Biology subjects

Dash, R.

Publications and source records attributed to Dash, R..

24 records · Page 2Linked to original sources

bioRxiv2020

SARS-CoV2 genome analysis of Indian isolates and molecular modelling of D614G mutated spike protein with TMPRSS2 depicted its enhanced interaction and virus infectivity

COVID-19 that emerged as a global pandemic is caused by SARS-CoV-2 virus. The virus genome analysis during disease spread reveals about its evolution and transmission. We did whole genome sequencing of 225 clinical strains from the state of Odisha in eastern India using ARTIC protocol-based amplicon sequencing. Phylogenetic analysis identified the presence of all five reported clades 19A, 19B, 20A, 20B and 20C in the population. The analyses revealed two major routes for the introduction of the disease in India i.e. Europe and South-east Asia followed by local transmission. Interestingly, 19B clade was found to be much more prevalent in our sequenced genomes (17%) as compared to other genomes reported so far from India. The haplogroup analysis for clades showed evolution of 19A and 19B in parallel whereas the 20B and 20C appeared to evolve from 20A. Majority of the 19A and 19B clades were present in cases that migrated from Gujarat state in India suggesting it to be one of the major initial points of disease transmission in India during month of March and April. We found that with the time 20A and 20B clades evolved drastically that originated from central Europe. At the same time, it has been observed that 20A and 20B clades depicted selection of four common mutations i.e. 241 C>T (5UTR), P323L in RdRP, F942F in NSP3 and D614G in the spike protein. We found an increase in the concordance of G614 mutation evolution with the viral load in clinical samples as evident from decreased Ct value of spike and Orf1ab gene in qPCR. Molecular modelling and docking analysis identified that D614G mutation enhanced interaction of spike with TMPRSS2 protease, which could impact the shedding of S1 domain and infectivity of the virus in host cells.

genomics↗

bioRxiv2020

CMTM6 drives cisplatin resistance in OSCC by regulating AKT mediated Wnt signaling

Chemoresistance is one of the important factors for treatment failure in OSCC, which can culminate in progressive tumor growth and metastatic spread. Rewiring tumor cells to undergo drug-induced apoptosis is a promising way to overcome chemoresistance, which can be achieved by identifying the causative factors for acquired chemoresistance. In this study, to explore the key cisplatin resistance triggering factors, we performed global proteomic profiling of OSCC lines representing with sensitive, early and late cisplatin-resistant patterns. The top ranked up-regulated protein appeared to be CMTM6. We found CMTM6 to be elevated in both early and late cisplatin-resistant cells with respect to the sensitive counterpart. Analyses of OSCC patient samples indicate that CMTM6 expression is upregulated in chemotherapy-non-responder tumors as compared to chemotherapy-naive tumors. Stable knockdown of CMTM6 restores cisplatin-mediated cell death in chemoresistant OSCC lines. Similarly, upon CMTM6 overexpression in CMTM6KD lines, the cisplatin resistant phenotype was efficiently rescued. Mechanistically, it was found that CMTM6 interacts with membrane bound Enolase-1 and stabilized its expression, which in turn activates the AKT-GSK3{beta} mediated Wnt signaling. CMTM6 triggers the translocation of {beta}-catenin into the nucleus, which elevates the Wnt target pro-survival genes like Cyclin D, c-Myc and CD44. Moreover, incubation with lithium chloride, a Wnt signaling activator, efficiently rescued the chemoresistant phenotype in CMTM6KD OSCC lines. In a patient-derived cell xenograft model of chemoresistant OSCC, knock-down of CMTM6 restores cisplatin induced cell death and results in significant reduction of tumor burden. CMTM6 has recently been identified as a stabilizer of PD-L1 and henceforth it facilitates immune evasion by tumor cells. Herewith for the first time, we uncovered another novel role of CMTM6 as one of the major driver of cisplatin resistance.

cancer biology↗

bioRxiv2020

RRBP1 rewires cisplatin resistance in Oral Squamous Cell Carcinoma by regulating YAP-1

Cisplatin-based chemotherapy still remains as one of the primary treatment modalities for OSCC. Several OSCC patients experience relapse owing to development of chemoresistance. To identify key resistance triggering molecules, we performed global proteomic profiling of human OSCC lines presenting with sensitive, early and late cisplatin resistance patterns. From the proteomic profiling study, human RRBP1 was identified to be upregulated in both early and late cisplatin-resistant cells with respect to the sensitive counterpart. Analysis of OSCC patient sample indicates that RRBP1 expression is elevated in chemotherapy-non-responder tumors as compared to chemotherapy-naive tumors. Knocking out RRBP1 resulted in restoring cisplatin mediated cell death in chemoresistant lines and patient derived cells (PDC). Mechanistically, RRBP1 regulates YAP-1 to induce chemoresistance in OSCC. The chemoresistant PDC xenograft data suggests that knock out of RRBP1 induces cisplatin mediated cell death and facilitates a significant reduction of tumor burden. We also found Radezolid, a novel oxazolidinone antibiotic represses the expression of RRBP1 and restores cisplatin-induced cell death in chemoresistant OSCC. This unique combinatorial approach needs further clinical investigation to target advanced OSCC. Here with for the first time, we uncover the novel role of RRBP1 as potential modulator of cisplatin resistance in advanced OSCC.

cancer biology↗

bioRxiv2020

In silico chemical profiling and identification of neuromodulators from Curcuma amada targeting Acetylcholinesterase

Curcuma amada or Mango ginger, a member of the Zingiberaceae family, has been revealed as a beneficiary medicinal plant having diverse pharmacological activities against a wide range of diseases. Due to having neuromodulation properties of this plant, the present study characterized the secondary metabolites of Curcuma amada for their drug-likeness properties, identified potent hits by targeting Acetylcholinesterase (AChE) and revealed neuromodulatory potentiality by network pharmacology approaches. Here in silico ADMET analysis was performed for chemical profiling, and molecular docking and molecular dynamics simulations were used to hit selection and binding characterizations. Accordingly, ADMET prediction showed that around 87.59% of compounds processed drug-likeness activity, where four compounds have been screened out by molecular docking. Guided from induced-fit docking, molecular dynamics simulations revealed phytosterol and curcumin derivatives as the most favorable AChE inhibitors with the highest binding energy, as resulted from MM-PBSA analysis. Furthermore, all of the four hits were appeared to modulate several signaling molecules and intrinsic cellular pathways in network pharmacology analysis, which are associated with neuronal growth survival, inflammation, and immune response, supporting their capacity to revert the condition of neuro-pathobiology. Together, the present in silico based characterization and system pharmacology based findings demonstrate Curcuma amada, as a great source of neuromodulating compounds, which brings about new development for complementary and alternative medicine for the prevention and treatment of neurodegenerative disorders.

bioinformatics↗

bioRxiv2019

Mechanistic insights into the deleterious role of nasu-hakola disease associated TREM2 variants

Recently, critical roles of genetic variants in Triggering Receptor Expressed on Myeloid cells 2 (TREM2) for myeloid cells to Alzhimers disease have been aggressively highlighted. However, little studies focused to the deleterious role of Nasu-Hakola disease (NHD) associated TREM2 variants. In order to get insights into the contributions of these variants in neurodegeneration, we investigated the influences of three well-known NHD associated TREM2 mutations (Y38C, T66M and V126G) on the loss-of-function by using conventional molecular dynamics simulation. Compared to the wild type, the mutants produced substantial differences in the collective motions in the loop regions, which not only promotes structural remodelling in complementarity-determining region 2 (CDR2) loop but also in CDR1 loop, through changing the inter and intra-loop hydrogen bonding network. In addition, the structural studies from free energy landscape showed that Y38, T66 and V126 are crucial for maintaining structural features of CDR1 and CDR2 loops, while their mutation at this position produced steric clash and thus contributes to the structural impact and loss of ligand binding. These results revealed that the presence of the mutations in TREM2 ectodomain induced flexibility and promotes structural alterations. Dynamical scenarios, which are provided by the present study, may be critical to our understanding of the role of the three TREM2 mutations in neurodegenerative diseases.

biochemistry↗

bioRxiv2018

In Silico Analysis of Non Synonymous Single Nucleotide Polymorphisms (nsSNPs) of SMPX Gene in Hearing Impairment

BackgroundMutations in SMPX gene can disrupt the normal activity of the SMPX protein which is involved in hearing process.\n\nObjectiveIn this study, deleterious non-synonymous single nucleotide polymorphisms were isolated from the neutral variants by using several bioinformatics tools.\n\nMethodFirstly, dbSNP database hosted by NCBI was used to retrieve the SNPs of SMPX gene, secondly, SIFT was used primarily to screen the damaging SNPs. Further, for validation PROVEAN, PredictSNP and PolyPhen 2 were used. I-Mutant 3 was utilized to analyze the protein stability change and MutPred predicted the molecular mechanism of protein stability change. Finally evolutionary conservation was done to study their conservancy by using ConSurf server.\n\nResultsA total of 26 missense (0.6517%) and 3 nonsense variants (0.075%) were retrieved and among them 4 mutations were found deleterious by all the tools of this experiment and are also highly conserved according to ConSurf server. rs772775896, rs759552778, rs200892029 and rs1016314772 are the reference IDs of deleterious mutations where the substitutions are S71L, N19D, A29T and K54N. Loss of Ubiquitination, loss of methylation, loss of glycosylation, and loss of MoRF binding motifs are the root causes of protein stability change.\n\nConclusionThis is the first study regarding nsSNPs of SMPX gene where the most damaging SNPs were screened that are associated with the SMPX gene and can be used for further research to study their effect on protein structure and function, their dynamic behavior and how they actually affect proteins flexibility.

bioinformatics↗