KEGG Analysis Research Articles

Amniotic fluid microbiota and metabolism with non-syndromic congenital heart defects: a multi-omics analysis

Background and aimsRecent studies have indicated possible links between the microbiota and the fetal heart, while the relevant mechanism is still unknown. This study is aims to investigate whether analyzing the microbiota and metabolic profiles of amniotic fluid collected from pregnant women whose fetuses with or without non-syndromic congenital heart defects (CHDs), during the second and third trimester of pregnancy, could offer valuable insights into CHDs.Methods and resultsA case-control study was conducted with 17 cases diagnosed with non-syndromic CHDs (CHDs group) and 34 controls without congenital anomalies (control group) at a ratio of 1:2. The 16 S rDNA gene sequencing and metabolomics methods were employed to assess 51 amniotic fluid samples. The amniotic fluid microbiome from the CHDs group exhibited significantly higher Shannon and Simpson indices compared to the control group. At the genus level, 240 bacterial taxa were substantially enriched in the two groups, with 93 of those taxa being highly enriched in the case group. Compared to the control group, the case group exhibited 177 metabolites that were significantly increased and 480 metabolites that were down-regulated. The differential metabolites were primarily enriched in the steroid hormone biosynthesis, bile secretion and ovarian steroidogenesis, according to KEGG analysis. The observed variations in nine metabolites could attributed to fifty-eight distinct bacterial taxa. The nine differential metabolites were mainly associated with pathways involving steroid hormone biosynthesis, bile secretion, glycolysis, tricarboxylic acid (TCA) cycle, NADPH metabolism, and acyl transfer pathways.ConclusionThe CHDs group has disturbed amniotic fluid microbiota and metabolites, and more research was required to elucidate the mechanism.

Exploring molecular disparities of H-type vasculature endothelial cells in osteonecrosis of the femoral head through single-cell analysis

ObjectiveRecent studies highlight the role of H-type vasculature in bone regeneration. This study, based on single-cell RNA sequencing (scRNA-seq), aims to explore the changes in H-type vasculature endothelial cells (H_ECs) in osteonecrosis of the femoral head (ONFH) and hip osteoarthritis (HOA), focusing on the death modes such as ferroptosis, pyroptosis, and parthanatos.MethodsWe re-analyzed the scRNA-seq data of femoral head samples publicly available in 2022. This study selected nine femoral head samples (3 each from HOA, ONFH stage 3 A, and ONFH stage 4). CD31 + EMCN + endothelial cells were classified as H_ECs. Molecular differences were assessed using Gene Ontology and KEGG analysis. Hypoxia, ferroptosis, pyroptosis, and parthanatos indices were calculated, and transcription factors were predicted using SENIC. Cell communication was analyzed with CellChat.ResultsAfter integrating the 9 samples, 14 cell types were identified: B cells, Mesenchymal stem cells, Osteoblasts, Endothelial cells, Monocytes, T cells, NK cells, Fibroblasts, Macrophages, Common myeloid progenitors, Chondrocytes, Myelocytes, Osteoclasts, and Pericytes. The number of endothelial cells and H_ECs decreased with necrosis severity. H_ECs showed higher angiogenic capacity but lower stress resistance compared to other endothelial cells. Angiogenic capacity decreased in necrotic samples, accompanied by an elevation in inflammation levels. The hypoxia index was higher, with ferroptosis increased in stage 3 A and parthanatos in stages 3 A and 4. No change was observed in pyroptosis. Cell communication analysis revealed downregulation of SLIT3-ROBO4 signaling during necrosis.ConclusionH_ECs show molecular differences compared to other endothelial cells. Ferroptosis and parthanatos contribute to the demise of H_ECs in ONFH, with pericytes and fibroblasts supporting H_EC angiogenesis.

Uncovering proteome variations and concomitant quality changes of different drying methods Cordyceps sinensis by 4D-DIA structural proteomics

IntroductionCordyceps sinensis is a fungus, serves dual purposes as both a medicinal herb and a food source. Due to its high water content, fresh Cordyceps sinensis is difficult to preserve, necessitating the drying necessary to process Cordyceps sinensis.MethodsUsing 4D-DIA proteomics, researchers analyzed the proteome profiles of fresh Cordyceps sinensis (CK) under three different drying conditions: vacuum freeze-drying (FD), oven-drying (OD), and air-drying (AD). In addition, it was found that the protein and free sulfhydryl content of Cordyceps sinensis decreased significantly and the disulfide bond content increased after different drying methods.Results and discussionA total of 3762 proteins were identified, showing variations between groups and high protein content. In the control groups consisting of fresh Cordyceps sinensis samples and the three drying methods, FD. vs CK exhibited the fewest differentially abundant proteins, with the majority being upregulated. On the other hand, CK vs OD displayed the greatest amount of distinct proteins, with a significant rise in both up-regulated and down-regulated proteins. Analysis of KEGG indicated that the distinct proteins were predominantly concentrated in pathways like the ribosome, synthesis of coenzymes, and metabolism of amino sugar and nucleotide sugar. Notably, there was a significant overlap between ribosome and ribosome biogenesis in eukaryotes pathways. The process of drying Cordyceps sinensis resulted in a significant upregulation of the expression of proteins linked to various metabolic pathways. This observation suggests that the drying treatment might activate or enhance certain biochemical processes within the organism, potentially influencing its overall metabolic activity. This finding highlights the importance of post-harvest dry methods on the biochemical properties of Cordyceps sinensis, which could have implications for its nutritional and medicinal value.This study provides a theoretical basis for the realization of Cordyceps sinensis resource utilization and storage methods, and provides theoretical support for guaranteeing the sustainable development of Cordyceps sinensis resources.

Protocatechuic Acid Suppresses Lipid Uptake and Synthesis through the PPARγ Pathway in High-Fat Diet-Induced NAFLD Mice.

Nonalcoholic fatty liver disease (NAFLD) has become one of the most concerning health problems in the world. Dietary intervention is an effective way to prevent and improve NAFLD. As one of the main metabolites of anthocyanins, protocatechuic acid (PCA) exhibited strong activity to improve NAFLD, but the specific mechanism remains unclear. Currently, proteomics has been used to identify that PCA treatment could significantly influence the expression of 224 proteins, including 89 downregulated proteins and 135 upregulated proteins. KEGG analysis showed that PCA obviously inhibited the peroxisome proliferator-activated receptor (PPAR) signaling pathway. Immunofluorescence and Western blot analyses further confirmed that PCA repressed the protein expression of PPARγ and subsequently inhibited the expression of free fatty acid (FFA) uptake proteins (CD36 and FABP2) and FFA synthesis proteins (ACC and FASN), respectively. These effects of PCA contributed to the inhibitory activity of excessive lipid accumulation in the liver. Our results highlighted that PCA could effectively alleviate high-fat diet-induced (HFD) NAFLD by inhibiting lipid absorption and synthesis through the PPARγ signaling pathway.

Role of microvascular pericyte dysfunction in antibody-mediated rejection following kidney transplantation

Objective To investigate the role of microvascular pericyte dysfunction in antibody-mediated rejection (ABMR) of transplanted kidneys. Methods A total of 160 patients who underwent kidney transplantation in our hospital from 2004 to 2020 were enrolled, divided into 4 groups: ABMR group (n = 79), TCMR group (n = 20), mixed rejection group (n = 25) and control group (n = 36). Postoperative renal function indicators were compared, and immunohistochemical and immunofluorescence staining was performed on graft tissues and mice models using the pericyte marker PDGFR-β. An in vitro pericyte dysfunction model was co-cultured with vascular endothelial cells for functional assessment through Western blotting, PCR, and wound healing tests. KEGG pathway analysis from the GEO database identified gene expression changes in pericytes, which were further analyzed using electron microscopy and Western blot techniques. Results There were statistically significant differences in creatinine, urea nitrogen, urine protein, and eGFR among the groups over time, with ABMR displaying the poorest outcomes. Immunohistochemistry revealed lower pericyte expression in ABMR, which was confirmed in mouse model studies showing reduced PDGFR-β expression in ABMR. KEGG analysis highlighted decreased autophagy in pericyte dysfunction, supported by electron microscopy and Western blot findings indicating reduced autophagy and pericyte damage, which could be reversed by chloroquine. Conclusion ABMR episodes worsened the long-term prognosis of transplanted kidneys. pericyte dysfunction appears to be one of the crucial causes of poor prognosis in ABMR patients. In vitro studies demonstrated that dysfunction of microvascular pericytes can result in damage to vascular endothelial cells, with autophagy impairment being a significant mechanism contributing to pericyte dysfunction.

Therapeutic Mechanism of Zhishi Decoction Regulating P38/MAPK Signaling Pathway on Functional Constipation (FC).

Zhishi decoction (ZSD) is one of the most common herb decoctions in traditional Chinese medicine (TCM), and it is used for the treatment of FC. However, its main therapeutic mechanism is not yet clear. This study aims to explore the possible pharmacodynamic material basis and potential molecular mechanism from network pharmacology and molecular docking and verify them through animal experiments. Firstly, the effective ingredients, potential targets, and key targets of ZSD in the treatment of FC were screened through network pharmacology. Go and KEGG analyses were performed for potential targets. Secondly, molecular docking was used to link the main active components of ZSD with target genes to predict their possible molecular mechanisms. Finally, 30 male BALB/c mice (20±2 g) were randomly divided into five groups (n=6), including the blank group, ZSD groups with two dosages (7.15, 14.3 g/kg), FC model group, and positive group (lactulose group). All the mice were given difenoxate tablets for 14 days to establish FC model except the blank group. Moreover, the mice in the blank group were given the same volume of normal saline. After admination for 14 days, the whole colon tissues were obtained for the analysis of small intestinal propulsion rate, and the expression of P38MAPK in colon tissues of mice was observed via immunohistochemistry and WesterBlot. In this study, 43 active ingredients in ZSD were identified. Four hundred and thirty potential therapeutic targets were selected, among which AKT1, MAPK12, and MAPK14 were key targets. 164 GO biological processes and 123 KEGG signaling pathways were identified after analysis， such as MAPK signaling pathway, TNF signaling pathway etc. The molecular docking results showed that Prangenin, 4-Hydroxyhomopterocarpin, isoponcimarin, and AKT1, MAPK12, MAPK14 had good binding degree. Additionally, ZSD could relieve the symptoms of FC in mice significantly. Compared with the model group, p38/MAPK positive expression cells and protein expression levels in the colon tissues of ZSD groups significantly increased in a dose-dependent manner (p<0.01). This study confirmed that ZSD could act on AKT1, MAPK12, and MAPK14 targets to activate the p38/MAPK signaling pathway to relieve FC induced by defenoxate tablets. The further development of ZSD provided a theoretical basis.

Circular RNA encoded by PPARG in the peripheral blood and a lipopolysaccharide-induced cardiomyocyte inflammation model is identified as a marker of fulminant myocarditis.

Fulminant myocarditis (FM), a critical cardiac disease, is characterised by atypical initial symptoms and rapid progression and tends to lead to cardiomyocyte degeneration or necrosis. Reliable biological markers for FM screening remain lacking. Circular RNAs (circRNAs) are highly stable in peripheral blood due to their special closed-loop structure, and reports have described their involvement in regulating inflammatory responses and cell injury in cardiomyocytes. This study attempted to identify the abnormal expression of circRNAs in the peripheral blood of patients with FM and to evaluate the potential diagnostic value. Peripheral blood was collected from 5 children with FM and 5 sex- and age-matched healthy controls; total RNA was extracted from each sample, and the extracted RNA from each group was pooled. After RNase R treatment, high-throughput sequencing was performed to screen for differentially expressed circRNAs in the peripheral blood of patients. Biological function classification and enrichment analysis were used to explore the main action pathways involving differentially expressed circRNAs. A lipopolysaccharide (LPS)-induced cardiomyocyte inflammation model was used to explore the effect of inflammation on the expression of these dysregulated circRNAs. Receiver operating characteristic (ROC) curves were used to evaluate the potential clinical value of FM-related circRNAs as biomarkers in a large sample of patients. CircRNA expression profiling of peripheral blood samples from patients revealed 6,435 and 3,678 circRNAs with upregulated and downregulated expression, respectively, compared with healthy controls. The expression of 1,749 circRNAs did not significantly differ between the groups. GO and KEGG analysis revealed that the genes encoding the dysregulated circRNAs were associated with various biological functions related to the risk of FM development, including infectious diseases, the immune system, and signal transduction. The high expression of hsa_circ_0064338 (circ_PPARG) was confirmed in both the myocardial cell inflammation model and peripheral blood from a large sample of FM patients. ROC curve analysis showed that the level of circ_PPARG in peripheral blood had a good ability to distinguish patients with FM from healthy controls. Large numbers of abnormally regulated circRNAs were identified in peripheral blood from patients with FM; among these, the highly expressed circ_PPARG could distinguish patients from healthy controls to a certain extent. It is expected to become a potential clinical biomarker of FM in the future.

Sulfonated albumin from hepatocytes accelerates liver fibrosis in nonalcoholic fatty liver disease through endoplasmic reticulum stress.

Posttranslational modifications (PTM) of albumin occur in liver diseases; however, little is known about the source and function of sulfonated albumin, a significant modification of albumin occurring in nonalcoholic fatty liver disease (NAFLD). We aimed to investigate the mechanism underlying sulfonated albumin production and its role in the progression of NAFLD-related liver fibrosis. Serum samples from healthy controls and patients with NAFLD were used to measure the proportion of sulfonated albumin. Mice models with NAFLD fed with high-fat diet (HFD) and methionine choline-deficient diet (MCD) were constructed. RNA sequencing, KEGG analysis, and GSEA were used to explore the mechanism of sulfonated albumin production and its mechanism of activating hepatic stellate cells (HSCs) and promoting the progression of liver fibrosis in NAFLD. Sulfonated albumin levels increased significantly in both human and mouse NAFLD serum samples. In vivo studies in mice have shown that the intraperitoneal injection of sulfonated albumin promotes inflammation, hepatic steatosis, and liver fibrosis in NAFLD. In addition, autophagy has been verified as a key mechanism in the regulation of sulfonated albumin production. We also demonstrated that reactive oxygen species (ROS) production depends on the accumulation of damaged mitochondria and affects the production of sulfonated albumin under the regulation of autophagy. Hepatocyte-derived sulfonated albumin activates HSCs through the GAL3 receptor, thereby activating the endoplasmic reticulum (ER) stress pathway and promoting profibrotic activation of HSCs. Our study demonstrated that sulfonated albumin activated HSCs through GAL3, thereby accelerating NAFLD-related liver fibrosis. Serum sulfonated albumin may be a potential diagnostic marker for liver fibrosis and an important target for the treatment of NAFLD-related liver fibrosis.

Comprehensive landscape of FGFR variations and prognosis revelance in colorectal cancer from circulating tumor DNA and tissue gene analyses in 2083 patients.

278 Background: FGFR genomic alterations have been identified, and several FGFR inhibitors are approved for various malignancies, including bladder and cholangiocarcinoma. However, limited studies have shown FGFR alterations and their prognostic impact in colorectal cancer (CRC). Methods: This retrospective analysis involved tissue and blood samples from a single-institute cohort (The Sixth Affiliated Hospital of Sun Yat-sen University) of stage I-IV CRC patients from 2014 to 2024. FGFR genomic alterations were analyzed using tissue NGS and plasma ctDNA. Disease-free survival (DFS) for stages I-III and progression-free survival (PFS) for stage IV were compared between FGFR-altered and negative CRC patients, matched in a 1:2 ratio. Validation of genomic alterations and their prognostic impact was conducted using cBioPortal and TCGA data. Results: FGFR alterations were found in 7.89% of 608 tissue samples and 10.95% of 2083 ctDNA samples. The most frequent alteration was FGFR1 amplification in all cohorts, along with FGFR2 p.R165W and FGFR3 p.A634T mutations in ctDNA. FGFR alterations correlated with younger age, left-sided colon tumors, adenocarcinomas, poor differentiation, advanced TNM staging, and multi-organ metastasis. Prognostic analysis showed a higher proportion of FGFR alterations in stage IV patients (66.23% vs. 59.14%), lower rates of no evidence of disease (NED) (6.62% vs. 17.68%), and significantly shorter PFS (median 17 vs. 20 months, HR 2.184, p=0.007). In stages I-III, FGFR-altered patients also had a lower NED rate (79.22% vs. 82.19%) and significantly shorter DFS (median 13 vs. 29 months, HR 2.833, p=0.002). Among frequent alterations, FGFR1 amplification was significantly associated with poor prognosis (PFS 17 vs. 20 months, HR 2.221, p=0.014; DFS 13 vs. 29 months, HR 2.964, p=0.002), while others showed no significant correlation. In stage IV patients receiving bevacizumab, FGFR1 alteration was linked to significantly shorter PFS (p=0.0021). KEGG analysis indicated FGFR1 was associated with angiogenesis pathways. FGFR alteration profiles and prognostic outcomes were consistent across tissue samples, ctDNA analyses, and databases. Conclusions: Our study outlines the genomic landscape and prognostic significance of FGFR in CRC, highlighting FGFR1 amplification as the dominant alteration. FGFR alterations were associated with poorer outcomes, as reflected in lower NED rates and shorter DFS and PFS. FGFR1 amplification was notably linked to reduced DFS and PFS, and it correlated with shorter PFS in patients receiving bevacizumab, indicating a potential link to resistance against bevacizumab. ctDNA n=2083 Tissue genen=608 cBioPortal Databasen=6998 FGFR Total 228/10.95% 48/7.89% 528/8.0% FGFR1 76/3.65% 29/4.77% 264/4.0% FGFR2 78/3.74% 10/1.64% 125/1.9% FGFR3 104/4.99% 10/1.64% 139/2.1%

Exosomes derived from colorectal cancer cells suppress B-cell mediated anti-tumor immunity.

Exosomes derived from cancer cells significantly influence the tumor immune microenvironment and can limit the efficacy of immunotherapy. However, the impact of exosomes on B cell-dependent anti-tumor immunity remains poorly understood. Here, we demonstrate that exosomes secreted by MC38 (MC38-Exos), a murine colorectal cancer cell line, induce B cells to adopt immunosuppressive phenotypes. MC38-Exos inhibits B cell proliferation and survival. Additionally, MC38-Exos induce B cells to acquire characteristics of regulatory B cells, including the upregulation of IL-10 and TGF-β. Finally, B cells treated with MC38-Exos impair the functional efficacy of CD8+ T cells. Transcriptome analysis reveals that MC38-Exos markedly suppresses gene pathways associated with B cell receptor (BCR) signaling, as well as antigen processing and presentation in B cells, but up-regulates genes involving apoptosis pathway. Mechanistically, NF-κB pathway was enriched in KEGG analysis, and was validated by western blot. Finally, inhibition of MC38-Exo in vivo activates B-cell mediated anti-tumor immunity. Thus, MC38-Exo has a profound effect of transcriptome of B cells and attenuates B cell-dependent anti-tumor immunity, supporting the rationale for targeted exosome therapy in human colorectal cancer.

Integration of single-cell RNA sequencing and network pharmacology to elucidate the effect of Yantiao Formula on alleviating ALI by regulating the polarization of alveolar macrophages.

Acute lung injury (ALI)/acute respiratory distress syndrome (ARDS) has a high mortality rate and often occurs in sepsis. Yantiao Formula (YTF) is used effectively in clinic but its mechanism in the treatment of ALI induced by sepsis remains unelucidated. This study aims to explore the potential molecular mechanisms of YTF in the treatment of sepsis- induced ALI. Using ACQUITY UPLC I-Class, the chemical components contained in YTF were characterized. The network pharmacology approach was used to predict the components and targets of YTF for treating sepsis- induce ALI. Single-cell RNA sequencing (scRNA-seq) was used to find changes in the lung microenvironment after CLP-induced sepsis. Experimental validation was also performed in vitro and in vivo. Using molecular docking, we speculated on the potential pharmacological substances of YTF. We detected 596 ingredients in YTF and identified 7 absorbed prototypes in serum. 1031 targets for 596 components were retrieved through TCMSP and SwissTargetPrediction databases. 365 potential targets for YTF and sepsis were identified. We observed that the targets of YTF for sepsis were significantly enriched in TNF and chemokine related pathway using GO and KEGG analysis. It was confirmed that at different time points, different doses of YTF increased the CLP-induced PaO2, reduced PaCO2 levels and W/D ratio of lung tissue. CLP- decreased survival rates was also significantly improved by YTF. YTF reversed the increase of IL-6 and IL-1β caused by CLP. Using scRNA-seq analysis, we found that changes in the proportion of cell types and the polarization state of macrophages were evident. Furthermore, the altered levels of biomarkers (M1: IL-1β, iNOS and TNF- α; M2: CD206/ Mrc1 and Arg-1) provided evidence of macrophages polarization. We found that CLP-challenged group presented enhanced iNOS and IL-1β expression and YTF increased CD206 and Arg-1 expression in CLP- induced sepsis using immunohistochemical analysis. Similarly, the same results were validated in LPS- induced ALI in NR8383 cells. The material basis and potential therapeutic targets of YTF were also demonstrated using molecular docking. YTF reduced the release of inflammatory factors and attenuated sepsis-induced ALI. The combined application of scRNA-seq, network pharmacology and molecular docking was helpful for revealing the mechanism of YTF, which was related to altering levels of M1 and M2 biomarkers to regulate macrophage polarization. The role of YTF in exerting its effects was closely relevant to the potential binding targets of its absorbed prototypes.

Molecular mechanism of Gancao Xiexin Decoction regulating EMT and suppressing hepatic metastasis of gastric cancer via the TGF-β1/SMAD pathway.

Gastric cancer (GC) is a highly malignant tumor of the digestive tract, posing a significant menace to human health. Gancao Xiexin Decoction (GCXXD), being a traditional Chinese medicine (TCM), has a good effect on inhibiting the proliferation and metastasis of GC. However, its mechanisms still need further investigation. To investigate the mechanism by which GCXXD inhibits GC metastasis through network pharmacology, and to verify through in vivo and in vitro experiments. The TCMSP and GEO databases, in combination with UPLC-MS/MS techniques, were employed to identify the hub genes, active ingredients, and critical pathways of GCXXD in the treatment of GC. Subsequently, molecular docking was conducted on both the hub genes and the core components. Finally, based on the results of the bioinformatics analysis, the role of GCXXD in inhibiting liver metastasis of GC was elucidated through in vivo and in vitro experiments, including scratch assays, Transwell assays, HE staining, immunohistochemistry, in vivo live imaging, qRT-PCR, and Western blotting. Utilizing UPLC-MS/MS and network pharmacology, we identified 20 active ingredients and 5 hub targets in the treatment of GC by GCXXD. Through KEGG analyses, GCXXD treatment of GC could through the TGF-beta pathway. In vivo and in vitro experiments, GCXXD downregulated the mRNA and protein expression level of hub genes involved in the TGF-β1/SMAD pathway and the EMT process. Additionally, GCXXD significantly reduced the incidence of liver metastases in GC. GCXXD inhibited EMT via blocking the TGF-β1/SMAD pathway, which suppressed GC cell growth and liver metastasis. This study provides data to support the treatment of liver metastasis in GC with TCM and holds significant importance for the research and development of new anticancer drugs.

FN1 and VEGFA Are Potential Therapeutic Targets in Glioblastoma as Determined by Bioinformatics Analysis.

Glioblastoma is the most malignant brain tumor, and despite advances in treatment, survival rates are still dismal. Therefore, a comprehensive understanding of the underlying molecular mechanisms of glioblastoma is needed. This study suggests potential therapeutic targets in glioblastoma that may provide new therapeutic insights. To identify hub genes in glioblastoma, three datasets were selected from the GEO database. After screening DEGs using GEO2R, GO and KEGG analyses were performed using DAVID. The PPI network was visualized using Cytoscape and 7 hub genes were extracted. The prognostic potential of 7 hub genes was investigated using the Gliovis and GEPIA2 databases. In total, 176 up-regulated and 263 down-regulated genes were identified. From the PPI network, 7 hub genes were identified including CAMK2A, DLG4, SNAP25, SYT1, MYC, FN1, and VEGFA. Out of the 7 hub genes identified, FN1 and VEGFA have been associated with a poor prognosis in glioblastoma based on the survival analysis. This study suggests that high levels of FN1 and VEGFA expression are associated with a poor prognosis in glioblastoma and that both genes are promising targets for glioblastoma therapy. Bioinformatics analysis of DEGs revealed putative targets that might reveal the molecular mechanisms underlying glioblastoma.

Lipid metabolism during seed germination of Pistacia chinensis and its response to gibberellic acid

Lipid metabolism may play a critical role in fueling seed germination, but the knowledge of lipid metabolism during germination is still ambiguous. Here, we hypothesize that gibberellic acid (GA) promotes germination by means of enhancing lipid mobilization in Chinese pistachio (Pistacia chinensis Bunge), a species belonging to Anacardiaceae with high oil content in its seeds. A multi-omics approach has been applied to measure lipid mobilization during seed germination, and to identify the key regulators involved in GA-mediated lipid metabolism. The results indicated that GA contents increased, while IAA, ABA and JA contents decreased during seed germination. GA3 increased significantly in the two germination stages (i.e. imbibition and radicle protrusion), and it was more abundant than GA1 and GA4. In addition, the relative content of most lipids decreased during germination, and the differentially changed metabolites were significantly enriched in lipid metabolic pathways based on KEGG analysis. WGCNA indicated that GA3 was correlated with more genes in lipid metabolic pathways. Transcriptomic analysis further revealed that differentially expressed genes (DEGs) related to fatty acid biosynthesis, glycerolipid metabolism, glycerophospholipid metabolism and starch and sucrose metabolism were upregulated under GA3 application, such as the acetyl-CoA carboxylase biotin carboxyl carrier protein (ACCB), fatty acyl-ACP thioesterase B (FATB), diacylglycerol acyltransferase (DGAT) and DEFECTIVE IN ANTHER DEHISCENCE 1 (DAD1). Therefore, our study supports the hypothesis that GA promotes seed germination in P. chinensis by enhancing lipid mobilization. This study proposes a novel mechanism of lipid responses to exogenous GA, which contributes to a deep understanding of germination of oleaginous seeds.

Improving sulforaphane content in broccoli sprouts by applying Se: transcriptome profiling and coexpression network analysis provide insights into the mechanistic response.

Sulforaphane (SF) is a sulfur (S)-containing isothiocyanate found in cruciferous vegetables and is known for its potent anticancer properties. Broccoli sprouts, in particular, are considered safe and healthy dietary choices due to their high SF content and other beneficial biological activities, such as enhanced metabolite ingestion. The application of selenium (Se) is an excellent approach to enhance the abundance of SF. Previous studies have often focused on gene expression and changes in the synthetic substrates of glucoraphanin (RAA) to explain SF variation in response to Se application. However, the regulatory network and other physiological and biochemical reactions involved in the regulation of SF biosynthesis are poorly understood. In this study, Se-treated broccoli sprouts had higher SF and RAA contents; they increased with increasing Se application. Using RNA-seq in combination with KEGG, GO, phenotypic, and WGCNA analyses, it was observed that not only gene expression was induced but also that glutathione serves as an S donor for SF biosynthesis and acts as an oxidative stress reliever as a result of Se treatment. Additionally, a module related to glucosinolate biosynthesis was identified. Yeast one-hybrid system and dual luciferase reporter assay were utilized. These assays demonstrated the hub transcription factors GATA22, ERF12-like, and MYB108 would directly bind to SUR1 promoter and positively regulate its expression. Our study presents the first global overview of the role of GSH metabolism in response to Se for SF biosynthesis, and provides a novel and valuable gene resource for the molecular breeding of high-SF broccoli.

Epigallocatechin gallate ameliorates retinal pigment epithelial cell damage via the CYFIP2 /AKT pathway.

Age-related macular degeneration (AMD) is a representative age-related ophthalmic disease, and the pathogenesis of AMD remains unclear. This research intended to determine whether epigallocatechin gallate (EGCG) could alleviate the progression of AMD and the possible mechanism. We constructed three groups of mice (young, aged, and EGCG), and HE and TUNEL staining of retinal tissues was performed to observe the structural changes in the retinal pigment epithelial (RPE) layer and the level of apoptosis, respectively. Through RNA-Sequencing analysis of retinal tissues and by RT-qPCR, GO, KEGG, and literature analyses, we identified cytoplasmic fragile X mental retardation 1-interacting protein 2 (CYFIP2) as a possible effector gene for EGCG action and validated its role by immunofluorescent and western blotting experiments. The CCK-8 and Hoechst 33342 apoptosis assays, and western blotting and qRT-PCR assays showed that EGCG reduced hydrogen peroxide (H2O2)-induced apoptosis in adult human RPE (ARPE-19) cells, and the expression of Cyfip2 was changed accordingly. RNA interference analysis indicated that Cyfip2 knockdown alleviated H2O2-induced ARPE apoptosis, while its overexpression weakened EGCG's protective effect. Western blot analysis showed that Cyfip2 mediated the anti-apoptotic effect of EGCG by modulating the level of protein kinase B (Akt) phosphorylation in ARPE cells, and the activation level of phosphorylated AKT (p-AKT Ser473) in retinal tissue of the EGCG-fed group was higher than that of the aged group. Taken together, this study suggests that EGCG plays a protective role in the development of AMD and the apoptosis of ARPE cells through the Cyfip2/AKT pathway.

Effects of drought stress on the secondary metabolism of Scutellaria baicalensis Georgi and the function of SbWRKY34 in drought resistance

The pharmacological properties of the dried root of Scutellaria baicalensis Georgi, a Chinese medicinal herb, include antioxidant, antibacterial, and antiviral effects. In S. baicalensis quality assessment, concentrations of baicalin, wogonoside, baicalein, and wogonin in the root are crucial. Drought stress commonly affects the biomass and build-up of active compounds in medicinal sections of medicinal plants and thus their quality. The molecular mechanisms underlying the response of S. baicalensis to drought stress remain unexplored. To delve into the impacts of drought stress on the growth and metabolic processes of S. baicalensis, as well as to unravel the underlying molecular mechanisms. We found prolonged and intensified drought treatment causes an initial surge in its fresh weight, plant height, and stem diameter followed by a gradual slowdown, while malondialdehyde (MDA) content rises; while the fresh weight, length, superoxide dismutase (SOD), and catalase (CAT) activities peak before declining, and the root’s diameter continuously narrows. In this study, flavonoid index ingredient levels in S. baicalensis initially decreased, then rose as the drought duration extended, followed by a notable post-rehydration increase in baicalin, wogonoside, and baicalein content and decrease in levels of wogonin and oroxylin A. Transcriptome sequencing and KEGG analysis revealed a significant enrichment of DEGs involved in phenylpropanoid biosynthesis and plant hormone signal transduction pathways. The expression levels of SbPAL, SbCCL, Sb4CL, SbCHI, SbFNSII, SbF6H, and SbUGT genes in the flavonoid biosynthetic pathway and PYR/PYL, PP2C, ABF, and SnRK2 genes in the abscisic acid signal transduction pathway were significantly changed. Drought responsive SbWRKY34 was selected for the subsequent investigation. SbWRKY34 showed the highest level in stems, and the encoding protein was localized in the nucleus. Overexpression of SbWRKY34 in Arabidopsis thaliana (OE-SbWRKY34 lines) resulted in increased sensitivity to drought stress, with considerably reduced MDA content and elevated SOD and CAT activities. Concurrently, the expression levels of AtCAT3, AtDREB, AtRD22, AtRD29A, and AtRD29B were significantly reduced in these lines, suggesting that SbWRKY34 functions to negatively regulate drought resistance in A. thaliana.

Carboxylesterase 4A Inhibits the Malignant Biological Behavior of Nasopharyngeal Carcinoma via the PI3K/AKT Pathway.

Carboxylesterase 4A (CES4A) belongs to the member of the carboxylesterase family, yet there has been limited research into its malignant biological behavior in malignant tumors. Here, we aim to investigate the expression, cellular biological functions, and the potential underlying mechanism of CES4A in nasopharyngeal carcinoma (NPC). A standardized mean difference (SMD) analysis was used to analyze the dysregulation of CES4A based on the gene expression omnibus (GEO) database. qRT-PCR and immunohistochemical staining (IHC) were used to identify the mRNA and protein levels of CES4A in NPC cell lines and tissues, respectively. CCK-8, colony formation, wound healing and transwell assays were utilized to estimate cellular growth and metastasis, respectively. Western blot was conducted to evaluate the activity of PI3K/AKT signaling pathway. Both mRNA and protein expression of CES4A was significantly diminished both in NPC cell lines and primary tumor tissues. Ectopic expression of CES4A restrains the proliferation, colony formation, migration and invasion of NPC. Additionally, KEGG analysis based on GEO data and high-throughput transcriptome sequencing of cell lines all strongly suggested that CES4A was involved in regulating phosphoinositide 3-kinase (PI3K)/protein kinase B (AKT) signaling pathway. It was observed that AKT and phosphorylated AKT were remarkably reduced in CES4A overexpressing NPC cells, indicating that PI3K/AKT signaling pathway is hindered by CES4A. CES4A expression is silenced in NPC, functioning as a tumor suppressor by negatively modulating the PI3K/AKT signaling pathway.

Effect of Leonurus japonicus alkaloids on endometrial inflammation and its mechanisms.

The aerial parts of Leonurus japonicus Houtt. (Chinese motherwort) are famous for their efficacy in treating obstetrical and gynecological diseases in traditional Chinese medicine (TCM). Alkaloids are the major bioactive components of motherwort and have gained extensive attention for alleviating several symptoms of obstetrical and gynecological diseases such as postpartum hemorrhage, postpartum rehabilitation, irregular menstruation, and dysmenorrhea. However, the effects of motherwort alkaloids on endometritis remain unclear. The aim of this study was to investigate the effect of motherwort total alkaloids (MTAs) on endometritis and explore the molecular mechanisms using an integrating network analysis and in vitro experimental verification. Ultra-high performance liquid chromatography-tandem quadrupole-orbitrap high-resolution mass spectrometry (UPLC-Q-Orbitrap HRMS) was used to analyze and identify the components in the MTAs. The effects of MTAs were evaluated using bacteria-induced endometritis in rats. Network pharmacology was conducted to predict possible mechanism pathways of MTAs in endometritis. Finally, lipopolysaccharide-stimulated mouse mononuclear macrophage (RAW 264.7) cells and human endometrial epithelial cells were used to identify signaling pathways through which MTAs exert their effects. Thirty-nine alkaloids were identified in MTAs using the UPLC-Q-Orbitrap HRMS analysis. Their corresponding putative targets were then predicted. The MTAs exerted pharmacological effects on endometritis through a multi-ingredient and multi-target pattern. Network pharmacology showed that the MTAs had 152 candidate targets in treating endometritis. According to the KEGG analysis, the MTAs were found to potentially affect the PI3K-AKT and NF-κB signaling pathways. The following experiments showed that the MTAs exhibited significant effects on endometritis in vivo, significantly reduced the overproduction of inflammatory mediators, and promoted endometrial cell repair via the PI3K/AKT/NF-κB signaling pathway. Motherwort alkaloids can be used to treat endometrial inflammation by regulating the PI3K/AKT/NF-κB pathway. This study provides a scientific basis for the use of MTAs for treating endometritis.

An Integrated Approach of Network Pharmacology, Bioinformatics, Molecular Docking, and Experimental Verification Uncovers Prunellae Spica as the potential Medicine of Prognosis Improvement for Oral Squamous Cell Carcinoma.

Prunellae Spica (PS), the spike from Prunella vulgaris L., is a traditional Chinese medicine that can treat Oral Squamous Cell Carcinoma (OSCC), whereas its molecular mechanisms and effects on the prognosis of patients remain unclear. Our study aimed to identify potential anti-OSCC targets of PS and explore its mechanisms and effects on prognosis through network pharmacology, bioinformatics analysis, molecular docking, and in vitro cell assays. Sixty-two potential targets of 11 active anti-OSCC ingredients of PS were identified, with Quercetin, the core ingredient of PS, exhibiting the most significant number of OSCC-related targets. GO analysis indicated that the primary biological processes involved in OSCC treatment by PS were the cellular response to nitrogen compound, response to xenobiotic stimulus, and cellular response to organonitrogen compound. KEGG analysis revealed that Pathways in cancer were the top highly enriched signaling pathway in the treatment of OSCC by PS. DisGeNET analysis is mainly about Lip and Oral Cavity Carcinoma. More importantly, 6 of the 62 targets were markedly related to prognosis. Molecular docking revealed high affinities between the key component and the prognosis-related target proteins. Treatment of OSCC cell line SCC-25 with Quercetin could inhibit malignant biological behaviors, such as cell proliferation, colony formation, invasion, and migration, as well as affect the targets related to prognosis and promote autophagy. Overall, these results suggest that PS plays a significant role in treating and improving the prognosis of OSCC by directly influencing various processes in OSCC.