Identification of hub genes associated with head and neck squamous cell carcinoma by integrated bioinformatics approach and RNA-seq validation analysis.

Head and neck squamous cell carcinoma (HNSC) is one of the most lethal malignancies around the globe. Due to its complex nature, the diagnostic and prognostic signatures of HNSC remain poorly understood. This study was launched to identify signature genes and their signaling pathways related to the development of HNSC. In the current study, we retrieved the GSE53819 dataset from the Gene Expression Omnibus (GEO) database to determine the differentially expressed genes (DEGs) using the "Limma" R package. Adjusted P values P < 0.05 and |logFC| ≥ 1 were selected as the filtering conditions. To identify hub genes, the protein-protein interaction (PPI) network construction of the DEGs was performed using STRING. We further used UALCAN, GEPIA, OncoDB, GENT2, MEXPRESS, and HPA databases for the expression, validation, survival, and methylation analyses of the hub genes. The cBioPortal tool was used to investigate the genetic alterations in hub genes. CancerSEA, TIMER, DAVID, ENCORI, and DrugBank were also used to explore a few more hub gene-associated parameters. Lastly, HOK, FaDu, and SCC25 cell lines were used to validate hub gene expression via RNA sequencing (RNA-seq) technique. A total of top 250 DEGs were selected for detailed analysis in this study. From these DEGs, prognostic and diagnostic associated four hub genes, which could serve as potential molecular biomarkers and therapeutic targets in HNSC patients were identified. Four hub genes, including down-regulated DNAH1 and DNALI1, while up-regulated DNAH9 and CCDC151 were strongly implicated in HNSC. We also validated the same expression pattern of the hub genes using RNA-seq analysis in HNSC and normal cell lines. Moreover, this study also revealed some novel links between DNAH1, DNALI1, DNAH9, and CCDC151 expression and genetic alterations, promoter methylation status, immune cell infiltration, miRNAs, gene enrichment terms, and various chemotherapeutic drugs. In conclusion, we indicated four hub genes (DNAH1, DNALI1, DNAH9, and CCDC151) and their associated signaling pathways, which may improve our understanding of HNSC and could be used as new therapeutic targets.

Comparative analysis of antioxidant activity, toxicity, and mineral composition of kernel and pomace of apricot (Prunus armeniaca L.) grown in Balochistan, Pakistan.

The present study aims to investigate some physical attributes, total phenolics content, total flavonoids content, mineral composition, bioluminescence toxicity assay and antioxidant activity in terms of DPPH, HPS, TAC and FRAP assays in the kernel and pomace samples of six apricot cultivars grown in Balochistan, Pakistan. TFC and TPC determined by the AlCl3 and Folin-Ciocalteu assays in apricot kernel extracts of six cultivars varied from 1797.5 (Chagali) to 4778.9 (Badoghur) mg QUE/100 g DW and from 1750.0 (Chagali) to 5005.8 (Badoghur) mg GAE/100 g DW. Apricot kernels exhibited higher antioxidant activity than pomace; antioxidant activity in terms of IC50 in kernels ranged from 24.88 to 98.61 µg/ml for DPPH, 334.84 to 516.63 µg/ml for HPS, from 22.02 to 110.80 µg/ml for TAC and from 96.27 to 163.35 µg/ml for FRAP. The apricot kernels showed higher TPC, TFC, bioluminescence toxicity to V. logei and antioxidant activity than the pomace. The correlation analysis demonstrated substantial contributions of polyphenols and flavonoids to antioxidant assays. The sample type was the leading factor affecting the amounts of K, Na, Ca, Fe, and Mn in the tested samples; mineral contents were higher in pomace than kernels. The highest inhibition to V. logei was found in the kernels of Badoghur (IC50 = 1.61 mg/ml). The PCA analysis showed significant contributions of phenolic and flavonoid contents towards antioxidant bioluminescence toxicity assays. Our results suggest Badoghur, Shakarpara and Sardai kernels are rich sources of secondary metabolites and possess remarkable antioxidant and antiluminescence activity and can make a significant contribution to the treatment and prevention of chronic health problems.

In Vitro Anti-Inflammatory, Anticancer (MCF-7, 3T3, and HeLa Cell Lines), and Brine Shrimp Lethality Assay and FTIR Analysis of the Extract and Fractions of the Whole Plant of Heliotropium europaeum.

In this study, anti-inflammatory, anticancer, brine shrimp lethality, and FTIR studies were evaluated. The oxidative burst assay using the chemiluminescence technique, MTT assay, brine shrimp lethality assay, and FTIR analysis were the methods used for the evaluation of anti-inflammatory, anticancer, brine shrimp lethality, and FTIR studies, respectively. The whole-plant butanol fraction of Heliotropium europaeum (WBFHE) showed anti-inflammatory activity on ROS having IC5014.7 ± 2.5 while the extract and other fractions of the whole plant of Heliotropium europaeum exhibited no anti-inflammatory activity. None of the extract and fractions of the whole plant of Heliotropium europaeum exhibited anticancer (MCF-7, 3T3, and HeLa cell lines) activities. The whole-plant aqueous fraction of Heliotropium europaeum (WAFHE) and whole-plant butanol fraction of Heliotropium europaeum (WBFHE) showed lethality at high concentration while at low concentration, no toxicity was shown. The whole-plant methanolic extract of Heliotropium europaeum (WMEHE) and whole-plant n-hexane fraction of Heliotropium europaeum (WHFHE) exhibited no toxicity. FTIR interpretation showed the functional groups for the aromatic compounds, phenols, carboxylic acids, esters, alkanes, alkenes, alcohols, alkyl halides, sulfate esters, phosphines, silanes, nitriles, thiols, amines, phosphoric acids, and nitro compounds.

In Vitro Anticancer MCF-7, Anti-Inflammatory, and Brine Shrimp Lethality Assay (BSLA) and GC-MS Analysis of Whole Plant Butanol Fraction of Rheum ribes (WBFRR).

In this study, GC-MS analysis has shown that whole plant butanol fraction of rheum ribes (WBFRR) comprises of 21 compounds which exhibited anticancer (MCF-7) activity having IC50 value of 36.01± 0.26. MTT assay (MCF-7), Oxidative Burst assay using chemiluminescence technique, and B-Hatching techniques were the methods used for anticancer MCF-7, anti-inflammatory, and Brine Shrimp Lethality Assay (BSLA). GC-MS was used for structural elucidation. Whole plant methanol extract of rheum ribes (WMERR), whole plant n-hexane fraction of rheum ribes (WHFRR), and whole plant aqueous fraction of rheum ribes (WAFRR) were inactive against anticancer (MCF-7) cell line. Whole plant methanol extract of rheum ribes (WMERR), whole plant aqueous fraction of rheum ribes (WAFRR) and whole plant butanol fraction of rheum ribes (WBFRR) showed anti-inflammatory activity on ROS having IC50 value of 23.2±1.9, 24.2±2.7 and 12.0±0.6. Whole plant butanol fraction of rheum ribes (WBFRR) showed Brine Shrimp Lethality with LD50 693.302 while whole plant methanol extract of rheum ribes (WMERR) and whole plant aqueous fraction of rheum ribes (WAFRR) showed high lethality at highest concentration. This study revealed that whole plant butanol fraction of rheum ribes (WBFRR) exhibited significant anticancer (MCF-7) activity. In the near future, the constituent of whole plant butanol fraction of rheum ribes (WBFRR) can be the alternative drug against MCF-7 cell line with least toxicity and side effects.