Expression of CD44 in Head and Neck Squamous Cell Carcinoma-An In-Silico Study.

Introduction CD44, a multistructural and multifunctional transmembrane glycoprotein, is a promising cancer stem cell (CSC) marker that regulates the properties of CSCs, including self-renewal, tumor initiation, and metastasis, and confers resistance to chemotherapy and radiotherapy. The aim of the present study was to evaluate the gene and protein expression of CD44 and explore its prognostic value in head and neck squamous cell carcinoma (HNSCC). Methodology The present observational study employs computational tools for analysis. The Cancer Genome Atlas Head-Neck Squamous Cell Carcinoma dataset (520 primary HNSCC and 44 normal tissues) from the University of Alabama at Birmingham Cancer platform was used to study the association of CD44 mRNA transcript levels with various clinicopathological characteristics of HNSCC including age, gender, tumor grade, tumor stage, human papillomavirus (HPV) status, p53 mutation status, and overall survival. The CD44 protein expression in HNSCC and normal tissues was ascertained using the National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium Head-and-Neck cancer dataset (108 primary HNSCC and 71 normal tissues). Results CD44 mRNA transcript and protein expression levels were significantly higher in HNSCC tissues than in normal tissues, and high CD44 expression was correlated with poor survival. CD44 was upregulated in Stage 1 and Grade 2 HNSCC compared with other stages and grades. Overexpression of CD44 was observed in HPV-negative and TP53-positive mutant status in HNSCC. Conclusion The pleiotropic roles of CD44 in tumorigenesis urge the need to explore its differential expression in HNSCC. The study concludes that CD44 can be a potential diagnostic and prognostic biomarker for HNSCC and offer new molecular targets for CD44-targeted therapy for cancer management.

Deciphering the genetic alterations in matrix metallo-proteinase gene family and its putative association with head and neck squamous cell carcinoma.

Matrix metallo-proteinases (MMPs) a group of zinc-dependent proteolytic enzymes which play a key role in tumorigenesis by degrading almost all extracellular matrix (ECM) components. MMPs are associated with tumour progression including invasion, angiogenesis, metastasis and poor prognosis. Genetic alterations such as single nucleotide variations and other gross chromosomal abnormalities have been found to drive the process of malignant transformation. In line with the above facts, the present study aims to analyse the genetic alterations, associated gene expression patterns and survival probability of HNSCC patients upon differential expression of the crucial members of the MMP family. The observational study utilised several computational tools. The cBioportal database was used as the primary source of identification of genetic alterations in the MMP family of genes. The Cancer Gene Atlas dataset (Firehose Legacy) was used for the investigations. The highest frequency of alteration was identified in the MMP20 gene (8%). The common gene alterations were amplifications, deep deletions, mis-sense and truncating mutations. Interestingly, amplification and deep deletion followed the same pattern in about 31 patients, in genes MMP1, 3, 7, 8, 10, 12, 20, and 27. The MMP20 gene expression analysis showed a significant difference between the normal subjects and the patients with primary tumors (6.95 x 10-4). The Kaplan-Meier survival curve analysis identified that female patients with high-level expression of the MMP20 gene had a low survival probability when compared to male HNSC patients. Taken together, the present study provides preliminary information about the involvement of the MMP20 gene of the MMP family with HNSCC. Further experimental analysis is required to derive a strong association between the gene alterations observed with HNSCC.

Computational approach towards identification of pathogenic missense mutations in AMELX gene and their possible association with amelogenesis imperfecta.

Amelogenin gene (AMEL-X) encodes an enamel protein called amelogenin, which plays a vital role in tooth development. Any mutations in this gene or the associated pathway lead to developmental abnormalities of the tooth. The present study aims to analyze functional missense mutations in AMEL-X genes and derive an association with amelogenesis imperfecta. The information on missense mutations of human AMEL-X gene was collected from Ensembl database (https://asia.ensembl.org). Three different computational tools viz., SIFT, PolyPhen and PROVEAN were used to identify the deleterious or pathogenic forms of mutations in the gene studied. I-Mutant Suit was used to identify the stability of the proteins identified as deleterious by the three tools. Further, MutPred analysis revealed the pathogenicity of these mutations. Among 96 missense variants reported in AMEL-X gene, 18 were found to be deleterious using the three prediction tools (SIFT, PolyPhen and PROVEAN). When these variants were subjected to protein stability analysis, about 14 missense variants showed decreased stability whereas the other 8 variants showed increased stability. Further, these variants were analyzed using MutPred which identified 9 variants to be highly pathogenic. ExAC database revealed that all the pathogenic mutations had a minor allele frequency less than 0.01. The in silico analysis revealed highly pathogenic mutations in amelogenin gene which could have a putative association with amelogenesis imperfecta. These mutations should be screened in patients for early diagnosis of susceptibility to AI.

In silico validation of the non-antibiotic drugs acetaminophen and ibuprofen as antibacterial agents against red complex pathogens.

BACKGROUND: Acetaminophen (APAP) and ibuprofen (IB) are drugs commonly used to alleviate pain due to their anti-inflammatory, anti-pyretic, and analgesic effect. The aim of the present study is to unravel the molecular mechanisms underlying the antimicrobial potential of these two drugs against red complex pathogens, namely, Porphyromonas gingivalis, Treponema denticola, and Tannerella forsythia, by using in silico tools, since they are potentially associated with inflammatory conditions related to periodontal infections. METHODS: The STITCH v5.0 pipeline was primarily used for identifying drug-protein interactions; VirulentPred and VICMPred were used for elucidating the virulence property and functional class of the proteins. The subcellular localization of virulent proteins was assessed using PSORTb v3.0 and the epitopes were identified using BepiPred v1.0 Linear Epitope Prediction tool. RESULTS: APAP and IB were found to interact with proteins involved in cellular process, metabolism, and virulence. The virulent proteins targeted by the drugs were located in the cytoplasm, which would further add to the effectiveness of the drugs to serve as antimicrobial agents. Finally, epitope prediction revealed multiple epitopes in the virulent proteins which can be specifically focused on. CONCLUSIONS: APAP and IB were found to target vital proteins involved in the cellular process, metabolism, and virulence of red complex pathogens. An in-depth knowledge on the interaction of these drugs and their antibacterial activity would add to the plethora of merits gained by these drugs in clinical settings. Further in vitro studies on a wide range of pathogens are warranted to substantiate the true interactions between the drugs and the protein repertoire of pathogens.

Anti-cancer effects of thymoquinone in mouse neuroblastoma (Neuro-2a) cells through caspase-3 activation with down-regulation of XIAP.

Thymoquinone (TQ) is a bioactive component derived from the medicinal plant Nigella sativa. Recent studies reported that TQ exhibited cytotoxic effects in several cancer cell lines. Currently, no information in the literature is found concerning its mechanisms and cytotoxicity on neuroblastoma cells. In this study, the cytotoxicity of TQ in mouse neuroblastoma cells (Neuro-2a) was investigated. Our results showed that TQ significantly reduced viability of Neuro-2a cells than normal neuronal cells. Apoptosis induction by TQ was confirmed by DAPI and AO/PI staining. TQ triggered the apoptotic pathway, which was characterized by increased Bax/Bcl-2 ratio. TQ significantly increased the expression of pro-apoptotic protein Bax, whereas decreased the expression of anti-apoptotic protein Bcl-2, which leads to the release of cytochrome c from mitochondria into the cytoplasm. Moreover, TQ treatment directs the activation of caspase-3 followed by the cleavage of poly(ADP-ribose) polymerase (PARP). Interestingly, we also observed that TQ down-regulated caspase inhibitor X-linked inhibitor of apoptosis protein (XIAP). These results indicate that TQ induces apoptosis via caspase-3 activation with down-regulation of XIAP in Neuro-2a cells.