Biology subjects

Patel, S.

Publications and source records attributed to Patel, S..

At least 145 records · Page 8Linked to original sources

bioRxiv2023

Bacteriophage therapy for the treatment of Mycobacterium tuberculosis infections in humanized mice

The continuing emergence of new strains of antibiotic-resistant bacteria has renewed interest in phage therapy; however, there has been limited progress in applying phage therapy to multi-drug resistant Mycobacterium tuberculosis (Mtb) infections. In this study, we tested three bacteriophage strains for their Mtb-killing activities and found that two of them efficiently lysed Mtb H37Rv in 7H10 agar plates. However, only phage DS6A efficiently killed H37Rv in liquid culture and in Mtb-infected human primary macrophages. In subsequent experiments, we infected humanized mice with aerosolized H37Rv, then treated these mice with DS6A intravenously to test its in vivo efficacy. We found that DS6A treated mice showed increased body weight and improved pulmonary function relative to control mice. Furthermore, DS6A reduced Mtb load in mouse organs with greater efficacy in the spleen. These results demonstrated the feasibility of developing phage therapy as an effective therapeutic against Mtb infection.

microbiology↗

bioRxiv2023

Genome assembly of the hybrid grapevine Vitis Chambourcin

Background Chambourcin is a French-American interspecific hybrid grape variety grown in the eastern and midwestern United States and used for making wine. Currently, there are few genomic resources available for hybrid grapevines like Chambourcin. ResultsWe assembled the genome of Chambourcin using PacBio HiFi long-read sequencing, Bionano optical map sequencing and Illumina short read sequencing. We produced an assembly for Chambourcin with 26 scaffolds with an N50 length of 23.3 Mb and an estimated BUSCO completeness of 97.9%. 33,791 gene models were predicted, of which 81% (27,075) were functionally annotated using Gene Ontology and KEGG pathway analysis. We identified 16,056 common orthologs between Chambourcin gene models, V. vinifera PN40024 12X.v2, VCOST.v3, Shine Muscat (Vitis labruscana x V. vinifera) and V. riparia Gloire. A total of 1,606 plant transcription factors representing 58 different gene families were identified in Chambourcin. Finally, we identified 304,571 simple sequence repeats (SSRs), repeating units of 1-6 base pairs in length in the Chambourcin genome assembly. ConclusionsWe present the genome assembly, genome annotation, protein sequences and coding sequences reported for Chambourcin. The Chambourcin genome assembly provides a valuable resource for genome comparisons, functional genomic analysis and genome-assisted breeding research.

bioinformatics↗

bioRxiv2023

An intravenous DNA-binding priming agent protects cell-free DNA and improves the sensitivity of liquid biopsies

Blood-based, or "liquid," biopsies enable minimally invasive diagnostics but have limits on sensitivity due to scarce cell-free DNA (cfDNA). Improvements to sensitivity have primarily relied on enhancing sequencing technology ex vivo. Here, we sought to augment the level of circulating tumor DNA (ctDNA) detected in a blood draw by attenuating the clearance of cfDNA in vivo. We report a first-in-class intravenous DNA-binding priming agent given 2 hours prior to a blood draw to recover more cfDNA. The DNA-binding antibody minimizes nuclease digestion and organ uptake of cfDNA, decreasing its clearance at 1 hour by over 150-fold. To improve plasma persistence and limit potential immune interactions, we abrogated its Fc-effector function. We found that it protects GC-rich sequences and DNase-hypersensitive sites, which are ordinarily underrepresented in cfDNA. In tumor-bearing mice, priming improved tumor DNA recovery by 19-fold and sensitivity for detecting cancer from 6% to 84%. These results suggest a novel method to enhance the sensitivity of existing DNA-based cancer testing using blood biopsies.

genomics↗

bioRxiv2023

A nanoparticle priming agent reduces cellular uptake of cell-free DNA and enhances the sensitivity of liquid biopsies

Liquid biopsies are enabling minimally invasive monitoring and molecular profiling of diseases across medicine, but their sensitivity remains limited by the scarcity of cell-free DNA (cfDNA) in blood. Here, we report an intravenous priming agent that is given prior to a blood draw to increase the abundance of cfDNA in circulation. Our priming agent consists of nanoparticles that act on the cells responsible for cfDNA clearance to slow down cfDNA uptake. In tumor-bearing mice, this agent increases the recovery of circulating tumor DNA (ctDNA) by up to 60-fold and improves the sensitivity of a ctDNA diagnostic assay from 0% to 75% at low tumor burden. We envision that this priming approach will significantly improve the performance of liquid biopsies across a wide range of clinical applications in oncology and beyond.

genomics↗

bioRxiv2022

Large-scale unsupervised discovery of excitatory morphological cell types in mouse visual cortex

Neurons in the neocortex exhibit astonishing morphological diversity which is critical for properly wiring neural circuits and giving neurons their functional properties. However, the organizational principles underlying this morphological diversity remain an open question. Here, we took a data-driven approach using graph-based machine learning methods to obtain a low-dimensional morphological "bar code" describing more than 30,000 excitatory neurons in mouse visual areas V1, AL and RL that were reconstructed from the millimeter scale MICrONS serial-section electron microscopy volume. Contrary to previous classifications into discrete morphological types (m-types), our data-driven approach suggests that the morphological landscape of cortical excitatory neurons is better described as a continuum, with a few notable exceptions in layers 5 and 6. Dendritic morphologies in layers 2-3 exhibited a trend towards a decreasing width of the dendritic arbor and a smaller tuft with increasing cortical depth. Inter-area differences were most evident in layer 4, where V1 contained more atufted neurons than higher visual areas. Moreover, we discovered neurons in V1 on the border to layer 5 which avoided deeper layers with their dendrites. In summary, we suggest that excitatory neurons morphological diversity is better understood by considering axes of variation than using distinct m-types.

neuroscience↗

bioRxiv2022

Improved Neutralization of Omicron BA.4/5, BA.4.6, BA.2.75.2, BQ.1.1, and XBB.1 with Bivalent BA.4/5 Vaccine

The BNT162b2 bivalent BA.4/5 COVID-19 vaccine has been authorized to mitigate COVID-19 due to current Omicron and potentially future variants. New sublineages of SARS-CoV-2 Omicron continue to emerge and have acquired additional mutations, particularly in the spike protein, that may lead to improved viral fitness and immune evasion. The present study characterized neutralization activities against new Omicron sublineages BA.4.6, BA.2.75.2, BQ.1.1, and XBB.1 after a 4th dose (following three doses of BNT162b2) of either the original monovalent BNT162b2 or the bivalent BA.4/5 booster in individuals >55 years of age. For all participants, the 4th dose of monovalent BNT162b2 vaccine induced a 3.0x, 2.9x, 2.3x, 2.1x, 1.8x, and 1.5x geometric mean neutralizing titer fold rise (GMFR) against USA/WA1-2020 (a strain isolated in January 2020), BA.4/5, BA.4.6, BA.2.75.2, BQ.1.1, and XBB.1, respectively; the bivalent vaccine induced 5.8x, 13.0x, 11.1x, 6.7x, 8.7x, and 4.8x GMFRs. For individuals without SARS-CoV-2 infection history, BNT162b2 monovalent induced 4.4x, 3.0x, 2.5x, 2.0x, 1.5x, and 1.3x GMFRs, respectively; the bivalent vaccine induced 9.9x, 26.4x, 22.2x, 8.4x, 12.6x, and 4.7x GMFRs. These data suggest the bivalent BA.4/5 vaccine is more immunogenic than the original BNT162b2 monovalent vaccine against circulating Omicron sublineages, including BQ.1.1 that is becoming prevalent globally.

microbiology↗

bioRxiv2022

The chemorepellent, SLIT2, bolsters innate immunity against Staphylococcus aureus

Neutrophils are essential for host defense against Staphylococcus aureus (S. aureus). The neuro-repellent, SLIT2, potently inhibits neutrophil chemotaxis, and might therefore be expected to impair antibacterial responses. We report here that, unexpectedly, neutrophils exposed to the N-terminal SLIT2 (N-SLIT2) fragment kill extracellular S. aureus more efficiently. N-SLIT2 amplifies reactive oxygen species production in response to the bacteria by activating p38 mitogen-activated protein kinase that in turn phosphorylates NCF1, an essential subunit of the NADPH oxidase complex. N-SLIT2 also enhances exocytosis of secondary granules. In a murine model of S. aureus skin and soft tissue infection (SSTI), local SLIT2 levels fall initially but increase subsequently, peaking {approx} 3 days after infection. Of note, neutralization of endogenous SLIT2 worsens SSTI. Temporal fluctuations in tissue SLIT2 levels may promote neutrophil recruitment and retention at the infection site and hasten bacterial clearance by augmenting neutrophil oxidative burst and degranulation. Collectively, these actions of SLIT2 coordinate innate immune responses to limit susceptibility to S. aureus. One-sentence summarySLIT2, a prototypic neuro-repellent, spatiotemporally coordinates host defense against Staphylococcus aureus infection.

cell biology↗

bioRxiv2022

Loss of Mfn1 but not Mfn2 enhances adipogenesis

ObjectiveA biallelic missense mutation in mitofusin 2 (MFN2) causes multiple symmetric lipomatosis and partial lipodystrophy, implicating disruption of mitochondrial fusion or interaction with other organelles in adipocyte differentiation, growth and/or survival. In this study, we aimed to document the impact of loss of mitofusin 1 (Mfn1) or 2 (Mfn2) on adipogenesis in cultured cells. MethodsWe characterised adipocyte differentiation of wildtype (WT), Mfn1-/- and Mfn2-/- mouse embryonic fibroblasts (MEFs) and 3T3-L1 preadipocytes in which Mfn1 or 2 levels were reduced using siRNA. ResultsMfn1-/- MEFs displayed striking fragmentation of the mitochondrial network, with surprisingly enhanced propensity to differentiate into adipocytes, as assessed by lipid accumulation, expression of adipocyte markers (Plin1, Fabp4, Glut4, Adipoq), and insulin-stimulated glucose uptake. RNA sequencing revealed a corresponding pro-adipogenic transcriptional profile including Pparg upregulation. Mfn2-/- MEFs also had a disrupted mitochondrial morphology, but in contrast to Mfn1-/- MEFs they showed reduced expression of adipocyte markers and no increase in insulin-stimulated glucose uptake. Mfn1 and Mfn2 siRNA mediated knockdown studies in 3T3-L1 adipocytes generally replicated these findings. ConclusionsLoss of Mfn1 but not Mfn2 in cultured pre-adipocyte models is pro-adipogenic. This suggests distinct, non-redundant roles for the two mitofusin orthologues in adipocyte differentiation.

cell biology↗

bioRxiv2022

Developing Novel Biologicals with Multiple Modes of Action (BM) to Combat the EarlyBlight Disease in Tomato (Solanum lycopersicum), Potato (Solanum tuberosum), and BellPepper (Capsicum annuum)

Early blight, a fungal disease, leads to annual crop losses of up to 79% in tomato, potato, and bell pepper crops. Current treatment requires repeated application of chemical fungicides, resulting in fungicidal resistance. Previous studies have identified microorganisms that enhance plant growth or prevent the growth of early blight spores. This study aims to develop a biological fungicide with multiple modes of action (BM) that can be used in fungicide rotation. The average area under the disease progress curve (AUDPC) values were calculated to quantify the disease progression; formulation 2, formulation 3, and formulation 3 produced the lowest AUDPC value for the tomato, potato, and bell pepper crops, respectively. All the treatments were compared with the current industry standard used to treat early blight, and analysis of variance (ANOVA) tests, with 95% confidence intervals (CIs), of the disease severity were conducted to determine the efficacy of the treatments.

plant biology↗

bioRxiv2022

Targeting IRS-1/2 in uveal melanoma inhibits in vitro cell growth, survival and migration, and in vivo tumor growth.

Uveal melanoma (UM) originating in the eye and metastasizing to the liver is associated with poor prognosis and has only one approved therapeutic option. We hypothesized that liver-borne growth factors may contribute to UM growth. Therefore, we investigated the role of insulin-like growth factor -1 and its receptor (IGF-1/IGF-1R) signaling in UM. We found that the insulin receptor substrate -1 (IRS-1) is overexpressed in UM cells and tumors. Since we previously observed that IGF-1R antibody therapy was not clinically effective in UM, we investigated the potential of NT157, a small molecule inhibitor of IRS-1/2 in blocking this pathway in UM. NT157 treatment in UM cells resulted in reduced cell survival and migration, and increased apoptosis. This treatment also significantly inhibited UM tumor growth in vivo, in the chicken egg chorioallantoic membrane (CAM) and subcutaneous mouse models, validating the in vitro effect. Mechanistically, through reverse phase protein array (RPPA), we identified significant proteomic changes in the PI3K/AKT pathway, a downstream mediator of IGF-1 signaling, with NT157 treatment. Together, these results suggest that NT157 inhibits cell survival, migration in vitro and tumor growth in vivo via inhibiting IGF-1 signaling in UM.

cell biology↗

bioRxiv2022

Type 1 interferon remodels normal and neoplastic hematopoiesis in human

Inflammation perturbs evolutionary dynamics of hematopoietic stem cell (HSC) clones in clonal hematopoiesis and myeloid neoplasms. We studied HSCs, progenitors and immune cells from patients with myeloproliferative neoplasm (MPN) at baseline and following interferon- (IFN) treatment, the only MPN therapy to deplete clonal stem cells. We focused on essential thrombocythemia, an informative model of early-phase neoplastic hematopoiesis. We integrated somatic genotyping, transcriptomes, immunophenotyping, and chromatin accessibility across single cells. IFN simultaneously activated HSCs into two polarized states, a lymphoid progenitor expansion associated with an anti-inflammatory state and an IFN-specific inflammatory granulocytic progenitor (IGP) state derived directly from HSCs. The augmented lymphoid differentiation balanced the typical MPN-induced myeloid bias, associated with normalized blood counts. Clonal fitness upon IFN exposure was due to resistance of clonal stem cells to differentiate into IGPs. These results support a paradigm wherein inflammation perturbs clonal dynamics by HSC induction into the precipitous IGP differentiation program. One-Sentence SummaryInflammation accelerates clonal evolution by driving stem cell differentiation into an alternate interferon--induced progenitor state.

cancer biology↗

bioRxiv2022

A mouse model of human mitofusin 2-related lipodystrophy exhibits adipose-specific mitochondrial stress and reduced leptin secretion

Mitochondrial dysfunction has been reported in obesity and insulin resistance, but primary genetic mitochondrial dysfunction is generally not associated with these, arguing against a straightforward causal relationship. A rare exception, recently identified in humans, is a syndrome of lower body adipose loss, leptin-deficient severe upper body adipose overgrowth, and insulin resistance caused by the p.Arg707Trp mutation in MFN2, encoding mitofusin-2. How this selective perturbation of mitochondrial function leads to tissue- and adipose depot-specific growth abnormalities and systemic biochemical perturbation is unknown. To address this, Mfn2R707W/R707W knock-in mice were generated and phenotyped on chow and high fat diets. Electron microscopy revealed adipose-specific mitochondrial morphological abnormalities. Oxidative phosphorylation by isolated mitochondria was unperturbed, but the cellular integrated stress response was activated in adipose tissue. Fat mass and distribution, body weight, and systemic glucose and lipid metabolism were unchanged, however serum leptin and adiponectin concentrations, and their secretion from adipose explants were reduced. Pharmacological induction of the integrated stress response in wild-type adipocytes also reduced secretion of leptin and adiponectin, suggesting an explanation for the in vivo findings. These data suggest that the p.Arg707Trp MFN2 mutation perturbs mitochondrial morphology and activates the integrated stress response selectively in adipose tissue. In mice, this does not disrupt most adipocyte functions or systemic metabolism, whereas in humans it is associated with pathological adipose remodelling and metabolic disease. In both species, disproportionate effects on leptin secretion may relate to cell autonomous induction of the integrated stress response.

cell biology↗

bioRxiv2022

A structural dendrogram of the actinobacteriophage major capsid proteins provides important structural insights into the evolution of capsid stability

Many double-stranded DNA viruses, including tailed bacteriophages (phages) and herpesviruses, use the HK97-fold in their major capsid protein to make the capsomers of the icosahedral viral capsid. Following the genome packaging at near-crystalline densities, the capsid is subjected to a major expansion and stabilization step that allows it to withstand environmental stresses and internal high pressure. Several different mechanisms for stabilizing the capsid have been structurally characterized, but how these mechanisms have evolved is still not understood. Using cryo-EM structure determination, structural comparisons, phylogenetic analyses, and Alphafold predictions, we have constructed a detailed structural dendrogram describing the evolution of capsid structural stability within the actinobacteriophages. The cryo-EM reconstructions of ten capsids solved to resolutions between 2.2 and 4 [A]ngstroms revealed that eight of them exhibit major capsid proteins that are linked by a covalent cross-linking (isopeptide bond) between subunits that was first described in the HK97 phage. Those covalent interactions ultimately lead to the formation of mutually interlinked capsomers that has been compared to the structure of chain mail. However, three of the closely related phages do not exhibit such an isopeptide bond as demonstrated by both our cryo-EM maps and the lack of the required residue. This work raises questions about the importance of previously described capsid stabilization mechanisms.

biochemistry↗

bioRxiv2022

Quantitative Census of Local Somatic Features in Mouse Visual Cortex

Mammalian neocortex contains a highly diverse set of cell types. These types have been mapped systematically using a variety of molecular, electrophysiological and morphological approaches. Each modality offers new perspectives on the variation of biological processes underlying cell type specialization. Cellular scale electron microscopy (EM) provides dense ultrastructural examination and an unbiased perspective into the subcellular organization of brain cells, including their synaptic connectivity and nanometer scale morphology. It also presents a clear challenge for analysis to identify cell-types in data that contains tens of thousands of neurons, most of which have incomplete reconstructions. To address this challenge, we present the first systematic survey of the somatic region of all cells within a cubic millimeter of cortex using quantitative features obtained from EM. This analysis demonstrates a surprising sufficiency of the perisomatic region to identify cell-types, including types defined primarily based on their connectivity patterns. We then describe how this classification facilitates cell type specific connectivity characterization and locating cells with rare connectivity patterns in the dataset.

neuroscience↗

bioRxiv2022

Salivary exosomal miR-1307-5p predicts disease aggressiveness and poor prognosis in oral squamous cell carcinoma patients

BackgroundSalivary exosomal miRNAs as biomarkers facilitate repeated sampling, real-time disease monitoring and assessment of therapeutic response. This study identifies a single salivary exosomal miRNA prognosticator that will aid in improved patient outcome using a liquid biopsy approach. MethodSmall RNA and transcriptome sequencing profiles of tumour tissues and salivary exosomes from oral cancer patients were compared to their non-cancerous counterparts. We validated these results using the Cancer Genome Atlas database and performing Real-time PCR on a larger patient cohort. Potential target genes, miRNA-mRNA networks and enriched biological pathways regulated by this microRNA were identified using computational tools. ResultsSalivary exosomes (size: 30-50nm) demonstrated a strong expression of CD47 and detectable expression of tetraspanins CD63, CD81 and CD9 by flow cytometry. miR-1307-5p was exclusively overexpressed in tissues and salivary exosomes of oral cancer patients compared to their non-cancerous counterparts. Enhanced expression of miR-1307-5p clinically correlated with poor patient survival, disease progression, aggressiveness and chemo-resistance in these patients. Transcriptome analysis suggested that miRNA-1307-5p could promote oral cancer progression by suppressing THOP1, EHF, RNF4, GET4, and RNF114. ConclusionSalivary exosomal miRNA-1307-5p is a potential prognosticator for predicting poor survival and poor patient outcome in oral cancers.

cancer biology↗

bioRxiv2022

Melanoma cells appropriate pericyte:endothelial cell crosstalk during perivascular invasion in the brain

Post brain colonization, cancer cells may adhere to and spread along the abluminal surface of the vasculature providing advantageous access to oxygen, nutrients, and vessel-derived paracrine factors. For example, brain-tropic melanoma cells are well-known to invade along or within blood vessels at the invasive front, but the molecular mechanisms that guide this process are not well-characterized. We have used melanoma cells of different phenotypic states (melanocytic versus mesenchymal) to characterize different modes of perivascular invasion in the brain. We find that Sox9hi mesenchymal state melanoma cells undergo pericyte-like spreading along brain blood vessels via a Snail1-dependent process; in contrast, Sox10hi melanocytic state melanoma form proliferative, perivascular clusters. Snai1 deletion in mesenchymal-state melanoma cells diminishes Tgf{beta}-induced expression of Pdgfr{beta} which impairs Tgf{beta}/Pdgf ligand-driven motility along the brain microvasculature and dramatically reduces perivascular dispersal of melanoma cells throughout the brain post-colonization. These data suggest that, depending on their transcriptional/phenotypic state, some melanoma cells may appropriate signals that typically mediate endothelial cell:pericyte cross talk as an adaptive mechanism for maintaining vessel proximity and motility within the brain microenvironment.

cancer biology↗

bioRxiv2022

Restoration of beta-GC trafficking improves the lysosome function in Gaucher disease

Lysosomes function as a primary site for catabolism and cellular signaling. These organelles digest a variety of substrates received through endocytosis, secretion and autophagy with the help of resident acid hydrolases. Lysosomal enzymes are folded in the endoplasmic reticulum (ER) and trafficked to lysosomes via Golgi and endocytic route. The inability of hydrolase trafficking due to mutations or mutations in its receptor or cofactor leads to cargo accumulation (storage) in lysosomes, resulting in lysosome storage disorder (LSD). In Gauchers disease (GD), the lysosomes accumulate glucosylceramide due to a lack of {beta}-glucocerebrosidase ({beta}-GC) activity that causes lysosome enlargement/dysfunction. We hypothesize that improving the trafficking of mutant {beta}-GC to lysosomes may delay the progression of GD. RNAi screen using high throughput based lysosomal enzyme activity assay followed by reporter trafficking assay utilizing {beta}-GC-mCherry lead to the identification of nine potential phosphatases. Depletion of these phosphatases in HeLa cells enhanced the {beta}-GC activity by increasing the folding and trafficking of Gauchers mutants to the lysosomes. Consistently, the lysosomes in primary fibroblasts from GD patients restored their function upon the knockdown of these phosphatases. Thus, these studies provide evidence that altering phosphatome activity possibly delays the GD and forms an alternative therapeutic strategy for this genetic disease. Key pointsO_LIPhosphatome RNAi screen identified both activators and inhibitors of cellular glucocerebrosidase activity C_LIO_LIDepletion of selective phosphatases in HeLa cells improved the folding and trafficking of mutant {beta}-glucocerebrosidase to lysosomes C_LIO_LIKnockdown of selective phosphatases restored the low basal {beta}-glucocerebrosidase activity to that of wild-type in primary cells derived from Gauchers disease patients C_LIO_LIDepletion of selective phosphatases displayed variable {beta}-GC activity in neuropathic and non-neuropathic Gauchers disease patient cells C_LI

cell biology↗

bioRxiv2022

Endogenous GDF15 and FGF21 additively alleviate hepatic steatosis and insulin resistance in obese mice.

Obesity in mice and humans is associated with elevated levels of at least two hormones responsive to cellular stress, namely GDF15 and FGF21. Over-expression of each of these is associated with weight loss and beneficial metabolic changes but where they are secreted from and what they are required for physiologically in the context of overfeeding remains unclear. Here we used tissue selective knockout mouse models to establish that, like FGF21, circulating GDF15 is primarily derived from the liver, rather than adipose tissue, muscle or macrophages in high fat fed mice. Combined whole body deletion of FGF21 and GDF15 does not result in any additional weight gain in high fat fed mice but is associated with significantly greater hepatic steatosis and insulin resistance. Collectively the data suggest that activation of the integrated stress response in hepatocytes is a major driver for GDF15 and FGF21 secretion in the context of overfeeding, and that they both act to alleviate this metabolic stress.

physiology↗