OBJECTIVE: Circadian rhythm disruption (CRD) is a risk factor that correlates with poor prognosis across multiple tumor types, including hepatocellular carcinoma (HCC). However, its mechanism remains unclear. This study aimed to define HCC subtypes based on CRD and explore their individual heterogeneity. METHODS: To quantify CRD, the HCC CRD score (HCCcrds) was developed. Using machine learning algorithms, we identified CRD module genes and defined CRD-related HCC subtypes in The Cancer Genome Atlas liver HCC cohort (n = 369), and the robustness of this method was validated. Furthermore, we used bioinformatics tools to investigate the cellular heterogeneity across these CRD subtypes. RESULTS: We defined three distinct HCC subtypes that exhibit significant heterogeneity in prognosis. The CRD-related subtype with high HCCcrds was significantly correlated with worse prognosis, higher pathological grade, and advanced clinical stages, while the CRD-related subtype with low HCCcrds had better clinical outcomes. We also identified novel biomarkers for each subtype, such as nicotinamide n-methyltransferase and myristoylated alanine-rich protein kinase C substrate-like 1. CONCLUSION We classify the HCC patients into three distinct groups based on circadian rhythm and identify their specific biomarkers. Within these groups greater HCCcrds was associated with worse prognosis. This approach has the potential to improve prediction of an individual's prognosis, guide precision treatments, and assist clinical decision making for HCC patients. Please cite this article as: Li XJ, Chang L, Mi Y, Zhang G, Zhu SS, Zhang YX, et al. Integrated-omics analysis defines subtypes of hepatocellular carcinoma based on circadian rhythm. J Integr Med. 2025; 23(4): 445-456.
Humans ; Carcinoma, Hepatocellular/pathology* ; Liver Neoplasms/pathology* ; Circadian Rhythm/genetics* ; Prognosis ; Male ; Female ; Biomarkers, Tumor/genetics* ; Middle Aged ; Machine Learning ; Computational Biology

The structure of intestinal tissue is complex. In vitro simulation of intestinal structure and function is important for studying intestinal development and diseases. Recently, organoids have been successfully constructed and they have come to play an important role in biomedical research. Organoids are miniaturized three-dimensional (3D) organs, derived from stem cells, which mimic the structure, cell types, and physiological functions of an organ, making them robust models for biomedical research. Intestinal organoids are 3D micro-organs derived from intestinal stem cells or pluripotent stem cells that can successfully simulate the complex structure and function of the intestine, thereby providing a valuable platform for intestinal development and disease research. In this article, we review the latest progress in the construction and application of intestinal organoids.
Organoids/cytology* ; Intestines/physiology* ; Humans ; Animals ; Pluripotent Stem Cells

OBJECTIVE: Pneumoconiosis, a lung disease caused by irreversible fibrosis, represents a significant public health burden. This study investigates the causal relationships between gut microbiota, gene methylation, gene expression, protein levels, and pneumoconiosis using a multi-omics approach and Mendelian randomization (MR). METHODS: We analyzed gut microbiota data from MiBioGen and Esteban et al. to assess their potential causal effects on pneumoconiosis subtypes (asbestosis, silicosis, and inorganic pneumoconiosis) using conventional and summary-data-based MR (SMR). Gene methylation and expression data from Genotype-Tissue Expression and eQTLGen, along with protein level data from deCODE and UK Biobank Pharma Proteomics Project, were examined in relation to pneumoconiosis data from FinnGen. To validate our findings, we assessed self-measured gut flora from a pneumoconiosis cohort and performed fine mapping, drug prediction, molecular docking, and Phenome-Wide Association Studies to explore relevant phenotypes of key genes. RESULTS: Three core gut microorganisms were identified: Romboutsia ( OR = 0.249) as a protective factor against silicosis, Pasteurellaceae ( OR = 3.207) and Haemophilus parainfluenzae ( OR = 2.343) as risk factors for inorganic pneumoconiosis. Additionally, mapping and quantitative trait loci analyses revealed that the genes VIM, STX8, and MIF were significantly associated with pneumoconiosis risk. CONCLUSIONS This multi-omics study highlights the associations between gut microbiota and key genes ( VIM, STX8, MIF) with pneumoconiosis, offering insights into potential therapeutic targets and personalized treatment strategies.
Humans ; Male ; East Asian People/genetics* ; Europe ; Gastrointestinal Microbiome ; Lung ; Macrophage Migration-Inhibitory Factors/metabolism* ; Mendelian Randomization Analysis ; Multiomics ; Pneumoconiosis/microbiology* ; Intramolecular Oxidoreductases

Objective:To discuss the effect of angiotensin(1-7)[Ang(1-7)]on high-turnover bone disease in the uremic rats,and to clarify its possible mechanism.Methods:Thirty SD rats were randomly divided into sham operation group(n=6)and experimental group(n=24).The rats in experimental group underwent 5/6 nephrectomy(Platt method)+high-phosphorus(P)diet[1.2％P,1.0％calcium(Ca)]to establish the model of uremic high-turnover bone disease.The successfully modeled rats were then randomly divided into model group,Ang(1-7)group,angiotensin-converting enzyme 2(ACE2)activator dimethylacetamide amidoxime(DIZE)group,and Mas receptor antagonist group(A779 group),with 6 rats in each group.The levels of Ca,P,blood creatinine(Scr),blood urea nitrogen(BUN),and 24 h urinary protein(UP)in serum of the rats in various groups were detected by automatic biochemical analyzer at 12 and 18 weeks after operation;immunofluorescence staining was used to detect the levels of intact parathyroid hormone(iPTH)in the rats in various groups;ELISA method was used to detect the levels of osteocalcin(OC),type Ⅰ collagen N-terminal peptide(NTX),and tartrate-resistant acid phosphatase(TRAP)-5b in serum of the rats in various groups;high-resolution micro-CT scan was used to detect the bone density(BMD),tissue mineral density(TMD),trabecular thickness(Tb.Th),and trabecular separation(Tb.Sp)in femur tissue of the rats in various groups;Von Kossa staining and Giemsa staining were used to observe the pathomorphology of cortical bone and trabecular bone of the rats in various groups,and the trabecular bone volume(TBV)was calculated;fluorescence microscope was used to detect the mineral apposition rates(MAR)of the rats in vanious groups,and the osteoblast index(OBI)and osteoclast index(OCI)of the rats in various groups were calculated.Results:At 12 and 18 weeks after operation,compared with sham operation group,the weights of the rats in model group,Ang(1-7)group,DIZE group,and A779 group were decreased(P＜0.05).At 12 and 18 weeks after operation,compared with sham operation group,the levels of 24 h UP,Scr,and BUN in serum of the rats in model group,Ang(1-7)group,DIZE group,and A779 group were increased(P＜0.05);at 18 weeks after operation,compared with model group,the levels of 24 h UP and Scr in serum of the rats in Ang(1-7)group and DIZZ group were decreased(P＜0.05),and the levels of 24 h UP,Scr and BUN in serum of the rats in A779 group were increased(P＜0.05).The successful establishment of the uremic high-turnover bone disease model was confirmed.At 12 and 18 weeks after operation,compared with sham operation group,the serum iPTH,P,OC,NTX,and TRAP-5b levels ofthe rats in model group,Ang(1-7)group,DIZE group,and A779 group were all significantly increased(P＜0.05);at 18 weeks after operation,compared with model group,the serum NTX and TRAP-5b levels of the rats in Ang(1-7)group and DIZE group were decreased(P＜0.05),while the serum iPTH,P,NTX and TRAP-5b levels in A779 group were increased(P＜0.05).The high-resolution micro-CT scan results showed that compared with sham operation group,the values of femur BMD and TMD of the rats in model group,Ang(1-7)group,DIZE group,and A779 group were all significantly decreased(P＜0.05);compared with model group,the values of femur BMD and TMD of the rats in Ang(1-7)group and DIZE group were increased(P＜0.05),while the values of BMD and TMD of the rats in A779 group were decreased(P＜0.05).Compared with sham operation group,the femur Tb.Th of the rats in model group was decreased(P＜0.05),and the Tb.Sp was increased(P＜0.05);the femur Tb.Th of the rats in Ang(1-7)group and DIZE group were increased(P＜0.05),and the Tb.Sp was decreased(P＜0.05).Compared with model group,the femur Tb.Th of the rats in A779 group was decreased(P＜0.05),and the Tb.Sp was increased(P＜0.05).The bone pathological examination results showed that compared with sham operation group,the femur TBV of the rats in model group,Ang(1-7)group,DIZZ group and A779 group were decreased(P＜0.05),and MAR,OBI and OCI were increased(P＜0.05);compared with model group,the OBI and OCI of the rats in Ang(1-7)group and DIZE group were decreased(P＜0.05),and TBV was increased(P＜0.05),while the OBI and OCI of the rats in A779 group were increased(P＜0.05),and TBV was decreased(P＜0.05).Conclusion:The ACE2/Ang(1-7)/Mas axis improves high-turnover bone disease in the uremic rats.

Objective To understand the changing composition and antibiotic resistance of bacterial species in the clinical isolates from outpatient and emergency department(hereinafter referred to as outpatients)and inpatient children over time in various hospitals,and to provide laboratory evidence for rational antibiotic use.Methods The data on clinically isolated pathogenic bacteria and antimicrobial susceptibility of isolates from outpatients and inpatient children in the CHINET program from 2015 to 2021 were collected and analyzed.Results A total of 278 471 isolates were isolated from pediatric patients in the CHINET program from 2015 to 2021.About 17.1％of the strains were isolated from outpatients,primarily group A β-hemolytic Streptococcus,Escherichia coli,and Staphylococcus aureus.Most of the strains(82.9％)were isolated from inpatients,mainly SS.aureus,E.coli,and H.influenzae.The prevalence of methicillin-resistant S.aureus(MRSA)in outpatients(24.5％)was lower than that in inpatient children(31.5％).The MRSA isolates from outpatients showed lower resistance rates to the antibiotics tested than the strains isolated from inpatient children.The prevalence of vancomycin-resistant Enterococcus faecalis or E.faecium and penicillin-resistant S.pneumoniae was low in either outpatients or inpatient children.S.pneumoniae,β-hemolytic Streptococcus and S.viridans showed high resistance rates to erythromycin.The prevalence of erythromycin-resistant group A β-hemolytic Streptococcus was higher in outpatients than that in inpatient children.The prevalence of β-lactamase-producing H.influenzae showed an overall upward trend in children,but lower in outpatients(45.1％)than in inpatient children(59.4％).The prevalence of carbapenem-resistant Klebsiella pneumoniae(CRKpn),carbapenem-resistant Pseudomonas aeruginosa(CRPae)and carbapenem-resistant Acinetobacter baumannii(CRAba)was 14％,11.7％,47.8％in outpatients,but 24.2％,20.6％,and 52.8％in inpatient children,respectively.The prevalence of multidrug-resistant E.coli,K.pneumoniae,Proteus mirabilis,P.aeruginosa and A.baumannii strains was lower in outpatients than in inpatient children.The prevalence of fluoroquinolone-resistant E.coli,ESBLs-producing K.pneumoniae,ESBLs-producing P.mirabilis,carbapenem-resistant E.coli(CREco),CRKpn,and CRPae was lower in children in outpatients than in inpatient children,but the prevalence of CRAba in 2021 was higher than in inpatient children.Conclusions The distribution of clinical isolates from children is different between outpatients and inpatients.The prevalence of MRSA,ESBL,and CRO was higher in inpatient children than in outpatients.Antibiotics should be used rationally in clinical practice based on etiological diagnosis and antimicrobial susceptibility test results.Ongoing antimicrobial resistance surveillance and prevention and control of hospital infections are crucial to curbing bacterial resistance.

Objective To investigate the changing antibiotic resistance profiles of E.coli isolated from patients in the 52 hospitals participating in the CHINET program from 2015 to 2021.Methods Antimicrobial susceptibility was tested for clinical isolates of E.coli according to the unified protocol of CHINET program.WHONET 5.6 and SPSS 20.0 software were used for data analysis.Results Atotal of 289 760 nonduplicate clinical strains ofE.coli were isolated from 2015 to 2021,mainly from urine samples(44.7±3.2)％.The proportion of E.coli strains isolated from urine samples was higher in females than in males(59.0％vs 29.5％).The proportion of E.coli strains isolated from respiratory tract and cerebrospinal fluid samples was significantly higher in children than in adults(16.7％vs 7.8％,0.8％vs 0.1％,both P＜0.05).The isolates from internal medicine department accounted for the largest proportion(28.9±2.8)％with an increasing trend over years.Overall,the prevalence of ESBLs-producing E.coli and carbapenem resistant E.coli(CREco)was 55.9％and 1.8％,respectively during the 7-year period.The prevalence of ESBLs-producing E.coli was the highest in tertiary hospitals each year from 2015 to 2021 compared to secondary hospitals.The prevalence of CREco was higher in children's hospitals compared to secondary and tertiary hospitals each year from 2015 to 2021.The prevalence of ESBLs-producing E.coli in tertiary hospitals and children's hospitals and the prevalence of CREco in children's hospitals showed a decreasing trend over the 7-year period.The prevalence of CREco in secondary and tertiary hospitals increased slowly.Antibiotic resistance rates changed slowly from 2015 to 2021.Carbapenem drugs(imipenem,meropenem)were the most active drugs amongβ-lactams against E.coli(resistance rate≤2.1％).The resistance rates of E.coli to β-lactam/β-lactam inhibitor combinations(piperacillin-tazobactam,cefoperazone-sulbactam),aminoglycosides(amikacin),nitrofurantoin and fosfomycin(for urinary isolates only)were all less than 10％.The resistance rate of E.coli strains to antibiotics varied with the level of hospitals and the departments where the strains were isolated,especially for cefazolin and ciprofloxacin,to which the resistance rate of E.coli strains from children in non-ICU departments was significantly lower than that of the strains isolated from other departments(P＜0.05).The E.coli isolates from ICU showed higher resistance rate to most antimicrobial agents tested(excluding tigecycline)than the strains isolated from other departments.The E.coli strains isolated from tertiary hospitals showed higher resistance rates to the antimicrobial agents tested(excluding tigecycline,polymyxin B,cefepime and carbapenems)than the strains from secondary hospitals and children's hospitals.Conclusions E.coli is an important pathogen causing clinical infection.More than half of the clinical isolates produced ESBL.The prevalence of CREco is increasing in secondary and tertiary hospitals over the 7-year period even though the overall prevalence is still low.This is an issue of concern.

This study was aimed at identifying the pathogenic bacteria responsible for the death of a young tiger at the Fujian Meihua Mountain South China Tiger Breeding Research Institute.Tissue samples from the lungs,liver,and intestines of the deceased tiger were collected,and the bacteria were cultured inasterile environment.The bacterial strains were characterized according to their morphological and molecular biological properties,including assessment of virulence genes and antibiotic resistance genes,mouse lethality tests,and antibiotic susceptibility evaluations.A predominant bacterial strain isolated from the liver of the deceased tiger was identified as enterotoxigenic Escherichia coli(ETEC)strain Tiger22513F.Phylogenetic analysis of the 16S rRNA gene revealed that the Tiger22513F strain exhibited close genetic similarity to the reference strain ETEC(MF919609.1),with 99.9%nucleotide similarity,and resided on the same evolutionary branch.The Tiger22513F strain contained 11 antibiotic resistance genes(tetA,sul1,sul3,cmlA,floR,blaTEM,blaSHV,blaCMY-2,qnrA,qnrS,and qnrD)along with five virulence genes(VT1,fyuA,tsh,iucD,and ST).Mouse lethality tests indicated significant pathogenicity toward mice,affecting primarily the lungs,liver,and intestines.Antibiotic susceptibility testing demonstrated that this strain exhibited resistance to various classes of beta-lactam antibiotics,as well as quinolones and aminoglycosides.This investigation successfully isolated a multi-drug resistant enterotoxigenic Escherichia coli strain with pronounced pathogenicity from the liver of a deceased tiger;thus providing valuable scientific insights for clinical diagnosis,as well as prevention and control measures,against ETEC infections in South China tigers.

Sodium-glucose cotransporter 2 inhibitor was initially developed and marketed as a novel oral hypoglycemic agent.Currently,it has been recommended as one of the main therapeu-tic agents for chronic heart failure by national and international guidelines,and it has a significant cardioprotective effect on heart failure with reduced ejection fraction,heart failure with im-proved ejection fraction,heart failure with mildly reduced ejec-tion fraction,and heart failure with preserved ejection fraction.However,cardiac tissues do not express sodium-glucose cotrans-porter 2,and the underlying mechanisms of clinical cardiovascu-lar benefits of sodium-glucose cotransporter 2 inhibitors remain unclear.This review intends to summarize the cardiovascular benefits of sodium-glucose cotransporter 2 inhibitors in clinical trials and the recommendations suggested by national and inter-national heart failure guidelines and to elucidate further the po-tential mechanisms of sodium-glucose cotransporter 2 inhibitor-mediated cardioprotective effects.