Many triterpenoid compounds have been successfully heterologously synthesized in Saccharomyces cerevisiae. To increase the yield of triterpenoids, various metabolic engineering strategies have been developed. One commonly applied strategy is to enhance the supply of precursors, which has been widely used by researchers. Squalene, as a precursor to triterpenoid biosynthesis, plays a crucial role in the synthesis of these compounds. This study primarily investigates the effect of different squalene levels in chassis strains on the synthesis of triterpenoids(oleanolic acid and ursolic acid), and the underlying mechanisms are further explored using real-time quantitative PCR(qPCR) analysis. The results demonstrate that the chassis strain CB-9-5, which produces high levels of squalene, inhibits the synthesis of oleanolic acid and ursolic acid. In contrast, chassis strains with moderate to low squalene production, such as Y8-1 and CNPK, are more conducive to the synthesis of oleanolic acid and ursolic acid. The qPCR analysis reveals that the expression levels of ERG1, βAS, and CrCYP716A154 in the oleanolic acid-producing strain CB-OA are significantly lower than those in the control strains C-OA and Y-OA, suggesting that high squalene production in the chassis strains suppresses the transcription of certain genes, leading to a reduced yield of triterpenoids. Our findings indicate that when constructing S. cerevisiae strains for triterpenoid production, chassis strains with high squalene content may suppress the expression of certain genes, ultimately lowering their production, whereas chassis strains with moderate squalene levels are more favorable for triterpenoid biosynthesis.
Squalene/analysis* ; Saccharomyces cerevisiae/genetics* ; Triterpenes/metabolism* ; Metabolic Engineering ; Oleanolic Acid/biosynthesis* ; Ursolic Acid

OBJECTIVE: The relationship between benign prostatic hyperplasia (BPH) and the oxidative balance score (OBS) will be discussed in this study. METHODS: The clinical data on 16 dimensions of diet and 4 dimensions of lifestyle from the National Health and Nutrition Examination Survey (NHANES) from 2001 to 2008 were used to calculate OBS. We considered BPH as the outcome and investigated the linear and nonlinear relationships between the two. Additionally, subgroup analyses and interaction tests were conducted as well. Furthermore, the methods of machine learning including XGBoost, support vector machine (SVM) and naive Bayes (NB) were used to establish a predictive model for BPH. RESULTS: Higher OBS was consistently associated with an increased prevalence of BPH, with Restricted Cubic Splines highlighting a significant positive nonlinear association (P=0.015). Subgroup analyses revealed differences and interactive relationships based on alcohol consumption. Among the seven machine learning models that we included the OBS score in, the XGBoost model emerged as the best, with an AUC value of 0.769. CONCLUSION There is a significant association between OBS and the prevalence of BPH in the American population, which provides a valuable insight for further diagnosis and research of the disease.
Humans ; Male ; Prostatic Hyperplasia/epidemiology* ; Machine Learning ; Bayes Theorem ; Nutrition Surveys ; Support Vector Machine ; Life Style ; Oxidative Stress ; Aged ; Diet ; Prevalence

Objective： To investigate the relationship between the lipid metabolism-related gene sterol carrier protein 2(SCP2) and prostate cancer (PCa) from a multi-omics perspective using single-cell transcriptomes combined with Mendelian randomization. Methods： Single-cell transcriptome data of benign and malignant prostate tissues were obtained from GSE120716, GSE157703 and GSE141445 datasets, respectively. Integration, quality control and annotation were performed on the data to categorize the epithelial cells into high and low SCP2 expression groups, followed by further differential and trajectory analyses. Single nucleotide polymorphism (SNP) data for SCP2 expression quantitative trait loci (eQTL) were subsequently downloaded from Genotype-Tissue Expression (GTEx) and investigated from the PCa Society Cancer-Related Genomic Alteration Panel for the Investigation of Cancer-Related Alterations (PRACTICAL) to obtain PCa outcome data for Mendelian randomization analysis to validate the causal relationship between SCP2 and PCa. Results： High SCP2-expressing epithelial cells had higher energy metabolism and proliferation capacity with low immunotherapy response and metastatic tendency. Trajectory analysis showed that epithelial cells with high SCP2 expression may have a higher degree of malignancy, and SCP2 may be a key marker gene for differentiation of malignant epithelial cells in the prostate. Further Mendelian randomization results showed a significant causal relationship between SCP2 and PCa development (OR=1.045, 95% CI: 1.010 －1.083, P=0.011). Conclusion： By combining single-cell transcriptome and Mendelian randomization, the role of the lipid metabolism-related gene SCP2 in PCa development has been confirmed, and new targets and therapeutic directions for PCa treatment have been provided.
Humans ; Prostatic Neoplasms/genetics* ; Male ; Mendelian Randomization Analysis ; Polymorphism, Single Nucleotide ; Quantitative Trait Loci ; Single-Cell Analysis ; Sequence Analysis, RNA ; Carrier Proteins/genetics* ; Transcriptome ; Lipid Metabolism

BACKGROUND: Prolonged occupational noise exposure poses potential health risks, but its impact on mitochondrial DNA (mtDNA) damage and methylation patterns remains unclear. METHOD: We recruited 306 factory workers, using average binaural high-frequency hearing thresholds from pure-tone audiometry to assess noise exposure. MtDNA damage was evaluated through mitochondrial DNA copy number (mtDNAcn) and lesion rate, and mtDNA methylation changes were identified via pyrophosphate sequencing. RESULTS: There was a reduction in MT-RNR1 methylation of 4.52% (95% CI: -7.43% to -1.62%) among workers with abnormal hearing, whereas changes in the D-loop region were not statistically significant (β = -2.06%, 95% CI: -4.44% to 0.31%). MtDNAcn showed a negative association with MT-RNR1 methylation (β = -0.95, 95% CI: -1.23 to -0.66), while no significant link was found with D-loop methylation (β = -0.05, 95% CI: -0.58 to 0.48). Mediation analysis indicated a significant increase in mtDNAcn by 10.75 units (95% CI: 3.00 to 21.26) in those with abnormal hearing, with MT-RNR1 methylation mediating 35.9% of this effect. CONCLUSIONS These findings suggest that occupational noise exposure may influence compensatory increases in mtDNA content through altered MT-RNR1 methylation.
Humans ; DNA, Mitochondrial ; DNA Methylation ; Male ; Adult ; Noise, Occupational/adverse effects* ; Middle Aged ; Occupational Exposure/adverse effects* ; Biomarkers/blood* ; Female

OBJECTIVE: To evaluate the dynamic changes of glucocorticoid (GC) dose and the feasibility of GC discontinuation in rheumatoid arthritis (RA) patients under the background of Chinese medicine (CM). METHODS: This multicenter retrospective cohort study included 1,196 RA patients enrolled in the China Rheumatoid Arthritis Registry of Patients with Chinese Medicine (CERTAIN) from September 1, 2019 to December 4, 2023, who initiated GC therapy. Participants were divided into the Western medicine (WM) and integrative medicine (IM, combination of CM and WM) groups based on medication regimen. Follow-up was performed at least every 3 months to assess dynamic changes in GC dose. Changes in GC dose were analyzed by generalized estimator equation, the probability of GC discontinuation was assessed using Kaplan-Meier curve, and predictors of GC discontinuation were analyzed by Cox regression. Patients with <12 months of follow-up were excluded for the sensitivity analysis. RESULTS: Among 1,196 patients (85.4% female; median age 56.4 years), 880 (73.6%) received IM. Over a median 12-month follow-up, 34.3% (410 cases) discontinued GC, with significantly higher rates in the IM group (40.8% vs. 16.1% in WM; P<0.05). GC dose declined progressively, with IM patients demonstrating faster reductions (median 3.75 mg vs. 5.00 mg in WM at 12 months; P<0.05). Multivariate Cox analysis identified age <60 years [P<0.001, hazard ratios (HR)=2.142, 95% confidence interval (CI): 1.523-3.012], IM therapy (P=0.001, HR=2.175, 95% CI: 1.369-3.456), baseline GC dose ⩽7.5 mg (P=0.003, HR=1.637, 95% CI: 1.177-2.275), and absence of non-steroidal anti-inflammatory drugs use (P=0.001, HR=2.546, 95% CI: 1.432-4.527) as significant predictors of GC discontinuation. Sensitivity analysis (545 cases) confirmed these findings. CONCLUSIONS RA patients receiving CM face difficulties in following guideline-recommended GC discontinuation protocols. IM can promote GC discontinuation and is a promising strategy to reduce GC dependency in RA management. (Trial registration: ClinicalTrials.gov, No. NCT05219214).
Adult ; Aged ; Female ; Humans ; Male ; Middle Aged ; Arthritis, Rheumatoid/drug therapy* ; Glucocorticoids/therapeutic use* ; Medicine, Chinese Traditional ; Retrospective Studies

Gene regulation relies on the precise binding of transcription factors (TFs) at regulatory elements, but simultaneously detecting hundreds of TFs on chromatin is challenging. We developed cFOOT-seq, a cytosine deaminase-based TF footprinting assay, for high-resolution, quantitative genome-wide assessment of TF binding in both open and closed chromatin regions, even with small cell numbers. By utilizing the dsDNA deaminase SsdAtox, cFOOT-seq converts accessible cytosines to uracil while preserving genomic integrity, making it compatible with techniques like ATAC-seq for sensitive and cost-effective detection of TF occupancy at the single-molecule and single-cell level. Our approach enables the delineation of TF footprints, quantification of occupancy, and examination of chromatin influences on TF binding. Notably, cFOOT-seq, combined with FootTrack analysis, enables de novo prediction of TF binding sites and tracking of TF occupancy dynamics. We demonstrate its application in capturing cell type-specific TFs, analyzing TF dynamics during reprogramming, and revealing TF dependencies on chromatin remodelers. Overall, cFOOT-seq represents a robust approach for investigating the genome-wide dynamics of TF occupancy and elucidating the cis-regulatory architecture underlying gene regulation.
Transcription Factors/genetics* ; Humans ; Chromatin/genetics* ; Animals ; Binding Sites ; Mice ; DNA Footprinting/methods*

Objective To observe the clinical efficacy of Chang'an Juntai Granules(mainly composed of Pseudostellariae Radix,Atractylodis Macrocephalae Rhizoma,Poria,Glycyrrhizae Radix et Rhizoma Praeparata cum Melle,Paeoniae Radix Alba,Saposhnikoviae Radix,Citri Reticulatae Pericarpium,Coptidis Rhizoma,and Aucklandiae Radix)in the treatment of diarrhea-predominant irritable bowel syndrome(IBS-D)with liver depression and spleen deficiency syndrome,and to evaluate its safety.Methods A single-center,randomized,double-blind,placebo-controlled clinical trial was designed.A total of 130 patients with IBS-D of liver depression and spleen deficiency were included.The patients were randomly divided into a treatment group and a control group by random number table method,with 65 cases in each group.The treatment group was treated with Chang'an Juntai Granules,and the control group was treated with Chang'an Juntai Placebo Granules.The course of treatment covered 12 weeks.The changes in the scores of IBS Symptom Severity Scale(IBS-SSS),Bristol Stool Form Scale(BSFS),IBS Quality of Life Questionnaire(IBS-QOL)and Hospital Anxiety and Depression Scale(HADS)in the two groups were observed before and after treatment.After treatment,the clinical efficacy and medication safety in the two groups were evaluated.Results(1)During the trial,six cases in the treatment group and eight cases in the control group fell off.Eventually,a total of 116 patients completed the clinical trial,including 59 cases in the treatment group and 57 cases in the control group.(2)After 12 weeks of treatment,the total effective rate of the treatment group was 88.14％(52/59),and that of the control group was 45.61％(26/57).The intergroup comparison(tested by chi-square test)showed that the clinical efficacy of the treatment group was significantly superior to that of the control group,and the difference was statistically significant(P＜0.01).(3)After treatment,the IBS-SSS scores of the two groups and the BSFS and IBS-QOL scores of the treatment group were significantly lower than those before treatment(P＜0.01),while the scores of Hospital Anxiety and Depression Scale-Anxiety subscale(HADA)and Hospital Anxiety and Depression Scale-Depression subscale(HADD)in the two groups and the BSFS and IBS-QOL scores in the control group showed no obvious changes(P＞0.05).Compared with the control group,the decrease of IBS-SSS,BSFS and IBS-QOL scores in the treatment group was significantly superior to that in the control group(P＜0.05 or P＜0.01).(4)During the trial,no serious adverse reactions or adverse events occurred in the two groups,no drug-related abnormalities of liver and kidney function,blood,and heart function were found,either.Conclusion Chang'an Juntai Granules are effective on improving the clinical symptoms and fecal characteristics of IBS-D patients with liver depression and spleen deficiency syndrome,and on enhancing the quality of life of patients.The granules excert definite curative effect and high safety,and has certain value of clinical application.