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Reddy, S.

Publications and source records attributed to Reddy, S..

At least 37 records · Page 2Linked to original sources

Exercise Mitigates Flow Recirculation and Activates Mechanosensitive Transcriptome to Uncover Endothelial SCD1-Catalyzed Anti-Inflammatory Metabolites

Exercise modulates vascular plasticity in multiple organ systems; however, the metabolomic transducers underlying exercise and vascular protection in the disturbed flow-prone vasculature remain under-investigated. We simulated exercise-augmented pulsatile shear stress (PSS) to mitigate flow recirculation in the lesser curvature of the aortic arch. When human aortic endothelial cells (HAECs) were subjected to PSS ({tau}ave = 50 dyne{middle dot}cm-2, {partial}{tau}/{partial}t = 71 dyne{middle dot}cm-2{middle dot}s-1, 1 Hz), untargeted metabolomic analysis revealed that Stearoyl-CoA Desaturase (SCD1) in the endoplasmic reticulum (ER) catalyzed the fatty acid metabolite, oleic acid (OA), to mitigate inflammatory mediators. Following 24 hours of exercise, wild-type C57BL/6J mice developed elevated SCD1-catalyzed lipid metabolites in the plasma, including OA and palmitoleic acid (PA). Exercise over a 2-week period increased endothelial SCD1 in the ER. Exercise further modulated the time-averaged wall shear stress (TAWSS or{tau} ave) and oscillatory shear index (OSIave), upregulated Scd1 and attenuated VCAM1 expression in the disturbed flow-prone aortic arch in Ldlr-/- mice on high-fat diet but not in Ldlr-/-Scd1EC-/- mice. Scd1 overexpression via recombinant adenovirus also mitigated ER stress. Single cell transcriptomic analysis of the mouse aorta revealed interconnection of Scd1 with mechanosensitive genes, namely Irs2, Acox1 and Adipor2 that modulate lipid metabolism pathways. Taken together, exercise modulates PSS ({tau}ave and OSIave) to activate SCD1 as a metabolomic transducer to ameliorate inflammation in the disturbed flow-prone vasculature.

physiology↗

Dietary sugar and protein exert opposing effects on key larval growth and metabolic regulators, the Drosophila insulin-like peptides Dilp2 and Dilp6.

Nutrient intake drives secretion of insulin and insulin-like peptides that stimulate glucose uptake, nutrient storage, protein synthesis and cell growth. The Drosophila genome encodes seven insulin-like peptides (Dilps) that bind to a single known insulin receptor to drive growth and nutrient storage. Whether Dilps respond uniformly to changes in dietary nutrients is unknown. Here we characterized the endocrine response to starvation and dietary sugar and protein in mid-third instar Drosophila larvae, measuring circulating Dilp2, derived from insulin-producing cells in the brain, and Dilp6, produced by the fat body. Starvation led to a 90% reduction in circulating Dilp2 without affecting circulating Dilp6 levels. Dietary protein, but not sugar, restored hemolymph Dilp2 from starved levels, while elevated and imbalanced ratios of sugar to protein led to modest reductions in circulating Dilp2. In contrast, hemolymph Dilp6 was increased by a sugar-only diet. Surprisingly, dietary protein strongly reduced circulating Dilp6 levels. Dietary sugar drives glycogen and triglyceride storage, and levels of these stored nutrients positively correlate with Dilp6. Protein in the diet promotes whole-animal growth, which correlates strongly with circulating Dilp2. Our data show that Dilp2 and Dilp6 secretion are regulated in opposite ways by distinct dietary nutrients. These findings raise the question of how the single known insulin receptor integrates divergent signals from distinct Dilps to control growth and metabolism.

physiology↗

Bill shape imposes biomechanical tradeoffs in cavity-excavating birds

Organisms are subject to a host of physical forces that influence morphological evolution. Birds, for instance, use their bills as implements to perform various functions, each exerting unique physical demands and selective influences on bill morphology. For example, birds that use their bills to excavate nesting or roosting cavities must resist a range of mechanical stresses to prevent fracture. However, the contribution of bill geometry and material composition to excavation stress resistance remains poorly understood. Here, we study the biomechanical consequences of bill diversification in two clades of cavity-excavating, frugivorous birds, the paleotropical barbets. Using multilayered finite element models and beam theory, we compare the excavation performance of different maxillary geometries for two loading regimes experienced by barbet bills during cavity excavation-dorsoventral impact and torsion. We find that deeper and wider maxillae perform better for impact loads than for torsional loads, with the converse for narrower maxillae. This results in a tradeoff between impact and torsion resistance imposed by bill geometry. Analytical beam models validate this prediction, showing that this relationship holds even when maxillae are simplified to solid elliptical beams. Finally, we find that composite bill structures broadly exhibit lower stresses than homogenous structures of the same geometry, indicating a functional synergy between the keratinous rhamphotheca and bony layers of the bill. Overall, our findings demonstrate the strong link between morphological evolution, behavior, and functional performance in organisms.

ecology↗

Cytosolic condensates enriched in polyserine repeats are preferred sites of tau fiber propagation

Tau aggregates are a hallmark of multiple neurodegenerative diseases and can contain RNAs and RNA binding proteins, including SRRM2 and PNN. How these resident nuclear proteins mislocalize and their influence on the prion-like propagation of tau fibers remains unknown. We demonstrate that polyserine repeats in SRRM2 and PNN are necessary and sufficient for recruitment to tau aggregates. Moreover, we demonstrate tau fibers preferentially grow in association with endogenous cytoplasmic assemblies - mitotic interchromatin granules and cytoplasmic speckles - which contain SRRM2 and PNN. Polyserine undergoes self-assembly in vitro and in cells, where polyserine-assemblies are sites of tau fiber propagation. Modulating the levels of polyserine containing proteins results in a corresponding change in tau aggregation. These findings define a specific protein motif, and cellular condensates, that promote tau fiber propagation. As cytoplasmic speckles form in iPSC neurons under inflammatory or hyperosmolar stress, they may promote tau fiber propagation in various neurodegenerative diseases.

neuroscience↗

Climate influences bill shape diversification in cavity-excavating birds

The remarkable structural and functional diversity of the avian bill serves as an ideal system to understand how ecological and environmental factors influence morphological diversification under physically demanding tasks. For example, in cavity-excavating birds where the bill experiences tremendous physical stresses, climate and habitat affect the mechanical properties of available nesting substrates and therefore can potentially influence the shape and performance of bills. Few studies have focused on the entire avian bill, a complex structure consisting of the rhamphotheca and bony core of the upper and lower mandibles, which may evolve as independent modules or as a single integrated unit. Here, we examined patterns and drivers of bill shape diversification in barbets using micro-computed tomography of museum study skins. We employed landmark-based geometric morphometrics and phylogenetic comparative methods to study the influence of climatic conditions, integration and phylogenetic constraints on bill shape diversification. Asian and African barbets have explored distinct maxillary shape spaces without corresponding change in mandibular shape after correcting for phylogenetic non-independence. Additionally, maxillary shape for both rhamphotheca and bony components was significantly correlated with climate variables and exhibited signatures of allometric scaling. All four bill components, however, covaried with each other and have evolved in a gradual and integrated fashion, exhibiting late-stage shape disparity. Through these findings, our study offers crucial insights into how ecological behaviors impact morphological evolution of complex, multifunctional features.

evolutionary biology↗

A comprehensive single-cell breast tumor atlas defines cancer epithelial and immune cell heterogeneity and interactions predicting anti-PD-1 therapy response

We present an integrated single-cell RNA-seq resource of the breast tumor microenvironment consisting of 236,363 cells from 119 biopsy samples across 8 publicly available datasets. In this computational study, we first leverage this novel resource to define cancer epithelial cell heterogeneity based on two clinically relevant markers and identify six new and distinct subsets of natural killer cells. We then illustrate how cancer epithelial cell heterogeneity impacts immune cell interactions. We develop T cell InteractPrint, which considers how cancer epithelial cell heterogeneity shifts the predicted strength of T cell interactions. We use InteractPrint to predict response to immune checkpoint inhibition (ICI) in two clinical trials testing immunotherapy in patients with breast cancer. T cell InteractPrint was predictive in both trials (AUC = 0.81 and 0.84), versus PD-L1 expression (AUC = 0.54 and 0.72). This result provides an alternative predictive biomarker to PD-L1 to select patients who should receive ICI. STATEMENT OF SIGNIFICANCEWe developed a novel integrated single-cell atlas of the breast tumor microenvironment to interrogate breast tumor cell heterogeneity and define how heterogenous cancer epithelial cell and immune cell interactions predict response to anti-PD-1 therapy.

cancer biology↗

The proteasomal degradation signal FAT10 modulates substrate stability to accelerate degradation

The proteasome controls levels of most cellular proteins, and its activity is regulated under stress, quiescence, and inflammation. However, factors determining the proteasomal degradation activity remain poorly understood. Proteasome substrates are conjugated with small proteins (tags) like ubiquitin and Fat10 to target them to the proteasome. It is unclear if the structural plasticity of proteasome-targeting tags influences substrate degradation. The tag Fat10 is activated during inflammation, and ambiguously, Fat10 and its substrates undergo rapid proteasomal degradation. We report that the rapid degradation of Fat10 substrates depends on its structural plasticity. While the ubiquitin tag is recycled at the proteasome, Fat10 is degraded with the substrate, and the mechanical unfolding kinetics of Fat10 regulates substrate degradation. Our studies reveal that long-range salt bridges are absent in the Fat10 structure, creating a plastic protein with partially unstructured regions suitable for proteasome engagement. Such a malleable structure also provides low resistance to mechanical unfolding and expedites proteasomal degradation. We also uncovered that the Fat10 plasticity destabilizes substrates significantly and creates partially unstructured regions in the substrate to enhance degradation. NMR-relaxation-derived order parameters and temperature dependence of chemical shifts identify the Fat10-induced partially unstructured regions in the substrate. They correlated excellently to the regions where Fat10 contacts the substrate, suggesting that the tag-substrate collision destabilizes the substrate. These results highlight a strong dependence of proteasomal degradation on the structural plasticity and thermodynamic properties of the proteasome-targeting tag.

biochemistry↗

Genetic Impairment of Succinate Metabolism Disrupts Bioenergetic Sensing in Adrenal Neuroendocrine Tumor

Metabolic dysfunction mutations can impair energy sensing and cause cancer. Loss of function of mitochondrial TCA cycle enzyme, succinate dehydrogenase B (SDHB) results in various forms of cancer typified by pheochromocytoma (PC). Here we delineate a signaling cascade where the loss of SDHB induces the Warburg effect in PC tumors, triggers dysregulation of Ca2+ homeostasis, and aberrantly activates calpain and the protein kinase Cdk5, through conversion of its cofactor from p35 to p25. Consequently, aberrant Cdk5 initiates a cascade of phospho- signaling where GSK3 inhibition inactivates energy sensing by AMP-kinase through dephosphorylation of the AMP-kinase {gamma} subunit, PRKAG2. Overexpression of p25-GFP in mouse adrenal chromaffin cells also elicits this phosphorylation signaling and causes PC tumor formation. A novel Cdk5 inhibitor, MRT3-007, reversed this phospho-cascade, invoking an anti- Warburg effect, cell cycle arrest, and senescence-like phenotype. This therapeutic approach halted tumor progression in vivo. Thus, we reveal an important novel mechanistic feature of metabolic sensing and demonstrate that its dysregulation underlies tumor progression in PC and likely other cancers. HighlightsO_LILoss of SDHB function in pheochromocytoma causes Ca2+ dysregulation, calpain activation, and aberrant activation of the protein kinase Cdk5. C_LIO_LIHyperactive Cdk5 deregulates a GSK3/PRKAG2/AMPK signaling cascade. C_LIO_LIp25 overexpression and consequent aberrant Cdk5 activity in chromaffin cells causes pheochromocytoma. C_LIO_LIInhibition of Cdk5 activates the PRKAG2/AMPK/p53 signaling to rescue cell senescence and block PC tumor progression. C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=175 SRC="FIGDIR/small/475410v2_ufig1.gif" ALT="Figure 1"> View larger version (49K): org.highwire.dtl.DTLVardef@16f0a48org.highwire.dtl.DTLVardef@10c1c7aorg.highwire.dtl.DTLVardef@21b100org.highwire.dtl.DTLVardef@1eb8674_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

Cloud-enabled Fiji for reproducible, integrated and modular image processing

Modern biomedical image analyses workflows contain multiple computational processing tasks giving rise to problems in reproducibility. In addition, image datasets can span both spatial and temporal dimensions, with additional channels for fluorescence and other data, resulting in datasets that are too large to be processed locally on a laptop. For omics analyses, software containers have been shown to enhance reproducibility, facilitate installation and provide access to scalable computational resources on the cloud. However, most image analyses contain steps that are graphical and interactive, features that are not supported by most omics execution engines. We present the containerized and cloud-enabled Biodepot-workflow-builder platform that supports graphics from software containers and has been extended for image analyses. We demonstrate the potential of our modular approach with multi-step workflows that incorporate the popular and open-source Fiji suite for image processing. One of our examples integrates fully interactive Fiji macros with Jupyter notebooks. Our second example illustrates how the complicated cloud setup of an computationally intensive process such as stitching 3D digital pathology datasets using BigStitcher can be automated and simplified. In both examples, users can leverage a form-based graphical interface to execute multi-step workflows with a single click, using the provided sample data and preset input parameters. Alternatively, users can interactively modify the image processing steps in the workflow, apply the workflows to their own data, change the input parameters and macros. By providing interactive graphics support to software containers, our modular platform supports reproducible image analysis workflows, simplified access to cloud resources for analysis of large datasets, and integrated workflows across imaging, genomics and transcriptomics data.

bioinformatics↗

Patterns of morphological diversification in the Ramphastoidea reveal the dramatic divergence of toucans from a conserved morphotype

BackgroundMorphological traits offer insights into an organisms ecological niche, species interactions, and patterns of community organisation. Pantropical lineages - animals and plants distributed across the three tropical continental regions of Asia, Africa, and America - provide a way to test how different environments and communities influence morphological diversification. Here, we examined a monophyletic group of frugivorous birds, the barbets and toucans (Ramphastoidea), which diversified independently on three continents, to investigate whether clades in each region exhibit similar (phylogenetically constrained) or distinct (ecologically influenced) patterns of morphological diversification. ResultsOur results show that despite differences in community dynamics in these regions, lineage accumulation patterns through time on all three continents are broadly similar, putatively due to phylogenetic niche conservatism. We quantified morphological variation in light of phylogenetic relatedness to further reveal that all barbet lineages across continents occupy a conserved region of morphospace after correcting for variation in size. However, in the Neotropics, one lineage, the toucans, have diverged dramatically from typical barbet space and converged toward (yet are distinct from) the trait space occupied by the distantly related hornbills in Asia and Africa. Additionally, we found no link between climatic variables and morphological traits. We conclude that barbets exhibit a conserved morphotype across continents and have diversified by scaling mainly in body size. However, the absence of other large frugivorous birds may have allowed toucans to diversify into a different region of morphospace of increased bill/wing to tail/wing ratios. ConclusionsA combination of photographic and specimen measurements enabled us to demonstrate the presence of a globally conserved barbet morphotype across three tropical continents. By examining different continental lineages of a single monophyletic bird group, we shed light on the contrasting effects of regional ecological factors and phylogenetic constraints on morphological diversification.

ecology↗

Cdk5 drives formation of heterogeneous pancreatic neuroendocrine tumors

Pancreatic neuroendocrine tumors (PanNETs) are a heterogeneous population of neoplasms that arise from hormone-secreting islet cells of the pancreas and have increased markedly in incidence over the past four decades. Non-functional PanNETs, which occur more frequently than hormone-secreting tumors, are often not diagnosed until later stages of tumor development and have poorer prognoses. Development of successful therapeutics for PanNETs has been slow, partially due to a lack of diverse animal models for pre-clinical testing. Here, we report development of an inducible, conditional mouse model of PanNETs by using a bitransgenic system for regulated expression of the aberrant activator of Cdk5, p25, specifically in {beta}-islet cells. This model produces a heterogeneous population of PanNETs that includes a subgroup of well-differentiated, non-functional tumors. The utility of this model is enhanced by ability to form tumor-derived allografts. Production of these tumors demonstrates the causative potential of aberrantly active Cdk5 for generation of PanNETs. Further, we show that human PanNETs express Cdk5 pathway components, are dependent on Cdk5 for growth, and share genetic and transcriptional overlap with the INS-p25OE model. This new model of PanNETs will facilitate molecular delineation of Cdk5-dependent PanNETs and the development of new targeted therapeutics.

cancer biology↗

A graphical, interactive and GPU-enabled workflow to process long-read sequencing data

We present a graphical cloud-enabled workflow for fast, interactive analysis of nanopore sequencing data using GPUs. Users customize parameters, monitor execution and visualize results through an accessible graphical interface. To facilitate reproducible deployment, we use Docker containers and provide an Amazon Machine Image (AMI) with all software and drivers pre-installed for GPU computing on the cloud. We observe a 34x speedup and a 109x reduction in costs for the rate-limiting basecalling step in the analysis of blood cancer cell line data. The graphical interface and greatly simplified deployment facilitate the adoption of GPUs for rapid, cost-effective analysis of long-read sequencing.

bioinformatics↗

Inactivation of SARS-CoV-2 by β-propiolactone Causes Aggregation of Viral Particles and Loss of Antigenic Potential

Inactivated viral preparations are important resources in vaccine and antisera industry. Of the many vaccines that are being developed against COVID-19, inactivated whole-virus vaccines are also considered effective. {beta}-propiolactone (BPL) is a widely used chemical inactivator of several viruses. Here, we analyze various concentrations of BPL to effectively inactivate SARS-CoV-2 and their effects on the biochemical properties of the virion particles. BPL at 1:2000 (v/v) concentrations effectively inactivated SARS-CoV-2. However, higher BPL concentrations resulted in the loss of both protein content as well as the antigenic integrity of the structural proteins. Higher concentrations also caused substantial aggregation of the virion particles possibly causing undesirable outcomes including a potential immune escape by infectious virions, and a loss in antigenic potential. We also identify that the viral RNA content in the culture supernatants can be a direct indicator of their antigenic content. Our findings may have important implications in the vaccine and antisera industry during COVID-19 pandemic.

microbiology↗

Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 isolates from Pennsylvania

Rapid whole genome sequencing of SARS-CoV-2 has presented the ability to detect new emerging variants of concern in near real time. Here we report the genome of a virus isolated in Pennsylvania in March 2021 that was identified as lineage B.1.1.7 (VOC-202012/01) that also harbors the E484K spike mutation, which has been shown to promote "escape" from neutralizing antibodies in vitro. We compare this sequence to the only 5 other B.1.1.7+E484K genomes from Pennsylvania, all of which were isolated in mid March. Beginning in February 2021, only a small number (n=60) of isolates with this profile have been detected in the US, and only a total of 253 have been reported globally (first in the UK in December 2020). Comparative genomics of all currently available high coverage B.1.1.7+E484K genomes (n=235) available on GISAID suggested the existence of 7 distinct groups or clonal complexes (CC; as defined by GNUVID) bearing the E484K mutation raising the possibility of 7 independent acquisitions of the E484K spike mutation in each background. Phylogenetic analysis suggested the presence of at least 3 distinct clades of B.1.1.7+E484K circulating in the US, with the Pennsylvanian isolates belonging to two distinct clades. Increased genomic surveillance will be crucial for detection of emerging variants of concern that can escape natural and vaccine induced immunity.

genomics↗

Combined Inhibition of AKT and KIT Restores Expression of Programmed Cell Death 4 (PDCD4) in Gastrointestinal Stromal Tumor

The majority of gastrointestinal stromal tumor (GIST) patients develop resistance to the first-line KIT inhibitor, imatinib mesylate (IM), through acquisition of secondary mutations in KIT or bypass signaling pathway activation. AKT is a relevant target for inhibition, in addition to KIT, since the PI3K/AKT pathway is crucial for IM-resistant GIST survival. We evaluated the activity of a novel pan-AKT inhibitor, MK-4440 (formerly ARQ 751), as monotherapy and in combination with IM in GIST cell lines and preclinical models with varying IM sensitivities. Dual inhibition of KIT and AKT demonstrated significant synergistic effects in IM-sensitive and -resistant GIST cell lines. Proteomic analyses revealed upregulation of the tumor suppressor, PDCD4, in combination treated cells. Enhanced PDCD4 expression correlated to cell cycle arrest and cell death. In vivo studies revealed superior efficacy of MK-4440/IM combination in an IM-sensitive preclinical model of GIST compared with either single agent. The combination demonstrated limited efficacy in two IM-resistant models, including a GIST patient-derived xenograft model possessing an exon 9 KIT mutation. These studies provide strong rationale for further use of AKT inhibition in combination with IM in primary GIST; however, alternative agents will need to be tested in combination with AKT inhibition in the resistant setting.

cancer biology↗

Optimized structure of monoubiquitinated FANCD2 (human) at Lys 561: a theoretical approach

Fanconi anaemia pathway repairs inter-strand cross linking damage (ICL) of the DNA. Monoubiquitination of FANCD2 and FANCI is very crucial for ICL repairing. In this work we have tried to understand the monoubiquitinated FANCD2 structure, which facilitates the FANCD2 for binding the damage part of the chromatin. Crystal structure of the monoubiquitinated FANCD2 alone is not available, therefore we have developed the optimized structure of the human monoubiquitinated (Lys 561) FANCD2. As there is no suitable software or web server we have developed a method for building up monoubiquitinated product and validated on simplest monoubiquitinated protein, diubiquitin. We have predicted the structure of human monoubiquitinated FANCD2 by using our method and studied the interaction with DNA by docking studies. Molecular Dynamics (MD) simulation was used to understand the stability of the structure. Large structural differences have been observed between FANCD2 and monoubiquitinated FANCD2. DNA docking studies suggest that the binding site varies for the FANCD2 and monoubiquitinated FANCD2.

bioinformatics↗

Development of Equine Immunoglobulin Fragment F(ab')2 with High Neutralizing Capability against SARS-CoV-2

The ongoing pandemic, COVID-19, caused by SARS-CoV-2 has taken the world, and especially the scientific community by storm. While vaccines are being introduced into the market, there is also a pressing need to find potential drugs and therapeutic modules. Remdesivir is one of the antivirals currently being used with a limited window of action. As more drugs are being vetted, passive immunotherapy in the form of neutralizing antibodies can provide immediate action to combat the increasing numbers of COVID-positive cases. Herein, we demonstrate that equines hyper-immunized with chemically inactivated SARS-CoV-2 generate high titers of antibody with a strong virus neutralizing potential. ELISA performed with pooled antisera displayed highest immunoglobulin titer on 42 days post-immunization, at 1:51,200 dilutions. F(ab)2 immunoglobulin fragments generated from the pools also showed very high, antigen-specific affinity at 1:102,400 dilutions. Finally, in vitro virus neutralization assays confirmed that different pools of F(ab)2 fragments could successfully neutralize SARS-CoV-2 with titers well above 25,000, indicating the potential of this strategy in treating severe COVID-19 cases with high titers. The F(ab)2 was able to cross neutralize another SARS-CoV-2 strain, demonstrating its efficacy against the emerging viral variants and the importance of this approach in our efforts of eradication of COVID-19. In conclusion, this study demonstrates that virus-neutralizing antibodies raised in equines can potentially be used as a treatment regimen in the form of effective passive immunotherapy to combat COVID-19.

immunology↗

Discovery and validation of novel human genomic safe harbor sites for gene and cell therapies

Existing approaches for the integration and expression of genes of interest in a desired human cellular context are marred by the safety concerns related to either the random nature of viral-mediated integration or unpredictable pattern of gene expression in currently employed targeted genomic integration sites. Disadvantages of these methods lead to their limited use in clinical practice, thus encouraging future research in identifying novel human genomic sites that allow for predictable and safe expression of genes of interest. We conducted a bioinformatic search followed by experimental validation of novel genomic sites and identified two that demonstrated stable expression of integrated reporter and therapeutic genes without detrimental changes to cellular transcriptome. The cell-type agnostic criteria used in our bioinformatic search suggest wide-scale applicability of our sites for engineering of a diverse range of tissues for therapeutic as well as enhancement purposes, including modified T-cells for cancer therapy and engineered skin to ameliorate inherited diseases and aging. Additionally, the stable and robust levels of gene expression from identified sites allow for their use in industry-scale biomanufacturing of desired proteins in human cells.

genomics↗