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Puri, M.

Publications and source records attributed to Puri, M..

7 recordsLinked to original sources

Malnourishment and expanded microbiome maintain superior efficacy of the recombinant tuberculosis vaccine BCG::ESAT-6-PE25SS

Tuberculosis (TB) remains the leading cause of infectious mortality. The limited efficacy of the only TB vaccine, Bacille Calmette-Guerin (BCG) against pulmonary disease necessitates improved vaccines. Host factors such as malnutrition and microbiome composition shape immune responses in humans, though these factors are overlooked in preclinical vaccine evaluation. Here we show that a recombinant BCG strain, BCG::ESAT-6-PE25SS, confers superior protection compared to BCG across murine models of malnutrition, antibiotic-induced dysbiosis and environmentally enriched microbiota. Unexpectedly, malnourished mice displayed reduced Mycobacterium tuberculosis (Mtb) burden, associated with altered host metabolism and immune composition. Microbiome disruption increased TB susceptibility, whereas diversification of microbiota enhanced resistance and immune heterogeneity. Vaccine efficacy correlated with enrichment of known immunomodulatory microbial taxa. These findings suggest diet-microbiome-immunity interactions as potential key determinants of TB pathogenesis and provide evidence for the importance of vaccine candidate evaluation under physiologically relevant co-morbid conditions

microbiology↗

mRNA-based prime-and-pull vaccination combines benefits of subcutaneous and mucosal BCG vaccination

Pulmonary vaccination has been proposed as a strategy to improve protection against tuberculosis, due to the generation of immune cells that more efficiently survey and eliminate infected cells within the lung. However, uncontrolled replication and excessive inflammation associated with mucosal delivery of live-attenuated vaccines highlight the need for alternative strategies that balance efficacy and safety. Here, we describe a prime-and-pull vaccination approach in which systemic immunity is established by subcutaneous BCG vaccination, followed by the induction of local lung immunity through mucosal delivery of lipid nanoparticle-formulated multi-antigen mRNA. Proof-of-concept studies using a model antigen demonstrated the induction of polyfunctional antigen-specific T cells in the lung with minimal inflammatory cell infiltration, compared with mucosal BCG vaccination. Eight Mycobacterium tuberculosis- and BCG-derived proteins were subsequently selected to generate four multi-antigen mRNA constructs. In vivo vaccination and challenge experiments demonstrated that this prime-and-pull strategy is well tolerated and confers protective immunity against tuberculosis in a murine model. Collectively, these data support a modular mRNA-based prime-and-pull vaccination strategy as a translational approach that bridges the improved immunogenicity and efficacy of mucosal BCG vaccination with the safety profile of parenteral BCG administration. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=110 SRC="FIGDIR/small/739464v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@c0635borg.highwire.dtl.DTLVardef@bb0357org.highwire.dtl.DTLVardef@1d87243org.highwire.dtl.DTLVardef@135bcd7_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

Pulmonary delivery of antigen-enhanced BCG overcomes safety barriers in immunocompromised hosts and protects against TB in the absence of adaptive immunity.

The low efficacy of Bacille Calmette-Guerin (BCG) in preventing pulmonary tuberculosis (TB) underscores the need for improved TB vaccines. Recombinant BCG (rBCG) strains secreting the virulence-associated effector molecule ESAT-6 from Mycobacterium tuberculosis (Mtb) markedly improve efficacy and immunogenicity in animal models of TB but have been considered unsuitable for clinical translation due to safety concerns identified in intravenous SCID mouse models. Here, we demonstrate that pulmonary delivery fundamentally reshapes the safety and protective efficacy of the ESAT-6-secreting rBCG strains, BCG::RD1 and BCG::ESAT6-PE25SS. In sharp contrast to intravenous delivery, pulmonary administration was markedly better tolerated, improved survival, and reduced systemic dissemination and brain pathology of severely immunocompromised mice. Strikingly, pulmonary rBCG vaccination also conferred superior protection against aerosol Mtb challenge in wild-type, type 2 diabetic, and adaptive immunity-deficient Rag1-/- and Rag2-/-Il2rg-/- mice, with BCG::RD1 showing the strongest adaptive immunity-independent protection. Mechanistically, pulmonary rBCG vaccination promoted lung innate immune activation, expansion of myeloid-biased progenitors in the bone marrow, and enhanced antimycobacterial activity of macrophages, consistent with trained innate immunity. Collectively, these findings reveal that pulmonary vaccination largely overcomes safety concerns of ESAT-6-secreting rBCG strains and provide preclinical evidence for a viable strategy to improve protection against TB in immunocompromised individuals.

immunology↗

Protein Language Models Outperform BLAST for Evolutionarily Distant Enzymes: A Systematic Benchmark of EC Number Prediction

Accurate prediction of Enzyme Commission (EC) numbers is foundational to genome annotation, metabolic reconstruction, and enzyme engineering. Protein language models (PLMs) have transformed protein function prediction, yet their systematic evaluation for EC number prediction across architectures, EC hierarchy levels, and sequence identity thresholds is lacking. Here we present a comprehensive benchmark of three PLMs (ESM2-650M, ESM2-3B, ProtT5-XL) combined with nine downstream neural architectures, evaluated across four EC hierarchy levels and four sequence identity thresholds with 1,296 trained models in total. Our results establish that simple MLP classifiers achieve 98.0% accuracy at EC1, 96.9% at EC2, 96.6% at EC3, and 97.0% at EC4, matching or marginally exceeding a train-set-matched BLASTp baseline ({+/-}0.7 pp) for in-distribution proteins. Crucially, PLM-based methods dramatically outperform BLAST for evolutionarily distant eukaryotes: gains reach +31.8 pp over a fair 90K-sequence BLAST baseline (Giardia lamblia) and +26.4 pp over a full 520K SwissProt database (Trichomonas vaginalis). For held-out prokaryotic proteomes, PLMs outperform BLAST by a mean of +16.9 pp at EC4. Our benchmark reveals that (i) MLP architectures are sufficient and consistently superior to CNN/ResNet/Transformer variants, (ii) ESM2-650M is statistically distinguishable from but practically equivalent to the 5x larger ESM2-3B, and (iii) Transformer re-encoding of PLM embeddings fails at a shared learning rate due to convergence instability. All code, models, and benchmark results are available at [https://github.com/r-mbio/plm_benchmark.git].

bioinformatics↗

A modular self-assembling and self-adjuvanting multiepitope peptide nanoparticle vaccine platform to improve the efficacy and immunogenicity of BCG

After more than a century since its initial development, Bacille Calmette-Guerin (BCG) remains the only licensed vaccine against tuberculosis (TB). Subunit boosters are considered a viable strategy to enhance BCG efficacy, which often wanes in adolescence. While many studies on booster subunit vaccines have concentrated on recombinant proteins, here we developed a novel modular peptide-based subunit vaccine platform that is flexible, cold-chain independent and customizable to diverse circumstances and populations. Each individual peptide building block consists of a linear arrangement comprising a 15-leucine self-assembly inducer moiety, a Mycobacterium tuberculosis (Mtb) target epitope and an HLA-E binding moiety, with each moiety separated by a triple lysine spacer. The building blocks, in any combination, were able to form a multiepitope nanoparticle. Six Mtb epitopes were selected to produce the self-assembling and self-adjuvanting peptide-based TB nano-vaccine candidate PNx6. In vivo vaccination-challenge experiments demonstrated that subcutaneous boost of parenteral BCG immunization with PNx6 significantly enhanced its immunogenicity and improved its protective efficacy in a murine model of TB by more than 5-fold. Our study present evidence that purely amphiphilic peptides self-assemble into self-adjuvanting nanoparticles with appropriate size and morphology for TB vaccination with great potential for a multitude of other diseases.

microbiology↗

Leishmania parasite arginine deprivation response pathway influences the host macrophage lysosomal arginine sensing machinery

Extensive interaction between the host and pathogen metabolic networks decidedly shapes the outcome of infection. Infection with Leishmania donovani, an intracellular protozoan parasite, leads to a competition for arginine between the host and the parasite. L. donovani transports arginine via a high-affinity transporter LdAAP3, encoded by the two genes LdAAP3.1 and LdAAP3.2. Earlier reports show that upon arginine starvation, cultured Leishmania parasites promptly activate an Arginine Deprivation Response (ADR) pathway, resulting in the stoichiometric up-regulation of LdAAP3.2 mRNA, protein and activity. Lysosomes, on the other hand, are known to employ a specific sensor and an arginine-activated amino acid transporter, solute carrier family 38 member 9 (SLC38A9) that monitors intra-lysosome arginine sufficiency and subsequently up-regulates cellular mTORkinase activity. The present study investigates the interaction between Leishmania and macrophage-lysosome arginine sensing machinery. We show that infection with L. donovani activates SLC38A9 arginine sensing in the human monocyte like-macrophage cell line (THP-1) when grown under physiological concentrations of arginine (0.1 mM). However, supplementing the macrophage growth medium with excess arginine (1.5 mM) followed by infection led to the down-regulation of SLC38A9. Similarly, THP-1 cells infected with LdAAP3.2 null mutants grown in 0.1 mM arginine resulted in reduced expression of SLC38A9 and mTOR. These results indicate that inside the host macrophage, Leishmania overcome low arginine levels by up-regulating the transport of arginine via LdAAP3 and SLC38A9 signalling. Furthermore, while LdAAP3.2 null mutants were impaired in their ability to develop inside THP-1 macrophages, their infectivity and intracellular growth were restored in SLC38A9 silenced macrophages. This study provides the first identification of regulatory role of SLC38A9 in the expression and role of LdAAP3. Author SummaryLeishmania donovani, the causative agent of kala-azar, exhibits a digenetic life cycle. Following infection of the mammalian host, promastigotes differentiate into intracellular amastigotes within the phagolysosome of macrophages. Arginine is a central point of competition between the host and the pathogen. L. donovani senses lack of arginine in the surrounding micro-environment and activates a unique ADR pathway, thus upregulating the expression of the arginine transporter (LdAAP3). The arginine-activated amino acid transporter SLC38A9 localizes to the lysosome surface of mammalian cells and acts as a sensor that transmits information about arginine levels in the lysosome lumen to the mechanistic target of rapamycin (mTOR) kinase. In the present study, we identified the functional interaction of host SLC38A9 and parasite LdAAP3 in macrophages infected with L. donovani. We report that host SLC38A9 upregulation is critical for enhancing and maintaining high LdAAP3 levels in intracellular L. donovani. Our results decode crucial information regarding the molecular mechanism involved in the arginine sensing response in L. donovani-infected host cells. These findings increase our understanding of the interaction of signalling intermediates during Leishmania infection which may lead to the discovery of novel therapeutic interventions.

molecular biology↗

The hunger games: sensing host arginine is essential for Leishmania parasite virulence

Arginine homeostasis in lysosomes is critical for growth and metabolism of mammalian cells. They employ a specific sensor (SLC38A9) that monitors intra-lysosome arginine sufficiency and subsequently up-regulates cellular mTORC1 activity. Lysosomes of macrophages (phagolysosomes) are the niche where the parasitic protozoan Leishmania resides and causes important human disease. Several years ago, we discovered that upon arginine starvation, cultured Leishmania parasites promptly activate a MAPK2-mediated Arginine Deprivation Response (ADR) pathway, resulting in up-regulation of the Leishmania arginine transporter (AAP3), as well as a small group of other transporters. Significantly, ADR is also activated during macrophage infection, implying that the intracellular parasite actively depletes arginine within the host phagolysosome, likely to prevent mTORC1 activation and enhance intracellular development. We hypothesize that ADR-mediated up-regulation of AAP3 activity is necessary to withstand the resultant arginine starvation. Both copies of the AAP3 genes are located (in tandem) on a tetrasomic chromosome (chr31), but only one (AAP3.2) is responsive to arginine deprivation. CRISPR/Cas9-mediated disruption of the AAP3 locus yielded mutants that retain a basal level of arginine transport (mediated by AAP3.1), but lack a functional copy of AAP3.2 and are therefore not responsive to arginine starvation. While these mutants grow normally in culture as promastigotes, they were impaired in their ability to develop inside THP1 macrophages grown under physiological concentrations of arginine (0.1 mM). However, flooding the macrophage growth medium with arginine (1.5 mM) restored parasite infectivity and intracellular growth to that of wild type. The results indicate that inside the host macrophage, Leishmania must overcome the arginine \"Hunger Games\" by up-regulating transport of arginine via the ADR. Furthermore, the AAP3.2 mutants were ~70-80% less virulent in Balb/C mice, showing, for the first time, that the ability to monitor and respond to changes in host metabolite levels is essential for pathogenesis.

cell biology↗