Thorough examination of the potential biological implications of the cuproptosis-related gene LIPT2 in the prognosis and immunotherapy in pan-cancer.

OBJECTIVES: To elucidate the expression levels and prognostic value of the Lipoyltransferase 2 (LIPT2) gene in a pan-cancer view. METHODOLOGY: Our study comprehensively investigated the role of LIPT2 in pan-cancer, combining bioinformatics analyses with experimental validations. RESULTS: Analysis of LIPT2 mRNA expression across various cancers revealed a significant up-regulation in 18 tumor types and down-regulation in 8 types, indicating its diverse involvement. Prognostic assessment demonstrated a correlation between elevated LIPT2 expression and poorer outcomes in Overall Survival (OS) and Disease-Free Survival (DFS), particularly in Glioblastoma Multiforme (GBM), Liver Hepatocellular Carcinoma (LIHC), and Pheochromocytoma and Paraganglioma (PCPG). Protein expression analysis in GBM, LIHC, and PCPG affirmed a consistent increase in LIPT2 levels compared to normal tissues. Examining the methylation status in GBM, LIHC, and PCPG, we found reduced promoter methylation levels in tumor samples, suggesting a potential influence on LIPT2 function. Genetic mutation analysis using cBioPortal indicated a low mutation frequency (< 2%) in LIPT2 across GBM, LIHC, and PCPG. Immune correlation analysis unveiled a positive association between LIPT2 expression and infiltration levels of immune cells in GBM, LIHC, and PCPG. Single-cell analysis illustrated LIPT2's positive correlation with functional states, including angiogenesis and inflammation. Enrichment analysis identified LIPT2-associated processes and pathways, providing insights into its potential molecular mechanisms. Drug sensitivity analysis demonstrated that elevated LIPT2 expression conferred resistance to multiple compounds, while lower expression increased sensitivity. Finally, RT-qPCR validation in HCC cell lines confirmed the heightened expression of LIPT2 compared to a control cell line, reinforcing the bioinformatics findings. CONCLUSION: Overall, our study highlights LIPT2 as a versatile player in cancer, influencing diverse aspects from molecular processes to clinical outcomes across different cancer types.

Decoding the DSCC1 gene as a pan-cancer biomarker in human cancers via comprehensive multi-omics analyses.

OBJECTIVES: While dysregulation of DSCC1 (DNA Replication And Sister Chromatid Cohesion 1) has been established in breast cancer and colorectal cancer, its associations with other tumors remain unclear. Therefore, this study was launched to explore the role of DSCC1 in pan-cancer. METHODOLOGY: In this study, we investigate the biological functions of DSCC1 across 33 solid tumors, elucidating its role in promoting oncogenesis and progression in various cancers through comprehensive analysis of multi-omics data. RESULTS: We conducted a comprehensive analysis of DSCC1 expression using RNA-seq data from TCGA and GTEx databases across 30 cancer types. Striking variations were observed, with significant overexpression of DSCC1 identified in numerous cancers. Elevated DSCC1 level was strongly associated with poorer prognosis, shorter survival, and advanced tumor stages in kidney renal papillary cell carcinoma (KIRP), liver hepatocellular carcinoma (LIHC), lung adenocarcinoma (LUAD), as indicated by Kaplan-Meier curves and GEPIA2 analysis. Further investigation into the molecular mechanisms revealed reduced DNA methylation in the DSCC1 promoter region in KIRP, LIHC, and LUAD, supporting enhanced RNA transcription. Protein expression analysis via the Human Protein Atlas (HPA) corroborated mRNA expression findings, showcasing elevated DSCC1 protein in KIRP, LIHC, and LUAD tissues. Mutational analysis using cBioPortal revealed alterations in 0.4% of KIRP, 17% of LIHC, and 5% of LUAD samples, predominantly characterized by amplification. Immune cell infiltration analysis demonstrated robust positive correlations between DSCC1 expression and CD8+ T cells, CD4+ T cells, and B cells, influencing the tumor microenvironment. STRING and gene enrichment analyses unveiled DSCC1's involvement in critical pathways, emphasizing its multifaceted impact. Notably, drug sensitivity analysis highlighted a significant correlation between DSCC1 mRNA expression and responses to 78 anticancer treatments, suggesting its potential as a predictive biomarker and therapeutic target for KIRP, LIHC, and LUAD. Finally, immunohistochemistry staining of clinical samples validated computational results, confirming elevated DSCC1 protein expression. CONCLUSION: Overall, this study provides comprehensive insights into the pivotal role of DSCC1 in KIRP, LIHC, and LUAD initiation, progression, and therapeutic responsiveness, laying the foundation for further investigations and personalized treatment strategies.

Cognitive performance in aged rats is associated with differences in distinctive neuronal populations in the ventral tegmental area and altered synaptic plasticity in the hippocampus.

Introduction: Deterioration of cognitive functions is commonly associated with aging, although there is wide variation in the onset and manifestation. Albeit heterogeneity in age-related cognitive decline has been studied at the cellular and molecular level, there is poor evidence for electrophysiological correlates. The aim of the current study was to address the electrophysiological basis of heterogeneity of cognitive functions in cognitively Inferior and Superior old (19-20 months) rats in the ventral tegmental area (VTA) and the hippocampus, having Young (12 weeks) rats as a control. The midbrain VTA operates as a hub amidst affective and cognitive facets, processing sensory inputs related to motivated behaviours and hippocampal memory. Increasing evidence shows direct dopaminergic and non-dopaminergic input from the VTA to the hippocampus. Methods: Aged Superior and Inferior male rats were selected from a cohort of 88 animals based on their performance in a spatial learning and memory task. Using in vivo single-cell recording in the VTA, we examined the electrical activity of different neuronal populations (putative dopaminergic, glutamatergic and GABAergic neurons). In the same animals, basal synaptic transmission and synaptic plasticity were examined in hippocampal slices. Results: Electrophysiological recordings from the VTA and hippocampus showed alterations associated with aging per se, together with differences specifically linked to the cognitive status of aged animals. In particular, the bursting activity of dopamine neurons was lower, while the firing frequency of glutamatergic neurons was higher in VTA of Inferior old rats. The response to high-frequency stimulation in hippocampal slices also discriminated between Superior and Inferior aged animals. Discussion: This study provides new insight into electrophysiological information underlying compromised cerebral ageing. Further understanding of brain senescence, possibly related to neurocognitive decline, will help develop new strategies towards the preservation of a high quality of life.

Targeting the NF-κB p65/Bcl-2 signaling pathway in hepatic cellular carcinoma using radiation assisted synthesis of zinc nanoparticles coated with naturally isolated gallic acid.

PURPOSE: Oral diethylnitrosamine (DEN) is a known hepatocarcinogen that damages the liver and causes cancer. DEN damages the liver through reactive oxygen species-mediated inflammation and biological process regulation. MATERIALS AND METHODS: Gallic acid-coated zinc oxide nanoparticles (Zn-GANPs) were made from zinc oxide (ZnO) synthesized by irradiation dose of 50 kGy utilizing a Co-60 γ-ray source chamber with a dose rate of 0.83 kGy/h and gallic acid from pomegranate peel. UV-visible (UV) spectrophotometry verified Zn-GANP synthesis. TEM, DLS, and FTIR were utilized to investigate ZnO-NPs' characteristics. Rats were orally exposed to DEN for 8 weeks at 20 mg/kg five times per week, followed by intraperitoneal injection of Zn-GANPs at 20 mg/kg for 5 weeks. Using oxidative stress, anti-inflammatory, liver function, histologic, apoptotic, and cell cycle parameters for evaluating Zn-GANPs treatment. RESULTS: DEN exposure elevated inflammatory markers (AFP and NF-κB p65), transaminases (AST, ALT), γ-GT, globulin, and total bilirubin, with reduced protein and albumin levels. It also increased MDA levels, oxidative liver cell damage, and Bcl-2, while decreasing caspase-3 and antioxidants like GSH, and CAT. Zn-GANPs significantly mitigated these effects and lowered lipid peroxidation, AST, ALT, and γ-GT levels, significantly increased CAT and GSH levels (p<0.05). Zn-GANPs caused S and G2/M cell cycle arrest and G0/G1 apoptosis. These results were associated with higher caspase-3 levels and lower Bcl-2 and TGF-ß1 levels. Zn-GANPs enhance and restore the histology and ultrastructure of the liver in DEN-induced rats. CONCLUSION: The data imply that Zn-GANPs may prevent and treat DEN-induced liver damage and carcinogenesis.

Design, synthesis, and lead optimization of piperazinyl-pyrimidine analogues as potent small molecules targeting the viral capping machinery of Chikungunya virus.

The worldwide re-emerge of the Chikungunya virus (CHIKV), the high morbidity associated with it, and the lack of an available vaccine or antiviral treatment make the development of a potent CHIKV-inhibitor highly desirable. Therefore, an extensive lead optimization was performed based on the previously reported CHVB compound 1b and the reported synthesis route was optimized - improving the overall yield in remarkably shorter synthesis and work-up time. Hundred analogues were designed, synthesized, and investigated for their antiviral activity, physiochemistry, and toxicological profile. An extensive structure-activity relationship study (SAR) was performed, which focused mainly on the combination of scaffold changes and revealed the key chemical features for potent anti-CHIKV inhibition. Further, a thorough ADMET investigation of the compounds was carried out: the compounds were screened for their aqueous solubility, lipophilicity, their toxicity in CaCo-2 cells, and possible hERG channel interactions. Additionally, 55 analogues were assessed for their metabolic stability in human liver microsomes (HLMs), leading to a structure-metabolism relationship study (SMR). The compounds showed an excellent safety profile, favourable physicochemical characteristics, and the required metabolic stability. A cross-resistance study confirmed the viral capping machinery (nsP1) to be the viral target of these compounds. This study identified 31b and 34 as potent, safe, and stable lead compounds for further development as selective CHIKV inhibitors. Finally, the collected insight led to a successful scaffold hop (64b) for future antiviral research studies.

Enhancement of Radiation Sensitivity by Cathepsin L Suppression in Colon Carcinoma Cells.

Cancer is one of the main causes of death globally. Radiotherapy/Radiation therapy (RT) is one of the most common and effective cancer treatments. RT utilizes high-energy radiation to damage the DNA of cancer cells, leading to their death or impairing their proliferation. However, radiation resistance remains a significant challenge in cancer treatment, limiting its efficacy. Emerging evidence suggests that cathepsin L (cath L) contributes to radiation resistance through multiple mechanisms. In this study, we investigated the role of cath L, a member of the cysteine cathepsins (caths) in radiation sensitivity, and the potential reduction in radiation resistance by using the specific cath L inhibitor (Z-FY(tBu)DMK) or by knocking out cath L with CRISPR/Cas9 in colon carcinoma cells (caco-2). Cells were treated with different doses of radiation (2, 4, 6, 8, and 10), dose rate 3 Gy/min. In addition, the study conducted protein expression analysis by western blot and immunofluorescence assay, cytotoxicity MTT, and apoptosis assays. The results demonstrated that cath L was upregulated in response to radiation treatment, compared to non-irradiated cells. In addition, inhibiting or knocking out cath L led to increased radiosensitivity in contrast to the negative control group. This may indicate a reduced ability of cancer cells to recover from radiation-induced DNA damage, resulting in enhanced cell death. These findings highlight the possibility of targeting cath L as a therapeutic strategy to enhance the effectiveness of RT. Further studies are needed to elucidate the underlying molecular mechanisms and to assess the translational implications of cath L knockout in clinical settings. Ultimately, these findings may contribute to the development of novel treatment approaches for improving outcomes of RT in cancer patients.

Antioxidant, carbonic anhydrase inhibition and diuretic activity of Leptadenia pyrotechnica Forssk. Decne.

Background: Leptadenia pyrotechnica Forssk. Decne is a member of family Apocynaceae and locally known as 'Khipp'. It is found in dry, sandy habitat of Pakistan and in several other regions around the world including Asia, Tropical Africa, Western Gulf and Mediterranean countries. It has nutritional value, containing 4 % lipids, 23 % proteins, 28 % carbohydrates, 4 % fibers, vitamin E and several minerals. Traditionally, this plant has been used by several communities for pain, different inflammatory and kidney disorders. Ethno-botanical studies have reported the use of L. pyrotechnica in nephrolithiasis, kidney disorders and induction of diuresis, which requires a detailed pharmacological study to validate the folkloric use of L. pyrotechnica as diuretic. Methods: The 70 % methanolic L. pyrotechnica (Lp.Cr) extract was prepared and qualitatively checked for the presence of various phytochemicals. Phenolic, flavonoid, tannin and saponin contents were quantified. GC-MS analysis of Lp.Cr was also performed. Antioxidant potential of Lp.Cr was evaluated by DPPH, ABTS and nitrite radical scavenging assays. CUPRAC and FRAP assay described the reducing potential of Lp.Cr. Diuretic activity was performed in both acute and prolonged models at different doses followed by the estimation of electrolytes, urea and creatinine levels. The mechanism of diuresis was described by pre-treatment with atropine, l-NAME, indomethacin and carbonic anhydrase inhibition. Results: Lp.Cr. indicated high phenolic and flavonoid contents which correlated with good antioxidant activity. GC-MS analysis showed the presence of 104 compounds from different phytochemical classes. Diuretic activity was performed at 10-300 mg/kg concentrations where the dose of 100 and 300 mg/kg showed good diuretic and saluretic activity comparable to furosemide. Lp.Cr exhibited diuresis both in acute and prolonged study protocols which can be attributed to carbonic anhydrase inhibition, effect on prostaglandins and cholinergic pathways. Conclusion: L. pyrotechnica contained several phytochemicals and exhibited good antioxidant activity. It induced diuresis and saluretic activity which was comparable to furosemide at higher doses. Diuretic activity can be attributed to carbonic anhydrase inhibition, prostaglandin synthesis and cholinergic pathways.

Proteolytic Activation of the Epithelial Sodium Channel (ENaC): Its Mechanisms and Implications.

Epithelial sodium channel (ENaC) are integral to maintaining salt and water homeostasis in various biological tissues, including the kidney, lung, and colon. They enable the selective reabsorption of sodium ions, which is a process critical for controlling blood pressure, electrolyte balance, and overall fluid volume. ENaC activity is finely controlled through proteolytic activation, a process wherein specific enzymes, or proteases, cleave ENaC subunits, resulting in channel activation and increased sodium reabsorption. This regulatory mechanism plays a pivotal role in adapting sodium transport to different physiological conditions. In this review article, we provide an in-depth exploration of the role of proteolytic activation in regulating ENaC activity. We elucidate the involvement of various proteases, including furin-like convertases, cysteine, and serine proteases, and detail the precise cleavage sites and regulatory mechanisms underlying ENaC activation by these proteases. We also discuss the physiological implications of proteolytic ENaC activation, focusing on its involvement in blood pressure regulation, pulmonary function, and intestinal sodium absorption. Understanding the mechanisms and consequences of ENaC proteolytic activation provides valuable insights into the pathophysiology of various diseases, including hypertension, pulmonary disorders, and various gastrointestinal conditions. Moreover, we discuss the potential therapeutic avenues that emerge from understanding these mechanisms, offering new possibilities for managing diseases associated with ENaC dysfunction. In summary, this review provides a comprehensive discussion of the intricate interplay between proteases and ENaC, emphasizing the significance of proteolytic activation in maintaining sodium and fluid balance in both health and disease.

The Significance of Cathepsin B in Mediating Radiation Resistance in Colon Carcinoma Cell Line (Caco-2).

Cathepsins (Caths) are lysosomal proteases that participate in various physiological and pathological processes. Accumulating evidence suggests that caths play a multifaceted role in cancer progression and radiotherapy resistance responses. Their proteolytic activity influences the tumor's response to radiation by affecting oxygenation, nutrient availability, and immune cell infiltration within the tumor microenvironment. Cathepsin-mediated DNA repair mechanisms can promote radioresistance in cancer cells, limiting the efficacy of radiotherapy. Additionally, caths have been associated with the activation of prosurvival signaling pathways, such as PI3K/Akt and NF-κB, which can confer resistance to radiation-induced cell death. However, the effectiveness of radiotherapy can be limited by intrinsic or acquired resistance mechanisms in cancer cells. In this study, the regulation and expression of cathepsin B (cath B) in the colon carcinoma cell line (caco-2) before and after exposure to radiation were investigated. Cells were exposed to escalating ionizing radiation doses (2 Gy, 4 Gy, 6 Gy, 8 Gy, and 10 Gy). Analysis of protein expression, in vitro labeling using activity-based probes DCG04, and cath B pull-down revealed a radiation-induced up-regulation of cathepsin B in a dose-independent manner. Proteolytic inhibition of cathepsin B by cathepsin B specific inhibitor CA074 has increased the cytotoxic effect and cell death due to ionizing irradiation treatment in caco-2 cells. Similar results were also obtained after cathepsin B knockout by CRISPR CAS9. Furthermore, upon exposure to radiation treatment, the inhibition of cath B led to a significant upregulation in the expression of the proapoptotic protein BAX, while it induced a significant reduction in the expression of the antiapoptotic protein BCL-2. These results showed that cathepsin B could contribute to ionizing radiation resistance, and the abolishment of cathepsin B, either by inhibition of its proteolytic activity or expression, has increased the caco-2 cells susceptibility to ionizing irradiation.

Elucidating the clinical and immunological value of m6A regulator-mediated methylation modification patterns in adrenocortical carcinoma.

N6-methyladenosine methylation (m6A) is a common type of epigenetic alteration that prominently affects the prognosis of tumor patients. However, it is unknown how the m6A regulator affects the tumor microenvironment (TME) cell infiltration in adrenocortical carcinoma (ACC) and how it affects the prognosis of ACC patients yet. The m6A alteration patterns of 112 ACC patients were evaluated, furthermore, the association with immune infiltration cell features was investigated. The unsupervised clustering method was applied to typify the m6A alteration patterns of ACC patients. The principal component analysis (PCA) technique was taken to create the m6A score to assess the alteration pattern in specific malignancies. We found two independent patterns of m6A alteration in ACC patients. The TME cell infiltration features were significantly in accordance with phenotypes of tumor immune-inflamed and immune desert in both patterns. The m6Ascore also served as an independent predictive factor in ACC patients. The somatic copy number variation (CNV) and patients prognosis can be predicted by m6A alteration patterns. Moreover, the ACC patients with high m6A scores had better overall survival (OS) and higher efficiency in immune checkpoint blockade therapy. Our work demonstrated the significance of m6A alteration to the ACC patients immunotherapy. The individual m6A alteration patterns analysis might contribute to ACC patients prognosis prediction and immunotherapy choice.

Quercus floribunda Lindl. Ex A. Camus; a tremendous remedy against inflammation and associated symptoms.

Crude extracts prepared from aerial parts and nut galls of Quercus floribunda Lindl. Ex. A. Camus were evaluated for phytochemical screening, in vitro antioxidant, and in vivo analgesic, anti-inflammatory and antipyretic activities. Various solvents including methanol (M), acetone (A), distilled water (DW), distilled water + methanol (DWM) were used for extraction. Highest total phenolic (66.9 ± 0.05 µg GAE/mgE) and flavonoid content (38.4 ± 0.72 µg QE/mgE) were measured in QFAA extract by colorimetric methods. Cumulative maximum concentrations of polyphenols were quantified in QFMG, QFAA, and QFMA extracts i.e. 19.036, 15. 574 and 11.647 µg/mg of extract by RP-HPLC analysis. From aerial parts extracts, apentacyclic tritepenoid, glutinol was isolated using column chromatography techniques and structure was elucidated using spectroscopic techniques. QFDWMA (205.5 ± 0.56 µg AAE/mg of extract) showed highest total reducing power while highest total antioxidant capacity (207.1 ± 0.49 AAE/mg of extract) and free radical scavenging potential (96.1 ± 0.42%) were observed in QFAA extract. QFAA extract showed significant (p ≤ 0.001) analgesic potential in different pain models i.e. hot plate method, cold plate method, Haffner's tail clip method and acetic acid induced writhing assay having 50.20%, 62.07%, 57.26% and 70.49% analgesia respectively at 300 mg/kg. QFAA extract showed maximum anti-inflammatory activity in croton oil induced edema (68.83%) and in carrageenan induced paw edema models (72.32%) at 300 mg/kg concentration. QFAA extract markedly reduced the rectal temperature at 300 mg/kg concentration, in brewer's yeast induced pyrexia model. Detailed investigations can be executed in future to determine the molecular mechanisms of these pharmacological attributes.

Comprehensively analyzing the genetic alterations, and identifying key genes in ovarian cancer.

Though significant improvements have been made in the treatment methods for ovarian cancer (OC), the prognosis for OC patients is still poor. Exploring hub genes associated with the development of OC and utilizing them as appropriate potential biomarkers or therapeutic targets is highly valuable. In this study, the differentially expressed genes (DEGs) were identified from an independent GSE69428 Gene Expression Omnibus (GEO) dataset between OC and control samples. The DEGs were processed to construct the protein-protein interaction (PPI) network using STRING. Later, hub genes were identified through Cytohubba analysis of the Cytoscape. Expression and survival profiling of the hub genes were validated using GEPIA, OncoDB, and GENT2. For exploring promoter methylation levels and genetic alterations in hub genes, MEXPRESS and cBioPortal were utilized, respectively. Moreover, DAVID, HPA, TIMER, CancerSEA, ENCORI, DrugBank, and GSCAlite were used for gene enrichment analysis, subcellular localization analysis, immune cell infiltration analysis, exploring correlations between hub genes and different diverse states, lncRNA-miRNA-mRNA co-regulatory network analysis, predicting hub gene-associated drugs, and conducting drug sensitivity analysis, respectively. In total, 8947 DEGs were found between OC and normal samples in GSE69428. After STRING and Cytohubba analysis, 4 hub genes including TTK (TTK Protein Kinase), (BUB1 mitotic checkpoint serine/threonine kinase B) BUB1B, (Nucleolar and spindle-associated protein 1) NUSAP1, and (ZW10 interacting kinetochore protein) ZWINT were selected as the hub genes. Further, it was validated that these 4 hub genes were significantly up-regulated in OC samples compared to normal controls, but overexpression of these genes was not associated with overall survival (OS). However, genetic alterations in those genes were found to be linked with OS and disease-free (DFS) survival. Moreover, this study also revealed some novel links between TTK, BUB1B, NUSAP1, and ZWINT overexpression and promoter methylation status, immune cell infiltration, miRNAs, gene enrichment terms, and various chemotherapeutic drugs. Four hub genes, including TTK, BUB1B, NUSAP1, and ZWINT, were revealed as tumor-promotive factors in OC, having the potential to be utilized as novel biomarkers and therapeutic targets for OC management.

Synthesis, In Silico Studies, and Antioxidant and Tyrosinase Inhibitory Potential of 2-(Substituted Phenyl) Thiazolidine-4-Carboxamide Derivatives.

Heterocyclic nuclei have shown a wide variety of biological activities, highlighting their importance in drug discovery. Derivatives of 2,4-subsituted thiazolidine have a structural similarity with the substrates of tyrosinase enzymes. Hence, they can be used as an inhibitor to compete against tyrosine in the biosynthesis of melanin. This study is focused on design, synthesis, biological activities, and in silico studies of thiazolidine derivatives substituted at positions 2 and 4. The synthesized compounds were evaluated to determine the antioxidant activity and tyrosine inhibitory potential using mushroom tyrosinase. The most potent tyrosinase enzyme inhibitor was compound 3c having IC50 value 16.5 ± 0.37 µM, whereas compound 3d showed maximum antioxidant activity in a DPPH free radical scavenging assay (IC50 = 18.17 µg/mL). Molecular docking studies were conducted using mushroom tyrosinase (PDB ID: 2Y9X) to analyze binding affinities and binding interactions of the protein-ligand complex. Docking results indicated that hydrogen bonds and hydrophobic interactions were mainly involved in the ligand and protein complex. The highest binding affinity was found to be -8.4 Kcal/mol. These results suggest that thiazolidine-4-carboxamide derivatives could serve as lead molecules for development of novel potential tyrosinase inhibitors.

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.

A pan-cancer analysis of HAVCR1 with a focus on diagnostic, prognostic and immunological roles in human cancers.

OBJECTIVES: Cancer is one of the most prominent causes of death world wide. Identification of novel cancer biomarkers woud help with cancer diagnosis and possible treatment. METHODS: In this study, we comprehensively studied the diagnostic, prognostic, and therapeutic values of the hepatitis A virus cellular receptor 1 (HAVCR1) gene across multiple cancers from a pan-cancer point of view via a detailed in silico approach. RESULTS: HAVCR1 expression was up-regulated in a variety of malignancies. The up-regulated HAVCR1 was closely related to the poor prognosis in patients with esophageal carcinoma (ESCA), lung adenocarcinoma (LUAD), and stomach adenocarcinoma (STAD). Moreover, DAVID analysis showed that HAVCR1, along with different other associated genes, was involved in numerous cancer-associated signaling pathways across ESCA, STAD, and LUAD. Furthermore, in these cancers, HAVCR1 was also found closely associated with some other parameters such as promoter methylation, tumor purity, level of CD8+ T immune cells, genomic alterations, and chemotherapeutic drugs. CONCLUSION: HAVCR1 was overexpressed in multiple tumors. However, the up-regulated HAVCR1 is a valuable diagnostic and prognostic biomarker as well as a therapeutic target in only ESCA, STAD, and LUAD patients.

Estimation of hub genes and exploration of multi-omics level alterations in the landscape of lung adenocarcinoma.

OBJECTIVES: Lung adenocarcinoma (LUAD) is recognized as one of the most prevalent and deadliest malignancies around the globe. The molecular mechanisms behind LUAD have not been fully elucidated. This study was launched to explore LUAD-associated hub genes and their enriched pathways using bioinformatics methods. METHODS: Information on GSE10072 was retrieved from the Gene Expression Omnibus (GEO) database and analyzed via the Limma package-based GEO2R tool to obtain the top 100 differentially expressed genes (DEGs) in LUAD. The protein-protein interaction (PPI) network of the DEGs was drawn using the STRING website and was shifted into Cytoscape to screen the top 6 hub genes via the CytoHubba application. Furthermore, the expression analysis and validation of hub genes in LUAD samples and cell lines were done using UALCAN, OncoDB, and GENT2 databases. Moreover, OncoDB was also used for analyzing hub gene DNA methylation levels. In addition, cBioPortal, GSEA tool, Kaplan-Meier (KM) plotter, Enrichr, CancerSEA, and DGIdb were performed to explore some other important aspects of hub genes in LUAD. RESULTS: We identified Interleukin 6 (IL6), Collagen, type I, alpha 1 (COL1A1), TIMP metallopeptidase inhibitor 1 (TIMP1), CD34 molecule (CD34), Decorin (DCN), and Secreted Phosphoprotein 1 (SPP1) genes as the hub genes in LUAD, out of which IL6, CD34, and DCN were significantly down-regulated while COL1A1, TIMP1, and SPP1 were significantly up-regulated in LUAD cell lines and samples of diverse clinical variables. In this study, we also documented some important correlations between hub genes and other parameters such as DNA methylation, genetic alterations, Overall Survival (OS), and 14 important states at the single cell level. Lastly, we also identified hub genes associated with the ceRNA network and 11 important chemotherapeutic drugs. CONCLUSION: We identified 6 hub genes involved in the development and progression of LUAD. These hub genes can also be helpful in the accurate detection of LUAD and provide novel ideas for treatment.

An in-silico approach leads to explore six genes as a molecular signatures of lung adenocarcinoma.

Due to heterogenetic-specific nature of the available biomarkers, the incidence of lung adenocarcinoma (LUAD) is on the rise worldwide. Previously reported LUAD-related hub genes were searched from the medical literature via literature mining and were processed to identify few top genes via degree method. Later, a comprehensive in silico methodology was applied on the selected real hub genes to identify their tumor driving, diagnostic, and prognostic roles in LUAD patients with divers clinicopathological variables. Out of total 145 extracted hub genes, six genes including CDC6, PBK, AURKA, KIF2C, OIP5, and PRC1 were identified as real hub genes. The expression analysis showed that all these genes were significantly up-regulated across LUAD samples of different clinicopathological variables. In addition, a variety of unique correlations among the expression and of real hub genes and some other parameters including promoter methylation status, overall survival (OS), genetic changes, tumor purity, and immune cell infiltration have also been explored in the present study. Moreover, via TFS-miRNA-mRNA regulatory network, one important TF (E2F1) and one important miRNAs (hsa-mir-34a-5p) that targeted all the real hub genes were also identified. Finally, a variety of drugs also predicted to be very useful in treating LUAD. The discovery of the real hub genes, TFS-miRNA-mRNA network, and chemotherapeutic drugs associated with LUAD provides new insights into underlying mechanisms and treatment of LUAD overcoming heterogeneity barriers.

Characterizing the oncogenic importance and exploring gene-immune cells correlation of ACTB in human cancers.

After cardiovascular diseases, cancer is the second deadliest malignancy in the world. The current study was launched to investigate the diagnostic and prognostic landscape of Beta-actin (ACTB) via a multi-layered bioinformatics approach. ACTB expression was analyzed and validated via UALCAN, TIMER, GENT2, GEPIA, and HPA. ACTB promoter methylation was evaluated via MREXPRES. Furthermore, ACTB prognostic values and their correlation with cancer metastasis were explored through the KM plotter and TNMplot, respectively. Then, cBioPortal, CancerSEA, Enrichr, TIMER, MuTarget, and CDT were used to analyze ACTB-related genetic alterations, transcription factors (TFS), MicroRNAs (miRNAs), chemotherapeutic drugs, and the correlation between its expression, immune cells, and different other parameters. We found that ACTB expression was remarkably higher in 24 major human cancer tissues than the normal samples. Additionally, elevated ACTB expression was associated with poorer survival and metastasis in only liver hepatocellular carcinoma (LIHC), head and neck squamous cancer (HNSC), and lung adenocarcinoma (LUAD). This implies that ACTB plays a significant role in the development and progression of LIHC, HNSC, and LUAD. Furthermore, enrichment analysis showed that ACTB-associated genes regulate different Biological Processes (BP), Molecular Functions (MF), and Kyoto Encyclopedia of Genes and Genomes (KEGG) terms. Moreover, ACTB up-regulation had interesting correlations with immune infiltration of CD4+ T, and CD8+ T, tumor purity, mutant genes, and a few other important parameters. At last, via this study, we also explored ACTB-associated clinically important expression regulators, including TFS, miRNAs, and different chemotherapeutic drugs. The results of the present study suggested that ACTB might be a potential candidate biomarker in LIHC, HNSC, and LUAD.

Genome Editing Technology: A New Frontier for the Treatment and Prevention of Cardiovascular Diseases.

Over the past 2 decades, genome-editing technique has proven to be a robust editing method that revolutionizes the field of biomedicine. At the genetic level, it can be efficiently utilized to generate various disease-resistance models to elucidate the mechanism of human diseases. It also develops an outstanding tool and enables the generation of genetically modified organisms for the treatment and prevention of various diseases. The versatile and novel clustered regularly interspaced short palindromic repeats (CRISPR/Cas9) system mitigates the challenges of various genome editing techniques such as zinc-finger nucleases, and transcription activator-like effector nucleases. For this reason, it has become a ground-breaking technology potentially employed to manipulate the desired gene of interest. Interestingly, this system has been broadly utilized due to its tremendous applications for treating and preventing tumors and various rare disorders; however, its applications for treating cardiovascular diseases (CVDs) remain in infancy. More recently, 2 newly developed genome editing techniques, such as base editing and prime editing, have further broadened the accuracy range to treat CVDs under consideration. Furthermore, recently emerged CRISPR tools have been potentially applied in vivo and in vitro to treat CVDs. To the best of our knowledge, we strongly enlightened the applications of the CRISPR/Cas9 system that opened a new window in the field of cardiovascular research and, in detail, discussed the challenges and limitations of CVDs.

Impact of Enniatin B and Beauvericin on Lysosomal Cathepsin B Secretion and Apoptosis Induction.

Enniatin B (ENN B) and Beauvericin (BEA) are cyclohexadepsipeptides that can be isolated from Fusarium and Beauveria bassiana, respectively. Both compounds are cytotoxic and ionophoric. In the present study, the mechanism of cell death induced by these compounds was investigated. Epidermal carcinoma-derived cell line KB-3-1 cells were treated with different concentrations of these compounds. The extracellular secretion of cathepsin B increased in a concentration-dependent manner, and the lysosomal staining by lysotracker red was reduced upon the treatment with any of the compounds. However, the extracellular secretion of cathepsin L and cathepsin D were not affected. Inhibition of cathepsin B with specific inhibitor CA074 significantly reduced the cytotoxic effect of both compounds, while inhibition of cathepsin D or cathepsin L did not influence the cytotoxic activities of both compounds. In vitro labelling of lysosomal cysteine cathepsins with Ethyl (2S, 3S)-epoxysuccinate-Leu-Tyr-Acp-Lys (Biotin)-NH2 (DCG04) was not affected in case of cathepsin L upon the treatment with both compounds, while it was significantly reduced in case of cathepsin B. In conclusion, ENN B and BEA increase lysosomal Ph, which inhibits delivery of cathepsin B from Golgi to lysosomes, thereby inducing cathepsin B release in cytosol, which activates caspases and hence the apoptotic pathway.