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Sharma, P.

Publications and source records attributed to Sharma, P..

At least 55 records · Page 3Linked to original sources

Macrophage-Dendritic Cell-T-Cell Tetrads Orchestrate Antitumor Immunity and Response to Checkpoint Blockade

Immune checkpoint inhibitors (ICIs) elicit durable responses in only a subset of patients with solid tumors, underscoring the need to define the cellular architectures that govern effective antitumor immunity. Here we identify a spatially organized multicellular immune unit comprising macrophages, cDC1s, CD4 T-cells, and CD8 T-cells that emerges in response to anti-CTLA-4 or dual checkpoint blockade. We term these structures tetrads. Using multiplexed imaging and spatial transcriptomics in mouse and human tumors, we show that tetrads assemble early during immune priming, depend on the ICOS-ICOSL pathway, and are enriched for ICOS Th1-like CD4 T cells and ICOSLhigh cDC1s. CD8 T-cells within tetrads exhibit an activated, non-terminally differentiated state, while tetrad-associated macrophages display an interferon-{gamma}-responsive program that sustains CD8 T-cell function and prevents dysfunction. Functionally, ICOSL cDC1s are required for tumor eradication in vivo. In patients with bladder cancer treated with neoadjuvant dual checkpoint blockade, tetrad, but not triad or dyad formation correlates with clinical response. These findings establish tetrads as a fundamental cellular unit coordinating antitumor immunity and responsiveness to ICIs.

immunology↗

A dietary pan-amino acid dropout screen in vivo reveals a critical role for histidine in T-ALL

Dietary interventions show therapeutic potential in cancer, but systematic comparisons are lacking. We performed a dietary pan-amino acid dropout screen in an orthotopic model of NOTCH1-driven T-cell acute lymphoblastic leukemia and identified histidine depletion as uniquely antileukemic. Histidine-restricted diets extended survival of leukemic mice in a dose-dependent manner, while remaining well-tolerated. Mechanistically, multiomic profiling revealed that histidine deprivation-induced ribosome stalling activates GCN2 to suppress cholesterol biosynthesis pathways critical for leukemic proliferation. Dietary cholesterol supplementation partially reverted the antileukemic effects of histidine restriction in vivo. These findings couple histidine levels and translational control to cholesterol metabolism, which can be therapeutically exploited for cancer treatment. Our results suggest that defined dietary amino acid restrictions may expose broader therapeutic opportunities in diseases beyond cancer.

cancer biology↗

The pharmacokinetics, bio-distribution and therapeutic efficacy of a trimeric nanobody against SARS-CoV-2 in the Syrian golden hamster COVID-19 model

The rapid emergence of SARS-CoV-2 prompted the development of anti-viral therapies and vaccines to combat the COVID-19 pandemic. The continuous emergence of variants of concern has necessitated the development of platforms that can be rapidly adapted. Nanobodies, offer advantages over conventional monoclonal antibodies, including low molecular weight, high antigen-binding affinity, enhanced tissue penetration, blood-brain barrier permeability, and simplified production. Previous studies have demonstrated the efficacy of nanobodies against respiratory viruses such as SARS-CoV-2, respiratory syncytial virus, and influenza A virus in animal models. We previously reported the protective effects of nanobody trimers against SARS-CoV-2. However, pharmacokinetic and biodistribution data for nanobodies remain limited. To address this, we evaluated the efficacy, biodistribution and longevity of action of a nanobody trimer (A8) administered intranasally (IN) or intraperitoneally (IP) in Syrian golden hamsters. Our findings revealed that the A8 trimer reached peak concentrations shortly after administration and was subsequently cleared from the system via both routes. Importantly, early administration of A8 trimer reduced virus mediated weight loss and viral load compared with untreated controls supporting its potential as a therapeutic candidate for SARS-CoV-2 infection.

microbiology↗

Alginate Nanohydroxyapatite Composite for Dental Tissue Engineering Application.

Traumatic dental tissue injury is a common health concern globally, with more than a billion people affected worldwide. In this study, we have synthesized green route nanohydroxyapatite utilizing green tea extract, which further enhances the osteogenesis, osteointegration, and biocompatibility of the synthesized hydroxyapatite. This Nanohydroxyapatite was capped with an antibiotic, integrated into an alginate scaffold, and coated with a painkiller to create a dual drug release system, providing rapid release of painkiller and sustained release of antibacterial drug. Biocompatibility and osteoblast proliferation were confirmed through MTT assays, and osteogenesis by ALP activity, validating the suitability of the scaffold for dental bone tissue engineering applications. The developed nanocomposite scaffold shows significant promise in enhancing dental bone repair by simultaneously addressing the inflammation, infection, and regeneration challenges. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=129 SRC="FIGDIR/small/693830v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@124b53forg.highwire.dtl.DTLVardef@f75868org.highwire.dtl.DTLVardef@cd20a6org.highwire.dtl.DTLVardef@11a7dfb_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

Modeling patient tissues at molecular resolution with Eva

Tissue structure is essential to function and homeostasis in all organs, and disruptions to structure usually indicate disease. Modeling relationships between structural, molecular, and clinical aspects of tissues could advance new diagnostics and treatment strategies. Although profiling techniques like spatial proteomics can capture these relationships, the data remain challenging to extract insight from. Here, we present Eva, a foundation model for tissue imaging data that learns multi-scale spatial representations of tissues at the molecular, cellular, and sample level. Eva uses a novel vision transformer architecture and is pre-trained on masked reconstruction of over 40 million matched spatial proteomics and histopathology images. We show that Eva excels at a variety of tasks, including cross-modal inference from H&E to proteomics stains, quality control, data annotation, zero-shot retrieval, survival modeling, and patient stratification. Extensive evaluations on held-out validation data demonstrate the versatility and generalizability of the learned embeddings. We anticipate that Eva will accelerate translational science by bridging basic research and clinical practice.

bioinformatics↗

A non-canonical MPK3-ACTPK1-RbcS signalling module fine-tunes photosynthesis in rice

Chloroplast protein import is essential for photosynthesis, yet whether and how cytosolic signaling pathways dynamically regulate this process remains largely unknown. Here we uncover a signaling module that links mitogen activated protein kinase (MAPK) activity to fine tune the import of small subunit of Rubisco (RbcS) into the chloroplast. We show that MPK3 negatively regulates the cytosolic Raf-like kinase ACTPK1, which directly phosphorylates the transit peptide of RbcS precursor at Thr12. MPK3 directly phosphorylates ACTPK1, attenuating its kinase activity and thereby limiting RbcS transit peptide phosphorylation. Genetic and physiological analyses demonstrate that loss of MPK3 elevates ACTPK1 activity, increases RbcS phosphorylation and enhances Rubisco accumulation and CO2 assimilation. On the other hand, ACTPK1 deficiency compromises these processes and photosynthetic performance. Phospho-mutant analyses further reveal that reversible phosphorylation of the RbcS transit peptide is required for efficient chloroplast import. Together, our findings establish chloroplast protein import as a signaling-regulated process and identify transit peptide phosphorylation a key check point integrating cytosolic MAPK signaling with photosynthetic capacity.

plant biology↗

Putative azithromycin-resistance mutations in Chlamydia trachomatis are globally distributed but arose before azithromycin was discovered

Azithromycin is widely used to treat Chlamydia trachomatis infections, yet the extent of resistance to the drug across the species has not been addressed. We surveyed mutations and substitutions linked to putative azithromycin resistance across 1,354 high-quality C. trachomatis genomes. Mutations in the rplV gene encoding three non-synonymous substitutions, compared to the canonical C. trachomatis reference strain D//TW-3/Cx sequence, were found to be common but largely conserved within lineages causing prevalent urogenital and anorectal infections and lymphogranuloma venereum (LGV). Time-scaled phylogenetic analysis suggested that these mutations predate the clinical introduction of azithromycin. In contrast, no consistent resistance-associated patterns were observed in 23S rRNA or rplD genes. This large-scale genomic surveillance provides critical insights into the evolutionary trends of putative azithromycin resistance in C. trachomatis and underscores the importance of integrating genomic monitoring with phenotypic susceptibility testing to accurately assess and manage antimicrobial resistance.

genomics↗

Cdh-2 modulates tissue stiffness and cortical F-actin distribution in neuroepithelial cells to drive forebrain roof plate invagination.

The invagination of the dorsal forebrain roof plate is critical for cerebral hemisphere formation. Although mutations in several genes have been linked to holoprosencephaly (HPE), and studies in chick embryos have implicated key signaling pathways, the mechanisms by which mechanical forces drive roof plate invagination remain poorly understood. To address this gap, we employed atomic force microscopy to map the spatiotemporal changes in tissue stiffness across the dorsal forebrain in the chick embryo during roof plate invagination. Our analysis revealed that neuroepithelium that is uniformly stiff initially, undergoes dramatic remodelling during this period of morphological change. Ultimately a pronounced stiffness gradient emerges, with the roof plate midline becoming markedly more compliant than the dorsolateral regions. Through expression screening, we identified Cdh2 as a candidate molecular regulator, whose spatiotemporal expression pattern closely mirrors the observed stiffness gradient. Mechanistically, we found that the interplay between Cdh2 and F-actin modulates tissue stiffness by regulating Cdh2 expression levels, apical adherens junction stability, and cortical F-actin distribution along the apico-basal axis of neuroepithelial cells. These findings underscore the importance of apico-basal localization of Cdh2 and provide critical insights into the mechanical forces and molecular interactions that govern forebrain roof plate morphogenesis, while also shedding light on the pathogenesis of HPE.

developmental biology↗

Epigenetic Reprogramming of Host Chromatin by the Transforming Parasite Theileria annulata

Theileria annulata, a transforming apicomplexan parasite, extensively reprograms the chromatin architecture of bovine leukocytes to facilitate infection and cellular transformation. To elucidate the underlying epigenetic mechanisms, we characterized the chromatin landscape of infected lymphocytes using integrated proteomic, imaging, and functional assays. Our findings reveal that T. annulata lacks the DNA damage marker {gamma}H2A.X and its associated SQ/TQ motif, indicating an evolutionary divergence from canonical DNA repair signalling pathways. High-resolution profiling of histone post-translational modifications (PTMs) demonstrated distinct nuclear compartmentalization, with host (H3K27me3, H3K9me1/2), parasite-predominant modifications (H3K4me3, H3K18me1, H3K27ac, H3K9ac, and H3K36me3), and shared modifications (e.g., H3K4me1/2, H3K36me2, H4K5/8/12/16ac, H3K9me3 and H4K91Ac) suggesting a coordinated epigenetic strategy driving host cell programs to sustain proliferation and survival. Our study delineates a novel host-parasite epigenetic interface, positioning T. annulata as a unique model of epigenetic parasitism. By bridging parasitology and cancer epigenetics, these findings unveil new therapeutic opportunities targeting chromatin vulnerabilities in parasite-induced transformation. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=106 SRC="FIGDIR/small/684985v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@1bd0e05org.highwire.dtl.DTLVardef@e37ea4org.highwire.dtl.DTLVardef@18f78d5org.highwire.dtl.DTLVardef@460eb4_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

Commensal Escherichia coli colonization triggers Peyer's patch development

The gut microbiota plays a pivotal role in shaping mucosal immunity, yet the specific microbes contributing to lymphoid tissue development remain poorly defined. Here, we identify Escherichia coli, a pioneer commensal bacterium, as a key driver of naive B cell accumulation in gut Peyers patches and lamina propria via a CXCR2-dependent mechanism. We show that E. coli promotes B cell recruitment through the production of curli amyloid fibers, which signal via Toll-like receptor 2 (TLR2). Notably, this effect extends beyond the neonatal period, revealing a broader temporal window for microbial modulation of mucosal immune development. These findings reveal a previously unrecognized role for a defined gut commensal bacterium and its molecular products in orchestrating the formation of gut-associated lymphoid tissue and B cell recruitment.

microbiology↗

Investigation of anti-SARS CoV-2 multimeric bicyclic peptide inhibitors in a range of pre-clinical therapeutic settings

The spread of respiratory viruses, such as Influenza and SARS-CoV-2 has presented significant challenges over the last 30 years with few effective therapeutic options available to this day. Bi-cyclic peptides represent a unique, modular, modality in the antiviral armamentarium against future pandemics. This study provides a deeper evaluation of multivalent bi-cyclic (Bicycle(R)) molecule efficacy in several preclinical SARS-CoV-2 challenge settings. We explore both pre-exposure prophylaxis and post-exposure therapeutic settings via subcutaneous and intranasal routes of administration. We contextualize this further in bespoke scenarios of immune compromisation, and viral transmission. Promisingly, in all studies we observe efficacy, significantly reducing infectious viral burden at each study endpoint. These data further support candidacy of Bicycle molecules as a differentiated antiviral therapeutic class in the context of pandemic preparedness. ImportanceThe COVID-19 pandemic, triggered a rapid wave of innovation, accelerating the delivery of new vaccine technology and anti-viral treatments. In our first paper, we described the discovery and molecular optimization of Bicycle molecules as a novel drug class for the potential treatment of SARS CoV-2. Here, we have performed deeper characterization of these molecules in established animal models that simulate SARS-CoV-2 transmission, testing more convenient delivery routes, such as intra-nasal. The Bicycle molecules demonstrated positive outcomes in each of these studies and suggest that Bicycle molecules, as convenient and effective anti-viral treatments, could be an important addition to help future preparedness against new viral pandemics.

pharmacology and toxicology↗

Proteomic Insights into Strong and Weak Biofilm Formation in Acinetobacter baumannii for Potential Therapeutic Targets

Acinetobacter baumannii is notable for its biofilm-forming abilities, which aid in its tolerance to antibiotics, adding to antimicrobial resistance. The clinical isolates present varied biofilm-forming capacity; hence, understanding the molecular determinants that result in strong biofilm development is crucial for drug target identification. This study is the first of its kind to compare proteome profiling of strong and weak biofilm-forming A. baumannii clinical isolates. Comparative proteomic profiling revealed 42 differentially regulated proteins. It was observed that in strong biofilm forming isolate NlpA, uL16, DNA gyrase B, acetyl-CoA carboxylase, and purl etc. were upregulated highlighting a dynamic reprogramming of cellular functions that promotes biofilm formation, stress adaptation, and immune evasion. In contrast, EF-Tu, ribosome hibernation factors, and T6SS components were downregulated, suggesting a lack of biosynthesis and stress adaptability. These findings suggest a metabolic downshift and a possible energy conservation mechanism under conditions less favorable for strong biofilm development. Additionally, several uncharacterized proteins were identified, highlighting potential novel factors in biofilm regulation and virulence that warrant further investigation. The proteomics data correlated with qPCR findings, providing support for the unknown regulators of biofilm formation that were identified in this study. Key proteins such as nlpA, 6,7-dimethyl-8-ribityllumazine synthase and DNA gyrase B emerged as potential therapeutic targets. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/680171v1_ufig1.gif" ALT="Figure 1"> View larger version (56K): org.highwire.dtl.DTLVardef@1c9b95aorg.highwire.dtl.DTLVardef@a7e781org.highwire.dtl.DTLVardef@14fe64aorg.highwire.dtl.DTLVardef@9804f2_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO C_FIG

microbiology↗

ALM enables contextual decision-making via dynamic reconfiguration of local circuits

Cognitive operations often require flexible implementation of stimulus-response contingencies, depending on context. We developed an olfactory task in which mice learned to associate a test odor with a directional lick response, conditional on a preceding context odor drawn from a different odor set. Two-photon imaging revealed that anterior lateral motor cortex (ALM) contains distinct populations encoding context, test odors, and choice. Optogenetic silencing during the context and delay periods impaired performance, suggesting that ALM contributes to configuring the appropriate contingency. Although context odors that instructed the same mapping were represented by separate populations, their influence converged at the level of choice-selective neurons. A subpopulation of these neurons exhibited dual selectivity for context and choice, forming what we term "contingency neurons." These findings suggest that ALM supports flexible behavior not by abstracting over context cues, but by dynamically reconfiguring local circuits to route sensory input to the appropriate motor output.

neuroscience↗

NRF2 upregulation by CDDO-Me protects AC16 human cardiomyocytes against doxorubicin-induced toxicity.

Doxorubicin (DOX) is an effective anticancer therapeutic but exhibits dose-dependent, potentially life-threatening cardiotoxicity. The specific mechanisms driving this cardiotoxicity are not fully understood but can include the induction of oxidative stress and subsequent cell death mechanism activation. This has prompted the exploration of NRF2, a master co-ordinator of antioxidant and largely cytoprotective pathways, as a potential approach for the alleviation of DOX-induced cardiotoxicity. Here, NRF2 was pharmacologically activated via CDDO-Me (hitherto referred to as CDDO) to reduce the negative consequences on AC16 human cardiomyocyte cell health and functions. NRF2 intracellular dynamics were quantitatively measured using live-cell imaging, demonstrating rapid ([~]10 min) yet sustained ([≥]24 h) induction of NRF2 expression and functional downstream activity. Genetic perturbations of the NRF2-KEAP1 system highlight that CDDO acts specifically through NRF2 to exert AC16 cytoprotection from DOX whilst not promoting human lung and pancreatic cancer cell line viability. Via RNA-seq analysis, we reveal that CDDO dampens DOX-mediated effects on p53 signalling, apoptosis and ferroptosis. This study provides novel insight into NRF2 dynamics in the widely utilised AC16 cells whilst further elucidating the molecular mechanisms contributing to DOX cardiotoxicity and potential NRF2-orchestrated defence. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=106 SRC="FIGDIR/small/675420v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@18c0bb5org.highwire.dtl.DTLVardef@154c707org.highwire.dtl.DTLVardef@d6c127org.highwire.dtl.DTLVardef@122ef0d_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

Sequential sampling from memory underlies perceptual decisions unyoked from actions

Perceptual decision-making refers to the class of decisions in which sensory evidence is used to categorize percepts and guide actions. Conventionally, categorical decisions are thought to precede motor actions. However, recent studies in nonhuman primates challenge this assumption -- when perceptual decisions were uncoupled from the actions they bear upon, animals postponed the decisions until relevant response options were revealed. To determine whether this postponement stems from cognitive limitations unique to nonhuman primates, we conducted a similar experiment with human subjects. Naive subjects viewed a random-dot motion (RDM) stimulus that was difficult to categorize. After a delay period following the RDM, two choice targets were presented and subjects decided which target lay closer to the perceived motion direction. Decision accuracy varied across subjects, reflecting individual differences in ability to integrate motion evidence. Notably, subjects with higher decision accuracy showed prolonged deliberation after choice-target presentation. Furthermore, the time they took to report their decisions depended on the strength of the motion evidence. This pattern of accuracy and decision reporting time could be accounted for by a bounded diffusion model in which subjects sequentially sample stored sensory information from memory during the target selection phase. When the RDM was challenging to categorize, the subsequent appearance of the targets provided a framework to interrogate stored evidence and render a decision. Our results reveal a strategic feature of working memory of retaining information based on its future utility. This observation opens new avenues for investigating how memory and decision-making interact.

neuroscience↗

Plasmodium ARK1 regulates spindle formation during atypical mitosis and forms a divergent chromosomal passenger complex

Mitosis in Plasmodium spp., the causative agent of malaria, is fundamentally different from model eukaryotes, proceeding via a bipartite microtubule organising centre (MTOC) and lacking canonical regulators such as Polo kinases. During schizogony, asynchronous nuclear replication produces a multinucleate schizont, while rapid male gametogony generates an octaploid nucleus before gamete formation. Here, we identify Aurora-related kinase 1 (ARK1) as a key component of inner MTOC and spindle formation, controlling kinetochore dynamics and driving mitotic progression. Conditional ARK1 depletion disrupts spindle biogenesis, kinetochore segregation, karyokinesis and cytokinesis in both stages, and affects parasite transmission. Interactome analysis shows that ARK1 forms the catalytic core of a non-canonical chromosomal passenger complex (CPC) containing two highly divergent inner centromere proteins (INCENPs), which we term INCENP-A and INCENP-B, and lacking the canonical chromatin-targeting subunits Survivin and Borealin. Comparative genomics suggests that apicomplexan INCENPs arose through recurrent lineage-specific duplications, reflecting an evolutionary rewiring of CPC architecture in this eukaryotic lineage. Together, these findings reveal key adaptations in Plasmodium mitosis involving ARK1 and its INCENP scaffolds, and identify the ARK1-INCENP interface as a potential multistage target for antimalarial intervention.

microbiology↗

Hypoxia inducible factors regulate Pneumovirus replication by enhancing innate immune sensing

The immune mechanisms responsible for protection and pathogenesis in pneumoviral infection are not well defined. We demonstrated that pharmacological activation of the hypoxic inducible factor (HIF) signalling axis using Daprodustat limited viral replication through enhanced immune signalling. Transcriptomic analysis revealed HIF augmented activation of innate immune response genes, including interferon-stimulated gene 15 (Isg15), in the lung and spleen of mice infected with pneumonia virus of mice (PVM). In human respiratory syncytial virus (hRSV) infected airway epithelial cells, Daprodustat inhibited viral replication and enhanced ISG15 expression in a HIF-dependent manner. Importantly, inhibition of type I interferon signalling or the RIG-I sensing pathway abrogated the antiviral activity of HIF. Moreover, Daprodustat increased interferon signalling in response to viral RNA, suggesting that HIF inhibits pneumovirus replication through enhancing viral RNA sensing. Mechanistically, Daprodustat reduced N6-methyladenosine modification of viral RNA through upregulation of RNA demethylases, promoting detection by innate immune sensors. This study highlights the intricate interplay between hypoxia and antiviral immunity and offers valuable insights into pneumovirus-host interactions and potential therapeutic interventions. SIGNIFICANCE STATEMENTThis study explores the role of the hypoxic inducible factor (HIF) signalling pathway in limiting pneumoviral infections, such as respiratory syncytial virus (hRSV) and pneumonia virus of mice (PVM). Using Daprodustat, a clinically approved activator of HIF signalling we demonstrated that stimulation of this pathway enhanced innate immune signalling and limited viral replication. Transcriptomic analysis showed that HIF promoted innate immune response genes in mice infected with PVM and human airway epithelial cells infected with hRSV. Importantly, inhibition of type I interferon signalling or the RIG-I sensing pathway abrogated the antiviral activity of HIF. We uncovered a role for HIF to regulate the levels of N6-methyladenosine modification of viral RNA transcripts, resulting in the increased activation of nucleic acid sensing.

microbiology↗

Polyamines buffer labile iron to suppress ferroptosis

Polyamines are essential and evolutionarily conserved metabolites present at millimolar concentrations in mammalian cells. Cells tightly regulate polyamine homeostasis through complex feedback mechanisms, yet the precise role necessitating this regulation remains unclear. Here, we show that polyamines contribute to endogenous buffering of redox-active iron, providing a molecular link between polyamine metabolism and ferroptosis. Using a genome-wide CRISPR screen, we identified a synthetic lethal dependency between polyamine depletion and the key ferroptosis suppressor, GPX4. Mechanistically, we show that polyamine deficiency triggers a redistribution of cellular iron, increasing the labile iron pool and upregulating ferritin. To directly visualize this iron buffering in living cells, we developed a genetically encoded fluorescent reporter for redox-active iron. Live-cell analysis revealed a striking inverse correlation between intracellular polyamine levels and redox-active iron at single-cell resolution. These findings reposition polyamines as key regulators of iron homeostasis, with implications for ferroptosis-linked disease states and cellular redox balance.

cell biology↗