Biology subjects

Singh, A. K.

Publications and source records attributed to Singh, A. K..

At least 109 records · Page 6Linked to original sources

bioRxiv2021

The Sugar Porter gene family of Piriformospora indica: Nomenclature, Transcript Profiling and Characterization

Piriformospora indica is one of the prominent mutualistic root endophyte known to overcome phosphate and nitrogen limitation in a wide variety of plant species, reciprocally takes up carbohydrates for its survival and growth. A total of nineteen potential hexose transporters have been identified from P. indica genome, that may contributes to its potential of carbohydrate assimilation from host plant. Phylogenetic analysis assembles it in 10 groups within 3 clusters. To ease the study, systematic nomenclature were provided to 19 putative hexose transporters as "PiST1-PiST19" in accordance to their appearance on the supercontigs genome sequence of P. indica. The protein length ranges from 487 to 608 amino acids. Out of 19 putative hexose transporters, 9 have been predicted to contain 12 transmembrane domains (PiST1, PiST2, PiST5, PiST6, PiST9, PiST10, PiST11, PiST12 and PiST17), along with MFS family and Sugar porter subfamily motif. Therefore, transcripts were detected for these 9 genes. During colonization, three P. indica genes PiST1, PiST5 and PiST9 have shown induction as compared to axenic culture. Similarly during phosphate starvation, revealed PiST12 to be strongly enhanced. Carbon starvation study in liquid axenic culture resulted in induction of 4 genes, PiST6, PiST9, PiST12 and PiST17. We found co-relation in the expression pattern of PiPT and PiST12 during phosphate starvation. In silico analysis revealed the presence of functional conserved fucose permease (FucP) domain, involved in fructose transport. Phylogenetic analysis revealed that PiST12 groups closely with basidiomycetes hexose transporters. Further, functional complementation of {Delta}hxt null mutant revealed, PiST12 is able to complement growth on fructose and galactose but negligible on glucose.

plant biology↗

bioRxiv2021

BMP signaling is necessary and sufficient for osteoarthritis and a target for disease modifying therapy

ObjectiveTo investigate the role of BMP signaling in osteoarthritis' pathogenesis and propose a disease-modifying therapy for OA. MethodsC57BL6/J mouse line was used to perform ACLT surgery at P120 to study the expression pattern of the BMP signaling readout pSMAD1/5/9. To investigate whether activation of BMP signaling is sufficient and necessary to induce osteoarthritis, we have used conditional GOF and LOF mouse lines in which BMP signaling can be activated or depleted, respectively, upon intra-peritoneal injection of tamoxifen. Finally, we locally inhibited BMP signaling through intra-articular injection of LDN-193189 pre- and post-onset surgically induced OA. Most of the analysis has been done through immunohistochemistry, histopathological staining, and micro-CT to evaluate the status of the pathogenesis of the disease. ResultsWe observed concomitant activation of BMP signaling, as judged by pSMAD1/5/9 immunoreactivity in the articular cartilage, upon induction of osteoarthritis with simultaneous depletion of SMURF1, an intra-cellular BMP signaling inhibitor in articular cartilage. Even without surgical induction of osteoarthritis, only BMP gain-of-function mutation induces OA in mouse articular cartilage. Also, genetic, or pharmacological inhibition of BMP signaling offered significant protection against OA pathogenesis. Interestingly, post-onset of the disease, inhibition of BMP signaling by intra-articular injection of LDN-193189 retarded OA progression with a significant reduction in inflammatory markers. ConclusionOur study demonstrated that BMP signaling plays an essential role in the pathogenesis of OA and that local BMP inhibition can be an effective therapeutic strategy to mitigate osteoarthritis.

developmental biology↗

bioRxiv2021

The biogenesis and function of nucleosome arrays

Numerous chromatin remodeling enzymes position nucleosomes in eukaryotic cells. Aside from these factors, transcription, DNA sequence, and statistical positioning of nucleosomes also shapes the nucleosome landscape. Precise contributions of these processes remain unclear due to their functional redundancy in vivo. By incisive genome engineering, we radically decreased their redundancy in Saccharomyces cerevisiae. The transcriptional machinery is strongly disruptive of evenly spaced nucleosomes, and proper nucleosome density and DNA sequence critical for their biogenesis. The INO80 remodeling complex spaces nucleosomes in vivo and positions the first nucleosome over genes in an H2A.Z-independent fashion. INO80 requires its Arp8 subunit but unexpectedly not the Nhp10 module for spacing. Spaced nucleosomes prevent cryptic transcription and protect cells against genotoxic stress such as DNA damage, recombination and transpositions. We derive a unifying model of the biogenesis of the nucleosome landscape and suggest that it evolved not only to regulate but also to protect the genome.

molecular biology↗

bioRxiv2021

Unravelling the Physiological Correlates of Mental Workload Variations in Tracking and Collision Prediction Tasks: Implications for Air Traffic Controllers

ObjectiveWe have designed tracking and collision prediction tasks to elucidate the differences in the physiological response to the workload variations in basic ATC tasks to untangle the impact of workload variations experienced by operators working in a complex ATC environment. BackgroundEven though several factors influence the complexity of ATC tasks, keeping track of the aircraft and preventing collision are the most crucial. MethodsPhysiological measures, such as electroencephalogram (EEG), eye activity, and heart rate variability (HRV) data, were recorded from 24 participants performing tracking and collision prediction tasks with three levels of difficulty. ResultsThe neurometrics of workload variations in the tracking and collision prediction tasks were markedly distinct, indicating that neurometrics can provide insights on the type of mental workload. The pupil size, number of blinks and HRV metric, root mean square of successive difference (RMSSD), varied significantly with the mental workload in both these tasks in a similar manner. ConclusionOur findings indicate that variations in task load are sensitively reflected in physiological signals, such as EEG, eye activity and HRV, in these basic ATC-related tasks. ApplicationThese findings have applicability to the design of future mental workload adaptive systems that integrate neurometrics in deciding not just when but also what to adapt. Our study provides compelling evidence in the viability of developing intelligent closed-loop mental workload adaptive systems that ensure efficiency and safety in ATC and beyond. PrecisThis article identifies the physiological correlates of mental workload variation in basic ATC tasks. The findings assert that neurometrics can provide more information on the task that contributes to the workload, which can aid in the design of intelligent mental workload adaptive system.

neuroscience↗

bioRxiv2021

H3K27me3 mediated KRT14 upregulation promotes TNBC peritoneal metastasis

Triple Negative Breast Cancer (TNBC) is known to have poor prognosis and adverse clinical outcome among all breast cancer subtypes due to the absence of available targeted therapy for it. Emerging literature indicates that epigenetic reprogramming is now appreciated as a driving force for TNBC pathophysiology. High expression of epigenetic modulator EZH2 (Enhancer of zeste homolog 2) has been shown to correlate with TNBC poor prognosis but the contribution of EZH2 catalytic (H3K27me3) versus non-catalytic EZH2 (NC-EZH2) function in TNBC growth and progression remains elusive. In the process of dissecting the impact of H3K27me3 versus NC-EZH2 function in TNBC pathogenesis, we reveal that selective hyperactivation of H3K27me3 over NC-EZH2 not only promotes TNBC metastasis but also alters the metastatic landscape of TNBC. Using extensive in- vivo live animal imaging, we present conclusive evidence that peritoneal metastasis, particularly splenic metastasis of TNBC is governed by H3K27me3. Transcriptome analyses of hyperactive H3K27me3 cells lead us to discover Cytokeratin-14 (KRT14) as a new target of H3K27me3. Unlike classical H3K27me3 mediated suppression of gene expression, here; we observe that H3K27me3 enhances KRT14 transcription by attenuating the binding of transcriptional repressor Sp1 to its promoter. Further, loss of KRT14 significantly reduces TNBC migration, invasion and splenic metastasis. Finally, genetic ablation of EZH2 or pharmacological inhibition of EZH2 catalytic function by FDA approved drug tazemetostat (EPZ6438) robustly inhibits TNBC peritoneal metastasis. Altogether, our preclinical findings posit a rational insight for the clinical development of H3K27me3 inhibitor like tazemetostat as a targeted therapy against TNBC.

cancer biology↗

bioRxiv2021

Immunogenic Potential of DNA Vaccine candidate, ZyCoV-D against SARS-CoV-2 in Animal Models

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), initially originated in China in year 2019 and spread rapidly across the globe within 5 months, causing over 96 million cases of infection and over 2 million deaths. Huge efforts were undertaken to bring the COVID-19 vaccines in clinical development, so that it can be made available at the earliest, if found to be efficacious in the trials. We developed a candidate vaccine ZyCoV-D comprising of a DNA plasmid vector carrying the gene encoding the spike protein (S) of the SARS-CoV-2 virus. The S protein of the virus includes the receptor binding domain (RBD), responsible for binding to the human angiotensin converting enzyme (ACE-2) receptor. The DNA plasmid construct was transformed into E. coli cells for large scale production. The immunogenicity potential of the plasmid DNA has been evaluated in mice, guinea pig, and rabbit models by intradermal route at 25, 100 and 500g dose. Based on the animal studies proof-of-concept has been established and preclinical toxicology (PCT) studies were conducted in rat and rabbit model. Preliminary animal study demonstrates that the candidate DNA vaccine induces antibody response including neutralizing antibodies against SARS-CoV-2 and also provided Th-1 response as evidenced by elevated IFN-{gamma} levels.

immunology↗

bioRxiv2020

Helicobacter pylori and Epstein-Barr virus coinfection stimulates the aggressiveness in gastric cancer through the regulation of gankyrin

Persistent coinfection of Helicobacter pylori (H. pylori) and Epstein-Barr virus (EBV) promotes aggressive gastric carcinoma. The molecular mechanisms underlying the aggressiveness in H. pylori and EBV coinfected gastric cancer is not well characterized. In the current study, we investigated the molecular mechanism involved in the cooperation of H. pylori and EBV-driven proliferation of gastric epithelial cells. Results showed that the coinfections are significantly more advantageous to the pathogens to create a microenvironment that favors the higher pathogen-associated gene expression. The EBV latent genes EBNA1 and EBNA3C are highly overexpressed in the coinfections compared to individual EBV infection at different time points (12 and 24 hrs). The H. pylori-associated genes 16s rRNA, CagA, and BabA has also been highly overexpressed in coinfections compared to H. pylori alone. Gankyrin is a small protein of 25 KDa involved in multiple biological and physiological processes. The upregulation of gankyrin modulates the various cell signaling pathways, leading to oncogenesis. The gankyrin shows a similar expression pattern as EBNA3C at both transcript and protein levels, suggesting a possible correlation. Further EBV and H. pylori create microenvironments that induce cell transformation and oncogenesis by dysregulation of the cell-cycle regulator, GC marker, cell migration, DNA response, and antiapoptotic genes in infected gastric epithelial cells by enhancing the expression of gankyrin. Our study provides new insights into the molecular mechanism where the interplay between two oncogenic agents (H. pylori and EBV) leads to the enhanced carcinogenic activity of gastric epithelial cells through overexpression of oncoprotein gankyrin. ImportanceIn the present study, we have evaluated the synergistic effect of EBV and H. pylori infection on gastric epithelial cells in various coinfection models. These coinfection models depict the first exposures of gastric epithelial cells with EBV and then the H. pylori. While other coinfection models narrated the first exposures of H. pylori followed by the infection of EBV. This led to an enhanced oncogenic phenotype in gastric epithelial cells. We determined the coinfection of EBV and H. pylori enhanced the expression of oncogenic protein gankyrin. The interplay between EBV and H. pylori promotes the oncogenic properties of AGS cells through the newly discovered oncoprotein gankyrin. EBV and H. pylori mediated upregulation of gankyrin further dysregulates various cancer-associated hallmarks of genes such as cell-migratory, gastric cancer marker, tumor suppressor, DNA damage response, and proapoptotic genes.

microbiology↗

bioRxiv2020

An epithelial Nfkb2 pathway exacerbates intestinal inflammation by supplementing latent RelA dimers to the canonical NF-κB module

Aberrant inflammation associated with human ailments, including inflammatory bowel disease (IBD), is typically fuelled by the inordinate activity of RelA/NF-{kappa}B transcription factors. As such, the canonical NF-{kappa}B module mediates controlled nuclear activation of RelA dimers from the latent cytoplasmic complexes. What provokes pathological RelA activity in the colitogenic gut remains unclear. The noncanonical NF-{kappa}B pathway promotes immune organogenesis involving Nfkb2 gene products. Because NF-{kappa}B pathways are intertwined, we asked if noncanonical signaling aggravated inflammatory RelA activity. Our investigation revealed frequent engagement of the noncanonical pathway in human IBD. In a mouse model, an Nfkb2 function exacerbated gut inflammation by amplifying the epithelial RelA activity induced upon intestinal injury. Our mechanistic studies clarified that cell-autonomous Nfkb2 signaling supplemented latent NF-{kappa}B dimers leading to hyperactive canonical RelA response in the inflamed colon. In sum, regulation of latent NF-{kappa}B dimers links noncanonical signaling to RelA-driven inflammatory pathologies and may provide for therapeutic targets. In briefNoncanonical NF-{kappa}B signals in intestinal epithelial cells supplement latent RelA dimers that, in turn, aggravated canonical NF-{kappa}B response in the colitogenic gut exacerbating intestinal inflammation. HighlightsO_LIHuman IBD involves the frequent engagement of the noncanonical NF-{kappa}B pathway. C_LIO_LIMice deficient in the noncanonical signal transducer Nfkb2 are resistant to experimental colitis. C_LIO_LINoncanonical NF-{kappa}B signaling supplements latent RelA NF-{kappa}B dimers. C_LIO_LINoncanonical NF-{kappa}B signaling amplifies canonical NF-{kappa}B response to TLR ligands. C_LI

immunology↗

bioRxiv2020

Meta-GWAS for quantitative trait loci identification in soybean

We report a meta-Genome Wide Association Study involving 73 published studies in soybean (Glycine max L. [Merr.]) covering 17,556 unique accessions, with improved statistical power for robust detection of loci associated with a broad range of traits. De novo GWAS and meta-analysis were conducted for composition traits including fatty acid and amino acid composition traits, disease resistance traits, and agronomic traits including seed yield, plant height, stem lodging, seed weight, seed mottling, seed quality, flowering timing, and pod shattering. To examine differences in detectability and test statistical power between single- and multi-environment GWAS, comparison of meta-GWAS results to those from the constituent experiments were performed. Using meta-GWAS analysis and the analysis of individual studies, we report 483 quantitative trait loci (QTL) at 393 unique loci. Using stringent criteria to detect significant marker trait associations, 66 candidate genes were identified, including 17 candidate genes for agronomic traits, 19 for seed related traits, and 33 for disease reaction traits. This study identified potentially valuable candidate genes that affect multiple traits. The success in narrowing down the genomic region for some loci through overlapping mapping results of multiple studies is a promising avenue for community-based studies and plant breeding applications.

genetics↗

bioRxiv2020

PATRIOT: A pipeline for tracing identical-by-descent chromosome segments to improve genomic prediction in self-pollinating crop species

The lowering genotyping cost is ushering in a wider interest and adoption of genomic prediction and selection in plant breeding programs worldwide. However, improper conflation of historical and recent linkage disequilibrium between markers and genes restricts high accuracy of genomic prediction (GP). Multiple ancestors may share a common haplotype surrounding a gene, without sharing the same allele of that gene. This prevents parsing out genetic effects associated with the underlying allele of that gene among the set of ancestral haplotypes. We present Parental Allele Tracing, Recombination Identification, and Optimal predicTion (i.e., PATRIOT) approach that utilizes marker data to allow for a rapid identification of lines carrying specific alleles, increases the accuracy of genomic relatedness and diversity estimates, and improves genomic prediction. Leveraging identity by descent, PATRIOT showed an improvement in GP accuracy by 16.6% compared to the traditional rrBLUP method. This approach will help to increase the rate of genetic gain and allow available information to be more effectively utilized within breeding programs.

genomics↗

bioRxiv2020

Using Machine Learning To Develop A Fully Automated Soybean Nodule Acquisition Pipeline (SNAP)

Nodules form on plant roots through the symbiotic relationship between soybean (Glycine max L. Merr.) roots and bacteria (Bradyrhizobium japonicum), and are an important structure where atmospheric nitrogen (N2) is fixed into bio-available ammonia (NH3) for plant growth and developmental. Nodule quantification on soybean roots is a laborious and tedious task; therefore, assessment is done on a less informative qualitative scale. We report the Soybean Nodule Acquisition Pipeline (SNAP) for nodule quantification that combines RetinaNet and UNet deep learning architectures for object (i.e., nodule) detection and segmentation. SNAP was built using data from 691 unique roots from diverse soybean genotypes, vegetative growth stages, and field locations; and has a prediction accuracy of 99%. SNAP reduces the human labor and inconsistencies of counting nodules, while acquiring quantifiable traits related to nodule growth, location and distribution on roots. The ability of SNAP to phenotype nodules on soybean roots at a higher throughput enables researchers to assess the genetic and environmental factors, and their interactions on nodulation from an early development stage. The application of SNAP in research and breeding pipelines may lead to more nitrogen use efficient soybean and other legume species cultivars, as well as enhanced insight into the plant-Bradyrhizobium relationship.

plant biology↗

bioRxiv2020

Direct observation of RAG recombinase recruitment to chromatin and the IgH locus in live pro-B cells

The RAG1 and RAG2 proteins introduce double-strand DNA breaks at antigen-receptor loci in developing lymphocytes to initiate V(D)J recombination. How RAG proteins find the correct target locus in a vast excess of non-specific chromatin is not known. Here we measured dynamics of RAG1/RAG2 interactions with chromatin in living pro-B cells. We found that the majority of RAG1 or RAG1/RAG2 complex is in a fast 3D diffusive state, and the residual slow diffusive (bound) fraction was determined by a non-core portion of RAG1, and the PHD domain of RAG2. The RAG proteins exhibited distinct dynamics at the IgH locus. In particular, RAG2 increased the probability of RAG1 binding to IgH, a property that likely explains its non-catalytic role in V(D)J recombination. Our observations reveal how RAG finds its targets in developing B cells. One Sentence SummarySingle-molecule imaging of the RAG recombinase reveals its search strategy for chromatin, H3K4me3 and antibody gene loci in living cells.

biophysics↗

bioRxiv2020

Chromatin State Dynamics Confers Specific Therapeutic Strategies in Enhancer Subtypes of Colorectal Cancer

The extent and function of chromatin state aberrations during colorectal cancer (CRC) progression is not completely understood. Here, by comprehensive epigenomic characterization of 56 tumors, adenomas, and their matched normal tissues, we define the dynamics of chromatin states during the progression of colorectal cancer. H3K27ac-marked active enhancer state could distinguish between different stages of CRC progression. By epigenomic editing, we present evidence that gains of tumor-specific enhancers for crucial oncogenes, such as ASCL2 and FZD10, was crucial for excessive proliferation. Consistently, combination of MEK plus bromodomain (BET) inhibition was found to have synergistic effects in CRC patient-derived xenograft (PDX) models. Probing inter-tumor heterogeneity, we identified four distinct enhancer subtypes (EpiC), three of which correlate well with previously defined transcriptomic subtypes (CMSs). Importantly, CMS2 can be divided into two EpiC subgroups with significant survival differences. Leveraging such correlation, we devised a combinatorial therapeutic strategy of enhancer-blocking bromodomain inhibitors with pathway-specific inhibitors (PARPi, EGFRi, and TGF{beta}i) for three EPIC groups. Our data suggest that the dynamics of active enhancer underlies colorectal cancer progression and the patient-specific active enhancer patterns govern their unique gene expression patterns which can be leveraged for precision combination therapy.

cancer biology↗

bioRxiv2020

Physiological, Biochemical and Microstructural Changes in Rice (Oryza sativa L.) under Varying pH Levels

Soil acidification exerts detrimental effects on rice plant leading to severe reduction in its yield. In the present study, we investigated the physiological, biochemical and microstructural changes in the leaves of rice cultivars, namely, Jhilli Dhan (JD) and Gora Dhan (GD), under varying pH conditions (pH 6.5, 5.5, 4.5 and 3.5). Seedlings were grown at varying pH levels for 14 days under controlled conditions. Root and shoot growth and chlorophyll content were found to be decreased with increasing acidity, whereas electrolyte leakage was increased with increasing acidity. Overall, seedling growth was significantly reduced at pH 3.5, while, it was maximum at pH 6.5 treatment, which might be the result of cumulative altered physiological parameters. Further, biochemical parameters, namely total soluble sugar (TSS), proline content and lipid peroxidation were found to be positively correlated with acidity. Microstructural changes were observed through Swept-Source Optical Coherence Tomography (SS-OCT) and Field Emission Scanning Electron Microscope (FESEM). The thickness between different layers of leaves was found to be disintegrating at low pH conditions and the thickness of parenchyma cells was reduced significantly. FESEM analysis revealed changes in characteristics of stomata under acidic stress. The understanding of physiological, biochemical and microstructural changes in rice leaves under varying pH conditions may help in developing rice with improved tolerance towards soil acidity stress.

plant biology↗

bioRxiv2020

A novel sialic acid-binding adhesin present in multiple species contributes to the pathogenesis of infective endocarditis

Bacterial binding to platelets is a key step in the development of infective endocarditis (IE). Sialic acid, a common terminal carbohydrate on host glycans, is the major receptor for streptococci on platelets. So far, all defined interactions between streptococci and sialic acid on platelets are mediated by serine rich repeat proteins (SRRPs). However, we identified Streptococcus oralis subsp. oralis IE-isolates that bind sialic acid but lack SRRPs. In addition to binding sialic acid, some SRRP-negative isolates also bind the cryptic receptor {beta}-1,4-linked galactose through a yet unknown mechanism. Using comparative genomics, we identified a novel sialic acid-binding adhesin, here named AsaA (associated with sialic acid adhesion A), present in IE-isolates lacking SRRPs. We demonstrated that S. oralis subsp. oralis AsaA is required for binding to platelets in a sialic acid-dependent manner. AsaA comprises a non-repeat region (NRR), consisting of a FIVAR/CBM and two Siglec-like and Unique domains, followed by 31 DUF1542 domains. When recombinantly expressed, Siglec-like and Unique domains competitively inhibited binding of S. oralis subsp. oralis and directly interacted with sialic acid on platelets. We further demonstrated that AsaA impacts the pathogenesis of S. oralis subsp. oralis in a rabbit model of IE. Additionally, we found AsaA orthologues in other IE-causing species and demonstrated that the NRR of AsaA from Gemella haemolysans blocked binding of S. oralis subsp. oralis, suggesting that AsaA contributes to the pathogenesis of multiple IE-causing species. Finally, our findings provide evidence that sialic acid is a key factor for bacterial-platelets interactions in a broader range of species than previously appreciated, highlighting its potential as a therapeutic target. Authors summaryInfective endocarditis (IE) is typically a bacterial infection of the heart valves that causes high mortality. Infective endocarditis can affect people with preexisting lesions on their heart valves (Subacute-IE). These lesions contain platelets and other host factors to which bacteria can bind. Growth of bacteria and accumulation of host factors results in heart failure. Therefore, the ability of bacteria to bind platelets is key to the development of IE. Here, we identified a novel bacterial protein, AsaA, which helps bacteria bind to platelets and contributes to the development of disease. Although this virulence factor was characterized in Streptococcus oralis, a leading cause of IE, we demonstrated that AsaA is also present in several other IE-causing bacterial species and is likely relevant to their ability to cause disease. We showed that AsaA binds to sialic acid, a terminal sugar present on platelets, thereby demonstrating that sialic acid serves as a receptor for a wider range of IE-causing bacteria than previously appreciated, highlighting its potential as a therapeutic target.

microbiology↗

bioRxiv2020

Liver-specific suppression of ANGPTL4 improves obesity-associated diabetes and mitigates atherosclerosis in mice

ABSTRACTAngiopoietin-like 4 (ANGPTL4) is a major regulator of lipoprotein lipase (LPL) activity, which is responsible for maintaining optimal levels of circulating triacylglycerol (TAG) for distribution to different tissues including the adipose tissues (ATs), heart, muscle and liver. Dysregulation of trafficking and portioning of fatty acids (FA) can promote ectopic lipid accumulation in metabolic tissues such as the liver, ultimately leading to systemic metabolic dysfunction. To investigate how ANGPTL4 regulates hepatic lipid and glucose metabolism, we generated liver-specific ANGPTL4 knockout mice (LKO). Using metabolic turnover studies, we demonstrate that hepatic ANGPTL4 deficiency facilitates catabolism of TAG-rich lipoprotein (TRL) remnants in the liver via increased hepatic lipase (HL) activity, which results in a significant reduction in circulating TAG and cholesterol levels. Deletion of hepatocyte ANGPTL4 protects against diet-induce obesity, glucose intolerance, liver steatosis, and atherogenesis. Mechanistically, we demonstrate that absence of ANGPTL4 in hepatocytes promotes FA uptake which results in increased FA oxidation, ROS production, and AMPK activation. Finally, we demonstrate the utility of a targeted pharmacologic therapy that specifically inhibits ANGPTL4 in the liver and protects against diet-induced obesity, dyslipidemia, glucose intolerance, and liver damage without causing any of the deleterious effects previously observed with neutralizing antibodies.Competing Interest StatementThe authors have declared no competing interest.View Full Text

physiology↗

bioRxiv2020

Talin Rod Domain Containing Protein 1 (TLNRD1) is a novel actin- bundling protein which promotes filopodia formation

Talin is a mechanosensitive adapter protein which couples integrins to the cytoskeleton and regulates integrin-mediated adhesion. Talin rod domain-containing protein-1 (TLNRD1) shares 22% homology with the R7R8 domains of talin, and is highly conserved throughout vertebrate evolution, however little is known about its function. Here we show that TLNRD1 is an -helical protein which shares the same atypical topology as talin R7R8, but forms a novel antiparallel dimer arrangement. Actin co-sedimentation assays and electron microscopy reveal TLNRD1 is an actin-bundling protein that forms tight actin bundles. In addition, TLNRD1 binds to the same LD-motif containing proteins, RIAM and KANK, as talin, and thus may act in competition with talin. Filopodia are cell protrusions supported by tightly bundled actin filaments and TLNRD1 localises to filopodia tips, increases filopodia number and promotes cell migration in 2D. Together our results suggest that TLNRD1 has similar functionality to talin R7R8, serving as a nexus between the actin and microtubule cytoskeletons independent of adhesion complexes.

cell biology↗

bioRxiv2020

Global Spread of SARS-CoV-2 Subtype with Spike Protein Mutation D614G is Shaped by Human Genomic Variations that Regulate Expression of TMPRSS2 and MX1 Genes

COVID-19 pandemic is a major human tragedy. Worldwide, SARS-CoV-2 has already infected over 3 million and has killed about 230,000 people. SARS-CoV-2 originated in China and, within three months, has evolved to an additional 10 subtypes. One particular subtype with a non-silent (Aspartate to Glycine) mutation at 614th position of the Spike protein (D614G) rapidly outcompeted other pre-existing subtypes, including the ancestral. We assessed that D614G mutation generates an additional serine protease (Elastase) cleavage site near the S1-S2 junction of the Spike protein. We also identified that a single nucleotide deletion (delC) at a known variant site (rs35074065) in a cis-eQTL of TMPRSS2, is extremely rare in East Asians but is common in Europeans and North Americans. The delC allele facilitates entry of the 614G subtype into host cells, thus accelerating the spread of 614G subtype in Europe and North America where the delC allele is common. The delC allele at the cis-eQTL locus rs35074065 of TMPRSS2 leads to overexpression of both TMPRSS2 and a nearby gene MX1. The cis-eQTL site, rs35074065 overlaps with a transcription factor binding site of an activator (IRF1) and a repressor (IRF2). IRF1 activator can bind to variant delC allele, but IRF2 repressor fails to bind. Thus, in an individual carrying the delC allele, there is only activation, but no repression. On viral entry, IRF1 mediated upregulation of MX1 leads to neutrophil infiltration and processing of 614G mutated Spike protein by neutrophil Elastase. The simultaneous processing of 614G spike protein by TMPRSS2 and Elastase serine proteases facilitates the entry of the 614G subtype into host cells. Thus, SARS-CoV-2, particularly the 614G subtype, has spread more easily and with higher frequency to Europe and North America where the delC allele regulating expression of TMPRSS2 and MX1 host proteins is common, but not to East Asia where this allele is rare.

genomics↗