Simrinder Singh Sodhi

The novel inhibitor BRM270 downregulates tumorigenesis by suppression of NF-κB signaling cascade in MDR-induced stem like cancer-initiating cells.

The nuclear factor κB (NF-κB) and interleukin-6 (IL-6) contribute to multidrug resistance (MDR) in tumor chemotherapy. The essential phenomenon of oncogenic activation of NF-κB in cancer-initiating cells showing MDR resulting from increased IL-6 expression is still unclear. Cancer stem cells (CSCs) have been the objective of intensive study. The aim of this study was to investigate the selective and potential efficacy of BRM270 against stem-like cancer-initiating cells (SLCICs) via the molecular mechanisms of its anticancer effects. Co-regulation of NF-κB and Cdk6 might be new arena to mitigate tumorigenesis. In the present study phyto-drug based approach provides a new avenue in understanding the amelioration and regulatory mechanisms in CSCs. In the present study, an in vivo tumor metastasis model of osteosarcoma was established by injecting Cal72 and SaOS-2 SLCICs into the right lower flank of nude mice. Later the development of tumor was analyzed by LICOR Biosciences (Pearl image analyzer). Significant suppression of activation of NF-κB and LPS-induced gene expression and apoptosis by BRM270 was confirmed by FACS, western blotting and qPCR. Further, both p65 and Cdk6 were significantly (P<0.05) overexpressed in BRM270 non-treated Cal72 SLCICs compared to treated group. BRM270 directly dephosphorylated RelA and selectively inhibited NF-κB transcriptional activity, resulting in decreased expression of interleukin-6, a cytokine implicated in cancer metastasis. BRM270-mediated cell shrinkage, pyknosis, karyorrhexis and programmed cell death (PCD) were observed by Hoechst 33342 staining while flow cytometry analysis showed significant (P<0.05) decrease in cell population from G0-G1 phases. These findings suggest that activation of the oncogenic Cdk6-NF-κB pathway, resulting from increased IL-6 expression, plays a central role in CD133 expressing SLCICs augmented MDR and neoplasia. This study proposes targeting of NF-κB, and Cdk6 with IL-6 as potential targets for PCD and treatment of chemotherapeutic resistance of CSCs to design novel therapies for their elimination.

Comparative transcriptomic analysis by RNA-seq to discern differential expression of genes in liver and muscle tissues of adult Berkshire and Jeju Native Pig.

RNA-seq is being rapidly adopted for the profiling of the transcriptomes in different areas of biology, especially in the studies related to gene regulation. The discovery of differentially expressed genes (DEGs) between adult animals of Jeju Native Pig (JNP) and Berkshire breeds of Sus scrofa, is of particular interest for the current study. For the better understanding of the gene expression profiles of the liver and longissimus dorsi muscle, DEGs were identified via RNA-seq. Sequence reads were obtained from Illumina HiSeq2000 and mapped to the pig reference genome (Sscrofa10.2) using Tophat2. We identified 169 and 39 DEGs in the liver and muscle of JNP respectively, by comparison with Berkshire breed. Out of all identified genes, 41 genes in the liver and 9 genes in the muscle have given significant expression. Gene ontology (GO) terms of developmental process and KEGG pathway analysis showed that metabolic, immune response and protein binding were commonly enriched pathways in the two tissues. Further the heat map analysis by ArrayStar has shown the different levels of expression in JNP with respect to the Berkshire breed. The validation through real time PCR and western blotting also confirmed the differential expression of genes in both breeds. Genes pertaining to metabolic process and inflammatory and immune system are more enriched in Berkshire breed. This comparative transcriptome analysis of two tissues suggests a subset of novel marker genes which expressed differently between the JNP and Berkshire.

Targeted inhibition of osteosarcoma tumor growth by bone marrow-derived mesenchymal stem cells expressing cytosine deaminase/5-fluorocytosine in tumor-bearing mice.

Mesenchymal stem cells (MSCs) are considered as an attractive approach for gene or drug delivery in cancer therapy. In the present study, the ability of human bone marrow‐derived MSCs expressing the cytosine deaminase/5‐fluorocytosine prodrug (CD/5‐FC MSCs) to target the human osteosarcoma cell line Cal72 was evaluated.

Evaluation of body growth and immunity-related differentially expressed genes through deep RNA sequencing in the piglets of Jeju native pig and Berkshire

This study was carried out with the objective to investigate the differentially expressed genes (DEGs) between Jeju native pig (JNP) and Berkshire piglets. The RNA-Seq technique was used to investigate the transcriptomes in the fat, liver and longissimus dorsi muscle from these two breeds. Paired-end reads of the sequences that passed the quality filters were aligned to the Sus scrofa genome using tophat2 (v2.0.2). In this study, 65% of muscle, 20% of fat and 54% of liver genes showed higher expression in the piglets of JNP than in Berkshire. Gene Ontology and signaling pathways showed that immune response and lipid metabolisms were commonly enriched pathways in all three tissues. It was found that the genes pertaining to body growth and immune system are significantly (P < 0.01) more highly expressed in Berkshire piglets. DEGs explored between the piglets of the two breeds might influence the identification of the genetic markers for further breed improvement programs. Our findings provide a new perspective for understanding and identifying candidate genes that are involved in various biological functions. Moreover, transcriptome analysis makes it easier to understand the differences between genetic mechanisms of breeds.

Anti-tumor activity of wogonin, an extract from Scutellaria baicalensis, through regulating different signaling pathways

Wogonin is a plant flavonoid compound extracted from Scutellaria baicalensis (Huang-Qin or Chinese skullcap) and has been studied thoroughly by many researchers till date for its anti-viral, anti-oxidant, anti-cancerous and neuro-protective properties. Numerous experiments conducted in vitro and in vivo have demonstrated wogonins excellent tumor inhibitory properties. The anti-cancer mechanism of wogonin has been ascribed to modulation of various cell signaling pathways, including serine-threonine kinase Akt (also known as protein kinase B) and AMP-activated protein kinase (AMPK) pathways, p53-dependent/independent apoptosis, and inhibition of telomerase activity. Furthermore, wogonin also decreases DNA adduct formation with a carcinogenic compound 2-Aminofluorene and inhibits growth of drug resistant malignant cells and their migration and metastasis, without any side effects. Recently, newly synthesized wogonin derivatives have been developed with impressive anti-tumor activity. This review is the succinct appraisal of the pertinent articles on the mechanisms of anti-tumor properties of wogonin. We also summarize the potential of wogonin and its derivatives used alone or as an adjunct therapy for cancer treatment. Furthermore, pharmacokinetics and side effects of wogonin and its analogues have also been discussed.

An Integrated In Silico Approach for the Structural and Functional Exploration of Lipocalin 2 and its Functional Insights with Metalloproteinase 9 and Lipoprotein Receptor-Related Protein 2.

Recent evidence demonstrated that Lipocalin 2 (LCN2) is garnering interest from a wide spectrum as biomarker. Here, we present an in silico characterization of LCN2 belonging to prominent organisms focusing for their physicochemical and structural differences. We found significant variations in physicochemical properties between organisms and low sequence similarity based on their amino acid properties alone. However, we identified three main structurally distinct motif regions that are conserved among all variants. Further investigation was carried out to understand the functional insights of LCN2. We selected LCN2 sequence from Gallus gallus as an input query to identify unique scoring-framework based on computational tools and confidence scores of various putative associations. Among all ten proteins associated with LCN2; highest confidence of prediction were seen for the associations between LCN2 and metalloproteinase 9 (MMP9) and lipoprotein receptor-related protein 2 (LRP2) which play vital roles in tumor growth and iron transportation, respectively. We attempted to determine binding affinities of LCN2 with MMP9 and LRP2 through molecular modeling and docking. Selected docked models were examined for complex stability by GROMACS. Alteration of binding affinity between LCN2 with MMP9 and LRP2 proteins that we found in this study may provide new direction for future therapeutic targets.

An approach to identify SNPs in the gene encoding acetyl-CoA acetyltransferase-2 (ACAT-2) and their proposed role in metabolic processes in pig

The novel liver protein acetyl-CoA acetyltransferase-2 (ACAT2) is involved in the beta-oxidation and lipid metabolism. Its comprehensive relative expression, in silico non-synonymous single nucleotide polymorphism (nsSNP) analysis, as well as its annotation in terms of metabolic process with another protein from the same family, namely, acetyl-CoA acyltransferase-2 (ACAA2) was performed in Sus scrofa. This investigation was conducted to understand the most important nsSNPs of ACAT2 in terms of their effects on metabolic activities and protein conformation. The two most deleterious mutations at residues 122 (I to V) and 281 (R to H) were found in ACAT2. Validation of expression of genes in the laboratory also supported the idea of differential expression of ACAT2 and ACAA2 conceived through the in silico analysis. Analysis of the relative expression of ACAT2 and ACAA2 in the liver tissue of Jeju native pig showed that the former expressed significantly higher (P<0.05). Overall, the computational prediction supported by wet laboratory analysis suggests that ACAT2 might contribute more to metabolic processes than ACAA2 in swine. Further associations of SNPs in ACAT2 with production traits might guide efforts to improve growth performance in Jeju native pigs.

An integrated in silico approach for functional and structural impact of non- synonymous SNPs in the MYH1 gene in Jeju Native Pigs

BackgroundThis study was performed to identify the non- synonymous polymorphisms in the myosin heavy chain 1 gene (MYH1) association with skeletal muscle development in economically important Jeju Native Pig (JNP) and Berkshire breeds. Herein, we present an in silico analysis, with a focus on (a) in silico approaches to predict the functional effect of non-synonymous SNP (nsSNP) in MYH1 on growth, and (b) molecular docking and dynamic simulation of MYH1 to predict the effects of those nsSNP on protein-protein association.ResultsThe NextGENe (V 2.3.4.) tool was used to identify the variants in MYH1 from JNP and Berkshire using RNA seq. Gene ontology analysis of MYH1 revealed significant association with muscle contraction and muscle organ development. The 95 % confidence intervals clearly indicate that the mRNA expression of MYH1 is significantly higher in the Berkshire longissimus dorsi muscle samples than JNP breed. Concordant in silico analysis of MYH1, the open-source software tools identified 4 potential nsSNP (L884T, K972C, N981G, and Q1285C) in JNP and 1 nsSNP (H973G) in Berkshire pigs. Moreover, protein-protein interactions were studied to investigate the effect of MYH1 mutations on association with hub proteins, and MYH1 was found to be closely associated with the protein myosin light chain, phosphorylatable, fast skeletal muscle MYLPF. The results of molecular docking studies on MYH1 (native and 4 mutants) and MYLFP demonstrated that the native complex showed higher electrostatic energy (−466.5 Kcal mol−1), van der Walls energy (−87.3 Kcal mol−1), and interaction energy (−835.7 Kcal mol−1) than the mutant complexes. Furthermore, the molecular dynamic simulation revealed that the native complex yielded a higher root-mean-square deviation (0.2–0.55 nm) and lower root-mean-square fluctuation (approximately 0.08–0.3 nm) as compared to the mutant complexes.ConclusionsThe results suggest that the variants at L884T, K972C, N981G, and Q1285C in MYH1 in JNP might represent a cause for the poor growth performance for this breed. This study is a pioneering in-depth in silico analysis of polymorphic MYH1 and will serve as a valuable resource for further targeted molecular diagnosis and population-based studies conducted for improving the growth performance of JNP.

Novel phyto-derivative BRM270 inhibits hepatocellular carcinoma cells proliferation by inducing G2/M phase cell cycle arrest and apoptosis in xenograft mice model.

Hepatocellular carcinoma (HCC) is a major threat to human health worldwide and development of novel antineoplastic drug is demanding task. BRM270 is a proprietary combination of traditional medicinal herbs, has been shown to be effective against a wide range of stem-like cancer initiating cells (SLCICs). However, the underlying mechanism and antitumor efficacy of BRM270 in human hepatocellular carcinoma (HCC) cells have not been well elucidated till date. Here we studied the tumoricidal effect of BRM270 on human-CD133+ expressing stem-like HepG-2 and SNU-398 cells. Gene expression profiling by qPCR and specific cellular protein expressions was measured using immunocytochemistry/western blot analysis. In vivo efficacy of BRM270 has been elucidated in the SLCICs induced xenograft model. In addition, 2DG-(2-Deoxy-d-Glucose) optical-probe guided tumor monitoring was performed to delineate the size and extent of metastasized tumor. Significant (P<0.05) induction of Annexin-V positive cell population and dose-dependent upregulation of caspase-3 confirmed apoptotic cell death by pre/late apoptosis. In addition, bright field and fluorescence microscopy of treated cells revealed apoptotic morphology and DNA fragmentation in Hoechst33342 staining. Levels of c-Myc, Bcl-2 and c-Jun as invasive potential apoptotic marker were detected using qPCR/Western blot. Moreover, BRM270 significantly (P<0.05) increased survival rate that observed by Kaplan-Meier log rank test. In conclusion, these results indicate that BRM270 can effectively inhibit proliferation and induce apoptosis in hepatoma cells by down-regulating CyclinD1/Bcl2 mediated c-Jun apoptotic pathway.

Differentiation dynamics of mammary epithelial stem cells from Korean holstein dairy cattle under ECM-free conditions

The “stem cells” are commonly defined as “cells capable of self-renewal through replication and differentiating into specific lineages”. The mammary gland contains functional stem/progenitor cells. The current study was planned with the objectives to study the differentiation dynamics of Korean Holstein mammary epithelial stem cells (KHMESCs) under the optimum culture conditions. Lineage negative KHMESCs isolated from mammary tissue of lactating cows have shown the typical differentiation dynamics with formation of lobulo–alveolar structures in in vitro culture. This suggests the existence of bipotential mammary epithelial stem cells in the mammary gland. The strong mRNA expression of pluripotency factors indicates stemness, whereas expression of milk protein genes and epithelial cell-specific gene indicate their differentiation capabilities. Further, immunostaining results have shown the differentiation capabilities of KHMESCs into both luminal and basal lineages under the extracellular matrix (ECM, matrigel) free environment. However, under matrigel, the differentiation process was comparatively higher than without matrigel. Immunostaining results also suggested that differentiated cells could secrete milk proteins such as β-casein. To our knowledge, these data represent the first report on the differentiation dynamics and establishment of mammary epithelial stem cells from Korean Holstein with typical stemness properties. It was observed that isolated KHMESCs had normal morphology, growth pattern, differentiation ability, cytogenetic and secretory activity even without ECM. Therefore, it is concluded that established KHMESCs could be used for further studies on Korean Holstein dairy cows related to lactation studies, as non-GMO animal bioreactors and stem cell-based management of bovine mastitis including post-mastitis damage.