Combinatorial Chemistry & High Throughput Screening - Volume 26, Issue 8, 2023

Background: Recently, laboratory information systems (LIS) have become necessary for every laboratory to improve the decision-making process and achieve better treatment and diagnostic results. By standardizing laboratory's tests, procedures, and workflows, the software enables laboratories to improve patient care, reduce human error, and constructively lower operating costs. Implementing LIS has a multidimensional impact on improving the delivery of laboratory services. Objectives: This paper aims to investigate how patient services can be improved by laboratory information system. Methods: This paper is based on a review conducted by searching PubMed, Google Scholar, Saudi Digital Library and Research Gate for English language articles published from 2015 to 2021 and focused primarily on laboratory information systems. Results: The literature searches yielded a total of 30 articles that were then initially screened based on the titles and abstracts. Seven articles were excluded because they did not primarily address LIMS for biosafety, automated verification of test results in the core clinical laboratory, clinical biochemistry, or the impact of health information technology on patient safety, or were not written in English. The remaining 23 articles were then screened in full text. Conclusion: Advanced laboratory information systems may eliminate diagnostic errors in the preanalytical, analytical, and postanalytical phases. In addition, they can incorporate genomic data at the analytical stage to generate useful reports for providers and patients.

Objective: Oral cancer is one of the most common malignant tumors in the head and neck. It is easy to relapse, and the prognosis is poor. However, the molecular mechanism in the development of oral cancer is still unclear. Methods: A total of 30 normal individuals and 30 patients with head and neck cancer who underwent surgery were recruited in the Fourth Hospital of Hebei Medical University between February 2019 and November 2021. Furthermore, Human Protein Atlas (HPA) analysis, RT-qPCR, and immunofluorescence were used to verify the expression of SOX9 and IL1A. The GSE69002 dataset was downloaded from the Gene Expression Omnibus (GEO) database. GEO2R was used to identify the differentially expressed genes (DEGs). The Protein-Protein Interaction (PPI) network was constructed by using the STRING, and Cytoscape software was performed for visualization. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) for enrichment analysis were made via the DAVID, Metascape, Gene Set Enrichment Analysis (GSEA), and Bin Gene Ontology (BINGO) analysis. Gene Expression Profiling Interactive Analysis (GEPIA) analysis was used to analyze the expression level of hub genes and pathological stage. The cBioPortal can be used for mutation analysis and pathway prediction of hub genes. Kaplan Meier Plotter was used for survival analysis of hub genes. Results: The relative expression level of SOX9 (P=0.021, t=4.332) and IL1A (P=0.011, t= -4.213) in oral cancer was significantly higher than that in the standard group (P<0.05). The DEGs are mainly enriched in cell division, inflammation, interleukin-12 beta-subunit binding, and interleukin- 10 receptor binding. All the differentially expressed gene pathways eventually converge in cell growth and apoptosis. No relationship between the pathologic stage and the expression of hub genes. The poor overall survival of patients with the high expression of SOX9 (Hazard Ratio (HR) = 1.46, P = 0.009) and IL1A (HR = 1.49, P = 0.008). There were strong correlations between the hub genes and the head and neck neoplasms via the Comparative Toxicogenomics Database (CTD). The immunofluorescence and PCR results showed that the level of SOX9 (P<0.001, t = -23.368) in the cancer group was significantly higher than that in the normal group; The level of IL1A in the cancer group was significantly higher than that in the normal group (P<0.001, t = -11.960). Conclusion: SOX9 and IL1A genes are highly expressed in oral cancer and might be potential therapeutic targets for oral cancer. The poor overall survival of patients with the high expression of SOX9 and IL1A.

Objective; We aimed to assess whole-brain imaging with contrast-enhanced (CE) 3- dimensional (3D) Cube T1WI in improving the diagnostic accuracy of acute optic neuritis (ON) compared to conventional CE 2-dimensional (2D) T1WI. Methods: At a field strength of 3 T, CE 3D Cube T1-weighted and conventional CE 2D T1- weighted MR images were retrospectively analyzed for 32 patients (64 optic nerves) with clinically confirmed acute ON. The study cohort included 36 pathological nerves. Image assessments including the overall image quality, clarity of the optic nerve, and visual contrast enhancement were performed by two blinded neuroradiologists using a 4-point scale. The sensitivity, specificity, and accuracy of the conventional 2D T1WI and 3D Cube T1WI were calculated according to the clinical diagnosis. Results: The application of 3D Cube T1WI improved the overall image quality compared to 2D Ax T1WI and 2D Cor T1WI (P < 0.05). The clarity of the optic nerve and the visual contrast enhancement were higher for the 3D Cube T1WI compared to the 2D Ax T1WI and 2D Cor T1WI for at least one reader. The sensitivity, specificity, and accuracy were 89%, 86%, 88% for the 3D Cube T1WI respectively, and 75%, 79%, 77% for the conventional 2D T1WI respectively. The lesions detected by the conventional 2D T1WI were all detected by the 3D Cube T1WI. Conclusion: Our data show that whole-brain imaging with CE 3D Cube T1WI is a viable alternative for the detection of acute ON without sacrificing scanning efficiency.

Background: Endometrial cancer (EC) is one of the most normal malignancies globally. Growing evidence suggests epithelial-mesenchymal transition (EMT) related markers are closely correlated with poor prognosis of EC. However, the relationship between multiple EMT-associated long non-coding RNAs (lncRNAs) and the prognosis of EC has not yet been studied. Methods: The transcriptome data and clinical information of EC cases were obtained from The Cancer Genome Atlas (TCGA). Then, we identified differentially expressed EMT-associated lncRNAs between tumor and normal tissue. Univariate cox regression analysis and multivariate stepwise Cox regression analysis were applied to identify EMT-associated lncRNAs related to overall survival (OS). Kaplan-Meier curve, receiver operating characteristic (ROC), nomograms and multi-index ROC curves were further established to evaluate the performance of the prognostic signature. In addition, we also investigated the distribution of immune cell characteristics, sensitivity to immune checkpoint inhibitor (ICI) and chemotherapeutics, and tumor mutation burden (TMB) between high- and low-risk scores predicated on a prognostic model. Results: We established nine EMT-associated lncRNA signatures to predict the OS of EC, the area under the ROC curve (AUC) of the risk score has better values than other clinical characteristics, indicating the accuracy of the prognostic signature. As revealed by multivariate Cox regression, the prognosis model independently predicted EC prognosis. Moreover, the signature and the EMTassociated lncRNAs showed significant correlations with other clinical characteristics,including. Multi-index ROC curves for estimating 1-, 3- and 5-year overall survival (OS) of EC patients showed good predictive accuracy with AUCs of 0.731, 0.791, and 0.782, respectively. The highrisk group had specific tumor immune infiltration, insensitive to ICI, higher chemotherapeutics sensitivity and higher expression of TP53 mutation. Finally, the five lncRNAs of signature were further verified by qRT-PCR. Conclusion: We constructed an EMT-associated lncRNA signature that can predict the prognosis of EC effectively, and the prognostic signature also played an essential role in the TME; thus, the establishment of an EMT-associated lncRNA signature may provide new perspectives for the treatment of EC.

Background: Emerging evidence indicates that long noncoding RNA (lncRNA) plays an important biological role in clear cell renal cell carcinoma (ccRCC); however, the clinical value of tumor mutation burden-related lncRNA in ccRCC patients is unknown yet. Methods: Somatic mutation profiles and lncRNA expression data of ccRCC were downloaded from the TCGA database. We retrospectively analyzed lncRNA expression data and survival information from 116 patients with ccRCC fromJanuary 2013 to January 2014. Univariate and multivariate Cox regression analyses were performed to construct lncRNA signature, and the prognosis value was determined by Kaplan-Mayer and receiver operating characteristic curve (ROC) analysis. Results: Based on 160 differentially expressed TMB-related lncRNAs, two TMB-related molecular clusters with distinct immune checkpoints expression and immune cells infiltration were established for ccRCC patients. Moreover, a novel TMB-related lncRNA signature was constructed based on five lncRNAs for individualized prognosis assessment. High-risk group represents significantly worse overall survival in all cohorts. The area under the ROC curve was 0.716, 0.775 and 0.744 in the training cohort, testing cohort and TCGA cohort, respectively. Results of qRT-PCR successfully validated the expression levels of AP002360.3, LINC00460, AL590094.1, LINC00944 and LINC01843 in HK-2, 786-O, 769-P and ACHN cells. More importantly, the predictive performance of TMB-related lncRNA signature was successfully validated in an independent cohort of 116 ccRCC patients at our institution. Conclusion: This study successfully developed and validated a novel TMB-related lncRNA signature for individualized prognosis assessment of ccRCC patients.

Aim: The study aims to investigate the effects and mechanism of flavonoids from stems and leaves of Scutellaria baicalensis Georgi (SSF) on the disorders in learning and memory and neuroplasticity induced by beta amyloid 25-35 (Aβ25-35) combined with aluminum trichloride (AlCl3) and human recombinant transfer factor-β1 (RHTGF-β1) (composited Aβ) in rats. Methods: A rat Alzheimer's disease (AD) model was established by intracerebroventricular injection of Aβ25-35 combined with AlCl3 and RHTGF-β1. The successful AD model of rats was screened with a Morris water maze. The successful model rats were randomly divided into a model group and three doses of SSF treated group. The Morris water maze was used to detect the rats’ learning and memory abilities. The real-time fluorescence quantitative (qPCR) was applied to assay the mRNA expressions of CaM, CamkIV and Ferritin, as well as the neuroplasticity factors of HuB, HuC and HuD. The Western blotting was used to measure the protein expressions of CaM, CamkIV, HuB/D, HuC+HuD and Ferritin in the CaM-CamkIV-CREB signal pathway. Results: Compared with the sham group, the abilities of learning and memory in the model group were significantly impaired (P<0.01), and the mRNA or protein expressions of CaM, CamkIV, HuB, HuC, HuD, HuB/D, HuC+HuD and Ferritin in CaM-CamkIV-CREB signal pathway were abnormally changed in model group. However, the three doses of SSF can differently ameliorate the impaired learning and memory and regulate the abnormal expressions of mRNA or protein in rats’ CaM, CamkIV, HuB, HuC, HuD, HuB/D, HuC+HuD and Ferritin induced by composited Aβ. Conclusion: The improvement of SSF on the learning and memory disorder induced by composited Aβ is primarily derived from the positive regulation in the CaM-CamkIV-CREB signal pathway and activation in neuroplasticity.

Background: Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has a serious threat to human health. Oral candidiasis (OC) may be one of the causes of morbidity in severe COVID-19 patients. However, there is currently no treatment for oral candidiasis and COVID-19 (OC/COVID-19). The purpose of this study was to use text mining and data analysis to investigate the target genes for treatment and explore potential therapeutic drugs for OC/COVID-19. Methods: We used the text mining tool pubmed2ensembl to detect genes associated with OC, and the dataset GSE164805 was used for the data analysis. Then, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed on two intersection genes using the Database of Annotation, Visualization and Integrated Discovery (DAVID) platform. The protein-protein interaction (PPI) networks were constructed by STRING software, and gene module analysis was performed using Molecular Complex Detection (MCODE), a plug-in in Cytoscape. The most significant genes were selected as hub genes and their functions and pathways were analyzed using Metascape. We revealed the upstream pathway activity of the hub genes. The drug-gene interaction database (DGIdb) and the traditional Chinese medicines integrated database (TCMID) were used to discover potential drugs for the treatment of OC/COVID-19. Results: The analysis indicated that there were 2869 differentially expressed genes (DEGs) in GSE164805. We identified 161 unique genes associated with oral candidiasis through text mining. A total of 20 intersection genes were identified as the therapeutic targets for OC/COVID-19. Based on the bioinformatics analysis, nine genes (TNF, IL1B, IFNG, CSF2, ELANE, CCL2, MMP9, CXCR4, and IL1A) were identified as hub genes that were mainly enriched in the IL-17 signaling pathway, TNF signaling pathway, AGE-RAGE signaling pathway in diabetic complications and NOD-like receptor signaling pathway. We identified four of the nine genes that target five existing drugs, including BKT140, mavorixafor, sivelestat, canakinumab, and rilonacept. Furthermore, twenty herb ingredients were also screened as potential drugs. Conclusion: In this study, TNF, IL1B, IFNG, CSF2, ELANE, CCL2, MMP9, CXCR4, and IL1A were potentially key genes involved in the treatment of OC/COVID-19. Taken together five drugs and twenty herb ingredients were identified as potential therapeutic agents for OC/COVID-19 treatment and management.

Background: Astragalus polysaccharides (APS) is a natural phytochemical which has been extensively utilized for anti-tumor therapy over the past few years. However, its impact on cervical cancer (CC) has rarely been studied. Objective: To clarify the exact mechanism of anti-cancer effects of Astragalus polysaccharides (APS) on Cervical Cancer (CC), we screened differentially expressed genes (DEGs) from The Cancer Genome Atlas (TCGA) to construct the cancer network. Methods: Then we performed functional enrichment analysis with gene ontology (GO) and KEGG pathway analyses, constructed protein-protein interaction (PPI) network, and performed molecular docking (MD) analysis to identify the key gene for docking with APS. Further, we observed the effects of APS on cell proliferation, cell cycle, and apoptosis experiments in HeLa cells. qRT-PCR and western blot were used to detect the expression of target genes. Results: A total of 793 DEGs were screened using criteria, which included 541 genes that were upregulated and 251 genes that were down-regulated. Using topological attributes for identifying critical targets, molecular docking (MD), and survival analyses, this study predicted the APS targets: POLO-like kinase 1(PLK1), Cyclin-cell division 20(CDC20), and Cyclin-dependent kinase 1 (CDK1), which regulated HeLa cells. The results of cell proliferation, cell cycle, and apoptosis experiments concluded that APS inhibited the development of HeLa cells in a concentrationdependent manner. Also, qRT-PCR and western blot experiments demonstrated that APS could significantly down-regulate the expression of PLK1, CDC20, and CDK1 in the CC cells. Conclusion: The result revealed that APS might have a therapeutic potential in treating CC and might permit intervention with treatments targeting PLK1, CDC20, and CDK1.

Objective: To explore the possible mechanism for treating NRR in arrhythmia using network pharmacology and molecular docking in this study. Methods: Active compounds and targets for NRR were retrieved from the Traditional Chinese Medicine Systems Pharmacology (TCMSP) Database and Analysis Platform, SymMap, and the Encyclopedia of Traditional Chinese Medicine (ETCM) databases. Arrhythmia-related genes were acquired from the Comparative Toxicogenomics Database (CTD) and the GeneCards database. Overlapping targets of NRR associated with arrhythmia were acquired and displayed via a Venn diagram. DAVID was applied for GO and KEGG pathway analyses. Cytoscape software and its plug-in were used for PPI network construction, module division and hub nodes screening. Auto- Dock Vina and qRT-PCR were carried out for validation. Results: In total, 21 active compounds and 57 targets were obtained. Of these, coumarin was the predominant category which contained 15 components and 31 targets. There were 5 key targets for NRR in treating arrhythmia. These targets are involved in the apoptotic process, extrinsic apoptotic signaling pathway in the absence of ligand, and endopeptidase activity involved in the apoptotic process by cytochrome c. The main pathways were the p53 signaling pathway, Hepatitis B and apoptosis. The molecular docking and qRT-PCR displayed good effects on hub node regulation in NRR treatment. Conclusion: NRR plays an important role in anti-apoptotic mechanisms that modulate the p53 signaling pathway, which may provide insight for future research and clinical applications focusing on arrhythmia therapy.

>Background and Objective: Dizziness is a common complication of gastrointestinal endoscopy under general anesthesia. Dizziness is primarily caused by a lack of energy and blood volume following fasting and water deprivation. Hypertonic glucose solution (HGS) is an intravenous energy replenishment, that increases blood volume due to its hyperosmotic characteristics and can be directly absorbed from blood circulation. This study aimed to HGS can prevent dizziness after gastrointestinal endoscopy. Methods: This was a double-blind, randomized, controlled study. Eligible patients were randomly allocated into two groups based on the intravenous agent administered before gastrointestinal endoscopy: Group A, saline (0.9%; 20 mL); and group B, HGS (50%; 20 mL). Overall, 840 patients were included in the statistical analysis. The scores and incidence of dizziness were assessed. Results: The dizziness score were higher in group A than in group B (1.92 ± 0.08 vs. 0.92 ± 0.06; p < 0.01). The incidence of mild dizziness and moderate-to-severe dizziness was significantly lower in group B than in group A (40.10% vs. 51.78% and 3.10% vs. 19.72%, respectively; p < 0.01). The incidence and score of dizziness were significantly lower in males than in females (30.81% vs. 51.82% and 0.64 ± 0.08 vs. 1.12 ± 0.08, respectively; p < 0.01) after pretreatment with HGS. Conclusion: Pretreatment with HGS effectively prevents dizziness after gastrointestinal endoscopy under general anesthesia. The mechanism of action is unclear but might be related to body energy replacement and an increase in blood volume following HGS administration.

Background: Copper-induced death (cuproptosis) is copper-dependent regulated cell death, which is different from known death mechanisms and is dependent on mitochondrial respiration. However, its effect on breast cancer (BRCA) is unclear. Objective: The objective of this study is to explore the important clinical significance of cuproptosis genes and to provide a new idea for guiding the personalized immunotherapy strategy of BRCA patients. Materials and Methods: We collected cuproptosis genes from published work. The gene alteration, differential expression, and prognostic value of cuproptosis genes were explored in BRCA based on TCGA database. We identified two subtypes (clusters A and B) by performing unsupervised clustering. The difference between two clusters was deeply explored, including clinical features, differential expressed genes (DEGs), pathways, and immune cell infiltration. Based on the DEGs between two clusters, a cuproptosis score was constructed and its predictive capability for overall survival of BRCA patients was validated. Results and Discussion: Patients with high cuproptosis score have worse survival status, with an increased infiltration level of most immune cells. Further analysis suggested that BRCA patients with high cuproptosis score may be sensitive to immune checkpoint inhibitor (ICI) treatment. Conclusion: Our findings may improve our understanding of cuproptosis in BRCA and may distinguish patients suitable for ICI treatment.

Background: Lung cancer (LC) is the leading cause of cancer-related deaths worldwide. Traditional Chinese medicine (TCM) reportedly has potential therapeutic effects against LC. Objective: This study aimed to investigate the antitumor efficacy of Yishen Qutong granule (YSQTG) in primary LC treatment, to identify its key active pharmaceutical ingredients (APIs), and to explore its possible mechanism of action. Methods: The antitumor role of YSQTG was validated via cell function assays and a xenograft tumor model. Then, high-performance liquid chromatography-mass spectrometry (HPLC-MS) was performed to determine the objective precipitation components of YSQTG, followed by target prediction through reference to databases. Subsequently, the proportion of the predicted targets that underwent actual changes was identified via RNA-sequencing. Enrichment analysis was performed to explore the possible mechanisms of action. Hub genes were screened, and western blotting was used to verify their protein expression levels to identify the core target. Molecular docking between the active compounds and the verified core target was performed, combined with an evaluation of the potential efficacy of candidate compounds using meta-analysis to screen the candidate key APIs. Results: Experiments confirmed that YSQTG could inhibit LC cell proliferation, induce apoptosis in vitro, and inhibit lung tumor growth in vivo. HPLC-MS, RNA-seq, and enrichment analysis showed that oxidative stress-related pathways were the possible mechanism of YSQTG in primary LC treatment. Western blot verification indicated that heme oxygenase 1 (HMOX1, HO-1) could be the core target. Molecular docking and meta-analysis suggested that genistein and quercetin were the candidate key APIs. Conclusion: YSQTG and its active ingredients, genistein and quercetin, may have therapeutic effects against LC through their action on the downregulation of oxidative stress-related HMOX1 protein expression.

Background: The cost of synthetic DNA has limited applications in frontier science and technology fields such as synthetic biology, DNA storage, and DNA chips. Objective: The objective of this study is to find an algorithm-optimized scheme for the in situ synthesis of DNA microarrays, which can reduce the cost of DNA synthesis. Methods: Here, based on the characteristics of in situ chemical synthesis of DNA microarrays, an optimization algorithm was proposed. Through data grading, the sequences with the same base at as many different features as possible were synthesized in parallel to reduce synthetic cycles. Results and Discussion: The simulation results of 10 and 100 randomly selected sequences showed that when level=2, the reduction ratio in the number of synthetic cycles was the largest, 40% and 32.5%, respectively. Subsequently, the algorithm-optimized scheme was applied to the electrochemical synthesis of 12,000 sequences required for DNA storage. The results showed that compared to the 508 cycles required by the conventional synthesis scheme, the algorithmoptimized scheme only required 342 cycles, which reduced by 32.7%. In addition, the reduced 166 cycles reduced the total synthesis time by approximately 11 hours. Conclusions: The algorithm-optimized synthesis scheme can not only reduce the synthesis time of DNA microarrays and improve synthesis efficiency, but more importantly, it can also reduce the cost of DNA synthesis by nearly 1/3. In addition, it is compatible with various in situ synthesis methods of DNA microarrays, including soft-lithography, photolithography, a photoresist layer, electrochemistry and photoelectrochemistry. Therefore, it has very important application value.

Background: Irritable bowel syndrome (IBS) is the most common gastrointestinal disease worldwide, with diarrhea-predominant irritable bowel syndrome (IBS-D) being the prevalent subtype. However, its pathogenesis remains unclear. Research has increasingly focused on identifying genetic factors in the mechanisms underlying IBS. Objective: We aimed to explore key gene nodes and potential microRNA-mRNA regulatory pairs of IBS-D using bioinformatics methods. Methods: We downloaded the GSE36701 microarray dataset from the Gene Expression Omnibus database and obtained 1358 differentially expressed mRNAs by analyzing mRNA profiles using the GEO2R analysis tool. Based on our previous study, we used TargetScan, miTarBase, and miRDB to predict the downstream genes of three known microRNAs (hsa-let-7b-5p, hsa-miR-19b-3p, and hsamiR- 20a-5p), and the microRNA-mRNA regulatory network was visualized using Cytoscape. Results: A total of 795 downstream target genes were found in TargetScan, miRTarBase, and miRDB databases, and 50 candidate genes were obtained. The Metascape and STRING databases were used to perform enrichment analysis and construct a protein-protein interaction network of candidate genes. Finally, we constructed a network of 3 microRNAs and 50 candidate mRNAs, among which 28 negative relation ship pairs and 5 key axes (hsa-miR-20a-5p/VEGFA, hsa-let-7b- 5p/MSN, hsa-let-7b-5p /PPP1R16B, hsa-19b-3p/ITGA2, and hsa-19b-3p/PIK3R3) were identified. Conclusion: We report five novel microRNA-mRNA regulatory axes in IBS-D pathogenesis and speculated that PIK3R3, negatively regulated by hsa-miR-19b-3p, may regulate NF-ΚB production through the PI3K/Akt pathway, which accounts for the occurrence of clinical symptoms in IBS-D patients. Our findings may offer key biomarkers for IBS-D diagnosis and treatment.