Polymerase Chain Reaction Experiments Research Articles

Identification of stable housekeeping genes in mouse liver for studying carbon tetrachloride-induced injury and cellular senescence

Acute liver injury (ALI) presents a challenging problem worldwide, prompting extensive research efforts. Cellular senescence has been found to be induced following ALI, and targeting cellular senescence has shown therapeutic potential. Therefore, understanding the expression of senescence-related genes in ALI can help to explore pathogenesis and treatment of this common disease. Carbon tetrachloride (CCl4) is commonly used to study ALI. Although polymerase chain reaction (PCR) is a convenient and economical molecular biology technique widely used in basic medicine, research on selecting suitable reference genes to obtain objective and reproducible PCR data is scarce. Moreover, evidence supporting the choice of reference genes for experimental studies of CCl4-induced ALI and hepatic senescence in mice is limited. In this study, we obtained murine livers at four time points (0, 12, 24, and 48 h) following CCl4 treatment. We used five algorithms (geNorm, BestKeeper, NormFinder, delta Ct, and RefFinder) to rank 12 candidate genes in real-time reverse-transcription quantitative PCR (RT-qPCR) experiments. Focusing on cellular senescence in this model, we adopted four senescence-associated secretory phenotype (SASP) genes (Il6, Il1b, Ccl2, and Ccl5) as target genes. Our results confirmed Gapdh and Tbp as suitable reference genes in murine CCl4-induced ALI models. Furthermore, we provide a table of published studies recommending reference genes for various liver disease models. This study provides a valuable reference for enhancing the reliability and reproducibility of ALI molecular findings.

The lncRNA AFAP1-AS1 is upregulated in metastatic triple-negative breast tumors and controls hypoxia-activated vasculogenic mimicry and angiogenesis

BackgroundVasculogenic mimicry (VM) is an alternative intratumoral microcirculation system that depends on the capacity of tumor cells to reorganize and grow in three-dimensional (3D) channel architectures like the capillaries formed by endothelial cells. Both VM and angiogenesis may coordinately function to feed cancer cells, allowing tumor growth. Long noncoding RNAs (lncRNAs) regulate critical cellular functions in cancer cells, including cell proliferation, apoptosis, angiogenesis, invasion, and metastasis. The lncRNA, known as actin filament-associated protein 1-antisense RNA 1 (AFAP1-AS1), has been described as an oncogene in diverse types of cancers. However, its role in VM and metastasis in triple-negative breast cancer (TNBC) is unknown.MethodsReverse transcription and quantitative polymerase chain reaction (RT‒qPCR) experiments were performed to evaluate the expression of 10 selected lncRNAs from literature in metastatic and nonmetastatic biopsies from TNBC patients. The expression of AFAP1-AS1 was analyzed in Genotype-Tissue Expression Genotype-Tissue Expression (GTEx) and The Cancer Genome Atlas (TCGA) datasets. The AFAP1-AS1 expression was knocked in TNBC Hs578T cells by transfection of specific siRNAs. Channel-like formation assays were performed using 3D cultures over Matrigel in hypoxia-treated Hs578T cancer cells with diminished expression of AFAP1-AS1. The angiogenesis tests were conducted using human umbilical vein endothelial cells (HUVECs) and AFAP1-AS1- silenced Hs578T cells on 3D cell cultures. The presence of VM (CD31-/PAS+) in tumor tissues from TNBC patients with and without metastasis was assessed through immunohistochemistry using endothelial marker CD31 antibodies and periodic acid-Schiff (PAS) staining.ResultsCompared with normal mammary tissues, AFAP1-AS1 expression was higher in breast cancer tissues. Moreover, AFAP1-AS1 expression was upregulated in the TNBC subtype compared to receptor-positive breast tumors. In addition, the expression of AFAP1-AS1 was correlated with the expression of the thirteen genes characteristic of a previously reported hypoxia signature. Interestingly, AFAP1-AS1 was upregulated in primary TNBC tumors from patients who developed metastasis compared with the nonmetastatic group. Functional analysis revealed that the knockdown of AFAP1-AS1 in Hs578T cells significantly impaired the hypoxia-induced VM, accompanied by a decrease in the development of 3D channel networks. Similarly, AFAP1-AS1 knockdown counteracts the angiogenic potential of cancer cells, as indicated by a reduction in the number of polygons, sprouting cells, and nodes in HUVEC cells. Remarkably, an increase in CD31-/PAS + staining of 3D channel networks in primary breast tumors from metastatic patients was found compared with the nonmetastatic group. Finally, we found that the number of blood vessels increased in the nonmetastatic group more than in the metastatic cohort.ConclusionsOur data suggested that AFAP1-AS1 controls both VM and angiogenesis in Hs578T breast cancer cells and that increased metastasis is associated with VM in TNBC patients.

RNAi of nuclear receptor E78 inhibits the cuticle formation in the molting process of spider mite, Tetranychus urticae.

The two-spotted spider mite, Tetranychus urticae, is an important pest mite in agriculture worldwide. E78, as a member of the nuclear receptor superfamily and a downstream responsive gene of ecdysteroids, plays a crucial role in regulating physiological behaviors such as development and reproduction in insects. However, its function in mites remains unclear. The aim of this study was to explore how E78 functions in the molting process of spider mites. In this study, reverse transcription quantitative polymerase chain reaction (RT-qPCR) experiments to analyze the expression pattern of TuE78 during the development of Tetranychus urticae, demonstrated that the expression level of TuE78 was higher during the molting state than that after the completion of molting, and it reached a peak expression level when the deutonymph mites entered the molting stage. RNA interference (RNAi)-mediated gene-silencing of TuE78 resulted in 95% deutonymph mite molt failure. A series of analysis under a light microscope, and scanning and transmission electron microscopy revealed that RNAi mites died within the exuvium without ecdysis, and that apolysis had started but the new cuticle was thin and the typical cuticular lamellae were absent, indicating blockage of the post-apolysial processes and explaining molt failure. Hence, transcriptome sequencing confirmed that the expression of cuticle protein and lipid metabolism-related genes was significantly affected after TuE78 silencing. This study demonstrated that TuE78 participates in the molting process of Tetranychus urticae by regulating the post-apolysial processes with the formation of new cuticle and successful ecdysis. This in turn suggests the potential of TuE78 as a target for pest mite control and provides a theoretical basis for further exploration of the molecular regulatory mechanism of spider mite molting. © 2024 Society of Chemical Industry. Published by John Wiley & Sons Ltd.

Thyroid Hormone Upregulates Cav1.2 Channels in Cardiac Cells via the Downregulation of the Channels' β4 Subunit.

Thyroid hormone binds to specific nuclear receptors, regulating the expression of target genes, with major effects on cardiac function. Triiodothyronine (T3) increases the expression of key proteins related to calcium homeostasis, such as the sarcoplasmic reticulum calcium ATPase pump, but the detailed mechanism of gene regulation by T3 in cardiac voltage-gated calcium (Cav1.2) channels remains incompletely explored. Furthermore, the effects of T3 on Cav1.2 auxiliary subunits have not been investigated. We conducted quantitative reverse transcriptase polymerase chain reaction, Western blot, and immunofluorescence experiments in H9c2 cells derived from rat ventricular tissue, examining the effects of T3 on the expression of α1c, the principal subunit of Cav1.2 channels, and Cavβ4, an auxiliary Cav1.2 subunit that regulates gene expression. The translocation of phosphorylated cyclic adenosine monophosphate response element-binding protein (pCREB) by T3 was also examined. We found that T3 has opposite effects on these channel proteins, upregulating α1c and downregulating Cavβ4, and that it increases the nuclear translocation of pCREB while decreasing the translocation of Cavβ4. Finally, we found that overexpression of Cavβ4 represses the mRNA expression of α1c, suggesting that T3 upregulates the expression of the α1c subunit in response to a decrease in Cavβ4 subunit expression.

Unraveling the mechanisms of RECQL4-mediated cervical cancer progression through the PI3K/AKT pathway

BackgroundRECQL4 is a member of the DNA helicase family and is critical for DNA replication, DNA damage repair, and tumor progression. However, its specific role in cervical cancer remains uncertain. MethodsIn this study, we aimed to investigate the impact of RECQL4 on cervical cancer prognosis using clinical specimens from The Cancer Genome Atlas. We evaluated the malignant effects of RECQL4 through various experimental assays including cell Cell Counting Kit-8, EdU, colony formation, cell cycle analysis, cell apoptosis, scratch, and Transwell assays. We explored the mechanisms of RECQL4-regulated malignancy using analyses of bioinformatics, RNA sequencing data, polymerase chain reaction (PCR), western blotting, and cell immunofluorescence experiments. Furthermore, we validated the effects of RECQL4 knockdown on tumor growth using subcutaneous tumor models in nude mice. ResultsRECQL4 was upregulated in cervical cancer and correlated with prognosis, demonstrating a positive relationship with tumor mutational burden. Knockdown of RECQL4 inhibits cervical cancer cell proliferation, migration, and invasion, suppresses epithelial-mesenchymal transition status, induces cell cycle arrest, and promotes apoptosis. Mechanistically, RECQL4 mediated malignancy through the PI3K/AKT pathway and reduced nuclear β-catenin expression. In vivo studies further confirmed that RECQL4 knockout significantly inhibited tumor growth. ConclusionsOur findings provide novel insights into the mechanism behind RECQL4-mediated cervical cancer progression through the PI3K/AKT pathway. Furthermore, our study suggests potential therapeutic strategies for targeting RECQL4 in cervical cancer treatment.

Identification of key regulatory genes involved in myelination after spinal cord injury by GSEA analysis

Multilayer dense myelin tissue provides insulating space and nutritional support for axons in healthy spinal cord tissue. Oligodendrocyte precursor cells (OPCs) are the main glial cells that complement myelin loss in the central nervous system and play an important role in the repair of spinal cord injury (SCI). However, the regulation of axonal remyelination after SCI is still insufficient. In this study, we focused on the changes in genes related to myelin repair after rat hemisection SCI by gene set enrichment analysis (GSEA). Key genes proteolipid protein 1 (Plp1), hexosaminidase subunit alpha (Hexa), and hexosaminidase subunit beta (Hexb) during remyelination after SCI were found. Through quantitative real-time polymerase chain reaction (qPCR) experiments, we confirmed that within 28 days after rat hemisection SCI, the mRNA expression of gene Plp1 gradually decreased, while the expressions of gene Hexa and Hexb gradually increased, which was consistent with RNA sequencing results. In vitro, we performed EdU proliferation assays on OPC cell line OLN-93 and primary rat OPCs. We found that interference of Plp1 promoted OPC proliferation, while interference of Hexa and Hexb inhibited OPC proliferation. In addition, we performed in vitro differentiation experiments on primary rat OPCs. By measuring myelin sheath branch outgrowth and the fluorescence intensity of the mature myelin sheath marker myelin basic protein (MBP), we found that interference of Hexa or Hexb promoted OPC differentiation and maturation, but interference of Plp1 inhibited this process. Finally, we injected Hexb siRNA in vivo and found that interfering Hexb could improve motor movements and myelin regeneration after SCI in rats. Our results provide new target genes that can selectively regulate the proliferation and differentiation of endogenous OPCs, providing new ideas for promoting remyelination and functional recovery after SCI.

Abstract P454: Screening of risk genes for carotid vulnerable plaque based on transcriptomics and experimental verification

Purpose and background: This study aims to conduct an in-depth analysis of human carotid atherosclerotic plaques using transcriptomic data to elucidate the relationship between hypoxia-related genes and the stability of carotid artery plaques and explore their connection with immune infiltration. Methods: Four GEO datasets (GSE21545, GSE24495, GSE159677, and GSE189300) were used. Initially, gene expression data from carotid artery plaque samples in GSE21545 and GSE24495 were analyzed. Hypoxia-related gene sets were obtained from MSigDB, and the "HALLMARK_HYPOXIA" gene set was explicitly selected. GSEA software was used for ultimately selecting CDKN1C and HAS1 as characteristic genes. Subsequently, sample clustering analysis was conducted to determin the optimal number of clusters. Gene set enrichment and differential analysis were performed. Real-time quantitative polymerase chain reaction (RT-qPCR) and Western blotting experiments were conducted for preliminary validation of CDKN1C and HAS1 expression levels in ApoE knockout mice at 16 and 6 weeks. Subsequently, single-cell data from GSE159677 were processed to determine the differential localization of CDKN1C in carotid atherosclerotic plaques, with functional analysis conducted using GSE189300. Results: CDKN1C and HAS1 genes were found to exhibit differential expression in plaques and were correlated with hypoxia and immune scores. Clustering analysis revealed two main clusters, with patients in cluster A showing a higher risk of adverse events and a stronger association with immunity. Genes with a positive effect on atherosclerosis were highly expressed in poorer prognosis cluster A. Validation dataset GSE24495 also confirmed the grouping ability of CDKN1C and HAS1 genes, showing enrichment in atherosclerosis-related pathways. RT-qPCR and protein immunoblotting experiments demonstrated no significant differences in HAS1 expression levels, while CDKN1C showed lower protein expression in 16-week ApoE knockout mice compared to 6 weeks. Single-cell data from GSE159677 localized differential expression of CDKN1C in plaque cells. Finally, immunofluorescence validation confirmed the coexistence of CDKN1C and vascular smooth muscle cells. Conclusion: This study comprehensively analyzed transcriptomics data from carotid atherosclerotic plaques, revealing the significant roles of CDKN1C and HAS1 genes. Immunofluorescence validation further supported the crucial role of these genes in carotid atherosclerosis.

Molecular Epidemiology and Horizontal Transfer Mechanism of optrA-Carrying Linezolid-Resistant Enterococcus faecalis.

The aim of this work was to provide a theoretical and scientific basis for the treatment, prevention, and control of clinical drug-resistant bacterial infections by studying the molecular epidemiology and horizontal transfer mechanism of optrA-carrying linezolid-resistant Enterococcus faecalis strains (LREfs) that were clinically isolated in a tertiary hospital in Kunming, China. Non-repetitive LREfs retained in a tertiary A hospital in Kunming, China. The strains were identified by Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The transferability and horizontal transfer mechanism of optrA gene were analyzed using polymerase chain reaction (PCR), whole-genome sequencing (WGS), and conjugation experiments. A total of 39 LREfs strains were collected, and all of them were multi-drug resistant. There were 30 LREfs strains (76.9%) carrying the optrA gene, The cfr, poxtA genes and mutations in the 23S rRNA gene were not detected. The conjugation experiments showed that only three of 10 randomly selected optrA-carrying LREfs were successfully conjugated with JH2-2. Further analysis of one successfully conjugated strain revealed that the optrA gene, located in the donor bacterium, formed the IS1216E-erm(A)-optrA-fexA-IS1216E transferable fragment under the mediation of the mobile genetic element (MGE) IS1216E, which was then transferred to the recipient bacterium via horizontal plasmid transfer. Carrying the optrA gene is the primary resistance mechanism of LREfs strains. The optrA gene could carry the erm(A) and fexA genes to co-transfer among E. faecalis. MGEs such as insertion sequence IS1216E play an important role in the horizontal transfer of the optrA gene.

Initial Evaluation of lncRNA A2M-AS1 Gene Expression in Multiple Sclerosis Patients.

Multiple sclerosis (MS) is one of the three leading neurodegenerative diseases worldwide. Gene expression profile studies play an important role in recognizing and preventing disease. Considering the inherent ability of biomarkers to diagnose and prognose the occurrence of a disease, with the aim of gene therapy and changing gene expression, it can be helped to treat it. In this study, by examining the gene interaction and expression of non-coding genes in patients with MS, using bioinformatics analyses, laboratory research and potential non-coding diagnostic biomarkers of MS were selected for further investigations. First, by using micro-array data analysis of the GEO database, the expression status of the long non-coding ribonucleic acid (RNA) (lncRNA) A2M-AS1 gene was investigated in patients with MS. lncRNA-mRNA interaction analysis was performed in the lncRRisearch database. After sample collection, the total RNA extracted using the RNA extraction kit from 20 patient samples and 20 healthy samples was synthesized into cDNA with the synthesis kit. The quantitative reverse transcriptase polymerase chain reaction experiment was performed for the final validation of expression change. Based on bioinformatic and laboratory analysis, the expression of the A2M-AS1 gene in MS samples showed a significant decrease in expression compared to healthy samples. Also, based on the receiver operating characteristic analysis, lncRNA A2M-AS1 can be introduced as an acceptable diagnostic biomarker to distinguish MS samples from healthy samples. lncRNA A2M-AS1, by reducing its expression as an acceptable diagnostic biomarker, can increase the risk of developing MS.

Hydrogen sulphide alleviates root growth inhibition induced by phosphate starvation.

Phosphorus (P) has crucial roles in plant growth and development. Hydrogen sulphide (H2S) has multiple functions in plants, particularly having the ability to promote tolerance to a variety of adversity stresses. However, it is unclear whether H2S has a function when plants suffer Pi-deficiency stress. DES1, encoding L-cysteine desulfhydrase1, is a crucial source of H2S in Arabidopsis thaliana by catalysing the substrate L-cysteine. Under phosphate starvation, the des1 mutant had a significantly shorter primary root length than the wild-type Col-0, and exogenous application of H2S donor NaHS could compensate for the root growth-sensitive phenotype. In contrast, the transgenic lines DES1ox overexpressing DES1 exhibited less sensitivity to phosphate starvation in terms of longer roots compared to the Col-0. These results demonstrate that H2S is involved in the regulation of Arabidopsis root growth under phosphate starvation. Moreover, using quantitative real-time polymerase chain reaction experiments to analyse the changes in genes induced by phosphate starvation in des1 mutant and Col-0, we screened to find that the expression of the Sulfoquinovosyl diacylglycerol 1 (SQD1) gene was significantly downregulated in the des1 mutant. Consistently, exogenous H2S significantly promoted SQD1 expression levels in roots of Col-0. Taken together, we demonstrate that DES1-mediated H2S participates in alleviating root growth inhibition by promoting the expression of SQD1 under Pi starvation.

Development of prognostic model incorporating a ferroptosis/cuproptosis-related signature and mutational landscape analysis in muscle-invasive bladder cancer

BackgroundMuscle-invasive bladder cancer (MIBC) is a prevalent and aggressive malignancy. Ferroptosis and cuproptosis are recently discovered forms of programmed cell death (PCD) that have attracted much attention. However, their interactions and impacts on MIBC overall survival (OS) and treatment outcomes remain unclear.MethodsData from the TCGA-BLCA project (as the training set), cBioPortal database, and GEO datasets (GSE13507 and GSE32894, as the test sets) were utilized to identify hub ferroptosis/cuproptosis-related genes (FRGs and CRGs) and develop a prognostic signature. Differential expression analysis (DEA) was conducted, followed by univariate and multivariate Cox’s regression analyses and multiple machine learning (ML) techniques to select genetic features. The performance of the ferroptosis/cuproptosis-related signature was evaluated using Kaplan–Meier (K–M) survival analysis and receiver-operating characteristics (ROC) curves. Mutational and tumour immune microenvironment landscapes were also explored. Real-time quantitative reverse transcription polymerase chain reaction (RT-qPCR) experiments confirmed the expression patterns of the hub genes, and functional assays assessed the effects of SCD knockdown on cell viability, proliferation, and migration.ResultsDEA revealed dysregulated FRGs and CRGs in the TCGA MIBC cohort. SCD, DDR2, and MT1A were identified as hub genes. A prognostic signature based on the sum of the weighted expression of these genes demonstrated strong predictive efficacy in the training and test sets. Nomogram incorporating this signature accurately predicted 1-, 3-, and 5-year survival probabilities in the TCGA cohort and GSE13507 dataset. Copy number variation (CNV) and tumour immune microenvironment analysis revealed that high risk score level groups were associated with immunosuppression and lower tumour purity. The associations of risk scores with immunotherapy and chemical drugs were also explored, indicating their potential for guiding treatment for MIBC patients. The dysregulated expression patterns of three hub genes were validated by RT-qPCR experiments.ConclusionsTargeting hub FRGs and CRGs could be a promising therapeutic approach for MIBC. Our prognostic model offers a new framework for MIBC subtyping and can inform personalized therapeutic strategies.

Research on preventive effect of Akkermansia muciniphilaAKKPROBIO on acute gouty arthritis in mice.

In mice with acute gouty arthritis, this study intends to examine the mechanism of action of Akkermansia muciniphila AKK PROBIO. We developed a mouse model of acute gouty arthritis using sodium urate. The efficiency and mechanism of AKK PROBIO in preventing acute gouty arthritis in mice were then determined by examining the degree of foot swelling, pain threshold, blood biochemical indicators, histological alterations, and messenger RNA (mRNA) expression changes. The results of the animal experiment showed that AKK PROBIO can lessen mouse foot edema severity and increase pain threshold. AKK PROBIO can enhance the enzyme activity of superoxide dismutase (SOD) and the level of glutathione (GSH) in the ankle joint tissues of mice with acute arthritis while decreasing the enzyme activity of myeloperoxidase (MPO) and the level of malondialdehyde (MDA). Interleukin 6 (IL-6), interleukin 10 (IL-10), interleukin 1 beta (IL-1β), and tumor necrosis factor-alpha (TNF-α) levels are all reduced by AKK PROBIO in the blood of mice with acute arthritis. Results from histopathology showed that AKK PROBIO reduced tissue damage in the mouse ankle and foot joints. In the tissues of the ankle joints of mice with acute arthritis, the results of the quantitative polymerase chain reaction (qPCR) and Western blot experiments suggested that AKK PROBIO may inhibit the mRNA and protein expression of extracellular signal-regulated kinase 1/2 (ERK1/2), cyclooxygenase-2 (COX-2), and prostaglandin E2 (PGE2) in the tissues. AKK PROBIO can also regulate gut microbiota, inhibit harmful bacteria, and enhance valeric acid in the intestine, isobutyric acid, and isovaleric acid. Therefore, it is evident that AKK PROBIO prevents acute gouty arthritis better than glucosamine sulfate. It is a strain that has probiotic potential.

Machine learning and bioinformatics analysis of diagnostic biomarkers associated with the occurrence and development of lung adenocarcinoma.

Lung adenocarcinoma poses a major global health challenge and is a leading cause of cancer-related deaths worldwide. This study is a review of three molecular biomarkers screened by machine learning that are not only important in the occurrence and progression of lung adenocarcinoma but also have the potential to serve as biomarkers for clinical diagnosis, prognosis evaluation and treatment guidance. Differentially expressed genes (DEGs) were identified using comprehensive GSE1987 and GSE18842 gene expression databases. A comprehensive bioinformatics analysis of these DEGs was conducted to explore enriched functions and pathways, relative expression levels, and interaction networks. Random Forest and LASSO regression analysis techniques were used to identify the three most significant target genes. The TCGA database and quantitative polymerase chain reaction (qPCR) experiments were used to verify the expression levels and receiver operating characteristic (ROC) curves of these three target genes. Furthermore, immune invasiveness, pan-cancer, and mRNA-miRNA interaction network analyses were performed. Eighty-nine genes showed increased expression and 190 genes showed decreased expression. Notably, the upregulated DEGs were predominantly associated with organelle fission and nuclear division, whereas the downregulated DEGs were mainly associated with genitourinary system development and cell-substrate adhesion. The construction of the DEG protein-protein interaction network revealed 32 and 19 hub genes with the highest moderate values among the upregulated and downregulated genes, respectively. Using random forest and LASSO regression analyses, the hub genes were employed to identify three most significant target genes.TCGA database and qPCR experiments were used to verify the expression levels and ROC curves of these three target genes, and immunoinvasive analysis, pan-cancer analysis and mRNA-miRNA interaction network analysis were performed. Three target genes identified by machine learning: BUB1B, CENPF, and PLK1 play key roles in LUAD development of lung adenocarcinoma.

Exploring the synergistic effects of chuanxiong rhizoma and Cyperi rhizoma in eliciting a rapid anti-migraine action based on pharmacodynamics and pharmacokinetics

Ethnopharmacological relevanceHerb-herb combination has been used to maximize the therapeutic efficacy in the theory of traditional Chinese medicine. Chuanxiong rhizoma (called Chuanxiong in Chinese, CX) and Cyperi rhizoma (called Xiangfu in Chinese, XF) have been used alone or in combination (CRCR) to treat migraine dating back to Eastern Jin Dynasty (AD317) of China. But no data demonstrate the possible necessities or advantages of combining CX and XF for migraine. Aim of the studyThis study explores the combination mechanism based on pharmacodynamics and pharmacokinetics. Materials and methodsA nitroglycerin-induced acute migraine model in rats was used to evaluate the anti-migraine effects of CRCR and the individual herbs using behavior, real time polymerase chain reaction and Western blot experiments. The absorption characteristics of active components involved in the anti-migraine action were analyzed by UPLC-MS/MS. ResultsCX and CRCR significantly reversed the abnormal levels of vasoactive substances (5-HT, CGRP, MMP-2 and MMP-9) to normal levels, but XF did not. XF and CRCR significantly decreased the pro-inflammatory cytokines (IL-1β, IL-6, and TNF-a), and increased the anti-inflammatory cytokines (IL-4 and IL-10). CRCR significantly decreased the mRNA expression levels of c-fos, iNos and nNos, and the corresponding protein expression levels of c-Fos, iNOS, and nNOS. CRCR inhibited NOS/NO pathway by downregulating the expression levels of NOS and NO. Furthermore, CRCR significantly increased the intestinal absorption rate and amount, and changed the pharmacokinetic parameters of active components in comparison with the individual herbs. ConclusionsCX had an advantage in regulating vasoactive substances, and XF focused on regulating inflammatory cytokines. CRCR is more effective in treating migraine than the individual herbs by depending on the synergistic action of CX and XF. This research provided some critical evidences on synergistic action between herb-herb interactions, and revealed the potential advantages of herb-herb combination in traditional Chinese medicine.

Key extracellular proteins and TF-miRNA co-regulatory network in diabetic foot ulcer: Bioinformatics and experimental insights.

Diabetic foot ulcers (DFUs), a serious complication of diabetes, are associated with abnormal extracellular protein (EP) metabolism. The identification of key EPs and their regulatory networks is crucial for the understanding of DFU formation and development of effective treatments. In this study, a large-scale bioinformatics analysis was conducted to identify potential therapeutic targets and experimental validation was performed to ensure the reliability and biological relevance of the findings. Due to the comprehensive profiling of DFU samples provided by the GSE80178 dataset, we initially selected it to derive differentially expressed genes (DEGs) associated with DFU. Subsequently, utilizing the UniProt database and annotated EP list from the Human Protein Atlas annotation database, we screened for extracellular protein-related differentially expressed genes (EP-DEGs) due to their crucial role in the pathogenesis and healing of DFU. We examined EP-DEG pathway enrichment and protein-protein interaction networks, analyzed paired full-thickness skin tissue samples from 24 patients with DFUs and healthy controls, and performed polymerase chain reaction (PCR) experiments to validate candidate genes. Ultimately, we constructed a transcription factor (TF)-microRNA (miRNA)-hub gene co-regulatory network to explore upstream and downstream regulatory connections based on validated DEGs. Four crucial candidate genes (FMOD, LUM, VCAN, and S100A12) were identified and verified via PCR analysis. The TF-miRNA-hub EP-DEG regulatory network contained the pivotal TFs TRIM28 and STAT3 and the miRNAs hsa-mir-20a-5p, hsa-miR-21, and hsa-miR-203. The findings of this study advance our understanding of the pathology of DFU by defining key roles of specific EPs and elucidating a comprehensive regulatory network. These insights pave the way for novel approaches to improve DFU treatment outcomes.

Icariin protects against acute graft-versus-host disease while preserving graft-versus-leukemia activity after allogeneic hematopoietic stem cell transplantation

BackgroundAcute graft-versus-host disease (aGVHD), which is mainly mediated by allogeneic T cells, is a decisive factor in the success of allogeneic hematopoietic stem cell transplantation (allo-HCT). Prophylaxis for aGVHD in clinical patients is unsatisfactory, and there is still a huge unmet need for novel approaches. Icariin (ICA) shows potent anti-inflammatory activity and suppresses T cell-mediated immune responses. Thus, ICA is a potential drug for the prevention of aGVHD. However, there is no data assessing the impact of ICA on aGVHD after allo-HCT. PurposeThis study aimed to investigate the protective effect of ICA against aGVHD and its mechanisms. Moreover, the impact of ICA on the graft-versus-leukemia (GVL) effect and engraftment of donor hematopoietic and immune cells were assessed. MethodsDifferent murine models of allo-HCT were developed to study the influence of the ICA on GVHD and GVL effect. Flow cytometry was used to analyze the growth of leukemia cells, alterations in different immune cells, and apoptosis. Cell proliferation was determined using a CCK-8 assay. RNA sequencing and quantitative proteomic analysis were performed to elucidate the underlying mechanisms, which were further verified by polymerase chain reaction or functional experiments. ResultsDifferent concentrations of ICA exhibited opposite effects: low-concentration ICA promoted, while high concentrations suppressed the proliferation and function of T cells. A high dose of ICA administration during days +3 to +5 post-allo-HCT can alleviate murine aGVHD but does not affect the course of chronic GVHD (cGVHD), the GVL effect against both acute myeloid and lymphoblastic leukemia, or the recovery of donor hematological and immune cells. ICA extensively represses the expansion, function, and infiltration of donor alloreactive T cells, while preserving regulatory T cells (Tregs) and myeloid-derived suppressor cells (MDSC). Quantitative proteomic analysis showed that downregulation of integrin-linked kinase (ILK) and lymphocyte cytosolic protein 2 (LCP2) expression was possibly associated with ICA-mediated aGVHD protective effects. Furthermore, an inhibitor of ILK, which can alleviate murine aGVHD administered early after allo-HCT. ConclusionThese findings suggest that the bioactivities of ICA are associated with its concentration and that ICA can effectively mitigate aGVHD without losing GVL activity or engraftment of donor hematopoietic and immune cells. Thus, ICA may be a promising drug for preventing aGVHD in clinical settings.

Pro-angiogenic effects of Guo Min decoction in a zebrafish model

ABSTRACT Objectives: Guo Min decoction (GMD) is a Chinese traditional medicine that can regulate allergy-related symptoms. Although GMD treatment was reported to treat allergy-associated symptoms by regulating the immune response, the rationale between GMD treatment and angiogenesis has not been reported yet. Our objective is to investigate the angiogenesis-modulating activity of GMD. Materials and Methods: In this study, we used fluorescence recording, alkaline phosphatase (AP) activity staining, and real-time polymerase chain reaction (PCR) experiments to examine the effects of GMD on angiogenesis in a zebrafish model. Results: GMD-treated zebrafish embryos exhibited more intercapillary spaces in the caudal vein plexus (Mock: 11.1 ± 1.8 [n = 20; n: numbers of embryos]; GMD-treated: 16.2 ± 1.9 [n = 20]). AP activity staining showed that treatment with GMD and liquorice (Gan Cao, a component of GMD) induced subintestinal vein outgrowth. However, glycyrrhizin (a component of Gan Cao) had no obvious pro-angiogenic effects on zebrafish. Furthermore, real-time PCR experiments indicated that GMD exposure might be through regulating angiogenesis-related genes (cdh5, nrp1a, and flt1) expressions. Conclusion: Based on these observations, we proposed that GMD had pro-angiogenic activity in a zebrafish model, and it might partially be contributed by one of the components, liquorice.

Developing an advanced diagnostic model for hepatocellular carcinoma through multi-omics integration leveraging diverse cell-death patterns.

Hepatocellular carcinoma (HCC), representing more than 80% of primary liver cancer cases, lacks satisfactory etiology and diagnostic methods. This study aimed to elucidate the role of programmed cell death-associated genes (CDRGs) in HCC by constructing a diagnostic model using single-cell RNA sequencing (scRNA-seq) and RNA sequencing (RNA-seq) data. Six categories of CDRGs, including apoptosis, necroptosis, autophagy, pyroptosis, ferroptosis, and cuproptosis, were collected. RNA-seq data from blood-derived exosomes were sourced from the exoRBase database, RNA-seq data from cancer tissues from the TCGA database, and scRNA-seq data from the GEO database. Subsequently, we intersected the differentially expressed genes (DEGs) of the HCC cohort from exoRBase and TCGA databases with CDRGs, as well as DEGs obtained from single-cell datasets. Candidate biomarker genes were then screened using clinical indicators and a machine learning approach, resulting in the construction of a seven-gene diagnostic model for HCC. Additionally, scRNA-seq and spatial transcriptome sequencing (stRNA-seq) data of HCC from the Mendeley data portal were used to investigate the underlying mechanisms of these seven key genes and their association with immune checkpoint blockade (ICB) therapy. Finally, we validated the expression of key molecules in tissues and blood-derived exosomes through quantitative Polymerase Chain Reaction (qPCR) and immunohistochemistry experiments. Collectively, we obtained a total of 50 samples and 104,288 single cells. Following the meticulous screening, we established a seven-gene diagnostic model for HCC, demonstrating high diagnostic efficacy in both the exoRBase HCC cohort (training set: AUC = 1; testing set: AUC = 0.847) and TCGA HCC cohort (training set: AUC = 1; testing set: AUC = 0.976). Subsequent analysis revealed that HCC cluster 3 exhibited a higher stemness index and could serve as the starting point for the differentiation trajectory of HCC cells, also displaying more abundant interactions with other cell types in the microenvironment. Notably, key genes TRIB3 and NQO1 displayed elevated expression levels in HCC cells. Experimental validation further confirmed their elevated expression in both tumor tissues and blood-derived exosomes of cancer patients. Additionally, stRNA analysis not only substantiated these findings but also suggested that patients with high TRIB3 and NQO1 expression might respond more favorably to ICB therapy. The seven-gene diagnostic model demonstrated remarkable accuracy in HCC screening, with TRIB3 emerging as a promising diagnostic tool and therapeutic target for HCC.

Knockdown of hsa_circ_0102231 Impedes the Progression of Liver Cancer through the miR-873-SOX4 Axis.

Hepatocellular carcinoma (HCC) is one of the most intractable tumors in the world due to its high rate of recurrence and heterogeneity. The objective of this study was to investigate the role of circular RNA 0102231 (hsa_circ_ 0102231) in the progression of liver cancer. In this study, quantitative polymerase chain reaction experiments were performed to quantify the hsa_circ_0102231 level in different liver cancer cell lines. Bioinformatics analysis, as well as a dual-luciferase reporter and RNA pull-down assay, were used to identify putative hsa_circ_ 0102231 downstream targets. Colony formation and CCK8 assays were utilized to examine cell proliferation, whereas Transwell assays were employed to monitor cell migration. Lastly, the role of hsa_circ_0102231 in liver cancer was assessed in a subcutaneous xenograft model. The expression of hsa_circ_0102231 increased significantly in HepG2 and Huh-7 cells compared with controls, and hsa_circ_0102231 knockdown inhibited cell proliferation and migration in vitro and in vivo. Bioinformatics analysis, as well as a dual-luciferase reporter and RNA pulldown assay, revealed that miR-873 and SOX4 were hsa_circ_0102231 downstream targets. miR-873 inhibition or SOX4 overexpression rescued the proliferation and migration of HepG2 and Huh-7 cells after hsa_circ_0102231 knockdown. Furthermore, SOX4 overexpression reversed the miR-873-induced inhibition of cell migration and proliferation in vitro. These results show that hsa_circ_0102231 knockdown impedes the progression of liver cancer by regulating the miR-873/SOX4 axis. However, further studies are needed to determine whether hsa_circ_0102231 may be a therapeutic target in liver cancer.

Investigating the Underlying Molecular Mechanisms of Yunke on Bone Metastases from Prostate Cancer.

To explore analgesic effect and bone repair mechanism of non-radioactive technetium-99 conjugated with methylene diphosphonate (99Tc-MDP, brand name, Yunke) on bone metastases (BM). In vivo experiment, mouse BM models of prostate cancer RM-1 cell were constructed and divided into Control, Yunke, 99Tc+SnCl2 and MDP groups based on medicine composition. Tumor specimens were inspected for size, X-ray, microCT and histopathology. In vitro experiment, with Cell Counting Kit-8 (CCK8), scratch, clone, apoptosis, Polymerase Chain Reaction (PCR) and Western Blot experiments, effects of Yunke on RM-1 cells and osteoclast-related cells were observed. In vivo experiment, there was no difference in tumor size between Yunke and control group. Contrasted with control group, in Yunke group, trabecular spacing (Tb.Sp) of tumor bone was lower, bone volume/total volume (BV/TV) on marrow cavity and bone cortex were higher. Tunnel staining showed that positive rate of apoptosis in Yunke group was higher than that in control group. Ki67 staining showed that Yunke could not inhibit proliferation of tumor cells. In vitro experiment, CCK8 and scratch experiments showed that Yunke neither can inhibit proliferation nor can inhibit migration of RM-1 cells. High concentration of Yunke promoted late apoptosis of RM-1 cells. Yunke could inhibit BMM cell proliferation, differentiation of osteoclasts, and osteoclast-related transcription factors. Yunke displayed different degrees of inhibitory effects on MAPKs signaling pathway during osteoclast differentiation. It had obvious inhibitory effects on osteoclast-related transcription factors, such as cFOS, NFATC1, ACP-5, CTSK, D2 and MMP-9, the strongest inhibitory effects were observed with ACP-5, CTSK and D2. Yunke also displayed different degrees of inhibitory effects on protein activities of JNK, pERK, ERK and pP38. Yunke cannot inhibit the proliferation and migration of RM-1 cells, so we think it is not recommended for the treatment of primary tumors and prevention of occurrence of tumors metastatic to bones. The mechanism of therapeutic effect of Yunke on BM by inhibiting proliferation of BMM, inhibiting MAPKs signal transduction and activation of transcription factors during differentiation process of BMM-derived osteoclasts, inhibiting number and size of osteoclasts, inhibiting bone resorption and protecting bone destruction through enhancing bone hardness and bone mass. Thereby, we believe that Yunke is more suitable for promoting the repair induced by BMs, delaying its progression and reducing the occurrence of SREs.