1.Proteomics combined with bioinformatics analysis of protein markers of dry eye
Yanting YANG ; Yajun SHI ; Guang YANG ; Haiyang JI ; Jie LIU ; Jue HONG ; Dan ZHANG ; Xiaopeng MA
International Eye Science 2025;25(1):104-111
AIM:To analyze differential proteins associated with the pathogenesis of dry eye(DE)using bioinformatics methods, in order to reveal their potential molecular mechanisms.METHODS: Articles published in PubMed and EMBASE databases from the inception of the database to August 31, 2023, that used proteomic methods to detect protein expression in clinical samples of dry eye were searched. Differential proteins were selected and further analyzed using the STRING database and Cytoscape software for hub gene screening and module analysis. Protein-protein interaction(PPI)analysis, gene ontology(GO)functional annotation, and Kyoto encyclopedia of genes and genomes(KEGG)pathway enrichment analysis were performed.RESULTS: A total of 21 articles were included, identifying 74 differentially expressed proteins. The most frequently occurring differential proteins were calgranulin A(SA1008), lipocalin-1(LCN1), lysozyme C(LYZ), mammaglobin-B(SCGB2A1), proline-rich protein 4(PRR4), transferrin(TF), and calgranulinB(S100A9). The top 10 hub genes were serum albumin(ALB), tumor necrosis factor(TNF), interleukin 6(IL6), IL1B, IL8, matrix metalloproteinase 9(MMP9), alpha-1-antitrypsin(SERPINA1), IL10, complement component 3(C3), and lactotransferrin(LTF). Module analysis suggested MMP9 and PRR4 as seed genes. KEGG analysis showed that differential proteins were mainly enriched in the IL17 signaling pathway(61.9%).CONCLUSION: The results reveal potential molecular targets and pathways for DE and confirm the association between the pathogenesis of DE and inflammation. Further in-depth research is needed to confirm the significance of these biomarkers in clinical practice.
2.Research advances in the effects of orexin and its receptor-related drugs on depression
Zhaoshu JIANG ; Ming CHENG ; Jie YANG ; Feng CAO ; Zhen ZHANG
China Pharmacy 2025;36(4):496-500
Depression is a psychiatric disorder whose main symptoms include low mood, loss of interest, anxiety, sleep disturbances, and changes in appetite. Orexin, a neuropeptide located in hypothalamic neurons, has a wide range of projections throughout the central nervous system and is involved in various behavioral modulations related to depression. This study systematically reviewed the effects of orexin and its receptor-related drugs on depression and found that orexin could exert complex regulatory effects on multiple brain regions by binding to related receptors, affecting emotions, sleep, anxiety, etc. The abnormal state of expression of plasma orexin in patients with depression was found. Exogenous orexin-A, selective orexin receptor 1 antagonists (SORA1s), selective orexin receptor 2 antagonists (SORA2s), and dual orexin receptor antagonists (DORAs) have demonstrated antidepressant-like effects in various animal models of depression. Among them, clinical trials involving exogenous orexin-A are relatively scarce. Drugs related to SORA1s and SORA2s, such as JNJ-61393215 and Setorexant, have made significant progress in the treatment of depression. DORAs, such as Suvorexant, Lemborexant, and Daridorexant, are primarily used to treat insomnia. Notably, Suvorexant has also shown potential in alleviating symptoms of anxiety and depression.
3.Treating diabetic kidney disease based on "using bitter herbs to nourish or purge" theory
Weimin JIANG ; Yaoxian WANG ; Shuwu WEI ; Jiale ZHANG ; Chenhui XIA ; Jie YANG ; Liqiao SUN ; Xinrong LI ; Weiwei SUN
Journal of Beijing University of Traditional Chinese Medicine 2025;48(1):1-7
The Huangdi Neijing proposes the " using bitter herbs to nourish or purge" theory to guide clinical prescription and formulation of herbal remedies based on the physiological characteristics and functions of the five zang viscera, along with the properties and flavors of medicinal herbs. This study explored diabetic kidney disease pathogenesis and treatment based on the " using bitter herbs to nourish or purge" theory. Kidney dryness is a key pathological factor in diabetic kidney disease, and the disharmony of kidney dryness is an essential aspect of its pathogenesis. Strengthening is the primary therapeutic principle, and kidney dryness is a persistent factor throughout the occurrence and progression of diabetic kidney disease. In the early stage, the pathogenesis involves heat-consuming qi and injuring yin, leading to kidney dryness. In the middle stage, the pathogenesis manifests as qi deficiency and blood stasis in the collaterals, resulting in turbidity owing to kidney dryness. In the late stage, the pathogenesis involves yin and yang deficiency, with kidney dryness and disharmony. This study proposes the staging-based treatment based on the " need for firmness" characteristic of the kidney. The aim is to provide new insights for clinical diagnosis and treatment in traditional Chinese medicine by rationally using pungent, bitter, and salty medicinal herbs to nourish and moisturize the kidney. This approach seeks to promote precise syndrome differentiation and personalized treatment for different stages of diabetic kidney disease, thereby enhancing clinical efficacy.
4.Exploring the inhibitory effect and mechanism of isorhamnetin therapy on oral squamous cell carcinoma based on network pharmacology and molecular docking
YU Fangfang ; ZHOU Jingjing ; YANG Jie ; QU Huijuan ; HUI Guangyan
Journal of Prevention and Treatment for Stomatological Diseases 2025;33(1):14-23
Objective :
To explore the mechanism of isorhamnetin (Iso) in the treatment of oral squamous cell carcinoma (OSCC) using network pharmacology and molecular docking methods and to verify it in vitro.
Methods :
The key targets were obtained by constructing the PPI protein interaction network based on the common intersection targets of Iso-OSCC. At the same time, gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) were used to analyze the related signaling pathways of the intersection targets. Iso and core targets were also analyzed through molecular docking and visualization. Colony formation assay and Transwell assay were used to identify the effect of Iso on the proliferation and invasion of Cal-27 cells. Western blot was used to analyze the regulatory effects of different concentrations of Iso on estrogen receptor-1 (ESR1), phosphoinositide-3-kinase regulatory subunit-1 (PIK3R1), Src tyrosine kinase (SRC), and phosphatidylinositol 3-kinase (PI3K)/protein kinase B (AKT) signaling pathway proteins.
Results:
A total of 269 potential intersection targets of Iso-regulated OSCC were obtained. According to the degree obtained by topological analysis, PIK3R1, AKT1, SRC, ESR1, and other core targets were screened out. KEGG analysis showed that 165 signaling pathways were enriched in the intersection targets of Iso-OSCC, among which the PI3K/AKT signaling pathway played an important role in the treatment of OSCC with Iso. Molecular docking results showed that the absolute value of binding energy between target proteins PIK3R1, AKT1, SRC, ESR1, and Iso was high. After Cal-27 cells were treated with Iso, the number of cell colony formations, the number of transmembrane cells, and the expression of PIK3R1, ESR1, SRC, p-PI3K, and p-AKT were negatively correlated with the increase in Iso concentration (P < 0.05).
Conclusion
Iso can inhibit PI3K/AKT signal transduction and influence the expression of PIK3R1, AKT1, SRC, and ESR1 proteins, thereby inhibiting the occurrence and development of OSCC.
5.Screening key genes of PANoptosis in hepatic ischemia-reperfusion injury based on bioinformatics
Lirong ZHU ; Qian GUO ; Jie YANG ; Qiuwen ZHANG ; Guining HE ; Yanqing YU ; Ning WEN ; Jianhui DONG ; Haibin LI ; Xuyong SUN
Organ Transplantation 2025;16(1):106-113
Objective To explore the relationship between PANoptosis and hepatic ischemia-reperfusion injury (HIRI), and to screen the key genes of PANoptosis in HIRI. Methods PANoptosis-related differentially expressed genes (PDG) were obtained through the Gene Expression Omnibus database and GeneCards database. Gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Set Enrichment Analysis (GSEA) were used to explore the biological pathways related to PDG. A protein-protein interaction network was constructed. Key genes were selected, and their diagnostic value was assessed and validated in the HIRI mice. Immune cell infiltration analysis was performed based on the cell-type identification by estimating relative subsets of RNA transcripts. Results A total of 16 PDG were identified. GO analysis showed that PDG were closely related to cellular metabolism. KEGG analysis indicated that PDG were mainly enriched in cellular death pathways such as apoptosis and immune-related signaling pathways such as the tumor necrosis factor signaling pathway. GSEA results showed that key genes were mainly enriched in immune-related signaling pathways such as the mitogen-activated protein kinase (MAPK) signaling pathway. Two key genes, DFFB and TNFSF10, were identified with high accuracy in diagnosing HIRI, with areas under the curve of 0.964 and 1.000, respectively. Immune infiltration analysis showed that the control group had more infiltration of resting natural killer cells, M2 macrophages, etc., while the HIRI group had more infiltration of M0 macrophages, neutrophils, and naive B cells. Real-time quantitative polymerase chain reaction results showed that compared with the Sham group, the relative expression of DFFB messenger RNA in liver tissue of HIRI group mice increased, and the relative expression of TNFSF10 messenger RNA decreased. Cibersort analysis showed that the infiltration abundance of naive B cells was positively correlated with DFFB expression (r=0.70, P=0.035), and the infiltration abundance of M2 macrophages was positively correlated with TNFSF10 expression (r=0.68, P=0.045). Conclusions PANoptosis-related genes DFFB and TNFSF10 may be potential biomarkers and therapeutic targets for HIRI.
6.Role of SWI/SNF Chromatin Remodeling Complex in Tumor Drug Resistance
Gui-Zhen ZHU ; Qiao YE ; Yuan LUO ; Jie PENG ; Lu WANG ; Zhao-Ting YANG ; Feng-Sen DUAN ; Bing-Qian GUO ; Zhu-Song MEI ; Guang-Yun WANG
Progress in Biochemistry and Biophysics 2025;52(1):20-31
Tumor drug resistance is an important problem in the failure of chemotherapy and targeted drug therapy, which is a complex process involving chromatin remodeling. SWI/SNF is one of the most studied ATP-dependent chromatin remodeling complexes in tumorigenesis, which plays an important role in the coordination of chromatin structural stability, gene expression, and post-translation modification. However, its mechanism in tumor drug resistance has not been systematically combed. SWI/SNF can be divided into 3 types according to its subunit composition: BAF, PBAF, and ncBAF. These 3 subtypes all contain two mutually exclusive ATPase catalytic subunits (SMARCA2 or SMARCA4), core subunits (SMARCC1 and SMARCD1), and regulatory subunits (ARID1A, PBRM1, and ACTB, etc.), which can control gene expression by regulating chromatin structure. The change of SWI/SNF complex subunits is one of the important factors of tumor drug resistance and progress. SMARCA4 and ARID1A are the most widely studied subunits in tumor drug resistance. Low expression of SMARCA4 can lead to the deletion of the transcription inhibitor of the BCL2L1 gene in mantle cell lymphoma, which will result in transcription up-regulation and significant resistance to the combination therapy of ibrutinib and venetoclax. Low expression of SMARCA4 and high expression of SMARCA2 can activate the FGFR1-pERK1/2 signaling pathway in ovarian high-grade serous carcinoma cells, which induces the overexpression of anti-apoptosis gene BCL2 and results in carboplatin resistance. SMARCA4 deletion can up-regulate epithelial-mesenchymal transition (EMT) by activating YAP1 gene expression in triple-negative breast cancer. It can also reduce the expression of Ca2+ channel IP3R3 in ovarian and lung cancer, resulting in the transfer of Ca2+ needed to induce apoptosis from endoplasmic reticulum to mitochondria damage. Thus, these two tumors are resistant to cisplatin. It has been found that verteporfin can overcome the drug resistance induced by SMARCA4 deletion. However, this inhibitor has not been applied in clinical practice. Therefore, it is a promising research direction to develop SWI/SNF ATPase targeted drugs with high oral bioavailability to treat patients with tumor resistance induced by low expression or deletion of SMARCA4. ARID1A deletion can activate the expression of ANXA1 protein in HER2+ breast cancer cells or down-regulate the expression of progesterone receptor B protein in endometrial cancer cells. The drug resistance of these two tumor cells to trastuzumab or progesterone is induced by activating AKT pathway. ARID1A deletion in ovarian cancer can increase the expression of MRP2 protein and make it resistant to carboplatin and paclitaxel. ARID1A deletion also can up-regulate the phosphorylation levels of EGFR, ErbB2, and RAF1 oncogene proteins.The ErbB and VEGF pathway are activated and EMT is increased. As a result, lung adenocarcinoma is resistant to epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs). Although great progress has been made in the research on the mechanism of SWI/SNF complex inducing tumor drug resistance, most of the research is still at the protein level. It is necessary to comprehensively and deeply explore the detailed mechanism of drug resistance from gene, transcription, protein, and metabolite levels by using multi-omics techniques, which can provide sufficient theoretical basis for the diagnosis and treatment of poor tumor prognosis caused by mutation or abnormal expression of SWI/SNF subunits in clinical practice.
7.Objective characteristics of tongue manifestation in different stages of damp-heat syndrome in diabetic kidney disease
Zhaoxi DONG ; Yang SHI ; Jiaming SU ; Yaxuan WEN ; Zheyu XU ; Xinhui YU ; Jie MEI ; Fengyi CAI ; Xinyue ZANG ; Yan GUO ; Chengdong PENG ; Hongfang LIU
Journal of Beijing University of Traditional Chinese Medicine 2025;48(3):398-411
Objective:
To investigate the objective characteristics of tongue manifestation in different stages of damp-heat syndrome in diabetic kidney disease (DKD).
Methods:
A cross-sectional study enrolled 134 patients with DKD G3-5 stages who met the diagnostic criteria for damp-heat syndrome in DKD. The patients were treated at Dongzhimen Hospital, Beijing University of Chinese Medicine, from May 2023 to January 2024. The patients were divided into three groups: DKD G3, DKD G4, and DKD G5 stage, with 53, 33, and 48 patients in each group, respectively. Clinical general data (gender, age, and body mass index) and damp-heat syndrome scores were collected from the patients. The YZAI-02 traditional Chinese medicine (TCM) AI Tongue Image Acquisition Device was used to capture tongue images from these patients. The accompanying AI Open Platform for TCM Tongue Diagnosis of the device was used to analyze and extract tongue manifestation features, including objective data on tongue color, tongue quality, coating color, and coating texture. Clinical data and objective tongue manifestation characteristics were compared among patients with DKD G3-5 based on their DKD damp-heat syndrome status.
Results:
No statistically significant difference in gender or body mass index was observed among the three patient groups. The DKD G3 stage group had the highest age (P<0.05). The DKD G3 stage group had a lower score for symptoms of poor appetite and anorexia(P<0.05) than the DKD G5 group. No statistically significant difference was observed in damp-heat syndrome scores among the three groups. Compared with the DKD G5 stage group, the DKD G3 stage group showed a decreased proportion of pale color at the tip and edges of the tongue (P<0.05). The DKD G4 stage group exhibited an increased proportion of crimson at the root of the tongue, a decreased proportion of thick white tongue coating at the root, a decreased proportion of pale color at the tip and edges of the tongue, an increased hue value (indicating color tone) of the tongue color in the middle, an increased brightness value (indicating color lightness) of the tongue coating color in the middle, and an increased thickness of the tongue coating (P<0.05). No statistically significant difference was observed in other tongue color proportions, color chroma values, body characteristics, coating color proportions, coating color chroma values, and coating texture characteristics among the three groups.
Conclusion
Tongue features differ in different stages of DKD damp-heat syndrome in multiple dimensions, enabling the inference that during the DKD G5 stage, the degree of qi and blood deficiency in the kidneys, heart, lungs, liver, gallbladder, spleen, and stomach is prominent. Dampness is more likely to accumulate in the lower jiao, particularly in the kidneys, whereas heat evil in the spleen and stomach is the most severe. These insights provide novel ideas for the clinical treatment of DKD.
8.A Case Report of Pachydermoperiostosis by Multidisciplinary Diagnosis and Treatment
Jie ZHANG ; Yan ZHANG ; Li HUO ; Ke LYU ; Tao WANG ; Ze'nan XIA ; Xiao LONG ; Kexin XU ; Nan WU ; Bo YANG ; Weibo XIA ; Rongrong HU ; Limeng CHEN ; Ji LI ; Xia HONG ; Yan ZHANG ; Yagang ZUO
JOURNAL OF RARE DISEASES 2025;4(1):75-82
A 20-year-old male patient presented to the Department of Dermatology of Peking Union Medical College Hospital with complaints of an 8-year history of facial scarring, swelling of the lower limbs, and a 4-year history of scalp thickening. Physical examination showed thickening furrowing wrinkling of the skin on the face and behind the ears, ciliary body hirsutism, blepharoptosis, and cutis verticis gyrate. Both lower limbs were swollen, especially the knees and ankles. The skin of the palms and soles of the feet was keratinized and thickened. Laboratory examination using bone and joint X-ray showed periostosis of the proximal middle phalanges and metacarpals of both hands, distal ulna and radius, tibia and fibula, distal femurs, and metatarsals.Genetic testing revealed two variants in
9.Study on Brain Functional Network Characteristics of Parkinson’s Disease Patients Based on Beta Burst Period
Yu-Jie HAO ; Shuo YANG ; Shuo LIU ; Xu LOU ; Lei WANG
Progress in Biochemistry and Biophysics 2025;52(5):1279-1289
ObjectiveThe central symptom of Parkinson’s disease (PD) is impaired motor function. Beta-band electrical activity in the motor network of the basal ganglia is closely related to motor function. In this study, we combined scalp electroencephalography (EEG), brain functional network, and clinical scales to investigate the effects of beta burst-period neural electrical activity on brain functional network characteristics, which may serve as a reference for clinical diagnosis and treatment. MethodsThirteen PD patients were included in the PD group, and 13 healthy subjects were included in the healthy control group. Resting-state EEG data were collected from both groups, and beta burst and non-burst periods were extracted. A phase synchronization network was constructed using weighted phase lag indices, and the topological feature parameters of phase synchronization network were compared between the two groups across different periods and four frequency bands. Additionally, the correlation between changes in network characteristics and clinical symptoms was analyzed. ResultsDuring the beta burst period, the topological characteristic parameters of phase synchronization network in all four frequency bands were significantly higher in PD patients compared to healthy controls. The average clustering coefficient of the phase synchronization network in the beta band during the beta burst period was negatively correlated with UPDRS-III scores. In the low gamma band during the non-burst period, the average clustering coefficient of phase synchronization network was positively correlated with UPDRS and UPDRS-III scores, while UPDRS-III scores were positively correlated with global efficiency and average degree. ConclusionThe brain functional network features of PD patients were significantly enhanced during the beta burst period. Moreover, the beta-band brain functional network characteristics during the beta burst period were negatively correlated with clinical scale scores, whereas low gamma-band functional network features during the non-burst period were positively correlated with clinical scale scores. These findings indicate that motor function impairment in PD patients is associated with the beta burst period. This study provides valuable insights for the diagnosis of PD.
10.Modified Buwangsan Ameliorates Cognitive Dysfunction in Rat Model of Type 2 Diabetes Mellitus by Regulating Autophagy in Hippocampus via PI3K/Akt/mTOR Pathway
Jie YANG ; Tonghua LIU ; Wei LIU ; Lili WU ; Lingling QIN
Chinese Journal of Experimental Traditional Medical Formulae 2025;31(13):104-113
ObjectiveTo evaluate the therapeutic effects of modified Buwangsan on cognitive dysfunction in the rat model of type 2 diabetes mellitus with mild cognitive impairment (T2DM-MCI) and explore the underlying mechanism. MethodsThirty-six 5-week-old SPF-grade SD rats were randomly assigned into 6 groups: Normal (Con, fed with a normal diet), model (DM, fed with a high-sugar and high-fat diet), low-dose modified Buwangsan (L-BWS, 1.86 g·kg-1), medium-dose modified Buwangsan (M-BWS, 3.72 g·kg-1), high-dose modified Buwangsan (H-BWS,7.44 g·kg-1), and huperzine A (SSJJ, 0.018 mg·kg-1). The rats were treated by gavage once a day for 12 weeks. The body weight and blood glucose level were monitored dynamically. Morris water maze was employed to test the cognitive function of rats. Hematoxylin-eosin and Nissl staining were employed to observe the pathological changes of the hippocampus. The levels of tumor necrosis factor-α (TNF-α), interleukin-1β (IL-1β), and interleukin-6 (IL-6) in the serum and hippocampus were assessed by enzyme-linked immunosorbent assay. Western blotting was employed to determine the expression levels of key autophagy-related proteins including microtubule-associated protein 1 light chain 3 (LC3), type Ⅲ phosphatidylinositol 3-kinase complex regulatory subunit (Beclin1), and phosphorylated UNC-51-like kinase (p-ULK) 1/2 in the hippocampus. Immunofluorescence staining was employed to observe the regulation of p-PI3K/PI3K, p-mTOR/mTOR, and p-Akt/Akt ratios. ResultsCompared with the DM group, the L-BWS, M-BWS, H-BWS, and SSJJ groups showed increases in body weight at the end of the experiment (P<0.05), and the M-BWS, H-BWS and SSJJ groups showed declines in fasting blood glucose level (P<0.05). In the water maze test, compared with the DM group, the M-BWS, H-BWS, and SSJJ groups presented shortened escape latency (P<0.001). The L-BWS, M-BWS, H-BWS, and SSJJ group showcased regularly arranged cells in the hippocampus and cortex, markedly increased number of neurons, and significantly recovered Nissl bodies. Compared with the DM group, the L-BWS, M-BWS, H-BWS, and SSJJ groups had reductions in the levels of IL-1β and IL-6 in the serum and hippocampus (P<0.05), increases in the LC3-II/LC3-I ratio and expression level of beclin1 in the hippocampus (P<0.05) and the p-ULK level (P<0.05). The p-PI3K/PI3K, p-Akt/Akt, and p-mTOR/mTOR ratios in the hippocampus decreased in the M-BWS, H-BWS, and SSJJ groups (P<0.01). ConclusionModified Buwangsan significantly ameliorates cognitive dysfunction and neurological damage in the rat model of T2DM through multiple mechanisms. It regulates metabolic disorders, lowers the blood glucose level, improves lipid metabolism, and alleviates oxidative stress. It promotes the protection and repair of neurons by inhibiting inflammatory responses and activating the autophagy pathway in the hippocampus. At the same time, modified Buwangsan relieves autophagy inhibition by regulating the PI3K/Akt/mTOR signaling pathway to alleviate the brain tissue injury.


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