneumoniae

Hypervirulent Klebsiella pneumoniae is associated with severe community-acquired infections. Hypervirulent K. pneumoniae colonies typically exhibit a mucoid phenotype. K. pneumoniae mucoidy is influenced by a complex combination of environmental factors and genetic mechanisms. Mucoidy results from altered capsular polysaccharide chain length, yet the specific environmental cues regulating this phenotype and their impact on pathogenesis remain unclear. This study demonstrates that casamino acids enhance the mucoidy phenotype but do not affect total capsular polysaccharide levels. Through targeted screening of each amino acid present in casamino acids, we identified that arginine is necessary and sufficient to stimulate the mucoid phenotype without altering capsule abundance. Furthermore, arginine activates the rmpADC promoter, increasing rmpD transcript levels, which in turn modulates capsular polysaccharide chain length and diversity. The arginine regulator, ArgR, plays a pivotal role in this regulatory cascade since deleting argR decreases mucoidy and increases capsular polysaccharide chain length diversity. Additionally, the {Delta}argR mutant displays increased macrophage association and has a substantial competitive defect in the lungs of mice, suggesting a link between arginine-dependent gene regulation, immune evasion and in vivo fitness. We discovered that arginine-dependent regulation of mucoidy is conserved in four additional hypervirulent K. pneumoniae isolates likely via a conserved ARG binding box present in rmp promoters. Our findings support a model in which arginine activates ArgR and increases mucoidy in hypervirulent K. pneumoniae. As a result, it is possible that arginine-dependent regulation of mucoidy allows hypervirulent K. pneumoniae to adapt the cell surface across different niches. This study underscores the significance of arginine as a regulatory signal in bacterial virulence. IMPORTANCEThe rise of hypervirulent Klebsiella pneumoniae as a global health threat underscores the urgent need to understand its pathogenic mechanisms. Its ability to cause severe infections in healthy individuals and spread beyond the endemic Asia-Pacific region demands a deeper investigation into the mechanisms driving hypervirulence. The hypermucoid phenotype is primarily associated with hypervirulent isolates and is regulated by RmpD, which increases capsular polysaccharide chain length and uniformity. Understanding how environmental and genetic factors influence mucoidy is vital for elucidating the mechanisms by which K. pneumoniae adapts and thrives in different ecological and host niches. Our study defines the role of amino acids, particularly arginine, in regulating the bacterial surface by modulating rmpD expression. These results reveal that mucoidy is not a constitutive phenotype, but rather a dynamic process finely tuned by nutrient availability. Our findings expand our understanding of how the rmp locus is controlled and how changes in arginine availability may optimize K. pneumoniae immune evasion.

microbiology↗

Structural basis of the human transcriptional Mediator complex modulated by its dissociable Kinase module

The eukaryotic Mediator, comprising a large Core (cMED) and a dissociable CDK8 kinase module (CKM), regulates RNA Polymerase II (Pol II)-dependent transcription. cMED recruits Pol II and promotes pre-initiation complex (PIC) formation in a manner inhibited by the CKM, which is also implicated in post-initiation control of gene expression. Herein we report cryo-electron microscopy structures of the human complete Mediator and its CKM, which explains the basis for CKM inhibition of cMED-activated transcription. The CKM binds to cMED through an intrinsically disordered region (IDR) in MED13 and HEAT repeats in MED12. The CKM inhibits transcription by allocating its MED13 IDR to occlude binding of Pol II and MED26 to cMED and further obstructing cMED-PIC assembly through steric hindrance with TFIIH and the +1 nucleosome. Notably, MED12 binds to the cMED Hook, positioning CDK8 downstream of the transcription start site, which sheds new light on its stimulatory function in post-initiation events.

biochemistry↗

Endogenous glucocorticoids are required for normal macrophage activation and gastric Helicobacter pylori immunity

Glucocorticoids are steroid hormones well-known for their potent anti-inflammatory effects. However, their immunomodulatory properties are multifaceted. Increasing evidence suggests that glucocorticoid signaling promotes effective immunity and that disruption of glucocorticoid signaling impairs immune function. In this study, we conditionally deleted the glucocorticoid receptor (GR) in the myeloid lineage using the LysM-Cre driver (myGRKO). We examined the impact on macrophage activation and gastric immune responses to Helicobacter pylori, the best-known risk factor of gastric cancer. Our results indicate that compared to WT, GRKO macrophages exhibited higher expression of proinflammatory genes in steroid-free conditions. However, when challenged in vivo, GRKO macrophages exhibited aberrant chromatin landscapes and impaired proinflammatory gene expression profiles. Moreover, gastric colonization with Helicobacter revealed impaired gastric immune responses and reduced T cell recruitment in myGRKO mice. As a result, myGRKO mice were protected from atrophic gastritis and pyloric metaplasia development. These results demonstrate a dual role for glucocorticoid signaling in preparing macrophages to respond to bacterial infection but limiting their pathogenic activation. In addition, our results support that macrophages are critical for gastric anti- Helicobacter immunity. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=159 SRC="FIGDIR/small/575574v1_ufig1.gif" ALT="Figure 1"> View larger version (34K): org.highwire.dtl.DTLVardef@7d5281org.highwire.dtl.DTLVardef@1b39ca2org.highwire.dtl.DTLVardef@f081caorg.highwire.dtl.DTLVardef@1d9215d_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

Comparison of gastric inflammation and metaplasia induced by Helicobacter pylori or Helicobacter felis colonization in mice

BackgroundGastric cancer is the fifth most diagnosed cancer in the world. Infection by the bacteria Helicobacter pylori (HP) is associated with approximately 75% of gastric cancer cases. HP infection induces chronic gastric inflammation, damaging the stomach and fostering carcinogenesis. Most mechanistic studies on Helicobacter-induced gastric cancer initiation are performed in mice and utilize either mouse-adapted strains of HP or the natural mouse pathogen Helicobacter felis (HF). Each of these infection models is associated with strengths and weaknesses. Here, we identified the differences in immunogenicity and gastric pathological changes associated with HP and HF infection in mice. Material and MethodsPMSS1 HP strain or with the CS1 HF strain were co-cultured with mouse peritoneal macrophages to assess their immunostimulatory effects. C57BL/6J mice were infected with HP or HF, and gastric inflammation, atrophy, and metaplasia development were assessed 2 months post-infection. ResultsHP and HF induced similar cytokine production from cultured mouse peritoneal macrophages. HP-infected mice caused modest inflammation within both the gastric corpus and antrum and did not induce significant atrophy within the gastric corpus. In contrast, HF induced significant inflammation throughout the gastric corpus and antrum. Moreover, HF infection was associated with significant atrophy of the chief and parietal cell compartments and induced expression of pyloric metaplasia markers. ConclusionsHP is poorly immunogenic compared to HF. HF induces dramatic CD4+ T cell activation, which is associated with increased gastric cancer risk in humans. Thus, HP studies in mice are better suited for studies on colonization, while HF is more strongly suited for pathogenesis and cancer initiation studies.

immunology↗

Anaplerotic nutrient stress drives synergy of angiogenesis inhibitors with therapeutics targeting tumor metabolism

Tumor angiogenesis is a cancer hallmark, and its therapeutic inhibition has provided meaningful, albeit limited, clinical benefit. While anti-angiogenesis inhibitors deprive the tumor of oxygen and essential nutrients, cancer cells activate metabolic adaptations to diminish therapeutic response. Despite these adaptations, angiogenesis inhibition incurs extensive metabolic stress, prompting us to consider such metabolic stress as an induced vulnerability to therapies targeting cancer metabolism. Metabolomic profiling of angiogenesis-inhibited intracranial xenografts showed universal decrease in tricarboxylic acid cycle intermediates, corroborating a state of anaplerotic nutrient deficit or stress. Accordingly, we show strong synergy between angiogenesis inhibitors (Avastin, Tivozanib) and inhibitors of glycolysis or oxidative phosphorylation through exacerbation of anaplerotic nutrient stress in intracranial orthotopic xenografted gliomas. Our findings were recapitulated in GBM xenografts that do not have genetically predisposed metabolic vulnerabilities at baseline. Thus, our findings cement the central importance of the tricarboxylic acid cycle as the nexus of metabolic vulnerabilities and suggest clinical path hypothesis combining angiogenesis inhibitors with pharmacological cancer interventions targeting tumor metabolism for GBM tumors.

cancer biology↗

Genetic depletion of de novo coenzyme A biosynthesis exacerbates puromycin toxicity

Puromycin is an amino nucleoside that inhibits protein synthesis by interrupting elongation of nascent peptide chains. It is a commonly used selection antibiotic in molecular biology research via engineered expression of a puromycin resistance transgene. The enzyme puromycin acetyl transferase (pac) or PuroR inactivates puromycin by N-acetylating its reactive amino group. Puromycin acetylation by pac requires the central metabolite and acetyl group donor acetyl-CoA as a substrate. We found that puromycin treatment exacerbates sensitivity of cancer cells to knockdown of pantothenate kinases, the proteins that catalyze the rate-limiting step of de novo coenzyme A production in cells. Mechanistically, we found that ablation of PANKs together with puromycin depletes acetyl-CoA levels, in a manner modulated by the dose of puromycin. Our findings provide a note of caution and context in the use of puromycin for metabolism research in that interference with the major acyl donor used for inactivating biotransformation may exacerbate toxicity under selection. Broadly, our findings also invite studies to explore how targeting CoA and acetyl-CoA synthesis may be exploited to enhance cytotoxic effects of cancer drugs that undergo acetylation.

cancer biology↗

Epitranscriptomic N6-methyladenosine profile of SARS-CoV-2-infected human lung epithelial cells

N6-methyladenosine (m6A) is a dynamic post-transcriptional RNA modification that plays an important role in determining transcript fate. Severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) has caused the global pandemic of coronavirus disease 2019 (COVID-19) and the virus has been extensively studied. However, how m6A modification of host cell RNAs change during SARS-CoV-2 infection has not been reported. Here we define the epitranscriptomic m6A profile of SARS-CoV-2-infected human lung epithelial cells compared to uninfected controls. Biological pathway analyses revealed that differentially methylated transcripts were significantly associated with cancer-related pathways, protein processing in the endoplasmic reticulum, cell death and proliferation. Upstream regulators predicted to be associated with the proteins encoded by differentially methylated mRNAs include proteins involved in the type I interferon response, inflammation, and cytokine signaling. These data suggest that m6A modification of cellular RNA is an important mechanism of regulating host gene expression during SARS-CoV-2 infection of lung epithelial cells.

microbiology↗

Regulation of Klebsiella pneumoniae mucoidy by the bacterial tyrosine kinase Wzc

Klebsiella pneumoniae is a frequent nosocomial pathogen associated with urinary tract infections (UTI), pneumonia, and septicemia. Two lineages of K. pneumoniae have emerged that challenge the treatment of these infections. One lineage includes hypervirulent strains, causing invasive community-acquired infections, and the other encompasses carbapenem-resistant isolates. Non-mucoid, carbapenem-resistant isolates are most frequently isolated from UTI. Therefore, we hypothesized that environmental conditions may drive K. pneumoniae adaptation to the urinary tract. We found that two rmp-positive, hypervirulent strains and two rmp-negative clinical UTI isolates all suppressed mucoidy when cultured in urine compared to rich LB medium without altering capsular polysaccharide (CPS) abundance. We then performed a transposon screen to identify genetic factors through which urine suppresses mucoidy. Due to variations within transposon hits, we performed whole genome sequencing on our hits and found 100% association between secondary mutations in Wzc and increased mucoidy. Wzc is an inner membrane tyrosine kinase that regulates CPS assembly. When Wzc mutations are encoded chromosomally we observed both increased mucoidy and increased cell-free extracellular polysaccharide (EPS). However, when Wzc mutations are expressed in trans we observed increased mucoidy without impacting CPS or cell-free EPS abundance. Functionally, one periplasmic mutation increased Wzc autophosphorylation, while four active site mutations reduced Wzc autophosphorylation. These four active site mutations are also sufficient to increase mucoidy in one of the rmp-negative clinical UTI isolates without affecting EPS abundance. Combined, these data implicate mutation-driven modulation of Wzc activity as a global, rmp-independent mechanism for increasing K. pneumoniae mucoidy, without altering EPS uronic acid content. Wzc activity may represent the lynchpin that coordinates both capsule biosynthesis and mucoidy, explaining why these two phenotypes have been historically intertwined.

microbiology↗

Shifting a Cellular Metabolic Landscape Identifies a Refractory Environment for Flavivirus Replication

Host-targeted therapeutics to control viral infection are gaining prominence given the vulnerability of viral replication at select host-interaction points and the limited possibility of developing drug resistant mutants. Nevertheless, the chemical and biological impact of many host-targeted therapeutics on both the cell and virus has not been elucidated and remains a key complication. Previously, it has been demonstrated that inhibition of fatty acid metabolism has significant antiviral potential. Here, we use a multidisciplinary approach to demonstrate how inhibition of fatty acid biosynthesis creates a metabolically refractory environment that drives viral dependence on alternate metabolic pathways for survival. By profiling the global metabolic landscape following inhibition of fatty acid biosynthesis, we identified additional biochemical pathways that, when inhibited in combination with fatty acid biosynthesis, displayed increased antiviral potential. Our studies also demonstrated that there was a direct link between changes in cellular chemical composition and the ultrastructural membrane architecture induced by viral gene products. Utilizing inhibitors to change these metabolic environments significantly impacted early viral replication and disrupted the membrane architecture critical for the viral life cycle. Here, we have defined at a molecular level how shifting metabolic landscapes can be exploited to identify combinations of therapeutics that have a greater antiviral effect. Author SummaryDengue viruses are transmitted by Aedes aegypti mosquitoes which are prevalent in the tropical and subtropical regions of the world. These viruses cause over 350 million infections annually. There are no antivirals to combat infection and the only vaccine available is suboptimal. Since these viruses are obligate pathogens, they hijack lipid metabolic pathways in host cells to drive new lipid synthesis critically required for their replication. Mechanisms of how lipid synthesis impacts viral replication is unknown. These viruses also rearrange cellular membranes to form platforms for assembly of viral replication complexes. Here, for the first time, we show that virus-hijacking of de novo fatty acid biosynthesis pathways is required for the formation of membranous replication platforms and if inhibited disrupted synthesis of replicative form viral RNA. Importantly, these inhibitors drastically rearranged the metabolic landscape of the cell resulting in an activation of compensatory nucleotide synthesis pathways that allowed the virus to survive at a low level through the inhibition. However, if both pathways were inhibited in combination, infectious virus release was reduced to below detection limits. The study demonstrates how understanding the metabolic landscape altered by specific inhibitors can lead to the discovery of compensatory metabolic pathways and targets that in combination can enhance intervention efficacy.

microbiology↗

Generation and validation of an anti-human PANK3 mouse monoclonal antibody

Coenzyme A (CoA) is an essential co-factor at the intersection of diverse metabolic pathways. Cellular CoA biosynthesis is regulated at the first committed step-- phosphorylation of pantothenic acid--catalyzed by pantothenate kinases (PANK1,2,3 in humans, PANK3 being the most highly expressed). Despite the critical importance of CoA in metabolism, the differential roles of PANK isoforms remain poorly understood. Our investigations of PANK proteins as precision oncology collateral lethality targets (PANK1 is co-deleted as part of the PTEN locus in some highly aggressive cancers) were severely hindered by a dearth of commercial antibodies that can reliably detect endogenous PANK3. While we successfully validated commercial antibodies for PANK1 and PANK2 using CRISPR knockout cell lines, we found no commercial antibody that could detect endogenous PANK3. We therefore set out to generate a mouse monoclonal antibody against human PANK3 protein. We demonstrate that clone (Clone MDA-299-62A) can reliably detect endogenous PANK3 protein in cancer cell lines, with band-specificity confirmed by CRISPR PANK3 knockout cell lines. Sub-cellular fractionation indicates that PANK3 is overwhelmingly cytosolic and expressed broadly across cancer cell lines. PANK3 monoclonal antibody MDA-299-62A should prove a valuable tool for researchers investigating this understudied family of metabolic enzymes in health and disease.

biochemistry↗

Quantification of phosphonate drugs by 1H-31P HSQC shows that rats are better models of primate drug exposure than mice

The phosphonate group is a key pharmacophore in many anti-viral, anti-microbial, and anti-neoplastic drugs. Due to its high polarity and short retention time, detecting and quantifying such phosphonate-containing drugs with LC/MS-based methods is challenging and requires derivatization with hazardous reagents. Given the emerging importance of phosphonate-containing drugs, developing a practical, accessible, and safe method for their quantitation in pharmacokinetics (PK) studies is desirable. NMR-based methods are often employed in drug discovery but are seldom used for compound quantitation in PK studies. Here, we show that proton-phosphorous (1H-31P) heteronuclear single quantum correlation (HSQC) NMR allows for quantitation of the phosphonate-containing enolase inhibitor HEX in plasma and tissue at micromolar concentrations. Although mice were shown to rapidly clear HEX from circulation (over 95% in <1 hr), the plasma half-life of HEX was more than 1hr in rats and nonhuman primates. This slower clearance rate affords a significantly higher exposure of HEX in rat models compared to mouse models while maintaining a favorable safety profile. Similar results were observed for the phosphonate-containing antibiotic, fosfomycin. Our study demonstrates the applicability of the 1H-31P HSQC method to quantify phosphonate-containing drugs in complex biological samples and illustrates an important limitation of mice as preclinical model species for phosphonate-containing drugs.

pharmacology and toxicology↗

Marburg and Ebola virus mRNA 3 untranslated regions contain negative regulators of translation that are modulated by ADAR1 editing

The filovirus family includes deadly pathogens such as Ebola virus (EBOV) and Marburg virus (MARV). A substantial portion of filovirus genomes encode 5 and 3 untranslated regions (UTRs) of viral mRNAs. Select viral genomic RNA sequences corresponding to 3UTRs are prone to editing by ADAR1. A reporter mRNA approach, in which different 5 or 3UTRs were inserted into luciferase encoding mRNAs, demonstrates that MARV 3UTRs yield different levels of reporter gene expression suggesting modulation of translation. The modulation occurs in cells unable to produce miRNAs and can be recapitulated in a minigenome assay. Deletion mutants identified negative regulatory regions at end of the MARV NP and L 3UTRs. Apparent ADAR1 editing mutants were previously identified within the MARV NP 3UTR. Introduction of these changes into the MARV nucleoprotein (NP) 3UTR or deletion of the region targeted for editing enhances translation, as indicated by reporter assays and polysome analysis. In addition, the parental NP 3UTR, but not the edited or deletion mutant NP 3UTRs, induce a type I interferon (IFN) response upon transfection into cells. Because some EBOV isolates from the West Africa outbreak exhibited ADAR1 editing of the VP40 3UTR, VP40 3UTRs with parental and edited sequences were similarly assayed. The EBOV VP40 3UTR edits also enhanced translation but neither the wildtype nor the edited 3UTRs induced IFN. These findings implicate filoviral mRNA 3UTRs as negative regulators of translation that can be inactivated by innate immune responses that induce ADAR1. ImportanceUTRs comprise a large percentage of filovirus genomes and are apparent targets of editing by ADAR1, an enzyme with pro- and antiviral activities. However, the functional significance of the UTRs and of ADAR1 editing have been uncertain. This study demonstrates that MARV and EBOV 3UTRs can modulate translation, in some cases negatively. ADAR1 editing or deletion of select regions within the translation suppressing 3UTRs, relieves the negative effects of the UTRs. These data indicate that filovirus 3UTRs contain translation regulatory elements that are modulated by activation of ADAR1, suggesting a complex interplay between filovirus gene expression and innate immunity.

microbiology↗