1.Network toxicology and its application in studying exogenous chemical toxicity
Yanli LIN ; Zehua TAO ; Zhao XIAO ; Chenxu HU ; Bobo YANG ; Ya WANG ; Rongzhu LU
Journal of Environmental and Occupational Medicine 2025;42(2):238-244
With the continuous development of society, a large number of new chemicals are continuously emerging, which presents a challenge to current risk assessment and safety management of chemicals. Traditional toxicology research methods have certain limitations in quickly, efficiently, and accurately assessing the toxicity of many chemicals, and cannot meet the actual needs. In response to this challenge, computational toxicology that use mathematical and computer models to achieve the prediction of chemical toxicity has emerged. In the meantime, as researchers increasingly pay attention to understanding the interaction mechanisms between exogenous chemical substances and the body from the system level, and multiomics technologies develop rapidly such as genomics, transcriptomics, proteomics, and metabolomics, huge amounts of data have been generated, providing rich information resources for studying the interactions between chemical substances and biological molecules. System toxicology and network toxicology have also developed accordingly. Of these, network toxicology can integrate these multiomics data to construct biomolecular networks, and then quickly predict the key toxicological targets and pathways of chemicals at the molecular level. This paper outlined the concept and development of network toxicology, summarized the main methods and supporting tools of network toxicology research, expounded the application status of network toxicology in studying potential toxicity of exogenous chemicals such as agricultural chemicals, environmental pollutants, industrial chemicals, and foodborne chemicals, and analyzed the development prospects and limitations of network toxicology research. This paper aimed to provide a reference for the application of network toxicology in other fields.
2.Acute Inflammatory Pain Induces Sex-different Brain Alpha Activity in Anesthetized Rats Through Optically Pumped Magnetometer Magnetoencephalography
Meng-Meng MIAO ; Yu-Xuan REN ; Wen-Wei WU ; Yu ZHANG ; Chen PAN ; Xiang-Hong LIN ; Hui-Dan LIN ; Xiao-Wei CHEN
Progress in Biochemistry and Biophysics 2025;52(1):244-257
ObjectiveMagnetoencephalography (MEG), a non-invasive neuroimaging technique, meticulously captures the magnetic fields emanating from brain electrical activity. Compared with MEG based on superconducting quantum interference devices (SQUID), MEG based on optically pump magnetometer (OPM) has the advantages of higher sensitivity, better spatial resolution and lower cost. However, most of the current studies are clinical studies, and there is a lack of animal studies on MEG based on OPM technology. Pain, a multifaceted sensory and emotional phenomenon, induces intricate alterations in brain activity, exhibiting notable sex differences. Despite clinical revelations of pain-related neuronal activity through MEG, specific properties remain elusive, and comprehensive laboratory studies on pain-associated brain activity alterations are lacking. The aim of this study was to investigate the effects of inflammatory pain (induced by Complete Freund’s Adjuvant (CFA)) on brain activity in a rat model using the MEG technique, to analysis changes in brain activity during pain perception, and to explore sex differences in pain-related MEG signaling. MethodsThis study utilized adult male and female Sprague-Dawley rats. Inflammatory pain was induced via intraplantar injection of CFA (100 μl, 50% in saline) in the left hind paw, with control groups receiving saline. Pain behavior was assessed using von Frey filaments at baseline and 1 h post-injection. For MEG recording, anesthetized rats had an OPM positioned on their head within a magnetic shield, undergoing two 15-minute sessions: a 5-minute baseline followed by a 10-minute mechanical stimulation phase. Data analysis included artifact removal and time-frequency analysis of spontaneous brain activity using accumulated spectrograms, generating spectrograms focused on the 4-30 Hz frequency range. ResultsMEG recordings in anesthetized rats during resting states and hind paw mechanical stimulation were compared, before and after saline/CFA injections. Mechanical stimulation elevated alpha activity in both male and female rats pre- and post-saline/CFA injections. Saline/CFA injections augmented average power in both sexes compared to pre-injection states. Remarkably, female rats exhibited higher average spectral power 1 h after CFA injection than after saline injection during resting states. Furthermore, despite comparable pain thresholds measured by classical pain behavioral tests post-CFA treatment, female rats displayed higher average power than males in the resting state after CFA injection. ConclusionThese results imply an enhanced perception of inflammatory pain in female rats compared to their male counterparts. Our study exhibits sex differences in alpha activities following CFA injection, highlighting heightened brain alpha activity in female rats during acute inflammatory pain in the resting state. Our study provides a method for OPM-based MEG recordings to be used to study brain activity in anaesthetized animals. In addition, the findings of this study contribute to a deeper understanding of pain-related neural activity and pain sex differences.
3.Interventional Effect and Mechanisms of Renqing Mangjue on MNNG-induced Malignant Transformation of Gastric Mucosal Epithelial Cells
Peiping CHEN ; Fengyu HUANG ; Xinzhuo ZHANG ; Xiangying KONG ; Ziqing XIAO ; Yanxi LI ; Xiaohui SU ; Na LIN
Chinese Journal of Experimental Traditional Medical Formulae 2025;31(8):69-77
ObjectiveThis study aimed to investigate the intervention effect of Renqing Mangjue on the malignant transformation of gastric mucosal epithelial cells induced by N-methyl-N′-nitro-N-nitrosoguanidine (MNNG) and to explore its molecular mechanism in preventing precancerous lesions of gastric cancer based on the cyclic guanosine monophosphate (cGMP)/protein kinase G (PKG)/mitogen-activated protein kinase (MEK)/extracellular signal-regulated kinase (ERK) signaling pathway. MethodsHuman gastric mucosal epithelial cells (GES-1) were initially induced by MNNG to establish a precancerous cell model (MC cells). The effective concentration of MNNG for inducing malignant transformation in GES-1 cells was screened using the cell proliferation activity decection (CCK-8) assay, and the effective concentration of Renqing Mangjue for inhibiting the proliferation of transformed GES-1 cells was also determined. GES-1 cells were divided into a blank control group, a model group, and treatment groups with Renqing Mangjue at concentrations of 1, 3, 10, and 30 mg·L-1. Furthermore, the effects of Renqing Mangjue on the migratory ability and epithelial-mesenchymal transition (EMT) characteristics of GES-1 malignant transformed cells were evaluated using Transwell migration assays, wound healing assays, and real-time quantitative reverse transcription polymerase chain reaction (Real-time PCR). Additionally, candidate chemical components and target sites of Renqing Mangjue were obtained from the TCMIP v2.0 database, and disease targets at various stages of gastric cancer precursors were sourced from the Gene Expression Omnibus (GEO) database. Pathway enrichment analysis was performed using the Metascape database to predict the potential mechanisms of action of Renqing Mangjue. Finally, the protective mechanism of Renqing Mangjue against gastric cancer precursors was validated through Western blot analysis. ResultsAt a concentration of 20 μmol·L-1, MNNG exhibited an inhibition rate of approximately 50% on GES-1 cells (P<0.01), and at this concentration, the GES-1 cells displayed biological characteristics indicative of malignant transformation. In contrast, Renqing Mangjue had no significant effect on the proliferation of normal GES-1 cells, but significantly inhibited the proliferation of MC cells (P<0.01) and markedly reduced their migratory capacity (P<0.01). Moreover, it also increased the mRNA expression level of E-cadherin during the EMT process (P<0.05), while inhibiting the expression of both N-cadherin and the transcription factor Snail mRNA (P<0.05, P<0.01). Network predictions suggested that Renqing Mangjue may prevent gastric cancer precursors through modulating the cGMP/PKG and MAPK/ERK signaling pathways. Furthermore, Western blot results indicated that Renqing Mangjue upregulated the expression of PKG and NPRB (B-type natriuretic peptide receptor) proteins in the cGMP/PKG pathway (P<0.01), while downregulating the expression of the downstream proteins MEK and ERK (P<0.05, P<0.01). ConclusionIn summary, Renqing Mangjue can prevent gastric cancer precursors by inhibiting the proliferation and migration of malignant transformed GES-1 cells, thereby delaying the EMT process. The underlying mechanisms may be related to the activation of the cGMP/PKG pathway and the inhibition of the MEK/ERK signaling pathway.
4.Progress in ablation therapy of pulmonary nodules
Xu SHEN ; Cheng SHEN ; Congjia XIAO ; Haonan LIN ; Yunke ZHU ; Feng LIN ; Hu LIAO
Chinese Journal of Clinical Thoracic and Cardiovascular Surgery 2025;32(03):401-405
In recent years, with the improvement of people's awareness of physical examination and the more accurate detection equipment, the detection rate of pulmonary nodules is getting higher and higher. Surgical resection is the first choice for the treatment of malignant pulmonary nodules, but multiple pulmonary nodules, nodules in complex areas and those with surgical contraindications are not suitable for surgery. As an effective, less invasive and low-cost treatment, ablation has developed rapidly in the treatment of multiple pulmonary nodules. This article introduces the progress of several common ablation techniques (radiofrequency ablation, microwave ablation, cryoablation) in the treatment of multiple pulmonary nodules, the indications and contraindications of ablation techniques, the efficacy evaluation and complications after ablation therapy, and the prospects of ablation techniques in the treatment of multiple pulmonary nodules.
5.Progress on antisense oligonucleotide in the field of antibacterial therapy
Jia LI ; Xiao-lu HAN ; Shi-yu SONG ; Jin-tao LIN ; Zhi-qiang TANG ; Zeng-ming WANG ; Liang XU ; Ai-ping ZHENG
Acta Pharmaceutica Sinica 2025;60(2):337-347
With the widespread use of antibiotics, drug-resistant bacterial infections have become a significant threat to human health. Finding new antibacterial strategies that can effectively control drug-resistant bacterial infections has become an urgent task. Unlike small molecule drugs that target bacterial proteins, antisense oligonucleotide (ASO) can target genes related to bacterial resistance, pathogenesis, growth, reproduction and biofilm formation. By regulating the expression of these genes, ASO can inhibit or kill bacteria, providing a novel approach for the development of antibacterial drugs. To overcome the challenge of delivering antisense oligonucleotide into bacterial cells, various drug delivery systems have been applied in this field, including cell-penetrating peptides, lipid nanoparticles and inorganic nanoparticles, which have injected new momentum into the development of antisense oligonucleotide in the antibacterial realm. This review summarizes the current development of small nucleic acid drugs, the antibacterial mechanisms, targets, sequences and delivery vectors of antisense oligonucleotide, providing a reference for the research and development of antisense oligonucleotide in the treatment of bacterial infections.
6.From Golgiphagy to Golgimedicine — a new strategy for disease prevention and treatment targeting the Golgi apparatus
Acta Pharmaceutica Sinica 2025;60(2):280-287
Functional disorders of the Golgi apparatus are harmful to the health of organisms, leading to various diseases. Removing damaged Golgi apparatus is crucial for maintaining cellular homeostasis, therefore, autophagy of Golgi apparatus has gradually attracted attention. This article summarizes Golgi autophagy, briefly describes its structure and functions, Golgi autophagy receptors, and the role of Golgi autophagy in disease treatment. It also proposes the new concept of Golgimedicine, which looks forward to the role of Golgi in disease diagnosis, treatment, prognosis, genetic diseases, and rare diseases. This article aims to explore the scientific connotations of Golgi autophagy, Golgi structure and function from the perspective of Golgimedicine, providing theoretical references for drug target research, new drug development, and the healthy development of humanity.
7.Research on compaction behavior of traditional Chinese medicine compound extract powders based on unsupervised learning
Ying FANG ; Yan-long HONG ; Xiao LIN ; Lan SHEN ; Li-jie ZHAO
Acta Pharmaceutica Sinica 2025;60(2):506-513
Direct compression is an ideal method for tablet preparation, but it requires the powder's high functional properties. The functional properties of the powder during compression directly affect the quality of the tablet. 15 parameters such as Py, FES-8KN,
8.Ten surgical pearls adapted from ancient Chinese allusions in managing severe proliferative diabetic retinopathy
Zhe CHEN ; Chan WU ; Yan ZHOU ; Shiqun LIN ; Xingyu XIAO ; Rongping DAI
International Eye Science 2025;25(5):698-705
AIM: To summarize 10 surgical pearls for managing proliferative diabetic retinopathy(PDR)adapted from the ancient Chinese allusions and analyze the application of these pearls in a real-world fashion.METHODS: Retrospective, noncomparative, interventional study. Ten surgical pearls were summarized and adapted from the ancient Chinese philosophy. Totally 346 cases(443 eyes)that underwent pars plana vitrectomy(PPV)at our hospial from January 2016 to February 2024 were selected. Flexible combinations of these pearls were applied according to the specific condition of each patient during surgeries. The efficacy and safety were analyzed, as well as the application frequencies according to the existence of tractional retinal detachment or not.RESULTS: A total of 473 times of surgeries were performed on all the patients. According to ancient Chinese allusions, ten surgical pearls were summarized from these surgeries. All PPVs went smoothly with the application of different combinations. Finally, almost all proliferative membranes were successfully peeled except for 10 patients(11 eyes), who went through strategy No.10(minimal membranectomy)that, only necessary relaxation incisions were made with most of the proliferative membranes left on purpose. The final visual acuities were mostly improved or stable(1.92±0.83 LogMAR preoperatively vs 1.16±0.85 LogMAR postoperatively, P<0.01). Postoperative complications mainly included early inflammatory responses in the anterior chamber and nuclear sclerosis. Recurrent vitreous hemorrhage, retinal detachment, and hyphema or neovascular glaucoma occurred in 1.9%(9/473), 3.2%(15/473), 0.4%(2/473)and 0.4%(2/473)times of PPVs, respectively. After 12/473(2.5%)times of PPVs, retinal detachment at the macular area still existed, and multiple times of subsequent PPVs were conducted. Final retinal attachment at the macular area was realized in 98.9% eyes. Those 5 unattached eyes were with heavily reproliferated membranes and subsequent tractional retinal detachment recurrence under the oil, and three of them were scleral buckled additionally.CONCLUSION:These 10 surgical strategies and technique pearls were mostly effective and safe in the management of severe PDR patients. They were relatively easy to be memorized and applicated once the meaning of each Chinese idiom was understood. One can use different combinations flexibly according to a patient's specific condition.
9.Terms Related to The Study of Biomacromolecular Condensates
Ke RUAN ; Xiao-Feng FANG ; Dan LI ; Pi-Long LI ; Yi LIN ; Zheng WANG ; Yun-Yu SHI ; Ming-Jie ZHANG ; Hong ZHANG ; Cong LIU
Progress in Biochemistry and Biophysics 2025;52(4):1027-1035
Biomolecular condensates are formed through phase separation of biomacromolecules such as proteins and RNAs. These condensates exhibit liquid-like properties that can futher transition into more stable material states. They form complex internal structures via multivalent weak interactions, enabling precise spatiotemporal regulations. However, the use of inconsistent and non-standardized terminology has become increasingly problematic, hindering academic exchange and the dissemination of scientific knowledge. Therefore, it is necessary to discuss the terminology related to biomolecular condensates in order to clarify concepts, promote interdisciplinary cooperation, enhance research efficiency, and support the healthy development of this field.
10.Analysis of Treatment of Diabetic Kidney Disease with Modified Buyang Huanwutang Based on 5hmC-Seal Sequencing Technology
Baixin ZHEN ; Haoyu CHEN ; Duolikun MAIMAITIYASEN ; Xuehui LI ; Hong XIAO ; Xiaxuan LI ; Kuerban SUBINUER ; Lei ZHANG ; Hangyu CHEN ; Jian LIN ; Linlin LI
Chinese Journal of Experimental Traditional Medical Formulae 2025;31(11):208-217
ObjectiveTo improve the therapeutic effect of Buyang Huanwutang(BYHW) on diabetic kidney disease (DKD) and explore new methods for developing new Chinese medicine decoctions,we utilized 5-hydroxymethylcytosine (5hmC)-Seal sequencing technology and network pharmacology to modify BYHW. MethodsWe selected 14 diabetes mellitus (DM) patients and 15 DKD patients hospitalized in the Department of Endocrinology of Peking University Third Hospital in 2021. Circulating free DNA (cfDNA) in the patients’ plasma was sequenced. After data processing and screening, we performed temporal clustering analysis to select a DKD 5hmC gene set, which was then cross-validated with a DKD database gene set to obtain the DKD gene set. We retrieved target genes of the seven herbal components of BYHW from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP) and the Encyclopedia of Traditional Chinese Medicine (ETCM), and performed cross-analysis with the DKD gene set to identify common genes shared by the disease and the Chinese medicines. A protein-protein interaction (PPI) network was constructed for the common genes to screen out the key genes. Chinese medicines targeting these key genes were searched against ETCM to identify removable Chinese medicines. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis was performed on non-common DKD genes, and key genes in DKD-related pathways were selected based on machine learning. The GSE30529 dataset was used to verify the expression trends of 5hmC-modified genes and the feasibility of target genes as drug targets. TCMBank was used to search for target genes and obtain compounds targeting these genes and the corresponding Chinese medicines to construct a "key target-compound-Chinese medicine" network. Molecular docking was employed to verify the binding affinity of compounds with key targets. TCMSP and ETCM were used to search and count the candidate Chinese medicines targeting DKD-related genes, and a new decoction was formed by adding the selected Chinese medicines. A mouse model of DKD was established to examine the efficacy of the new decoction based on the mouse body mass, random blood glucose, urinary microalbumin (mALB), serum creatinine (Scr), and blood urea nitrogen (BUN) and by hematoxylin-eosin staining, periodic acid-Schiff staining, Masson staining, immunofluorescence assay, and Real-time PCR. ResultsThe cross-analysis results showed that the DKD gene set included 507 genes, of which 30 were target genes of BYHW. The PPI analysis indicated that the top 15% target genes regarding the degree were interleukin-6 (IL-6), Toll-like receptor 4 (TLR4), lactotransferrin (LTF), lipoprotein lipase (LPL), and sterol regulatory element-binding transcription factor 1 (SREBF1). Persicae Semen and Pheretima in BYHW were unrelated to key genes and removed. Machine learning identified 10 potential target genes, among which TBC1 domain family member 5 (TBC1D5), RAD51 paralog B (RAD51B), and proteasome 20S subunit alpha 6 (PSMA6) had expression trends consistent with the GSE30529 dataset and could serve as drug targets. The "key target-compound-Chinese medicine" network and molecular docking results indicated that the compounds with good binding affinity to target proteins were arginine, glycine, myristicin, serine, and tyrosine, corresponding to 121 Chinese medicines. The top 10 Chinese medicines targeting DKD-related genes were Lycii Fructus, Ginseng Radix et Rhizoma, Dioscoreae Rhizoma, Rehmanniae Radix Praeparata, Isatidis Radix, Glehniae Radix, Ophiopogonis Radix, Allii Sativi Bulbus, Isatidis Folium, and Bolbostemmatis Rhizoma. Based on traditional Chinese medicine theory, the new decoction was obtained after removal of Persicae Semen and Pheretima and addition of Rehmanniae Radix Praeparata and Dioscoreae Rhizoma. Animal experiment results indicated that the modified BYHW improved the kidney function and inhibited renal fibrosis in DKD mice, with better effects than the original decoction. ConclusionThe BYHW modified based on 5hmC-Seal sequencing demonstrates better performance in inhibiting fibrosis and ameliorating DKD than the original decoction. This elucidates the biomedical theory behind the epigenetic modification of traditional Chinese medicine prescriptions, potentially offering new perspectives for the exploration of these prescriptions

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