1.Prediction of Potential Regulatory Pathways Involving The Notch Signaling Pathway and Its Associated Non-coding RNAs in Alzheimer’s Disease Based on Database Analysis
Meng-Lin LÜ ; Xing-Ran LIU ; Xian-Juan KOU
Progress in Biochemistry and Biophysics 2025;52(8):1942-1957
Alzheimer’s disease (AD) is a chronic, progressive, and irreversible neurodegenerative disorder that typically begins with a subtle onset and progresses slowly. Pathologically, it is characterized by two hallmark features: the extracellular accumulation of amyloid β-protein (Aβ), forming senile plaques, and the intracellular hyperphosphorylation of tau protein, resulting in neurofibrillary tangles (NFTs). These pathological changes are accompanied by substantial neuronal and synaptic loss, particularly in critical brain regions such as the cerebral cortex and hippocampus. Clinically, AD presents as a gradual decline in memory, language abilities, and spatial orientation, significantly impairing the quality of life of affected individuals. With the aging population steadily increasing in China, the incidence of AD is rising, making it a major public health concern that requires urgent attention. The growing societal and economic burden of AD underscores the pressing need to identify effective diagnostic biomarkers and develop novel therapeutic strategies. Among the various molecular signaling pathways involved in neurological disorders, the Notch signaling pathway is especially noteworthy due to its evolutionary conservation and regulatory roles in cell proliferation, differentiation, development, and apoptosis. In the central nervous system, Notch signaling is essential for neurodevelopment and synaptic plasticity and has been implicated in several neurodegenerative processes. Although some studies suggest that Notch signaling may influence AD-related pathology, its precise role in AD remains poorly understood. In particular, the interaction between Notch signaling and non-coding RNAs (ncRNAs)—key regulators of gene expression—has received limited attention. NcRNAs, including long non-coding RNAs (lncRNAs) and microRNAs (miRNAs), are known to exert extensive regulatory functions at both transcriptional and post-transcriptional levels. Dysregulation of these molecules has been widely associated with various diseases, including cancers, cardiovascular conditions, and neurodegenerative disorders. Notably, interactions between ncRNAs and major signaling pathways such as Notch can produce widespread biological effects. While such interactions have been increasingly reported in several disease models, comprehensive studies investigating the regulatory relationship between Notch signaling and ncRNAs in the context of AD remain scarce. Given the capacity of ncRNAs to modulate signaling cascades and form complex regulatory networks, a deeper understanding of their crosstalk with the Notch pathway could provide novel insights into AD pathogenesis and reveal potential targets for diagnosis and treatment. In this study, we investigated the regulatory landscape involving the Notch signaling pathway and associated ncRNAs in AD using bioinformatics approaches. By integrating data from multiple public databases, we systematically identified significantly dysregulated Notch pathway-related genes and their interacting ncRNAs in AD. Based on this analysis, we constructed a lncRNA-miRNA-mRNA regulatory network to elucidate the potential mechanisms linking Notch signaling to ncRNA-mediated gene regulation in AD pathogenesis. Furthermore, we explored the internal relationships and molecular mechanisms within this network and assessed the feasibility and clinical relevance of these molecules as early diagnostic biomarkers and potential therapeutic targets for AD. This study aims to deepen our understanding of the molecular basis of AD and offer novel strategies for its diagnosis and treatment.
2.Mechanism of Sanhuang Xiexintang in Protecting Stress Gastric Ulcer in Rats
Yilin ZHONG ; Ran XIE ; Jiameng LI ; Shuang LIU ; Junying LI ; Mengnan ZANG ; Xing LIU ; Jinsong LIU ; Feng SUI ; Pengqian WANG
Chinese Journal of Experimental Traditional Medical Formulae 2024;30(10):45-53
ObjectiveTo explore the molecular mechanism of Sanhuang Xiexintang (SHXXT) in protecting stress gastric ulcer (SGU) in rats through network pharmacology, molecular docking, and animal experiments. MethodThe active ingredients and corresponding targets in SHXXT were collected and screened from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP), Traditional Chinese Medicine Information Database (TCMID), Bioinformation Analysis Tool for Molecular Mechanism of Traditional Chinese Medicine (BATMAN-TCM), and Swiss Target Prediction database. SGU-related targets were screened from the Online Mendelian Inheritance in Man (OMIM), Therapeutic Target Database (TTD), GeneCards database, and PharmGKB database. Herbal-ingredient-target (H-C-T) network was constructed by using Cytoscape 3.9.1 software. Protein-protein interaction (PPI) of drug and disease intersection targets was analyzed by using the Protein Interaction Platform (STRING) database. Gene ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were conducted through the Database for Annotation Visualization and Integrated Discovery (DAVID). The active ingredients and key targets were validated using AutodockVina 1.2.2 molecular docking software, and the experimental results were further validated through animal experiments. ResultThe 55 active ingredients were screened, and 255 potential target genes for SHXXT treatment of SGU were predicted. The PPI analysis showed that protein kinase B (Akt), phosphatase and tensin homolog deleted on chromosome ten (PTEN), tumor necrosis factor-α (TNF-α), interleukin-1β (IL-1β), and cyclooxygenase-2 (COX-2) are the core targets of SHXXT for protecting SGU. GO and KEGG analyses showed that SHXXT may affect the development of SGU by regulating various biological processes such as the phosphoinositide 3-kinase (PI3K)/Akt signaling pathway and inflammatory processes. The molecular docking results showed that both the active ingredients and key targets had good binding ability. Animal experiments showed that compared with the blank group, the ulcer index (UI) of the model group was significantly increased (P<0.01), and the serum levels of TNF-α and IL-1β significantly increased (P<0.01). The phosphorylation level of PTEN in gastric mucosal tissue was significantly down-regulated (P<0.05). The phosphorylation levels of PI3K, Akt, and nuclear factor kappa-B (NF-κB) were significantly up-regulated (P<0.05). Compared with the model group, the UI of the treatment group was significantly reduced (P<0.01), and the serum levels of TNF-α and IL-1β were significantly reduced (P<0.01). The phosphorylation level of PTEN in gastric mucosal tissue was significantly up-regulated (P<0.01), and the phosphorylation levels of PI3K, Akt, and NF-κB were significantly downregulated (P<0.01). ConclusionThe application of network pharmacology prediction, molecular docking simulation, and animal experimental validation confirms that SHXXT regulates the PI3K/Akt/NF-κB signaling pathway to regulate the inflammatory response of rats and thus protects the gastric mucosa of SGU rats.
3.Regulation and Function of Protein Histidine Phosphorylation
Xiao-Ran LIU ; Mei-Ning XING ; Wan-Tao YING
Progress in Biochemistry and Biophysics 2024;51(10):2694-2704
Protein phosphorylation modification is one of the key regulatory mechanisms in cellular signaling transduction and metabolic processes. The phosphorylation state of target proteins is regulated by specific protein kinases and phosphatases, which add or remove phosphate groups. Histidine phosphorylation (pHis) plays a crucial role in both prokaryotes and eukaryotes life activities and is linked to various pathological processes. Unlike the stable phosphorylation of proteins via phosphate ester bonds, histidine phosphorylation is linked through phosphoramide bonds, making it highly sensitive to high temperatures and low pH. This sensitivity has historically impeded progress in identifying and studying histidine phosphorylation. In recent years, the development of new techniques in phosphoproteomics and the emergence of pHis-specific antibodies have promoted the identification and functional research of pHis-modified substrates. For the first time, more than 700 pHis-modified proteins have been identified in mammalian cells, and pHis-modified substrates such as focal adhesion kinase (FAK) and phosphoglycerate mutase 1 (PGAM1) have been found to promote tumor development. This article mainly reviewed the key mechanisms and functions of histidine kinases and histidine phosphatases in regulating the histidine phosphorylation of specific substrates, and highlights their significant roles in human physiological and pathological processes, aiming to provide guidance for further research into the biological functions of histidine phosphorylation.
4.Network meta-analysis for efficacy and safety of TACE combined with anti-angiogenic drugs in the treatment of unresectable primary liver cancer
Fenping LU ; Guangyan XING ; Bowen LIU ; Xiaobin LI ; Kai ZHAO ; Yun RAN ; Fenfang WU ; Shiping HU
China Pharmacy 2024;35(20):2533-2540
OBJECTIVE To systematically evaluate the efficacy and safety of transcatheter arterial chemoembolization (TACE) combined with anti-angiogenic drugs for the treatment of unresectable primary liver cancer (PLC). METHODS Retrieved from Chinese and English databases such as CNKI, the Cochrane Library, Google, and Baidu Academic, randomized controlled trial (RCT) about TACE combined with anti-angiogenic drugs for the treatment of unresectable PLC were collected from the inception to May 27, 2024. After screening the literature, extracting data, and evaluating the quality of the literature, network meta-analysis was performed using R 4.2.2 and Stata 17.0. RESULTS A total of 44 RCT were included, involving 5 607 patients and 8 interventions. The network meta-analysis results showed that for prolonging median overall survival (mOS) and median progression- free survival (mPFS), TACE+apatinib had the best efficacy, with TACE+apatinib and TACE+sorafenib ranking as the top two. For improving objective response rate (ORR) and disease control rate (DCR), TACE+donafenib had the best efficacy, with TACE+ donafenib and TACE+ lenvatinib ranking as the top two. In terms of safety, TACE+donafenib was the best, with TACE+donafenib and TACE+apatinib ranking as the top two. CONCLUSIONS TACE+apatinib and TACE+donafenib have good efficacy for patients with unresectable PLC, and TACE+donafenib has the best safety profile.
5.The Potential Mechanism of Hippo Signaling Pathway and Its Related miRNA Intervention in Alzheimer’s Disease and Parkinson’s Disease
Xing-Ran LIU ; Meng ZHANG ; Xian-Juan KOU
Progress in Biochemistry and Biophysics 2024;51(7):1485-1509
The main characteristics of neurodegenerative diseases represented by Alzheimer’s disease (AD) and Parkinson’s disease (PD) is the progressive irreversible loss of neurons, leading to varying degrees of pathological changes and loss of cognitive function. There is still no effective treatment. With the acceleration of global aging society, the incidence of neurodegenerative diseases is rapidly increasing, becoming a serious global public health concern that urgently requires the development of effective therapeutic strategies. The Hippo signaling pathway, a highly evolutionarily conserved pathway, consists of the core components MST1/2, LATS1/2, and downstream effectors, transcriptional co-activators YAP and TAZ. It plays a crucial role in the regulation of various biological processes such as cell proliferation, differentiation, development, and apoptosis. Dysregulation of the Hippo pathway contributes to the development of many diseases, including cancer, cardiovascular diseases, immune disorders, etc. Therefore, targeting the dysregulated components of the Hippo pathway may be an effective strategy for treating various diseases. Increasing evidence indicates that the Hippo pathway is excessively activated in the development of neurodegenerative diseases, manifested by increased expression of MST1 and downregulation of YAP. Stabilizing the Hippo pathway levels has shown improvements in AD and PD. However, most studies on the Hippo pathway in AD and PD focus on changes in the expression levels of Hippo pathway components, and research in other neurodegenerative diseases is still lacking. Therefore, further investigation is needed to fully understand the mechanistic role of the Hippo pathway in neurodegenerative diseases. Meanwhile, miRNA, similarly dysregulated in neurodegenerative diseases and serving as biomarkers, is a primary target for miRNA therapy in neurodegenerative diseases, including AD and PD. Activating or inhibiting dysregulated miRNAs is the main strategy of miRNA therapy during the neurodegenerative disease development. Evidence suggests that the interaction between the Hippo pathway and miRNA can result in widespread biological effects and crosstalk in the occurrence of different types of diseases. However, studies on the interplay between the Hippo pathway and miRNA in neurodegenerative diseases are relatively scarce. In this paper, we predicted the miRNAs related to Hippo pathway through bioinformatics database, and further screened the miRNAs with crosstalk relationship with Hippo signaling pathway through experiments in combination with PubMed. Then, the mechanism of action of Hippo signaling pathway related miRNAs in AD and PD is further elucidated. It is reported that the Hippo pathway and its related miRNA may exert neuroprotective effects by reducing oxidative stress, improving neuroinflammation, stabilizing autophagy levels, maintaining neuronal mitochondrial function, and ameliorating blood-brain barrier dysfunction, thereby delaying the progression of AD and PD. However, research on miRNA directly regulating the Hippo pathway to improve AD and PD is limited, and observations of the Hippo pathway and its related miRNA in other neurodegenerative diseases are scarce. However, considering the regulatory relationship between the Hippo pathway and miRNA in multiple diseases and their respective roles in key mechanisms of neurodegenerative diseases, such as oxidative stress and neuroinflammation, the crosstalk between miRNA and the Hippo pathway holds a crucial regulatory role in the development of neurodegenerative diseases. Thus, the interaction pathways of the Hippo pathway and its related miRNA may be a pivotal avenue for exploring effective therapeutic strategies for neurodegenerative diseases in the future.
6.CiteSpace-based visualization and analysis of Chinese medicine diagnostic and treatment equipment
Dan-Dan CUI ; Yi-Xing LIU ; Dong-Ran HAN
Chinese Medical Equipment Journal 2024;45(3):76-80
Relevant literature on TCM diagnostic and treatment equipment from January 1994 to May 2023 was collected with three Chinese databases,namely,China National Knowledge Infrastructure,Wanfang and Wipu.CiteSpace software was used for the analyses of the trend of annual publication volume,co-occurrence of publication institutions,co-occurrence of keywords,cluster and burst and the generation of corresponding knowledge graphs.It's pointed out TCM diagnostic and treatment equipment had problems in low publication volume and collaboration between research institutions,hotspots of Chinese medicine diagnosis and treatment,diagnosis and treatment equipment,diagnosis device,Chinese medicine diagnosis,diagnosis and treatment technology and traditional Chinese medicine,and research frontiers of artificial intelligence,medical alliance,curriculum design and innovation and entrepreneurship.References were provided for relevant research in China.[Chinese Medical Equipment Journal,2024,45(3):76-80]
7.Linezolid-induced fatal lactic acidosiss:an adverse reaction easily confu-sed with septic shock
Ran ZHU ; Shao-Wan YANG ; Xing-Han TIAN ; Xiao-Li LI ; Yan LIU
Chinese Journal of Infection Control 2024;23(7):897-900
Clinical data of 3 patients with linezolid-induced lactic acidosis treated in 2 hospitals in Beijing and Shandong were retrospectively analyzed,and relevant literatures at home and abroad were retrieved.The pathogene-sis,risk factors,clinical manifestations,and treatment scheme were valuated.Three patients received linezolid anti-infection treatment due to their disease condition.At different phases of treatment,they developed lactic acidosis that was difficult to be explained with septic shock.After discontinuing linezolid and receiving bedside continuous veno-venous hemofiltration(CVVH)treatment,patient's blood lactate levels decreased significantly.It is clinically diagnosed linezolid-induced lactic acidosis finally,but the initial diagnosis was septic shock by all doctors.After ac-tive treatment,2 patients recovered and 1 patient died.Linezolid-induced lactic acidosis is easily to be misdiagnosed as septic shock.Clinicians should enhance their understanding and recognition of the early diagnosis of the adverse reactions,take effective measures,so as to improve patient prognosis.
8.Comparison of the Prognostic Value of C-Reactive Protein to Albu-min Ratio and Glasgow Prognostic Score in Patients with Diffuse Large B-Cell Lymphoma
Hong-Yan WANG ; Hong DENG ; Mei-Jiao HUANG ; Liang ZHANG ; Tai-Ran CHEN ; Yu LIU ; Xing-Li ZOU
Journal of Experimental Hematology 2024;32(3):742-749
Objective:To compare the prognostic value of two predictive models based on C-reactive protein(CRP)and albumin(ALB),namely the CRP to ALB ratio(CAR)and the Glasgow prognostic score(GPS),in newly diagnosed patients with diffuse large B-cell lymphoma(DLBCL).Methods:The data of newly diagnosed DLBCL patients admitted to our center from May 2014 to January 2022 were reviewed.A total of 111 patients who completed at least 4 cycles of R-CHOP or R-CHOP-like chemotherapy with detailed clinical,laboratory data and follow-up information were included.The receiver operating characteristic(ROC)curve was performed to evaluate the predictive value of pre-treatment CAR on disease progression and survival.Furthermore,the association between CAR and baseline clinical,laboratory characteristics of patients was evaluated,and progression-free survival(PFS)and overall survival(OS)were compared between different CAR and GPS subgroups.Finally,the univariate and multivariate COX propor-tional hazard regression models were used to analyze the factors affecting disease outcomes.Results:ROC curve showed that the area under the curve(AUC)of CAR predicting PFS and OS in DLBCL patients was 0.687(P=0.002)and 0.695(P=0.005),respectively,with the optimal cut-off value of 0.11 for both predicting PFS and OS.Compared with the lower CAR(<0.11)group,the higher CAR(≥0.11)group had more clinical risk factors,including age>60 years(P=0.025),ECOG score ≥2(P=0.004),Lugano stage Ⅲ-Ⅳ(P<0.001),non-germinal center B-cell-like(non-GCB)subtype(P=0.035),elevated lactate dehydrogenase(LDH)(P<0.001),extranodal involved site>1(P=0.004)and IPI score>2(P<0.001).The interim response evaluation of patients showed that the overall response rate(ORR)and complete response rate(CRR)in the lower CAR group were both significantly better than those in the higher CAR group(ORR:96.9%vs 80.0%,P=0.035;CRR:63.6%vs 32.5%,P=0.008).With a median follow-up of 24 months,patients with lower CAR had significantly longer median PFS and OS than those with higher CAR(median PFS:not reached vs 67 months,P=0.0026;median OS:not reached vs 67 months,P=0.002),while there was no statistical difference in PFS(P=0.11)and OS(P=0.11)in patients with GPS of 0,1,and 2.Multivariate Cox regression analysis indicated that only sex(male)and IPI score>2 were independent risk factors for both PFS and OS.Conclusion:CAR is significantly correlated with disease progression and survival in DLBCL patients;And compared with GPS,CAR has more advantages in predicting disease outcomes in DLBCL patients.
9.Efficacy and Safety of Flumatinib and Imatinib as First-line Treatments for Newly-diagnosed Chronic Myeloid Leukemia in Chronic Phase:A Real-world Study
Liang ZHANG ; Hong DENG ; Yu LIU ; Tai-Ran CHEN ; Mei-Jiao HUANG ; Hong-Yan WANG ; Xing-Li ZOU
Journal of Experimental Hematology 2024;32(6):1676-1681
Objective:To compare the efficacy and safety of flumatinib (FM)and imatinib (IM)as first-line treatment in newly-diagnosed patients with chronic myeloid leukemia in chronic phase (CML-CP ) in real world. Methods:A total of 84 newly-diagnosed CP-CML patients in our center from December 2019 to December 2022 were retrospectively analyzed.Among them,32 cases received FM as first-line treatment,and 52 cases received IM. Molecular response (MR),disease progression,survival and incidence of adverse events (AEs)were compared between the two groups.Results:At 3 months of treatment,the incidences of early molecular response (EMR ),MR2.0 and MR3.0 were 96.7%,70.0% and 20.0% in FM group,respectively,which were significantly higher than 77.1%,29. 2% and 0 in IM group (all P<0.05 ).At 6,9 and 12 months of treatment,the incidences of major molecular response (MMR)in FM group were 68.2%,85.7% and 90.0%,respectively,which were significantly higher than 22.9%,34.0% and 51.1% in IM group (all P<0.01).The median time to achieve MMR in FM group was 6(6-9)months,which was significantly shorter than 18(12-22)months in IM group (P<0.001 ).The 3-year progression-free survival rate and 3-year event-free survival rate in FM group were 100% and 68.8%,respectively,while in IM group were 98.1% and 55.8%.There were no significant differences between the two groups (P>0.05). The incidence of grade 3-4 hematologic AEs in FM group was 21 .9%,which was slightly lower than 25.0% in IM group,but the difference was not significant (P>0.05 ).Conclusion:In real clinical practice,FM as first-line treatment achieves MMR earlier than IM,and exhibits good safety profile in newly-diagnosed CML-CP patients,which potentially leads to improved long-term survival and treatment-free remission.
10.Simultaneous determination of eight constituents in Lianhua Qingwen Capsules by LC-MS/MS
Piao-Ran QIN ; Jia-Ye TIAN ; Su-Xia LI ; Fan GAO ; Wen-Hua YU ; Xing-Chao LIU ; Qiu-Hong GUO
Chinese Traditional Patent Medicine 2024;46(11):3564-3568
AIM To establish an LC-MS/MS method for the simultaneous content determination of forsythin,forsythoside A,chlorogenic acid,neochlorogenic acid,amygdalin,emodin,rhein and salidroside in Lianhua Qingwen Capsules.METHODS The analysis was performed on a 35℃thermostatic ACQUITY UPlC-HSS T3 column(100 mm×2.1 mm,1.8 μm),with the mobile phase comprising of 0.1%formic acid-acetonitrile flowing at 0.3 mL/min in a gradient elution manner,and electron spray ionization source was adopted in negative ion scanning with multiple reaction monitoring mode.RESULTS Eight constituents showed good linear relationships within their own ranges(r≥0.999 5),whose average recoveries were 99.20%-100.96%with the RSDs of 0.62%-1.23%.CONCLUSION This simple,sensitive and reliable method can be used for the quality control of Lianhua Qingwen capsules.

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