Vellore Institute of Technology (VIT) is a private university located in&nbsp;Tamil Nadu, India. Founded in 1984, as Vellore Engineering College, the institution offers 20 undergraduate, 34 postgraduate, four integrated and four research programs. It has campuses in Vellore, Amravati, Bhopal and Chennai.

VIT is one of the top ranked private universities in India according to NIRF, THE and QS Rankings.&nbsp;Govt. of India has recognized&nbsp;VIT, Vellore as an&nbsp;Institution of Eminence. This has allowed VIT to take independent quality initiatives and move up in world ranking.

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VIT University

Department of Bio-Sciences

Acute Pancreatitis (AP) refers to the inflammatory state of the pancreatic mass caused by an abnormal release of digestive enzymes characterized by pancreatic acinar cell injury. It is mainly caused by gallstones, which primarily block sphincter of Oddi opening into the duodenum, heavy alcohol use, systemic diseases, etc. Stimulator of interferon genes known as STING uniquely senses the apoptotic and necrotic DNA fragments. Through the expression of TMEM173 (transmembrane protein 173) or STING protein in macrophages, downstream signaling pathways are activated in AP and are responsible for promoting inflammation. STING elicits a cascade of downstream signaling events such as activation of TBK1, IRF-3 phosphorylation, and IFN-β production along with other cytokines, which result in the excessive manufacture of the type-I IFNs and different kinds of proinflammatory cytokines that take part in the immune defense system of the host. Research findings suggest that STING regulates an array of innate immunity pathways, and the absence of proper treatment measures for AP provides the opportunity of evaluating STING as a striking therapeutic target for AP associated inflammation. Although the understanding of STING hyperactivation and its association with inflammation is relative of recent interest among researchers, extensive studies are going on to identify inhibitors that can directly target STING and inhibits the downstream signaling in AP. Therefore, this review aims to collectively compile the available pieces of evidence, which could help to better understand the role of STING signaling in AP and its promising role as a therapeutic target. © 2021 Elsevier B.V.

World University root node

School of Bio Sciences and Technology

Vellore Campus

Gene

Sting pathway – A futuristic therapeutic target for acute pancreatitis?

BAG3, a co-chaperone protein with a Bcl-2-associated athanogene (BAG) domain, has diverse functionalities in protein-folding, apoptosis, inflammation, and cell cycle regulatory cross-talks. It has been well characterised in cardiac diseases, cancers, and viral pathogenesis. The multiple roles of BAG3 are attributed to its functional regions like BAG, Tryptophan-rich (WW), isoleucine-proline-valine-rich (IPV), and proline-rich (PXXP) domains. However, to study its structural impact on various functions, the experimental 3D structure of BAG3 protein was not available. Hence, the structure was predicted through in silico modelling and validated through computational tools and molecular dynamics simulation studies. To the best of our knowledge, the role of BAG3 in bacterial infections is not explicitly reported. We attempted to study them through an in-silico protein–protein interaction network and host-pathogen interaction analysis. From structure-function relationships, it was identified that the WW and PXXP domains were associated with cellular cytoskeleton rearrangement and adhesion-mediated response, which might be involved in BAG3-related intracellular bacterial proliferation. From functional enrichment analysis, Gene Ontology terms and topological matrices, 18 host proteins and 29 pathogen proteins were identified in the BAG3 interactome pertaining to Legionellosis, Tuberculosis, Salmonellosis, Shigellosis, and Pertussis through differential phosphorylation events associated with serine metabolism. Furthermore, it was evident that direct (MAPK8, MAPK14) and associated (MAPK1, HSPD1, NFKBIA, TLR2, RHOA) interactors of BAG3 could be considered as therapeutic markers to curb down intracellular bacterial propagation in humans. © 2021 Wiley Periodicals LLC

Department of Biotechnology

Journal of Cellular Biochemistry

In silico structure evaluation of BAG3 and elucidating its association with bacterial infections through protein–protein and host-pathogen interaction analysis

Cyclin-dependent kinases (CDKs) belong to the serine/threonine kinase family, and their unique interactions with a variety of cyclin complexes influence its catalytic activity to ensure unimpaired cell cycle progression. In addition to their cell cycle regulatory roles, it is becoming increasingly clear that the CDKs can have multiple functional roles like transcription, epigenetic regulation, metabolism, stem cell self-renewal, neuronal functions, and in spermatogenesis. Further in addition, recent reports suggest that CDKs have a remarkable regulatory role in influencing the pro-inflammatory functions of various cytokines during the clinical inflammatory responses. CDKs initiate the inflammatory responses by triggering the activity of prominent pro-inflammatory transcription factors such as nuclear factor kappa B (NF-kB), signal transducer and activator of transcription 3 (STAT3), and activator protein 1 (AP-1). The transcriptional CDKs (tCDKs) is crucial for organizing various transcription events and associated processes such as RNA capping, splicing, 3ʹ end formation, and chromatin remodeling. Although the in-depth mechanism of certain mammalian CDKs is explored with respect to inflammation, the role of other tCDKs or any synergistic play among the members still remains unexplored. Until today, there is only supportive and palliative care available most of the inflammatory disorders, and thus it is the right time to explore novel pharmacological targets. In this regard, we focus on the pathophysiological role of CDK7, CDK8 and CDK9 and their impact on the development of inflammatory disorders within the mammals. Additionally, we discuss the potential trends of having tCDKs as a therapeutic target for fine-tuning inflammatory disorders. © 2020

Transcriptional cyclin-dependent kinases as the mediators of inflammation-a review

Injectable calcium phosphate cement is a promising biomaterial for hard tissue repair due to its osteoinductivity, biocompatibility properties, and its use to correct defect areas involving narrow cavities with limited accessibility by the minimally invasive technique. Microwave-synthesized hydroxyapatite (HA) was used for the preparation of cement. In recent years, both magnesium and strontium calcium phosphate cements have exhibited rapid setting, improved mechanical strength, and a good resorption rate. A big step still remains to develop injectable magnesium and strontium phosphate cements with ideal self-setting properties, adequate mechanical strength, and good biocompatibility for clinical applications. In this study, both magnesium and strontium were doped with synthesized semiamorphous and crystalline hydroxyapatite (HA). The powder mixture was mixed with Na2HPO4, NaH2PO4, and a carboxymethyl cellulose (CMC) solution to develop the novel magnesium and strontium calcium phosphate cement. The setting time, physiochemical properties of hardened cement, microstructure, mechanical strength, and injectability of the prepared cement were studied. The toxicity evaluation and cell adhesion, which are necessary to identify the suitability of the material for different applications, were quantified and investigated using fibroblast cells. The setting time of cement was reduced substantially for magnesium-or strontium-doped cement by 2 min. The phase composition of the hardened cement expresses the semiamorphous or crystalline phase of HA with additives. Smooth and complete injection of cement paste was observed in semiamorphous HA-based cement. The intercellular reactive oxygen stress (ROS) of the Sr2+-doped cement sample showed varied degrees of toxicity to cells in terms of different concentrations. The Mg2+-doped cement showed significant attachment of cells after treatment at varying incubation times. © 2021 The Authors. Published by American Chemical Society.

Department of Manufacturing Engineering

School of Mechanical Engineering

Fulltext

ACS Omega

Characterization and in Vitro Evaluations of Injectable Calcium Phosphate Cement Doped with Magnesium and Strontium

HOX proteins are homeodomain-containing transcription factors that play a central role in development. We have applied genome-wide approaches to develop time-dependent profile of differentially expressed genes in early and mature adipocytes. The list of differentially expressed HOX genes were developed by analyzing the microarray datasets of murine adipocyte samples at different time points of development. Since these datasets were obtained from Gene Expression Omnibus (GEO), we were able to find a new HOX gene, HOXC13 in adipogenesis. To investigate whether these members of the homeobox gene family are expressed and regulated in preadipocytes or mature adipocytes, RNA was isolated from 3T3-L1 preadipocyte cells at different time point's through-out the preadipocyte and adipocyte state. A reverse transcriptase-polymerase chain reaction strategy was applied for the analysis of gene expression. We have observed that HOXA5 and HOXC13 were differentially expressed in preadipocytes and HOXD4 and HOXD8 in mature adipocytes. To understand this difference in expression pattern, we have considered to investigate the role of the major regulators of adipogenesis in HOX gene regulation. Since Retinoic acid receptor (RAR) was reported previously as a regulator of Hox genes, we chose the combination of Peroxisome proliferator-activated receptor gamma (PPARγ) and Retinoic X receptor (RXR) which are modulated by the presence of RAR. To provide a detailed analysis of retinoic acid (RA) and/or PPARγ induced transcriptional and epigenetic changes within the homeotic clusters of mouse fibroblast cells (3T3-L1), we have performed a promoter mapping of HOX genes and observed an enriched binding site for PPARγ and RXR in their promoter regions. We further confirmed this PPARγ and RXR binding to HOX gene promoters by re-analyzing the anti-PPARγ/anti-RXR ChIP-Seq data. Based on the results, we modulated the PPARγ expression at the transcriptional and translational levels by using 5 different pharmacological molecules (TSA, GW9662, ATRA, FH535, and Pioglitazone) to elucidate their effect on the HOX gene transcription. These pharmacological molecules had a direct or indirect regulatory effect on the PPARγ activity. We observed that PPARγ suppression alone is enough for the upregulation of HOXA5 and HOXD4 genes. In addition, HOXD8 regulation was mediated by RAR activation in mature adipocytes but the regulation of HOXC13 gene expression was not clear. We suggest that it might be partially mediated through suppressing PPARγ activation. Further insights are required to provide a mechanistic detail about HOX gene regulation through PPARγ. In this study, we have reported a time-dependent expression analysis of HOXA5, HOXD4, HOXD8, and HOXC13 in preadipocytes and mature adipocytes. Also, we have suggested PPARγ/RAR dependent regulation for these genes during adipogenesis. © 2020 Elsevier B.V.

Dynamics of HOX gene expression and regulation in adipocyte development

Aims: Gender disparities exist in smoking-related lung cancer epidemiology, but the molecular basis has not been explored so far. We aimed at identifying genes with gender-bias expression pattern in smoking lung cancer patients for understanding the molecular basis of gender bias in smokers using meta-analysis of microarray gene expression data. Materials and methods: Transcriptome of around 1100 samples from 13 studies were used in the meta-analysis to identify ‘Lung Cancer genes specific to Female-Smokers’ (LCFS) and ‘Lung Cancer genes specific to Male-Smokers’ (LCMS). The expression profiles of these genes were validated with an independent microarray report and TCGA-RNA-sequencing data. The molecular interactions, pathway, and other functional annotations were portrayed for the key genes identified. Key findings: We identified 1159 gender-biased genes in smoking lung cancer patients. Of these, 400 and 474 genes showed differential expression in cancerous compared to normal lung of women (LCFS) and men (LCMS), respectively. While many up-regulated LCFS were involved in ‘immune responses’ including T-cell activation, leukocyte cell-cell adhesion, the LCMS were mainly involved in ‘positive regulation of gene expression’, signaling pathways including RAS, VEGF, insulin-receptor signaling, and ‘cell cycle’. Significance: The strategic-method identified genes, particularly, SNX20, GIMAP6, MTMR2, FAM171B, IDH1, MOBP, FBXO17, LPXN and WIPF1, which were consistently differentially expressed in at least 4 studies, and in agreement with RNA-Seq data. Exploring their functions could be beneficial to the gender-based diagnosis, prognosis, and treatment of lung cancer in smokers. The current meta-analysis supports existing knowledge of sexual-dimorphism of immune responses in cancer. © 2020

Life Sciences

The molecular basis of gender disparities in smoking lung cancer patients

Moyamoya disease (MMD), a cerebrovascular disorder caused by the RNF213 gene, is a cerebrovascular, neurological disorder leading to ischemic strokes. Our previous work suggested that RNF213 might be involved in the pro-inflammatory TNFα-mediated insulin-resistance pathway in adipocytes. Insulin resistance can lead to cerebrovascular diseases and ischemic strokes. Though p. R4810 K has been reported as the founder mutation for Asian population with this disease, there are several mutations continuously reported in clinical diagnosis. We are interested to know whether these mutations can modulate insulin resistance. Also, we are intended to understand the causalities of RNF213 and its associated mutations in MMD. For this, we have adopted a computational approach to characterize RNF213 and its naturally occurring SNPs. Clinically reported SNPs and the predicted SNPs were analyzed for their pathogenicity and effect on the biological function of the protein. To increase accuracy, this was performed through three different analysis software (PROVEAN, SIFT, and SNAP2). The mutations that were found to be deleterious in all the three platforms were further analyzed for their effect on the thermal stability of the protein through I-mutant and iStable. It was found that R4810 K and other mutations decreased the thermodynamic stability of the protein. Loss of function of RNF213 was suggested in some reports. Contrary to this, some studies reported a gain of function state due to the R4810K mutation. To understand this we have measured the ligand-binding ability of this mutated protein through COFACTOR and COACH. An increase in ligand binding is always related to the functional stability of a protein. We have observed that the R4810K mutation might increase the iron-binding efficiency of the amino acid residues. This increase in binding was further validated by analyzing the binding efficiencies by docking. Since RNF213 was previously reported as a target for Protein Tyrosine Phosphatase 1B (PTP1B), we have also analyzed whether PTP1B-binding positions are susceptible to mutations. We have re-analyzed our earlier report on the differential expression pattern of RNF213 in cancer and obese samples. We have provided a detailed analysis of the most deleterious SNPs related to RNF213. Also, we provide a prediction for the loss of function and gain of function attributes of RNF213 and its predicted causalities in MMD and insulin resistance. © 2021 Elsevier Ltd

Computational Biology and Chemistry

In silico explanation for the causalities of deleterious RNF213 SNPs in Moyamoya disease and insulin resistance

Proteus mirabilis is one among the most frequently identified pathogen in patients with the urinary tract infection. The multidrug resistance exhibited by P. mirabilis renders the treatment ineffective, and new progressive strategies are needed to overcome the antibiotic resistance (AR). We have analyzed the evolutionary relationship of 29 P. mirabilis strains available in the National Center for Biotechnology Information-Genome database. The antimicrobial resistance genes of P. mirabilis along with the enriched pathways and the Gene Ontology terms are analyzed using gene networks to understand the molecular basis of AR. The genes rpoB, tufB, rpsl, fusA, and rpoA could be exploited as potential drug targets as they are involved in regulating the vital functions within the bacterium. The drug targets reported in the present study will aid researchers in developing new strategies to combat multidrug-resistant P. mirabilis. © 2020 Wiley Periodicals LLC

Journal of Cellular Physiology

Gene interaction network approach to elucidate the multidrug resistance mechanisms in the pathogenic bacterial strain Proteus mirabilis

The complex and heterogeneous nature of neuroblastoma poses a great challenge to the scientific community for developing an effective therapeutic drug. Neuroblastoma tumors show relapse and resistance to available drugs and it is proving to be an obstacle for efficient treatment options. The tumor accounts for about 7% of the malignancies worldwide and is seen mostly in children around one year. Our present study aims to understand various mechanisms underlying Neuroblastoma. The gene interaction network of 92 Neuroblastoma related genes along with a total of 339 functional interactions are used for the gene interaction network construction and analysis. The clustering analysis resulted in four densely interconnected gene clusters. We further performed functional enrichment analysis and found important pathways associated with neuroblastoma in PI3K/AKT pathway, MAPK pathway, Ras pathway, Rap1 pathway, Cytokine- cytokine interaction, Neurotrophin signaling, EGFR tyrosine kinase inhibitor resistance, and VEGF signaling pathways. The predominant genes involved in the enriched pathways are ANGPT2, FGF2, NGFR, NTRK1, NTRK2, PDGFC, TGFA, TP53, VEGFB, VEGFC, BDNF, NRAS, and VEGFA. The topological parameter analysis has shown the genes with more direct interactions are considered as the hub genes and are important in the network. The genes TP53, VEGFA, BDNF, MYCN, and FGF2 with the maximum number of functional interactors, can be used as potential therapeutic targets for Neuroblastoma. The results obtained in our study will be helpful for researchers in better understanding the molecular level associations during the Neuroblastoma progression. © 2021 Elsevier Inc.

Gene Reports

Integrated systems biology approach using gene network analysis to identify the important pathways and new potential drug targets for Neuroblastoma

Long noncoding RNAs (lncRNAs) are widely known for their regulatory function in transcriptional and posttranscriptional processes. The involvement of such non-protein-coding RNAs in nuclear organization and chromatin remodeling is often associated with an increased risk of human malignancies. In cancer, lncRNAs either promote cell survival or may act as a growth suppressor, thus conferring a key regulatory function other than their established role in fundamental cellular processes. Interestingly, lncRNAs interfere with the stages of apoptosis and related pathways involving p53. Many of these molecules either regulate or are regulated by p53 while mounting oncogenic events. Consequently, they may confer both prosurvival or proapoptotic functions depending upon the tissue type. Since the mechanism of cell death is bypassed in many human cancers, it has emerged that the lncRNAs are either overexpressed or knocked down to sensitize cells to apoptotic stimuli. Nonetheless, the abundant expression of lncRNAs in tumor cells renders them suitable targets for anticancer therapies. Although the role of lncRNAs in the p53 network and apoptosis has been independently defined, their interplay in activating p53-target genes during cell cycle arrest remains unexplored. Thus, we have specifically reviewed the possible involvement of lncRNAs in the p53-mediated apoptosis of human cancer cells. In particular, we summarize the growing evidence from individual studies and analyze whether lncRNAs are essential to facilitate apoptosis in a p53-dependent manner. This may lead to the identification of p53-associated lncRNAs that are suitable therapeutic targets or diagnostic/prognostic markers. © 2021 International Federation for Cell Biology