1.Computational pathology in precision oncology: Evolution from task-specific models to foundation models.
Yuhao WANG ; Yunjie GU ; Xueyuan ZHANG ; Baizhi WANG ; Rundong WANG ; Xiaolong LI ; Yudong LIU ; Fengmei QU ; Fei REN ; Rui YAN ; S Kevin ZHOU
Chinese Medical Journal 2025;138(22):2868-2878
With the rapid development of artificial intelligence, computational pathology has been seamlessly integrated into the entire clinical workflow, which encompasses diagnosis, treatment, prognosis, and biomarker discovery. This integration has significantly enhanced clinical accuracy and efficiency while reducing the workload for clinicians. Traditionally, research in this field has depended on the collection and labeling of large datasets for specific tasks, followed by the development of task-specific computational pathology models. However, this approach is labor intensive and does not scale efficiently for open-set identification or rare diseases. Given the diversity of clinical tasks, training individual models from scratch to address the whole spectrum of clinical tasks in the pathology workflow is impractical, which highlights the urgent need to transition from task-specific models to foundation models (FMs). In recent years, pathological FMs have proliferated. These FMs can be classified into three categories, namely, pathology image FMs, pathology image-text FMs, and pathology image-gene FMs, each of which results in distinct functionalities and application scenarios. This review provides an overview of the latest research advancements in pathological FMs, with a particular emphasis on their applications in oncology. The key challenges and opportunities presented by pathological FMs in precision oncology are also explored.
Humans
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Precision Medicine/methods*
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Medical Oncology/methods*
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Artificial Intelligence
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Neoplasms/pathology*
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Computational Biology/methods*
2.Expert consensus on evaluation index system construction for new traditional Chinese medicine(TCM) from TCM clinical practice in medical institutions.
Li LIU ; Lei ZHANG ; Wei-An YUAN ; Zhong-Qi YANG ; Jun-Hua ZHANG ; Bao-He WANG ; Si-Yuan HU ; Zu-Guang YE ; Ling HAN ; Yue-Hua ZHOU ; Zi-Feng YANG ; Rui GAO ; Ming YANG ; Ting WANG ; Jie-Lai XIA ; Shi-Shan YU ; Xiao-Hui FAN ; Hua HUA ; Jia HE ; Yin LU ; Zhong WANG ; Jin-Hui DOU ; Geng LI ; Yu DONG ; Hao YU ; Li-Ping QU ; Jian-Yuan TANG
China Journal of Chinese Materia Medica 2025;50(12):3474-3482
Medical institutions, with their clinical practice foundation and abundant human use experience data, have become important carriers for the inheritance and innovation of traditional Chinese medicine(TCM) and the "cradles" of the preparation of new TCM. To effectively promote the transformation of new TCM originating from the TCM clinical practice in medical institutions and establish an effective evaluation index system for the transformation of new TCM conforming to the characteristics of TCM, consensus experts adopted the literature research, questionnaire survey, Delphi method, etc. By focusing on the policy and technical evaluation of new TCM originating from the TCM clinical practice in medical institutions, a comprehensive evaluation from the dimensions of drug safety, efficacy, feasibility, and characteristic advantages was conducted, thus forming a comprehensive evaluation system with four primary indicators and 37 secondary indicators. The expert consensus reached aims to encourage medical institutions at all levels to continuously improve the high-quality research and development and transformation of new TCM originating from the TCM clinical practice in medical institutions and targeted at clinical needs, so as to provide a decision-making basis for the preparation, selection, cultivation, and transformation of new TCM for medical institutions, improve the development efficiency of new TCM, and precisely respond to the public medication needs.
Medicine, Chinese Traditional/standards*
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Humans
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Consensus
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Drugs, Chinese Herbal/therapeutic use*
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Surveys and Questionnaires
3.Research progresses on the mechanism of macrophages in tendon bone healing.
Liang WANG ; Yinshuan DENG ; Tao QU ; Chaoming DA ; Yunfei HE ; Rui LIU ; Weimin NIU ; Weishun YAN ; Zhen CHEN ; Shuo LI ; Zhiyun YANG ; Binbin GUO ; Xueqian LAI
Chinese Journal of Cellular and Molecular Immunology 2025;41(2):183-187
The connection between tendons and bones is called the tendon bone connection. With the continuous improvement of national sports awareness, excessive exercises and the related intensity are prone to damage the tendon bone connection. Tendon bone healing is a complex repair and healing process involving multiple factors, and good tendon bone healing is a prerequisite for its physiological function. The complexity of tendon bone structure also poses great challenges to the repair of tendon bone injuries. In recent years, researches have found that stem cells, growth factors, macrophages, and other factors are closely related to the healing process of tendon bone injuries, among which macrophages play an important role in the healing process. The authors reviewed relevant research literature in recent years and summarized the role of macrophages in tendon bone healing, in order to provide new ideas and directions for treatment strategies to promote tendon bone healing.
Humans
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Macrophages/metabolism*
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Wound Healing
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Animals
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Tendons/physiology*
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Bone and Bones/injuries*
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Tendon Injuries
4.Expression and Clinical Significance of Co-inhibitory Molecules TIGIT/CD155 and PD-1 in Chronic Lymphocytic Leukemia.
Rui ZHANG ; Shuang CHEN ; Ting-Ting LUO ; Jian-Hua QU
Journal of Experimental Hematology 2025;33(1):54-61
OBJECTIVE:
To investigate the expression of co-inhibitory molecules TIGIT/CD155 and PD-1 on CD4+T cells and Treg cells in peripheral blood of patients with chronic lymphocytic leukemia (CLL) and analyze their clinical significance.
METHODS:
The expression of PD-1 and TIGIT on CD4+T cells and Treg cells was detected by flow cytometry in 40 CLL patients and 20 healthy controls. Additionally, the expression of CD155 on peripheral blood B cells and DC cells of the enrolled subjects was detected.
RESULTS:
The proportions of PD-1+TIGIT+CD4+T cells, PD-1+TIGIT+Treg cells and CD155+DC cells in peripheral blood of CLL patients were significantly higher than those of healthy controls ( P < 0.05). The proportions of PD-1+TIGIT+CD4+T cells and PD-1+TIGIT+Treg cells in CLL patients were significantly higher than those of PD-1+TIGIT-CD4+T cells and PD-1+TIGIT-Treg cells, respectively ( P < 0.05). Both PD-1+TIGIT+CD4+T cells and PD-1+TIGIT+Treg cells were positively correlated with the level of CD155+DC cells (r =0.742, r =0.766). With the progression of Binet stage, the proportions of PD-1+TIGIT+CD4+T cells, PD-1+TIGIT+Treg cells, and CD155+DC cells gradually increased ( P < 0.05), and the aforementioned three types cells were all increased in patients with CD38≥30%, IGVH unmutated, or poor prognosis due to chromosomal abnormalities ( P < 0.05).
CONCLUSION
Co-inhibitory molecules PD-1 and TIGIT may be involved in immunodepletion in patients with advanced CLL, which has clinical prognostic value. Dual inhibitor molecular targeted therapy provides a new direction for the individualized treatment of CLL.
Humans
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Leukemia, Lymphocytic, Chronic, B-Cell/immunology*
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Receptors, Immunologic/metabolism*
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Programmed Cell Death 1 Receptor/metabolism*
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T-Lymphocytes, Regulatory/metabolism*
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Receptors, Virus/metabolism*
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CD4-Positive T-Lymphocytes/metabolism*
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Male
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Female
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Middle Aged
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Flow Cytometry
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Clinical Relevance
5.Genetic and clinical phenotypic analysis of Usher syndrome-associated gene variants.
Heng ZHAO ; Xiuli MA ; Yanli QU ; Guo LI ; Ken LIN ; Rui HUANG ; Lijuan ZHOU ; Jing MA
Journal of Clinical Otorhinolaryngology Head and Neck Surgery 2025;39(8):736-742
Objective:To investigate the molecular characteristics and clinical heterogeneity of Usher syndrome(USH) -related gene variants in patients with hereditary hearing loss in southwest China, providing a basis for early diagnosis and clinical management. Methods:Thirteen patients from twelve families with hearing loss who attended the Affiliated Children's Hospital of Kunming Medical University between January 2017 and March 2021 were enrolled. All patients were identified as carrying USH-related gene variants through next-generation sequencing. Sanger sequencing was performed for all patients and their parents to validate the pathogenic variants. Comprehensive clinical evaluations, including medical history collection, otologic and ophthalmologic examinations, and vestibular function assessments, were conducted. Results:Among the 13 patients, 4 were diagnosed with USH type 1 and 2 with USH type 2. A total of 19 pathogenic or likely pathogenic variants were detected in USH-related genes, including MYO7A,CDH23,USH1C, and USH2A. The causative gene was MYO7A in 3 probands, CDH23 in 5, USH1C in 3, and USH2Ain 2. All patients exhibited an autosomal recessive inheritance pattern. Vestibular dysfunction was observed in 4 patients, and retinitis pigmentosa(RP) in 3 patients. Based on the genotype-phenotype correlation, 6 patients were initially diagnosed with USH, while 7 were classified as having non-syndromic hearing loss(NSHL). Conclusion:This study revealed the clinical heterogeneity of USH-related gene variants in patients with hereditary deafness in southwest China. Although the clinical manifestations of USH are complex and there are overlapping characteristics between different subtypes, genetic testing provides an important basis for early diagnosis and precise clinical management. Especially for those with typical hearing loss, early genetic diagnosis can provide a window of time for early detection and intervention of retinitis pigmentosa.
Humans
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Usher Syndromes/genetics*
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Myosin VIIa
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Phenotype
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Male
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Female
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Myosins/genetics*
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Mutation
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Cadherins/genetics*
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Child
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Extracellular Matrix Proteins/genetics*
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Adolescent
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Pedigree
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High-Throughput Nucleotide Sequencing
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Cadherin Related Proteins
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Cytoskeletal Proteins
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Cell Cycle Proteins
6.Identification and expression analysis of β-amylase gene family members in alfalfa under saline-alkali stress.
Hongyu QU ; Lishuang ZHANG ; Yahui TANG ; Lei LIU ; Rui GUO ; Weileng GUO ; Changhong GUO
Chinese Journal of Biotechnology 2025;41(2):719-735
Beta-amylases (BAMs), key enzymes in starch hydrolysis, play an important role in plant growth, development, and resistance to abiotic stress. To mine the saline-alkali tolerance-related BAM genes in alfalfa (Medicago sativa L.), we identified MsBAM genes in the whole genome. The physicochemical properties, phylogeny, gene structures, conserved motifs, secondary structures, promoter cis-acting elements, chromosome localization, and gene replication relationships of BAM gene family members were analyzed. RNA-seq and quantitative real-time PCR (qRT-PCR) were employed to analyze the expression patterns of BAM family members under saline-alkali stress. The results showed that 54 BAM genes were identified in the genome, which were classified into 8 subgroups according to the phylogenetic tree. The members of the same subgroup had similar gene structures except that those of subgroups 1 and 7 had large differences. Conserved motif analysis showed that all MsBAM proteins had a typical glycohydrolysis domain. The chromosome localization analysis showed that MsBAM gene family members were unevenly distributed on 27 chromosomes. The duplication of gene segments led to the increase in BAM gene number in alfalfa. The promoters of BAM genes contained a large number of elements in response to plant hormones and stress. Transcriptome data and qRT-PCR results showed that the expression levels of most MsBAM genes were up-regulated in response to saline-alkali stress. Under the saline-alkali stress, the expression levels of 28 genes, including MsBAM6, were up-regulated on days 1 and 7, and those of 5 genes, including MsBAM9, were up-regulated by over 2 folds. In addition, under salt-alkali stress, BAM activity and soluble sugar content were significantly increased. These results indicate that BAM genes play a key role in alfalfa in response to saline-alkali stress, laying a foundation for further research in this field.
Medicago sativa/physiology*
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beta-Amylase/metabolism*
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Phylogeny
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Gene Expression Regulation, Plant
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Stress, Physiological/genetics*
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Multigene Family
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Alkalies
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Plant Proteins/genetics*
7.PCBP1-mediated regulation of iron homeostasis suppresses ferroptosis against cadmium-induced neurotoxicity in mouse neuroblastoma cells
Sheng JIE ; Rui TIAN ; Yuchen QU ; Li TIAN ; Jia XIE ; Mengyan CHEN ; Mindi HE ; Zhengping YU ; Huifeng PI ; Ping DENG
Journal of Army Medical University 2025;47(19):2315-2326
Objective To investigate the role of poly(rC)-binding protein 1(PCBP1)in cadmium(Cd)-induced ferroptosis in mouse neuroblastoma Neuro-2a(N2A)cells.Methods N2A cells were exposed to a concentration gradient of CdCl?(0,1,2,4 μmol/L)for 72 h.Cell viability was assessed by trypan blue staining.Western blotting was employed to detect the expression of ferroptosis-related proteins(GPX4,HMOX1,ACSL4)and PCBP1.Intracellular Fe2? level and lipid peroxidation were detected using FerroOrange and BODIPY581/591 C11 probes,respectively.Ferrostatin-1(Fer-1),a ferroptosis inhibitor,was applied to confirm the critical role of ferroptosis in Cd-induced cytotoxicity.Molecular docking was performed to elucidate the interaction between PCBP1 and ferritin,as well as the binding sites of Cd2?.PCBP1 overexpression plasmid was further constructed for functional validation.Results Cd exposure suppressed cell viability in N2A cells in a dose-dependent manner(P<0.01),significantly down-regulated GPX4 expression(P<0.05),up-regulated HMOX1 expression(P<0.01),and induced Fe2? overload and lipid peroxidation(P<0.01).Molecular docking revealed that Cd2? directly bound to the KH2 domain of PCBP1 and then co-localized on the outer surface of ferritin heavy chain.Overexpression of PCBP1 markedly reversed Cd-induced Fe2? accumulation,GPX4 down-regulation,lipid peroxidation,and cell death.Conclusion Cd exposure disrupts PCBP1-mediated iron homeostasis via transcriptional suppression and competitive displacement of metal ions,and then synergistically drives Fe2? overload-triggered ferroptosis cascades,ultimately leading to neurotoxicity.Targeting PCBP1-mediated iron homeostasis can effectively mitigate Cd-induced neurotoxicity,and may serve as a novel therapeutic strategy.
8.Serum MST4 and HSP70 levels in children with idiopathic immune thrombocytopenia and their clinical significance
Huishuang XU ; Mingli QU ; Fang YAN ; Rui YUE ; Jing GUO ; Yinsha MIAO
International Journal of Laboratory Medicine 2025;46(1):49-53
Objective To explore serum levels of serine/threonine protein kinase 4(MST4)and heat shock protein 70(HSP70)in children with idiopathic immune thrombocytopenia(ITP)and their clinical signifi-cance.Methods Totally 98 children with ITP admitted to Northwest Women and Children's Hospital from April 2019 to April 2023 were retrospectively selected as the ITP group,and 50 healthy children who under-went physical examination during the same period were selected as the control group.Enzyme linked immu-nosorbent assay was used to detect serum levels of MST4 and HSP70,and the serum MST4 and HSP70 levels in children with different ITP levels were compared.The correlation between the indicators were analyzed by Pearson correlation.Logistic regression model was used to screen the prognostic factors of ITP,and the as-sessment value of serum MST4 and HSP70 on ITP prognosis was analyzed by subject working characteristic curve.Results Serum MST4,HSP70,and CD8 in the ITP group were higher than those in the control group,while PLT,CD3+,CD4+,CD4+/CD8+were lower than those in the control group,with statistical significance(P<0.05).Serum MST4 and HSP70 levels in mild group,moderate group and severe group were increased successively,with statistical significance(P<0.05).Correlation analysis showed that serum MST4 and HSP70 were positively correlated with CD8+(P<0.05),and negatively correlated with PLT,CD3+,CD4+,CD4+/CD8+(P<0.05).The disease course,serum MST4 and HSP70 of ITP children in the poor prognosis group were higher than those in the good prognosis group,and the differences were statistically significant(P<0.05).Logistic regression analysis showed that the course of disease(OR=1.579,P<0.001),serum MST4(OR=1.451,P<0.001)and serum HSP70(OR=1.442,P<0.001)were independent risk factors af-fecting the prognosis of children with ITP.The area under the curve of serum MST4 and HSP70 combined in the assessment of poor prognosis of ITP children was larger than that of serum MST4 and HSP70,and the difference was statistically significant(Z=4.568,4.672,both P<0.001).Conclusion The elevated serum MST4 and HSP70 levels in children with ITP are related to the severity of the disease and cellular immune function.The combination of the two has a high evaluation value for the prognosis of children with ITP.
9.Glaucocalyxin A alleviates inflammatory response in rats with traumatic fracture
Bowen JIANG ; Rui MA ; Peng WANG ; Zhe QU ; Aiqun LI
Basic & Clinical Medicine 2025;45(2):210-215
Objective To investigate whether glaucocalyxin A can reduce inflammatory response in rats with trau-matic fracture.Methods The rats were randomly divided into control group,model group,low GLA(GLA-L),high GLA dose group(GLA-H)and GLA?H+YC?1(HIF?1α inhibitor)group.The level of TNF?α,IL?6,CTX?Ⅰ,CTX?Ⅱ,S?Ca,S?P,BGP and the activities of iNOS and ALP were detected by ELISA.The density and thickness of bone trabeculae were measured by computed tomography.Apoptosis of femur tissue was detected by TUNEL.The cartilage morphology was observed by saffranin O?fast green staining.Western blot was applied to de?tect the expression of HIF?1α,VEGF,CD31,BMP?2,and collagenⅠ proteins in femoral tissue.Results Compared with the control group,the cartilage morphology of rats in the model group was significantly damaged,the level of serum TNF?α,IL?6,CTX?Ⅰ,CTX?Ⅱ,iNOS activity and apoptosis rate of femur tissue were in?creased.Serum S?Ca,S?P,BGP levels,ALP activity,bone trabecular density and thickness,HIF?1α,VEGF,CD31,BMP?2,collagen Ⅰ protein expression levels in femur tissue were all decreased(P<0.05).The mor?phology of cartilage tissue in GLA?L and GLA?H groups was significantly improved,and the level of serum TNF?α,IL?6,CTX?Ⅰ,CTX?Ⅱ,iNOS activity and apoptosis rate of femur tissue were all significantly de?creased.Serum levels of S?Ca,S?P,BGP,ALP activity,bone trabecular density and thickness,HIF?1α,VEGF,CD31,BMP?2,collagen Ⅰ protein expression level in femur tissue were significantly increased(P<0.05).YC?1 was able to weaken the therapeutic effect of GLA on traumatic fracture rats(P<0.05).Conclusions GLA alleviates inflammation and cartilage damage in rats with traumatic fractures,promotes angio?genesis and improves femoral morphology,possibly by activating the HIF?1α/VEGF signaling pathway.
10.Ophiopogon japonicus (L. f.) Ker Gawl. extract treats dry eye disease via anti-inflammatory, antioxidant, and goblet cell-stimulating effects
Guoliang Li ; Rui Feng ; Jiayi Yu ; Boliang Li ; Yanni Luo ; Hongyi Luo ; Cheng Zhang ; Guanghong Zhang ; Jianglong Li ; Chao Qu
Journal of Traditional Chinese Medical Sciences 2025;2025(3):422-433
ObjectiveTo investigate the anti-inflammatory, antioxidant, and goblet cell-stimulating effects of a suspension of Ophiopogon japonicus (L. f.) Ker Gawl. (O. japonicus, Mai Dong) extract combined with hyaluronic acid (HA) in the mouse model with dry eye disease (DED).MethodsA DED mouse model was induced using benzalkonium chloride (BAK), followed by treatment with O. japonicus extract-containing eye drops at varying concentrations. Experimental groups included a normal control, a DED model control, a positive control, and an O. japonicus extract-treated group. Corneal fluorescein staining and tear break-up time (TBUT) were used to assess tear film stability and ocular surface integrity. Enzyme-linked immunosorbent assay (ELISA) measured inflammatory factor levels in corneal and conjunctival tissues, whereas Western blot (WB) analyzed key antioxidant and inflammatory markers, including nuclear factor erythroid 2-related factor (2Nrf2) and heme oxygenase 1 (HO-1). Periodic acid-schiff (PAS) staining and immunofluorescence were used to evaluate goblet cell density and mucin secretion.ResultsO. japonicus extract significantly improved corneal damage, reduced fluorescein staining scores, prolonged TBUT, and increased tear secretion. It downregulated inflammatory markers, including interleukin-8 (IL-8), interleukin-1β (IL-1β), and interferon-γ (IFN-γ) while upregulating Nrf2, HO-1, and the interleukin-13 (IL-13)/IFN-γ ratio, alleviating oxidative stress and inflammation. PAS staining showed increased conjunctival goblet cell density and restored mucin secretion, enhancing tear film stability.ConclusionO. japonicus extract demonstrated significant anti-inflammatory, antioxidant, and goblet cell-stimulating effects in a DED model, with good biocompatibility and promising therapeutic potential. Future research should optimize extraction processes and validate their efficacy and safety in clinical settings.


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