bioRxiv Science⌕ Search

Biology subjects

Mehra, S.

Publications and source records attributed to Mehra, S..

At least 19 recordsLinked to original sources

PRNP mutations initially generate an alternatively misfolded PrP species that dissuades prion replication

Mutations in the PRNP gene, which encodes the prion protein (PrP), cause genetic prion disease. However, how PRNP mutations lead to spontaneous prion formation remains poorly understood. Building off the observation that expression of mutant bank vole PrP (BVPrP) in mice causes spontaneous prion disease, we sought to identify early events in prion formation by expressing mutant BVPrP in cultured cells lacking endogenous PrP. Expression of D178N- and E200K-mutant, but not wild-type BVPrP, in CAD5-PrP-/- and N2a-PrP-/- cells generates an alternatively misfolded PrP species, which we term PrPAM, that is detergent-insoluble and resistant to digestion with the protease thermolysin. PrPAM is also present in the brains of young, asymptomatic knock-in mice expressing mutant BVPrP. However, PrPAM does not appear to be a direct precursor of prions since 1) the prion disease-protective G127V substitution enhances PrPAM levels when coupled with the D178N or E200K mutations; 2) small molecule anti-prion drugs fail to reduce PrPAM accumulation in cells; 3) unlike cells expressing wild-type BVPrP, cells expressing D178N- or E200K-mutant BVPrP are largely resistant to infection with several prion strains; and 4) PrPAM-containing cell homogenate does not contain seeds that induce misfolding of wild-type BVPrP in either cells or the RT-QuIC assay. These results raise the possibility that prion disease-causing PRNP mutations initially generate a protective misfolded PrP species that is refractory to prion formation, which provides a potential explanation for why genetic prion diseases manifest later in life despite the presence of a mutation from birth.

neuroscience↗

Dengue virus-induced thrombocytopenia is mediated by dysregulation of the RUNX1-MYH9 axis

Dengue virus (DENV) infection causes an acute febrile illness that is usually self-limiting but can become fatal. Thrombocytopenia, or a decrease in circulating platelets, is a major clinical feature of dengue and is strongly associated with the progression to dengue hemorrhagic fever and dengue shock syndrome. In this report, MYH9, a cytoskeletal protein involved in platelets maturation and release, was found to be down-regulated in DENV-infected Huh7 cell lines. The expression of RUNX1, an important transcription factor involved in megakaryopoiesis, was also decreased following DENV-infection. In-silico analysis identified three potential RUNX1 transcription-factor binding site in the promoter-region of MYH9 gene. We therefore investigated whether RUNX1 regulates MYH9 expression during DENV-infection. Luciferase-assay and ChIP assays showed that DENV-infection affect the binding of RUNX1 to the MYH9 promoter, providing insight into the molecular basis underlying the reduced expression of MYH9 expression. Furthermore, the megakaryocyte differentiation markers GATA1, ITGB3, and MYH9 were upregulated in PMA-induced K562-cells. However, DENV infection downregulated these genes and increased the expression of apoptosis marker gene CYCS. These findings suggest that the dengue affects megakaryopoiesis through multiple mechanisms, potentially reducing platelets production while also promoting platelets destruction. Additionally, Fluorescence and electron microscopy revealed that functional defects of MYH9 may affects megakaryopoiesis biogenesis. Overall, this study provides insights into the molecular mechanisms contributing to thrombocytopenia during DENV infection.

molecular biology↗

α-Synuclein strain homogeneity in multiple system atrophy clinical subtypes

Conformationally distinct strains of -synuclein aggregates are believed to contribute to the clinical and pathological diversity observed among synucleinopathies such as multiple system atrophy (MSA) and Parkinsons disease. Cases of MSA can be classified into two distinct clinical subtypes: the cerebellar variant, MSA-C, and the parkinsonian variant, MSA-P. To assess whether distinct -synuclein strains may be present in individuals with MSA-C versus MSA-P, we characterized the conformational and seeding properties of -synuclein aggregates in various brain regions from MSA-C and MSA-P patients and performed propagation studies in M83 transgenic mice. Biochemical fingerprinting of -synuclein aggregates using limited proteolysis and a conformational stability assay failed to reveal differences between MSA-C and MSA-P either before or after propagation in mice. Similarly, using brain extracts from either MSA patients or MSA-inoculated mice, MSA-C and MSA-P -synuclein aggregates exhibited indistinguishable seeding attributes in a seed amplification assay. Finally, no differences were observed in either the kinetics of disease progression or the extent of cerebral -synuclein deposition in M83 mice inoculated with either MSA-C or MSA-P, regardless of the brain region from which the injected -synuclein aggregates were derived. These results suggest that MSA clinical subtypes are unlikely to arise due to distinct -synuclein strains. Instead, our findings support a model in which the same -synuclein strain initially forms in different brain regions, leading to differences in disease manifestation.

neuroscience↗

Bronchus associated lymphoid tissue induced by an attenuated Mycobacterium tuberculosis vaccine prevents tuberculosis from heterologous TB challenge

Tuberculosis (TB) remains a leading cause of death from infectious disease worldwide, underscoring the urgent need for vaccines with greater and more consistent efficacy than Bacille Calmette-Guerin (BCG). We previously showed that mucosal vaccination with an isogenic Mycobacterium tuberculosis (Mtb) mutant lacking the stress-response transcription factor SigH ({Delta}sigH) prevents pulmonary TB in two macaque species. In the absence of SigH, Mtb is unable to effectively counter host oxidative stress. Vaccinated macaques were notably protected from disease, exhibiting an absence of granulomatous pathology together with the formation of lymphoid follicles and robust antigen-specific CD4+ and CD8+ T cell responses, identifying{Delta} sigH as a promising live-attenuated TB vaccine candidate. The{Delta} sigH mutant used in prior studies was generated in the Mtb CDC1551 background, a commonly used laboratory strain for challenge studies. Here, we evaluated whether{Delta} sigH-mediated protection extends to heterologous challenge with the more virulent Mtb Erdman strain. Mucosal{Delta} sigH vaccination conferred significant protection against heterologous challenge, markedly reducing pulmonary bacterial burden and TB-associated pathology. Longitudinal high-resolution PET/CT imaging demonstrated that aerosol{Delta} sigH vaccination induced robust inducible bronchus-associated lymphoid tissue (iBALT) responses in the lung. Unlike granulomas, these iBALT structures resolved over time while remaining associated with protection against subsequent Mtb challenge. Protection of highly susceptible rhesus macaques against virulent heterologous Mtb challenge following aerosol{Delta} sigH vaccination supports the further preclinical development of{Delta} sigH-based live-attenuated TB vaccines and highlights iBALT induction as a potential correlate and mechanistic driver of protective immunity against TB.

immunology↗

MMV687794 blocks Plasmodium falciparum invasion of red blood cells by targeting a Surface-associated Lipid-Interacting Rhoptry Protein, PfSLIRP

Invasion of red blood cells (RBCs) by the human malaria parasite, Plasmodium falciparum, drives disease. During invasion, the parasite pushes its way into the RBC while wrapping the RBC membrane around itself to establish the parasitophorous vacuole, a stable niche within the RBC where the parasite grows. To better understand invasion, we investigated the mechanism of action of an invasion-inhibitory compound, MMV687794 (MMV794). Lattice light-sheet microscopy revealed that MMV794 blocks parasite entry by preventing parasitophorous vacuole formation. In vitro drug resistance selection of parasites with MMV794 found mutations to the /{beta} hydrolase, PF3D7_0403800, and engineering one of these mutations (C36W) into parasites by CRISPR/Cas9 recapitulated the resistance phenotype. Expansion microscopy demonstrated that this protein is expressed in schizonts, localising to the surface of rhoptries, which are specialised apical secretory organelles that function during invasion. Lipidomics and proteomics analyses of C36W parasites uncovered widespread changes to lipid composition/homeostasis and altered abundance of proteins involved in invasion, indicating a role for PF3D7_0403800 in invasion-associated lipid metabolism. Finally, we used solvent-induced proteome profiling and reactivity assays to confirm drug-target engagement. Together, our findings identify a novel Surface-associated Lipid-Interacting Rhoptry Protein (PfSLIRP) that coordinates lipid metabolism at the rhoptries to enable RBC invasion.

microbiology↗

Efflux pump regulation and metabolic rewiring define the ceiling of efflux-mediated drug resistance in Mycobacteria

Multidrug-resistant efflux pumps play a critical role in antimicrobial resistance, yet the physiological limits of their overexpression remain poorly understood. While gene amplifications and regulatory mutations commonly drive this overexpression, these pumps remain transcriptionally inactive under normal cellular conditions due to their high energetic cost, making it challenging to assess their full impact on resistance evolution and the maximum attainable minimum inhibitory concentration (MIC). To delineate the extent and spectrum of efflux-based resistance, we subjected Mycobacterium smegmatis mc{superscript 2}155(Msm) wild-type and efflux pump-deleted strains ({Delta}lfrA and {Delta}efpA) to adaptive laboratory evolution in the presence of a broad-spectrum efflux substrate ethidium bromide (EtBr). Despite prolonged selection, resistance plateaued at 8-16x MIC, revealing an intrinsic ceiling to efflux-based adaptation. Evolved populations integrated multiple layers of adaptation: enhanced efflux kinetics, reduced intracellular EtBr accumulation, and mutations spanning global regulators, ribosomal genes, and membrane components. Notably, deletion of specific pumps ({Delta}lfrA) triggered compensatory upregulation of alternative efflux systems, highlighting functional redundancy. Beyond efflux activation, evolved strains exhibited metabolic reprogramming, including downregulation of the tricarboxylic acid cycle and upregulation of lipid biosynthesis and {beta}-oxidation, which altered NAD/NADH homeostasis and membrane potential. Extending this adaptive evolution approach to Mycobacterium tuberculosis H37Ra (Mtb) demonstrated that these adaptive constraints and metabolic alterations are conserved across mycobacterial species. Together, these results uncover fundamental limits to efflux evolution and reveal how bacteria integrate regulatory and metabolic plasticity to maximize drug resistance. Targeting these interconnected networks may offer a powerful strategy to contain the rise of multidrug resistance. ImportanceEfflux pumps are widely recognized as major contributors to antimicrobial resistance; however, the extent to which resistance can be driven solely by efflux remains unclear. Here, we define the limits of efflux-mediated resistance using adaptive laboratory evolution to ethidium bromide in Mycobacterium smegmatis and Mycobacterium tuberculosis. We show that resistance reproducibly plateaus despite continued selection and the presence of multiple efflux pumps in the genome, indicating a physiological ceiling to efflux-based adaptation. This limit is achieved through distinct evolutionary trajectories involving regulatory mutations that converge on enhanced efflux activity. Importantly, upregulation of efflux pumps is coupled to extensive cellular remodelling, including metabolic rewiring, and changes in membrane energetics, revealing system-wide trade-offs associated with resistance. Together, our findings demonstrate that efflux-driven resistance is constrained by cellular physiology and shaped by global adaptive costs, thereby refining current models of antimicrobial resistance and identifying vulnerabilities that may be exploited to limit the evolution of resistance.

systems biology↗

Adaptive Laboratory Evolution under gradual ciprofloxacin stress leads to efflux-mediated ciprofloxacin resistance and an increase in endogenous antibiotic production in Streptomyces coelicolor.

Streptomyces are soil-dwelling bacteria harboring a vast reservoir of transcriptionally silent antibiotic-resistant genes. Mobilization of these resistance genes to pathogens results in the dissemination of multidrug resistance when exposed to differential antibiotic pressure. To determine the evolution of resistance, we employed adaptive laboratory evolution (ALE) in Streptomyces coelicolor under gradually increasing concentrations of ciprofloxacin, starting at the minimum inhibitory concentration (MIC) to 4X MIC. The evolved strain CipRr exhibited elevated resistance towards ciprofloxacin with cross-resistance to other fluoroquinolones, such as ofloxacin and moxifloxacin, and collateral sensitivity to the protein synthesis inhibitors chloramphenicol and tetracycline. Compared to the WT cells, CipRr showed elevated production of secondary metabolites actinorhodin and undecylprodigiosin, altered morphology, and reduced ROS production. Whole Genome Sequencing revealed mutations in transcriptional regulators and other metabolic genes, leading to enhanced activity of efflux pumps that conferred high-level ciprofloxacin resistance. Overall, this study demonstrates that evolutionary strategies in antibiotic producers such as streptomyces can help uncover the genetic determinants linked to antibiotic resistance, secondary metabolism, and morphological differentiation. ImportanceThis study employs adaptive laboratory evolution in the antibiotic-producing bacterium Streptomyces coelicolor to investigate how exposure to gradually increasing concentrations of the fluoroquinolone ciprofloxacin drives the emergence of high-level resistance and cross-resistance to related drugs, while simultaneously resulting in collateral sensitivity towards other antimicrobial agents. This study also highlights that the evolution of high-level resistance towards ciprofloxacin significantly alters the production of secondary metabolites and cellular morphology. Furthermore, we identify mutations in regulatory and metabolic genes that result in enhanced efflux pump activation, advancing our understanding of the molecular mechanisms underlying high-level resistance. This study thus highlights the complex interplay between antibiotic resistance, metabolism, and morphological development.

microbiology↗

Targeting CREB remodels the immune microenvironment to enhance immunotherapy responses in pancreatic cancer

Pancreatic ductal adenocarcinoma (PDAC) remains a challenging disease in need of improved treatments. Cyclic adenosine monophosphate response element binding protein 1 (CREB) is an emerging therapeutic target whose oncogenic effects in PDAC have been largely attributed to a key molecular interplay between oncogenic KrasG12D/+ (Kras*) and chronic inflammation driving irreversible acinar to ductal reprogramming. Here, we demonstrate that CREB activation fosters tumor associated macrophage (TAM) mediated immunosuppression and promotes PDAC growth in an aggressive LSL-KrasG12D/+;Trp53R172H/+;Pdx1Cre/+(KPC) genetically engineered mouse model. Selective deletion of CREB (Crebfl/fl) in KPC(KPCC-/-) mice attenuates primary disease burden. Unbiased transcriptomic analysis and validation using diverse molecular, genetic and pharmacological approaches in vitro and in vivo identify CREB-mediated transcriptional regulation of leukemia inhibitory factor (Lif) as one of the potential mediators of tumor cell-macrophage crosstalk promoting a pro-tumor polarization of TAMs, thereby attenuating the infiltration of effector T cells. Mechanistically, cancer cell derived LIF facilitates an immunosuppressive, pro-tumorigenic state. Importantly, pharmacological targeting of the CREB-LIF signaling axis between cancer cells and macrophages, using a CREB-specific inhibitor (CREBi), significantly suppresses tumor growth and sensitizes PDAC to immunotherapy, highlighting the therapeutic potential of this treatment combination to improve outcomes in this aggressive disease.

cancer biology↗

Therapeutic remodeling of the tuberculosis granuloma with 1-methyl-D-tryptophan enhances CD8+ T cell-macrophage interactions

Granulomas, the hallmark of tuberculosis (TB) disease, can both restrict Mycobacterium tuberculosis (Mtb) dissemination and impede its clearance. Recent studies indicate that indoleamine 2,3-dioxygenase (IDO1), an immunosuppressive metabolic enzyme, limits infiltration of activated T cells and can contribute to TB disease progression. Treatment with 1-methyl-D-tryptophan (D-1MT), a small molecule inhibitor that restores mTOR signaling, has been shown to improve immune responses Mtb-infected rhesus macaques. Here, we investigated the impact of D-1MT treatment on TB granuloma architecture using 30-plex high-dimensional issue imaging in rhesus macaques. By spatially mapping 13 distinct cell populations, we found D-1MT treatment corresponded with significantly increased infiltration CD8+ T cells into granulomas compared to untreated controls. Notably, these CD8+ T cells expressed markers of cell proliferation and cytotoxicity. D-1MT enhanced CD8+ T cell infiltration throughout the granuloma, with particularly pronounced effects in the myeloid core, where we observed significantly enhanced spatial interactions between macrophages and CD8+, but not CD4+ T cells. Our results demonstrate that: (i) effective intra-granulomatous Mtb control is associated with the close spatial proximity between CD8+ T cells and macrophages, a feature less abundant in uncontrolled pulmonary TB; (ii) IDO1 induction blocks CD8+ T cell infiltration and reduces T cell activation and proliferation; and (iii) therapeutic strategies, including D-1MT, that improve intra-granulomatous killing hold strong translational potential. Significance statementOur understanding of immune mechanisms within the TB granuloma has advanced greatly with the advent of high-resolution single cell multiplexed imaging. Using such imaging, we show that TB granulomas in rhesus macaques, a highly translational model of human TB pathology, are characterized by IDO1-mediated immunoregulation. Early pharmacologic restoration of mTOR signaling via D-1MT treatment can reduce IDO1 enzymatic activity and facilitate the recruitment and function of CD8+ T cells within the granulomas. These findings reveal specific mechanisms exploited by Mtb to maintain intra-granuloma persistence and underscore immune responses. Future vaccine and therapeutic design should consider these immunoregulatory features to achieve better control of Mtb infection.

immunology↗

Deconvolution of the on-target activity of plasmepsin V peptidomimetics in P. falciparum parasites

Plasmepsin V (PMV), an essential aspartyl protease, plays a critical role during the asexual blood stage of infection of Plasmodium by enabling the export of parasite proteins into the host red blood cell. This export is vital for parasite survival and pathogenesis, making PMV an attractive target for antimalarial drug development. Peptidomimetic inhibitors designed to mimic the natural substrate of PMV have demonstrated potent parasite-killing activity by blocking protein export. While these compounds have been instrumental in validating PMV as a bona fide antimalarial target, inconsistencies between their biochemical potency and cellular activity have raised questions regarding their precise mechanism of action. In this study, we employed chemoproteomic approaches, including solvent induced protein precipitation (SIP) and intact-cell thermal PISA profiling, to demonstrate PMV target engagement by the peptidomimetics. To further support these findings, we generated parasite lines exhibiting reduced sensitivity to peptidomimetics. Through whole-genome sequencing of these parasite lines, a single nucleotide variant (SNV) within the pmv gene was revealed. This mutation was later validated using reverse genetics, confirming its role in mediating resistance. Together, these data provide strong evidence that the peptidomimetics exert their antimalarial activity by directly targeting PMV. These findings further support the potential of PMV as a validated and promising target for future antimalarial drug development.

cell biology↗

Increased vaccine efficacy against tuberculosis with a recombinant BCG overexpressing the STING agonist cyclic di AMP

Tuberculosis (TB) remains the leading cause of death due to infection globally. Bacillus Calmette Guerin (BCG), a live attenuated bacterial strain, is the only available TB vaccine, but it has poor efficacy in preventing pulmonary TB in adults. There are advantages associated with the BCG platform however, including a remarkable safely profile, billions of administered doses and a public health ecosystem associated with its production, administration and care. A recombinant/modified BCG (rBCG/modBCG) anti-TB vaccine candidate would be able to leverage these advantages while improving on efficacy. BCG-STING is a recombinant BCG strain which overexpresses the mycobacterial diadenylate cyclase disA gene leading to the release of [~]15-fold greater levels of the endogenous small molecule STING agonist cyclic di-AMP. We evaluated vaccination with BCG-STING compared to its parental BCG-WT strain in rhesus macaques challenged with virulent Mycobacterium tuberculosis (Mtb). BCG-STING given intradermally was well-tolerated, and during life serial BAL samples showed that BCG-STING vaccinated animals had lower Mtb CFU counts than those receiving BCG-WT. At necropsy, BCG-STING vaccinated animals had significantly lower Mtb lung CFU counts, and a higher percentage of sterile lobes and granuloma lesions than the BCG-WT recipients. The enhanced protection observed in BCG-STING vaccinated animals was associated with significant elevations of antigen-specific CD4+ and CD8+ T cells. Modifying BCG to overexpress a small molecule recognized by the innate immune system significantly improves protection and cell-mediated immune responses against TB the non-human primate (NHP) model.

microbiology↗

Navigating parasite antigen genetic diversity in the design of Plasmodium vivax serological exposure markers for malaria

BackgroundPlasmodium vivax poses a major obstacle to malaria elimination because it can lie dormant in the liver for weeks or months before reactivating and causing a relapse of infection. These dormant forms (hypnozoites) cannot be detected using standard diagnostics, but recent P. vivax exposure and by proxy, hypnozoite carriage, can be inferred using antibody-based tests (serological markers). In this study, we examined how genetic variation in P. vivax affects the utility of these antibody markers, and whether redesigned antigens could improve performance. MethodsWe analysed global P. vivax genetic data to assess variation in leading serological markers. Based on this, we produced new antigen versions (haplotypes) that better reflect global sequence diversity, compared to the commonly used reference strain (Sal-1). Antibody responses against these new constructs were then tested using samples from well-characterised cohorts in Brazil and Thailand. Antibody levels were assessed in relation to how recently participants had a qPCR-detectable blood-stage P. vivax infection. We compared the ability of the haplotypes and reference constructs to correctly identify individuals infected within the prior 9-months. FindingsExtensive genetic diversity was identified in two P. vivax antigens, DBPII and MSP5. Several antigens had large numbers of circulating haplotypes globally, with the percentage with similar sequence identity to the reference Sal-1 ranging from 0.4% (MSP5) to 99% (S16). Two antigens exhibited strong differences in immunogenicity by region and construct (RBP2a and DBPII). However, for most proteins (5 out of 8), these differences had little impact on the accuracy of identifying recent exposure. In cases where performance was affected (e.g. RBP2a), this could be overcome by adding multiple antigens into the classification model. InterpretationEven highly diverse antigens can be effective serological exposure markers. Our findings highlight the importance of testing the impact of genetic diversity when designing serological tests and suggest practical strategies, such as using a mix of antigens, to ensure consistent performance across regions.

microbiology↗

Using Imaris to rigorously track PET-defined sites of lung inflammation in Mycobacterium tuberculosis-exposed non-human primates

Aerosol exposure of non-human primates (NHPs) to Mycobacterium tuberculosis (Mtb) typically results in discrete sites of inflammation of the lung that is detectable by 2-deoxy-2-[fluorine-18]fluoro-D-glucose (18F-FDG)-based PET/CT scans. Such scans are often analyzed using software such as Invicro VivoQuant or OsiriX as 3D images by manual labeling sites of PET signal using 2D slices and by reporting maximal standardized uptake value (SUVmax) either of the whole lung or of individual lesions. Here we propose a pipeline for analysis of the same PET/CT scans using Imaris, a proprietary software typically used for analysis of fluorescent microscopy data. We show that by using locations of spine vertebra (denoted as "landmarks") we can align serials scans of the same animal, and by using automated (with some manual corrections) image segmentation of PET scans in 3D as "surfaces", we can accurately define location of all sites of inflammation in the lung and lung-associated thoracic lymph nodes (LNs). We show that there is an excellent correlation between individual lesions SUVmax determined by VivoQuant and maximum intensity determined by Imaris suggesting utility of this approach. Imaris also provides wealth of additional information for each of the identified lesions such as volume, location, shape, surface area, and others, and each lesion can be exported in Virtual Reality file format (.wrl) allowing for detailed and rigorous analyses of how features of these PET-defined lesions evolve over time and correlate with the outcome of infection and/or treatment.

immunology↗

The Brain Interactome of a Permissive Prion Replication Substrate

Bank voles are susceptible to prion strains from many different species, yet the molecular mechanisms underlying the ability of bank vole prion protein (BVPrP) to function as a universal prion acceptor remain unclear. Potential differences in molecular environments and protein interaction networks on the cell surface of brain cells may contribute to BVPrPs unusual behavior. To test this hypothesis, we generated knock-in mice that express physiological levels of BVPrP (M109 isoform) and employed mass spectrometry to compare the interactomes of mouse (Mo) PrP and BVPrP following mild in vivo crosslinking of brain tissue. Substantial overlap was observed between the top interactors for BVPrP and MoPrP, with established PrP-interactors such as neural cell adhesion molecules, subunits of Na+/K+-ATPases, and contactin-1 being equally present in the two interactomes. We conclude that the molecular environments of BVPrP and MoPrP in the brains of mice are very similar. This suggests that the unorthodox properties of BVPrP are unlikely to be mediated by differential interactions with other proteins.

neuroscience↗

Cell-specific nanoengineering strategy disrupts tolerogenic signaling from myeloid-derived suppressor cells to invigorate antitumor immunity in pancreatic cancer

Pancreatic ductal adenocarcinoma (PDAC) is characterized by intratumoral abundance of neutrophilic/polymorphonuclear myeloid-derived suppressor cells (PMN-MDSC) which inhibit T-cell function through JAK2/STAT3-regulated arginase activity. To overcome limitations of systemic inhibition of PMN-MDSCs in cancer-bearing patients--i.e., neutropenia and compensatory myelopoietic adaptations--we develop a nanoengineering strategy to target cell-specific signaling exclusively in PMN-MDSCs without provoking neutropenia. We conjugate a chemically modified small-molecule inhibitor of MDSC-surface receptor CXCR2 (AZD5069) with polyethylene glycol (PEG) and chemically graft AZD5069-PEG constructs onto amphiphilic polysaccharide derivatives to engineer CXCR2-homing nanoparticles (CXCR2-NP). Cy5.5 dye-loaded CXCR2-NP showed near-exclusive uptake in PMN-MDSCs compared with PDAC tumor-cells, cancer-associated fibroblasts, and macrophages. Encapsulation of JAK2/STAT3i Ruxolitinib (CXCR2-NPRuxo) resulted in more durable attenuation in STAT3-regulated arginase activity from PMN-MDSCs and induction of cytolytic T-cell activity vs. free Ruxolitinib in-vitro and in-vivo. Cell-specific delivery of payloads via CXCR2-homing immunonanoparticles represents a novel strategy to disrupt MDSC-mediated immunosuppression and invigorate antitumor immunity in PDAC.

cancer biology↗

Systematic bias in malaria parasite relatedness estimation

Genetic studies of malaria parasites increasingly feature estimates of relatedness. However, various aspects of malaria parasite relatedness estimation are not fully understood. For example, estimates of relatedness based on whole-genome-sequence (WGS) data often exceed those based on more sparse data types. We explore systematic bias in relatedness estimation using theoretical, numerical and empirical approaches. Specifically, we use a non-ancestral model of pairwise relatedness to derive theoretical results; a simulation model of ancestry to independently verify and expand our theoretical results; and data on parasites sampled from Guyana to explore how theoretical and numerical results translate empirically. We show that allele frequencies encode, locus-by-locus, relatedness averaged over the set of sampled parasites used to compute them. These sample allele frequencies are typically plugged into the models used to estimate pairwise relatedness. Consequently, models of pairwise relatedness are misspecified and pairwise relatedness values are systematically underestimated. However, systematic underestimation can be viewed as population-relatedness calibration, i.e., a way of generating measures of relative relatedness. Systematic underestimation is unavoidable when relatedness is estimated assuming independence between genetic markers. It is mitigated when estimated using WGS data under a hidden Markov model (HMM), which exploits linkage between proximal markers. Estimates of absolute relatedness generated under a HMM using relatively sparse data should be treated with caution because the extent to which underestimation is mitigated is unknowable. That said, analyses dependent on absolute values and high relatedness thresholds are relatively robust. In summary, practitioners have two options: resolve to use relative relatedness estimated under independence or try to estimate absolute relatedness under a HMM. We propose various practical tools to help practitioners evaluate their situation on a case-by-case basis. Author summaryMalaria genomic epidemiology is increasingly recognised as a tool for public health. Relatedness, which captures likeness derived from common ancestry, is a useful concept for malaria parasites. Analyses of malaria parasite relatedness are important for generating results on spatiotemporal scales relevant to disease control. Since shared ancestry is unobservable, relatedness must be estimated under a statistical model. However, not all aspects of malaria parasite estimation are fully understood, including the effects of different data types. In this work, we characterise systematic biases in estimates of malaria parasite relatedness. Our analysis is three-fold: we mathematically interrogate a non-ancestral model of relatedness to derive theoretical results; simulate parasite ancestries from first principles to yield numerical results; and perform an empirical case study of parasites sampled from Guyana. We show that bias may be particularly pronounced when using sparse marker data from inbred parasite populations, which are often found in pre-elimination settings. We chart out a practical roadmap to enable practitioners to assess epidemiological settings on a case-by-case basis. Our findings are relevant to applications in malaria genomic epidemiology that use relatedness directly or indirectly, including molecular surveillance and the genetic-based classification of treatment failure.

genetics↗

The Molecular Determinants of a Universal Prion Acceptor

In prion diseases, the species barrier limits the transmission of prions from one species to another. However, cross-species prion transmission is remarkably efficient in bank voles, and this phenomenon can be recapitulated in mice by expression of the bank vole prion protein (BVPrP). The molecular determinants of BVPrPs ability to function as a universal or near-universal acceptor for prions remain incompletely defined. Building on our finding that cultured cells expressing BVPrP can replicate both mouse and hamster prion strains, we conducted a systematic analysis to identify key residues in BVPrP that permit cross-species prion replication. Consistent with previous findings, we demonstrate that residues N155 and N170 of BVPrP, which are absent in mouse PrP but present in hamster PrP, are critical for cross-species prion replication. Additionally, BVPrP residues V112, I139, and M205, which are absent in hamster PrP but present in mouse PrP, are also required to enable replication of both mouse and hamster prions. Unexpectedly, we found that residues E227 and S230 near the C-terminus of BVPrP severely restrict the accumulation of prions following cross-species prion challenge, suggesting that they may have evolved to counteract the inherent propensity of BVPrP to misfold. PrP variants with an enhanced ability to replicate both mouse and hamster prions displayed accelerated spontaneous aggregation kinetics in vitro. These findings suggest that BVPrPs unusual properties are governed by a key set of amino acids and that the enhanced misfolding propensity of BVPrP may enable cross-species prion replication.

neuroscience↗

Insight into the regulatory mechanism of the MFS transporter, SCO4121 by the MarR regulator, SCO4122

MarR group of transcriptional regulators are ubiquitous in bacteria and found to be involved in regulation of efflux pumps that confer multidrug resistance phenotype. While most characterized MarR regulators act as transcriptional repressors, we earlier identified a MarR regulator SCO4122 in Streptomyces coelicolor, playing an essential role in transcriptional activation of the MFS transporter SCO4121 in response to multiple substrates of the latter, including streptomycin, ciprofloxacin and chloramphenicol. In this study, using Surface Plasmon Resonance, we demonstrate that SCO4122 interacts directly with the diverse substrates of SCO4121 with the highest affinity for streptomycin with a KD of 0.73 M. Further, in-vitro and in-vivo studies reveal that SCO4122 also binds to the intergenic region between sco4121 and sco4122, where the interaction is dependent on the cooperative binding of SCO4122 to three motifs in this region. A conserved Methionine, M93, in SCO4122 is identified to be an integral amino acid residue that is involved in activation of SCO4121 in response to ciprofloxacin, streptomycin and EtBr but not chloramphenicol. Furthermore, our studies also indicate that upon binding to different substrates, the affinity of SCO4122 to the sco4121 promoter increases 50-1000 fold, thereby leading to enhanced expression of the transporter, SCO4121. This study thus highlights that SCO4122 is a novel MarR regulator that functions as a strong transcriptional activator of an efflux pump, SCO4121, through intricate molecular mechanisms in presence of structurally dissimilar substrates. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=97 SRC="FIGDIR/small/577416v1_ufig1.gif" ALT="Figure 1"> View larger version (15K): org.highwire.dtl.DTLVardef@3394e2org.highwire.dtl.DTLVardef@73afb1org.highwire.dtl.DTLVardef@113c724org.highwire.dtl.DTLVardef@1772ac9_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗