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Joshi, S.

Publications and source records attributed to Joshi, S..

At least 73 records · Page 4Linked to original sources

ALCAM-mediated synapses between DC1 and CD8 T cells are inhibited in advanced lung tumors

Conventional type 1 dendritic cells (DC1) control anti-tumoral CD8 T responses, in lymph nodes and tumor tissues. T-cell activation depends on the establishment of a tight physical interaction with antigen-presenting cell, the immunological synapse (IS). The molecular determinants of DC1-CD8 IS in tumor tissues and how they are regulated during cancer progression remain poorly investigated. Using a reporter for DC1 in a genetic model of non-small cell lung cancer (KP-XCR1venus) we show that IS in lung tissues are abundant and productive at early stages of tumor development but progressively diminish in advanced tumors. Transcriptional profiling and flow cytometry of lung resident DC1 identified a module of adhesion molecules downregulated in advanced tumors. We focused on ALCAM and LFA-1, ligands for CD6 and ICAM-1 on T cells, to investigate their role and functional impact. By immobilizing single receptor agonists on artificial cell surfaces, we demonstrate that ALCAM and LFA-1 are sufficient to trigger cytoskeletal remodeling in early tumor DC1, whereas late tumors DC1 are not responsive. Blocking ALCAM-CD6 interactions in functional assays impairs the acquisition of effector functions in CD8 T cells. Together these data highlight that adhesion molecules required to establish IS in early, immune-reactive, tumors are targeted during tumor progression blunting cross-talk within the IS.

immunology↗

Tim4 enables large peritoneal macrophages to cross-present tumor antigens at early stages of tumorigenesis

Cross-presentation of tumor antigens by subsets of macrophages at different stages along tumor progression may have divergent impacts on anti-tumoral immune responses. Here we show that TIM4+ large peritoneal macrophages (LPM) avidly capture tumor cells and cross-present tumor-associated antigens at early stages of peritoneal infiltration by ovarian cancer cells. The phosphatidylserine (PS) receptor TIM4 promotes maximal uptake and triggers inflammatory and metabolic gene programs in combination with cytoskeletal remodeling and upregulation of transcriptional signatures related to antigen processing. At the cellular levels, TIM4 is recruited with F-actin at the phagocytic cup and translocates in nascent phagosomes, controlling the kinetic of phagosomal acidification and cargo degradation. TIM4 deletion abrogates cross-presentation of tumor-associated antigens and blunts expansion of effector CD8 T cells at tumor inception. In addition, targeting tumor antigens to LPM by PS liposomes can trigger CD8 T cell activation. Together these results suggest that TIM4 enables LPMs to scan the antigenic content of incoming tumor cells to promote immune surveillance by CD8 T cells and, at defined temporal windows, may be exploited for therapeutic purposes.

immunology↗

Progesterone receptor activation regulates sensory sensitivity

Women develop chronic pain during their reproductive years more often than men, and estrogen and progesterone regulate this susceptibility. We tested whether brain progesterone receptor (PR) signaling regulates pain susceptibility. During the estrous cycle, animals were more sensitive to pain during the estrus stage than in the diestrus stage, suggesting a role for reproductive hormones, estrogen, and progesterone. We measured the pain threshold daily for four days in ovariectomized, estrogen-primed animals treated with progesterone. The pain threshold was lower 2 days later and stayed that way for the duration of the testing. A specific progesterone-receptor (PR) agonist, segesterone, promoted pain, and mice lacking PR in the brain (PRKO) did not experience lowered pain threshold when treated with progesterone or segesterone. PR activation increased the cold sensitivity but did not affect the heat sensitivity and had a small effect on light sensitivity. Finally, we evaluated whether PR activation altered experimental migraine. Segesterone and nitroglycerin (NTG) when administered sequentially, reduced pain threshold but not separately. These studies have uncovered a pain-regulating function of PRs. Targeting PRs may provide a novel therapeutic avenue to treat chronic pain in women.

neuroscience↗

Does enforcing glenohumeral joint stability matter? A new rapid muscle redundancy solver highlights the importance of non-superficial shoulder muscles

The complexity of the human shoulder girdle enables the large mobility of the upper extremity, but also introduces instability of the glenohumeral (GH) joint. Shoulder movements are generated by coordinating large superficial and deeper stabilizing muscles spanning numerous degrees-of-freedom. How shoulder muscles are coordinated to stabilize the movement of the GH joint remains widely unknown. Musculoskeletal simulations are powerful tools to gain insights into the actions of individual muscles and particularly of those that are difficult to measure. In this study, we analyze how enforcement of GH joint stability in a musculoskeletal model affects the estimates of individual muscle activity during shoulder movements. To estimate both muscle activity and GH stability from recorded shoulder movements, we developed a Rapid Muscle Redundancy (RMR) solver to include constraints on joint reaction forces (JRFs) from a musculoskeletal model. The RMR solver yields muscle activations and joint forces by minimizing the weighted sum of squared-activations, while matching experimental motion. We implemented three new features: first, computed muscle forces include active and passive fiber contributions; second, muscle activation rates are enforced to be physiological, and third, JRFs are efficiently formulated as linear functions of activations. Muscle activity from the RMR solver without GH stability was not different from the computed muscle control (CMC) algorithm and electromyography of superficial muscles. The efficiency of the solver enabled us to test 3600 trials sampled within the uncertainty of the experimental movements to test the differences in muscle activity with and without GH joint stability enforced. We found that enforcing GH stability significantly increases the estimated activity of the rotator cuff muscles but not of most superficial muscles. Therefore, a comparison of shoulder model muscle activity to EMG measurements of superficial muscles alone is insufficient to validate the activity of rotator cuff muscles estimated from musculoskeletal models.

systems biology↗

Platelet-Localized ST6Gal1 Does Not Impact IgG Sialylation

The IgG antibody class forms an important basis of the humoral immune response, conferring reciprocal protection from both pathogens and autoimmunity. IgG function is determined by the IgG subclass, as defined by the heavy chain, as well as the glycan composition at N297, the conserved site of N-glycosylation within the Fc domain. For example, lack of core fucose promotes increased antibody-dependent cellular cytotoxicity, whereas 2,6-linked sialylation by the enzyme ST6Gal1 helps to drive immune quiescence. Despite the immunological significance of these carbohydrates, little is known about how IgG glycan composition is regulated. We previously reported that mice with ST6Gal1-deficient B cells have unaltered IgG sialylation. Likewise, ST6Gal1 released into the plasma by hepatocytes does not significantly impact overall IgG sialylation. Since IgG and ST6Gal1 have independently been shown to exist in platelet granules, it was possible that platelet granules could serve as a B cell-extrinsic site for IgG sialylation. To address this hypothesis, we used a platelet factor 4 (Pf4)-Cre mouse to delete ST6Gal1 in megakaryocytes and platelets alone or in combination with an albumin-Cre mouse to also remove it from hepatocytes and the plasma. The resulting mouse strains were viable and had no overt pathological phenotype. We also found that despite targeted ablation of ST6Gal1, no change in IgG sialylation was apparent. Together with our prior findings, we can conclude that in mice, neither B cells, the plasma, nor platelets have a substantial role in homeostatic IgG sialylation.

immunology↗

Cell Type-Specific Regulation by a Heptad of Transcription Factors in Human Hematopoietic Stem and Progenitor Cells

Hematopoietic stem and progenitor cells (HSPCs) rely on a complex interplay of transcription factors (TFs) to regulate differentiation into mature blood cells. A heptad of TFs - FLI1, ERG, GATA2, RUNX1, TAL1, LYL1, LMO2 - bind regulatory elements in bulk CD34+ HSPCs. However, whether specific heptad-TF combinations have distinct roles in regulating hematopoietic differentiation remained unknown. We mapped genome-wide chromatin contacts and TF binding profiles in HSPC subsets (HSC, CMP, GMP, MEP) and found that heptad occupancy and enhancer-promoter interactions varied significantly across cell types and were associated with cell-type-specific gene expression. Distinct regulatory elements were enriched with specific heptad-TF combinations, including stem-cell-specific elements with ERG, and myeloid- and erythroid-specific elements with combinations of FLI1, RUNX1, GATA2, TAL1, LYL1, and LMO2. These findings suggest that specific heptad-TF combinations play critical roles in regulating hematopoietic differentiation and provide a valuable resource for development of targeted therapies to manipulate specific HSPC subsets.

developmental biology↗

Divergent phenotypes in germline versus conditional mutant mouse models of Sifrim-Hitz- Weiss Syndrome

Chromatin remodellers are among the most important risk genes associated with neurodevelopmental disorders (NDDs), however, their functions during brain development are not fully understood. Here, we focused on Sifrim-Hitz-Weiss Syndrome (SIHIWES) - a brain overgrowth/intellectual disability disorder caused by mutations in the CHD4 chromodomain helicase gene. We utilized mouse genetics to excise the Chd4 ATPase/helicase domain - either in the germline, or conditionally in the developing telencephalon. Conditional heterozygotes exhibited little change in cortical size and cellular composition, and had only subtle behavioral phenotypes. Telencephalon-specific conditional knockouts had marked reductions in cortical growth, reduced numbers of upper-layer neurons, and exhibited alterations in anxiety and repetitive behaviors. Despite the fact that germline heterozygotes exhibited comparable growth defects, they were unaffected in these behaviors, but instead exhibited female-specific alterations in learning and memory. These data reveal unexpected phenotypic divergence arising from differences in the spatiotemporal deployment of loss-of-function manipulations, underscoring the importance of context in chromatin remodeller function during neurodevelopment. Graphical Abstract. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=90 SRC="FIGDIR/small/528754v1_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@ffdb72org.highwire.dtl.DTLVardef@1a0231corg.highwire.dtl.DTLVardef@613242org.highwire.dtl.DTLVardef@12ac3ab_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

A new microphysiological system shows hypoxia primes human ISCs for interleukin-dependent rescue of stem cell activity

Background & AimsHypoxia in the intestinal epithelium can be caused by acute ischemic events or conditions like Inflammatory Bowel Disease (IBD) where immune cell infiltration produces inflammatory hypoxia, a chronic condition that starves the mucosa of oxygen. Epithelial regeneration after ischemia and IBD suggests intestinal stem cells (ISCs) are highly tolerant to acute and chronic hypoxia; however, the impact of acute and chronic hypoxia on human ISC (hISC) properties have not been reported. Here we present a new microphysiological system (MPS) to investigate how hypoxia affects hISCs isolated from healthy human tissues. We then test the hypothesis that some inflammation-associated interleukins protect hISCs during prolonged hypoxia. MethodshISCs were exposed to <1.0% oxygen in the MPS for 6-, 24-, 48- & 72hrs. Viability, HIF1 response, transcriptomics, cell cycle dynamics, and hISC response to cytokines were evaluated. ResultsThe novel MPS enables precise, real-time control and monitoring of oxygen levels at the cell surface. Under hypoxia, hISCs remain viable until 72hrs and exhibit peak HIF1 at 24hrs. hISCs lose stem cell activity at 24hrs that recovers at 48hrs of hypoxia. Hypoxia increases the proportion of hISCs in G1 and regulates hISC capacity to respond to multiple inflammatory signals. Hypoxia induces hISCs to upregulate many interleukin receptors and hISCs demonstrate hypoxia-dependent cell cycle regulation and increased organoid forming efficiency when treated with specific interleukins ConclusionsHypoxia primes hISCs to respond differently to interleukins than hISCs in normoxia through a transcriptional response. hISCs slow cell cycle progression and increase hISC activity when treated with hypoxia and specific interleukins. These findings have important implications for epithelial regeneration in the gut during inflammatory events.

cell biology↗

Broad-spectrum antiviral inhibitors targeting pandemic potential RNA viruses

RNA viruses continue to remain a clear and present threat for potential pandemics due to their rapid evolution. To mitigate their impact, we urgently require antiviral agents that can inhibit multiple families of disease-causing viruses, such as arthropod-borne and respiratory pathogens. Potentiating host antiviral pathways can prevent or limit viral infections before escalating into a major outbreak. Therefore, it is critical to identify broad-spectrum antiviral agents. We have tested a small library of innate immune agonists targeting pathogen recognition receptors, including TLRs, STING, NOD, Dectin and cytosolic DNA or RNA sensors. We observed that TLR3, STING, TLR8 and Dectin-1 ligands inhibited arboviruses, Chikungunya virus (CHIKV), West Nile virus (WNV) and Zika virus, to varying degrees. Cyclic dinucleotide (CDN) STING agonists, such as cAIMP, diABZI, and 2,3-cGAMP, and Dectin-1 agonist scleroglucan, demonstrated the most potent, broad-spectrum antiviral function. Comparative transcriptome analysis revealed that CHIKV-infected cells had larger number of differentially expressed genes than of WNV and ZIKV. Furthermore, gene expression analysis showed that cAIMP treatment rescued cells from CHIKV-induced dysregulation of cell repair, immune, and metabolic pathways. In addition, cAIMP provided protection against CHIKV in a CHIKV-arthritis mouse model. Cardioprotective effects of synthetic STING ligands against CHIKV, WNV, SARS-CoV-2 and enterovirus D68 (EV-D68) infections were demonstrated using human cardiomyocytes. Interestingly, the direct-acting antiviral drug remdesivir, a nucleoside analogue, was not effective against CHIKV and WNV, but exhibited potent antiviral effects against SARS-CoV-2, RSV (respiratory syncytial virus), and EV-D68. Our study identifies broad-spectrum antivirals effective against multiple families of pandemic potential RNA viruses, which can be rapidly deployed to prevent or mitigate future pandemics.

microbiology↗

Segmenting functional tissue units across human organs using community-driven development of generalizable machine learning algorithms

The development of a reference atlas of the healthy human body requires automated image segmentation of major anatomical structures across multiple organs based on spatial bioimages generated from various sources with differences in sample preparation. We present the setup and results of the "Hacking the Human Body" machine learning algorithm development competition hosted by the Human Biomolecular Atlas (HuBMAP) and the Human Protein Atlas (HPA) teams on the Kaggle platform. We showcase how 1,175 teams from 78 countries engaged in community- driven, open-science code development that resulted in machine learning models which successfully segment anatomical structures across five organs using histology images from two consortia and that will be productized in the HuBMAP data portal to process large datasets at scale in support of Human Reference Atlas construction. We discuss the benchmark data created for the competition, major challenges faced by the participants, and the winning models and strategies.

bioinformatics↗

CineFinch: An animated female zebra finch for studying courtship interactions

Dummies, videos and computer animations have been used extensively in animal behaviour to study simple social interactions. These methods allow complete control of one interacting animal, making it possible to test hypotheses about the significance and relevance of different elements of animal displays. Recent studies have demonstrated the potential of videos and interactive displays for studying more complex courtship interactions in the zebra finch, a well-studied songbird. Here, we extended these techniques by developing an animated female zebra finch and showed that ~40% of male zebra finches (n=5/12) sing to this animation. To study real-time social interactions, we developed two possible methods for closed loop control of animations; (1) an arduino based system to initiate videos/animations based on perch hops and (2) a video game engine based system to change animations. Overall, our results provide an important tool for understanding the dynamics of complex social interactions during courtship. SUMMARY STATEMENTWe develop and test an animation of a female zebra finch to study song and courtship interactions in the male zebra finch.

animal behavior and cognition↗

Limbic progesterone receptors regulate spatial memory

Progesterone and its receptors (PRs) participate in mating and reproduction, but their role in spatial declarative memory, is not understood. Male and female mice express PRs in regions that support spatial memory: the hippocampus and entorhinal cortex. PRs were predominantly expressed in excitatory neurons in Pgr-Cre mice injected with AAV-delivered flexed tdTomato. Furthermore, segesterone, a specific PR agonist, activated neurons in the entorhinal cortex (EC) and the hippocampus. We assessed the PR function in these spatial memory circuit neurons by examining the performance of mice lacking this receptor (PRKO) in novel object recognition, object placement, and Y-maze alternation tasks. In the recognition test, wild-type littermates spent significantly more time exploring the new object than male PRKO mice. The EC-specific deletion of PRs was sufficient to induce a deficit in detecting familiar versus never experienced or new objects. We confirmed deficits in spatial memory of PRKO mice by testing them on the Y-maze forced alternation task. In contrast to spatial tasks, PR removal did not alter the response to fear conditioning. PRs also support spatial memory in female mice. These studies provide novel insights into the role of PR in facilitating spatial, declarative memory in males and females, which may help with finding reproductive partners. SIGNIFICANCE STATEMENTBrain progesterone receptors play an essential role in facilitating mating and reproductive behaviors, but their role in spatial memory and, therefore, mate-finding is not described. Principal, excitatory neurons of the entorhinal cortex and hippocampus express progesterone receptors. These receptors facilitate spatial memory in male and female mice, which may enhance mate-finding reproductive function and food foraging.

neuroscience↗

Impaired hepatic autophagy exacerbates xenobiotics induced liver injury

Xenobiotics can activate the hepatic survival pathway, but it is not clear how impaired hepatic survival pathways may affect xenobiotic-induced liver injury. We investigated the role of hepatic autophagy, a cellular survival pathway, in cholestatic liver injury driven by a xenobiotic. Here we demonstrate that DDC diet impaired autophagic flux, resulting in the accumulation of p62-Ub-intrahyaline bodies (IHBs) but not the Mallory Denk-Bodies (MDBs). Impaired autophagic flux was linked to a deregulated hepatic protein-chaperonin system and a significant decline in Rab family proteins. In addition, we demonstrate that heterozygous deletion of Atg7, a key autophagy gene, aggravated the p62-Ub-IHB accumulation and cholestatic liver injury. Moreover, we showed that p62-Ub-IHB accumulation did not activate the proteostasis-related ER stress signaling pathway, but rather activated the NRF2 pathway and suppressed the FXR nuclear receptor, resulting in cholestatic liver injury. Conclusion: Impaired autophagy exacerbates xenobiotic-induced cholestatic liver injury. Promotion of autophagy may represent a new therapeutic approach for xenobiotic-induced liver injury.

pharmacology and toxicology↗

Olfactory receptor neurons generate multiple response motifs, increasing coding space dimensionality

Odorants binding to olfactory receptor neurons (ORNs) trigger bursts of action potentials, providing the brain with its only experience of the olfactory environment. Our recordings made in vivo from locust ORNs showed odor-elicited firing patterns comprise four distinct response motifs, each defined by a reliable temporal profile. Different odorants could elicit different response motifs from a given ORN, a property we term motif switching. Further, each motif undergoes its own form of sensory adaptation when activated by repeated plume-like odor pulses. A computational model constrained by our recordings revealed that organizing responses into multiple motifs provides substantial benefits for classifying odors and processing complex odor plumes: each motif contributes uniquely to encode the plumes composition and structure. Multiple motifs and motif switching further improve odor classification by expanding coding dimensionality. Our model demonstrated these response features could provide benefits for olfactory navigation, including determining the distance to an odor source.

neuroscience↗

Multi-modal Imaging of Disease Progression in TH-MYCN Mouse Models of Neuroblastoma

MYCN is a major driver for neuroblastoma (NB) and the tyrosine hydroxylase (TH)-MYCN transgenic mouse model is extensively used for preclinical NB studies. However, spatio-temporal NB progression in the TH-MYCN model has not been studied, and questions remain about the value of implanted models as a surrogate for transgenic mice. In this work, we used magnetic resonance imaging (MRI) to study tumor progression and nanoparticle contrast-enhanced computed tomography (n-CECT) to assess tumor vascular architecture in TH-MYCN transgenic mice (2-7 weeks of age) and TH-MYCN+/+-derived orthotopic allograft and syngeneic mice (2-5 weeks post-tumor implantation). Tumors in TH-MYCN transgenic mice became evident in the abdominal paraspinal region at week 5. A delayed thoracic paraspinal mass became evident at week 6 and most mice succumbed by week 7. In allograft and syngeneic mice, single mass tumor growth was restricted to the peritoneal cavity. N-CECT revealed a predominantly microvascular network in TH-MYCN tumors while implanted tumors exhibited heterogeneous and tortuous vessels. N-CECT quantitative analysis demonstrated high vascularity (tumor fractional blood volume ~ 0.12) in all models. Multi-modal imaging of TH-MYCN transgenic and implanted models revealed differences in growth patterns and vascular architecture that should be considered in designing preclinical studies.

cancer biology↗

ECS1 and ECS2 regulate polyspermy and suppress the formation of haploid plants by promoting double fertilization

In flowering plants, the number of pollen tubes that provide sperm cells to the female gametes is restricted by a pollen tube block. This safeguard mechanism is only activated after successful fertilization of both female gametes and involves the disintegration of pollen tube attracting synergid cells. Yu and coworkers previously reported that the endopeptidase ECS1 and ECS2, which are secreted by fertilized egg cells, prevent the attraction of supernumerary pollen tubes by cleaving the pollen tube attractant LURE11. Here we report on an earlier defect in ecs1 ecs2 mutants that is manifested by single rather than double fertilization of either egg or central cell. The defect is accompanied by a delay in synergid disintegration providing an alternative explanation for the extra pollen tubes observed in the double mutant. These results are corroborated by our finding that ecs1 ecs2 plants segregate both, haploid as well as polyspermy derived triploid plants.

plant biology↗

Characterization of metabolic compartmentalization in the liver using spatially resolved metabolomics

Cells adapt their metabolism to physiological stimuli, and metabolic heterogeneity exists between cell types, within tissues, and subcellular compartments. The liver plays an essential role in maintaining whole-body metabolic homeostasis and is structurally defined by metabolic zones. These zones are well-understood on the transcriptomic level, but have not been comprehensively characterized on the metabolomic level. Mass spectrometry imaging (MSI) can be used to map hundreds of metabolites directly from a tissue section, offering an important advance to investigate metabolic heterogeneity in tissues compared to extraction-based metabolomics methods that analyze tissue metabolite profiles in bulk. We established a workflow for the preparation of tissue specimens for matrix-assisted laser desorption/ionization (MALDI) MSI and achieved broad coverage of central carbon, nucleotide, and lipid metabolism pathways. We used this approach to visualize the effect of nutrient stress and excess on liver metabolism. Our data revealed a highly organized metabolic compartmentalization in livers, which becomes disrupted under nutrient stress conditions. Fasting caused changes in glucose metabolism and increased the levels of fatty acids in the circulation. In contrast, a prolonged high-fat diet (HFD) caused lipid accumulation within liver tissues with clear zonal patterns. Fatty livers had higher levels of purine and pentose phosphate related metabolites, which generates reducing equivalents to counteract oxidative stress. This MALDI MSI approach allowed the visualization of liver metabolic compartmentalization at high resolution and can be applied more broadly to yield new insights into metabolic heterogeneity in vivo.

biochemistry↗

A versatile mitochondria isolation- and analysis-pipeline generates 3D nano-topographies and mechano-physical surface maps of single organelles

Living eukaryotic cells typically contain large quantities of highly dynamic mitochondria, which sustain the cells energy and redox homeostasis. Growing evidence suggests that mitochondria can functionally differ among but also within cells. The extent and biological significance of mitochondrial diversity is still largely unexplored, due to technical limitations that hamper profiling of individual organelles. Previous measurements of the cells interior have shown that membrane-bound compartments respond to metabolic manipulation by changes in their surface stiffness, suggesting that mechano-physical properties are a valuable readout of mitochondrial function. We here present the establishment of a robust multi-step analysis pipeline that allows one to profile mechano-physical properties of single mitochondria at the nanoscale using Atomic Force Microscopy (AFM). Firstly, we developed a rapid cell-type specific isolation protocol (mRACE), which selectively functionalizes mitochondria with biotin, facilitating isolation by streptavidin decorated microbeads. We established the technique for human and rat cell cultures, the invertebrate Caenorhabditis elegans, and the model plant Arabidopsis thaliana. Based on this versatile tool, we detected diversity of mitochondrially associated proteins among different tissues, reflecting the trophic condition of the source material. Secondly, a rapid filtration-based mitochondria isolation protocol was established, which was combined with mRACE. Lastly, we established an AFM analysis platform, which generates 3D maps of the nano-topography and mechano-physical properties of individual mitochondria. The comparison of mitochondria with each other revealed an unprecedented diversity in their mechano-physical properties and suggests that shape is not the sole determining parameter for outer membrane stiffness. We expect our results to not only introduce a new dimension for basic mitochondrial research, but in addition to open the door for the exploitation of individual mitochondria for diagnostic characterization.

plant biology↗