1.Molecular Mechanisms of RNA Modification Interactions and Their Roles in Cancer Diagnosis and Treatment
Jia-Wen FANG ; Chao ZHE ; Ling-Ting XU ; Lin-Hai LI ; Bin XIAO
Progress in Biochemistry and Biophysics 2025;52(9):2252-2266
RNA modifications constitute a crucial class of post-transcriptional chemical alterations that profoundly influence RNA stability and translational efficiency, thereby shaping cellular protein expression profiles. These diverse chemical marks are ubiquitously involved in key biological processes, including cell proliferation, differentiation, apoptosis, and metastatic potential, and they exert precise regulatory control over these functions. A major advance in the field is the recognition that RNA modifications do not act in isolation. Instead, they participate in complex, dynamic interactions—through synergistic enhancement, antagonism, competitive binding, and functional crosstalk—forming what is now termed the “RNA modification interactome” or “RNA modification interaction network.” The formation and functional operation of this interactome rely on a multilayered regulatory framework orchestrated by RNA-modifying enzymes—commonly referred to as “writers,” “erasers,” and “readers.” These enzymes exhibit hierarchical organization within signaling cascades, often functioning in upstream-downstream sequences and converging at critical regulatory nodes. Their integration is further mediated through shared regulatory elements or the assembly into multi-enzyme complexes. This intricate enzymatic network directly governs and shapes the interdependent relationships among various RNA modifications. This review systematically elucidates the molecular mechanisms underlying both direct and indirect interactions between RNA modifications. Building upon this foundation, we introduce novel quantitative assessment frameworks and predictive disease models designed to leverage these interaction patterns. Importantly, studies across multiple disease contexts have identified core downstream signaling axes driven by specific constellations of interacting RNA modifications. These findings not only deepen our understanding of how RNA modification crosstalk contributes to disease initiation and progression, but also highlight its translational potential. This potential is exemplified by the discovery of diagnostic biomarkers based on interaction signatures and the development of therapeutic strategies targeting pathogenic modification networks. Together, these insights provide a conceptual framework for understanding the dynamic and multidimensional regulatory roles of RNA modifications in cellular systems. In conclusion, the emerging concept of RNA modification crosstalk reveals the extraordinary complexity of post-transcriptional regulation and opens new research avenues. It offers critical insights into the central question of how RNA-modifying enzymes achieve substrate specificity—determining which nucleotides within specific RNA transcripts are selectively modified during defined developmental or pathological stages. Decoding these specificity determinants, shaped in large part by the modification interactome, is essential for fully understanding the biological and pathological significance of the epitranscriptome.
2.Adolescent Smoking Addiction Diagnosis Based on TI-GNN
Xu-Wen WANG ; Da-Hua YU ; Ting XUE ; Xiao-Jiao LI ; Zhen-Zhen MAI ; Fang DONG ; Yu-Xin MA ; Juan WANG ; Kai YUAN
Progress in Biochemistry and Biophysics 2025;52(9):2393-2405
ObjectiveTobacco-related diseases remain one of the leading preventable public health challenges worldwide and are among the primary causes of premature death. In recent years, accumulating evidence has supported the classification of nicotine addiction as a chronic brain disease, profoundly affecting both brain structure and function. Despite the urgency, effective diagnostic methods for smoking addiction remain lacking, posing significant challenges for early intervention and treatment. To address this issue and gain deeper insights into the neural mechanisms underlying nicotine dependence, this study proposes a novel graph neural network framework, termed TI-GNN. This model leverages functional magnetic resonance imaging (fMRI) data to identify complex and subtle abnormalities in brain connectivity patterns associated with smoking addiction. MethodsThe study utilizes fMRI data to construct functional connectivity matrices that represent interaction patterns among brain regions. These matrices are interpreted as graphs, where brain regions are nodes and the strength of functional connectivity between them serves as edges. The proposed TI-GNN model integrates a Transformer module to effectively capture global interactions across the entire brain network, enabling a comprehensive understanding of high-level connectivity patterns. Additionally, a spatial attention mechanism is employed to selectively focus on informative inter-regional connections while filtering out irrelevant or noisy features. This design enhances the model’s ability to learn meaningful neural representations crucial for classification tasks. A key innovation of TI-GNN lies in its built-in causal interpretation module, which aims to infer directional and potentially causal relationships among brain regions. This not only improves predictive performance but also enhances model interpretability—an essential attribute for clinical applications. The identification of causal links provides valuable insights into the neuropathological basis of addiction and contributes to the development of biologically plausible and trustworthy diagnostic tools. ResultsExperimental results demonstrate that the TI-GNN model achieves superior classification performance on the smoking addiction dataset, outperforming several state-of-the-art baseline models. Specifically, TI-GNN attains an accuracy of 0.91, an F1-score of 0.91, and a Matthews correlation coefficient (MCC) of 0.83, indicating strong robustness and reliability. Beyond performance metrics, TI-GNN identifies critical abnormal connectivity patterns in several brain regions implicated in addiction. Notably, it highlights dysregulations in the amygdala and the anterior cingulate cortex, consistent with prior clinical and neuroimaging findings. These regions are well known for their roles in emotional regulation, reward processing, and impulse control—functions that are frequently disrupted in nicotine dependence. ConclusionThe TI-GNN framework offers a powerful and interpretable tool for the objective diagnosis of smoking addiction. By integrating advanced graph learning techniques with causal inference capabilities, the model not only achieves high diagnostic accuracy but also elucidates the neurobiological underpinnings of addiction. The identification of specific abnormal brain networks and their causal interactions deepens our understanding of addiction pathophysiology and lays the groundwork for developing targeted intervention strategies and personalized treatment approaches in the future.
3. Analysis of cerebral gray matter structure in multiple sclerosis and neuromyelitis optica
Xiao-Li LIU ; Ai-Xue WU ; Ru-Hua LI ; An-Ting WU ; Cheng-Chun CHEN ; Lin XU ; Cai-Yun WEN ; Dai-Qian CHEN
Acta Anatomica Sinica 2024;55(1):17-24
Objective The volume and cortical thickness of gray matter in patients with multiple sclerosis (MS) and neuromyelitis optica (NMO) were compared and analyzed by voxel⁃based morphometry (VBM) and surface⁃based morphometry (SBM), and the differences in the structural changes of gray matter in the two diseases were discussed. Methods A total of 21 MS patients, 16 NMO patients and 19 healthy controls were scanned by routine MRI sequence. The data were processed and analyzed by VBM and SBM method based on the statistical parameter tool SPM12 of Matlab2014a platform and the small tool CAT12 under SPM12. Results Compared with the normal control group (NC), after Gaussian random field (GRF) correction, the gray matter volume in MS group was significantly reduced in left superior occipital, left cuneus, left calcarine, left precuneus, left postcentral, left central paracentral lobule, right cuneus, left middle frontal, left superior frontal and left superior medial frontal (P<0. 05). After family wise error (FWE) correction, the thickness of left paracentral, left superiorfrontal and left precuneus cortex in MS group was significantly reduced (P<0. 05). Compared with the NC group, after GRF correction, the gray matter volume in the left postcentral, left precentral, left inferior parietal, right precentral and right middle frontal in NMO group was significantly increased (P<0. 05). In NMO group, the volume of gray matter in left middle occipital, left superior occipital, left inferior temporal, right middle occipital, left superior frontal orbital, right middle cingulum, left anterior cingulum, right angular and left precuneus were significantly decreased (P<0. 05). Brain regions showed no significant differences in cortical thickness between NMO groups after FWE correction. Compared with the NMO group, after GRF correction, the gray matter volume in the right fusiform and right middle frontal in MS group was increased significantly(P<0. 05). In MS group, the gray matter volume of left thalamus, left pallidum, left precentral, left middle frontal, left middle temporal, right pallidum, left inferior parietal and right superior parietal were significantly decreased (P<0. 05). After FWE correction, the thickness of left inferiorparietal, left superiorparietal, left supramarginal, left paracentral, left superiorfrontal and left precuneus cortex in MS group decreased significantly (P<0. 05). Conclusion The atrophy of brain gray matter structure in MS patients mainly involves the left parietal region, while NMO patients are not sensitive to the change of brain gray matter structure. The significant difference in brain gray matter volume between MS patients and NMO patients is mainly located in the deep cerebral nucleus mass.
4.Simultaneous content determination of nine constituents and chemical pattern recognition for Fuyang Granules
Chun-Xia XIAO ; Xiao-Jing HUANG ; Li XU ; Ting-Ting LI ; Ji LI ; Xiao-Qin ZHAO
Chinese Traditional Patent Medicine 2024;46(2):365-370
AIM To simultaneously determine the contents of neochlorogenic acid,caffeic acid,chlorogenic acid,cryptochlorogenic acid,hydroxysafflor yellow A,ferulic acid,senkyunolide I,senkyunolide H and senkyunolide A in Fuyang Granules,and to make chemical pattern recognition.METHODS The UHPLC was performed on a 35℃thermostatic Waters Acquity UPLC?BEH C18 column(150 mm×2.1 mm,1.7 μm),with the mobile phase comprising of acetonitrile-0.01%phosphoric acid flowing at 0.4 mL/min in a gradient elution manner,and the detection wavelengths were set at 278,322,325,390 nm.Then heatmap clustering analysis and principal component analysis were adopted.RESULTS Nine constituents showed good linear relationships within their own ranges(r>0.999 0),whose average recoveries were 93.89%-102.25%with the RSDs of 0.85%-2.88%.Different batches of samples from the same enterprises demonstrated consistent overall qualities,while the overall qualities of samples from different enterprises exhibited obvious differences.CONCLUSION This simple and accurate method can be used for the quality control of Fuyang Granules.
5.Variation rules of main secondary metabolites in Hedysari Radix before and after rubbing strip
Xu-Dong LUO ; Xin-Rong LI ; Cheng-Yi LI ; Peng QI ; Ting-Ting LIANG ; Shu-Bin LIU ; Zheng-Ze QIANG ; Jun-Gang HE ; Xu LI ; Xiao-Cheng WEI ; Xiao-Li FENG ; Ming-Wei WANG
Chinese Traditional Patent Medicine 2024;46(3):747-754
AIM To investigate the variation rules of main secondary metabolites in Hedysari Radix before and after rubbing strip.METHODS UPLC-MS/MS was adopted in the content determination of formononetin,ononin,calycosin,calycosin-7-glucoside,medicarpin,genistein,luteolin,liquiritigenin,isoliquiritigenin,vanillic acid,ferulic acid,γ-aminobutyric acid,adenosine and betaine,after which cluster analysis,principal component analysis and orthogonal partial least squares discriminant analysis were used for chemical pattern recognition to explore differential components.RESULTS After rubbing strip,formononetin,calycosin,liquiritigenin and γ-aminobutynic acid demonstrated increased contents,along with decreased contents of ononin,calycosin-7-glucoside and vanillic acid.The samples with and without rubbing strip were clustered into two types,calycosin-7-glucoside,formononetin,γ-aminobutynic acid,vanillic acid,calycosin-7-glucoside and formononetin were differential components.CONCLUSION This experiment clarifies the differences of chemical constituents in Hedysari Radix before and after rubbing strip,which can provide a reference for the research on rubbing strip mechanism of other medicinal materials.
6.Application status and research progress of tranexamic acid in the perioperative period of joint replacement and arthroscopic surgery
Bao-Hua YUAN ; Hai-Ping LIU ; Xing-Yong LI ; Xiao-Ting LIU ; Ji-Hai MA ; Xu-Sheng ZHANG ; Hao-Fei YANG ; Jin-Sheng LI ; Sheng-Long HAN
The Chinese Journal of Clinical Pharmacology 2024;40(7):1080-1084
Tranexamic acid is widely used in joint orthopedic surgery.At the same time,it has high safety and few adverse drug reactions.It can effectively improve intraoperative bleeding and promote early functional recovery of patients.This article reviews the mode of administration,safe dose,administration time and adverse drug reactions of tranexamic acid in the perioperative period of joint replacement and arthroscopic surgery,in order to provide reference for the clinical application of tranexamic acid.
7.Clinical trial on the use of ω-3 fish oil fat milk in the treatment of total parenteral nutrition after radical resection of gastric cancer
Yan XU ; Xiao-Ting YU ; Shuai YIN
The Chinese Journal of Clinical Pharmacology 2024;40(18):2690-2694
Objective To explore the application effect of ω-3 fish oil fat emulsion in total parenteral nutrition(TPN)after radical resection of gastric cancer.Methods Patients with gastric cancer undergoing radical resection in the hospital were divided into control group and treatment group.The patients in the control group were treated with TPN after operation,and the energy was mainly glucose and conventional fat emulsion.The daily calorie supply was 100-125 kJ·kg-1,and the deep venous catheter was dripped for 10-12 h.On the basis of the control group,the patients in the treatment group were added with ω-3 fish oil fat emulsion 100 mL,and the daily calorie supply and infusion conditions were the same as those in the control group.Both groups were treated for 7 days.All patients were treated for 7 d.The nutritional status(total protein,transferrin,albumin,nitrogen balance),gastrointestinal function recovery,immune function[CD4+/CD8+,natural killer(NK)cells],inflammatory factors[interleukin-6(IL-6),IL-12p70,tumor necrosis factor-α(TNF-α)]in abdominal drainage fluid and the safety was evaluated.Results There were 40 cases in treatment group and 42 cases in control group,respectively.After treatment,total response rates in treatment group and control group were 90.00%(36 cases/40 cases)and 71.43%(30 cases/42 cases),and the difference was statistically significant(P<0.05).In the two groups,total protein,transferrin and albumin decreased at 3 d after surgery,but they all increased at 7 d after surgery,and nitrogen balance increased after surgery.There was no significant difference in total protein,transferrin,albumin or nitrogen balance between the two groups at different time periods(all P>0.05).The first exhaust time in treatment group and control group were(55.72±9.75)and(61.52±10.43)h.At 7 d after surgery,proportions of peripheral blood CD4+/CD8+levels in treatment group and control group were 1.50±0.38 and 1.29±0.30;proportions of NK cells were(19.64±3.04)%and(17.24±2.96)%;IL-6 levels in drainage fluid were(18.77±4.69)and(32.36±5.18)pg·mL-1;IL-12p70 levels were(6.14±1.86)and(8.93±2.17)pg·mL-1;TNF-α levels were(25.62±4.95)and(30.75±4.88)pg·mL-1,the differences were statistically significant(all P<0.05).During treatment,main adverse drug reactions included vomiting,nausea and persistent abdominal distension in treatment group,while main adverse drug reactions included vomiting,nausea and persistent abdominal distension in control group.There was no significant difference in total incidence of adverse drug reactions between treatment group and control group(20.00%vs 26.19%,P>0.05).Conclusion ω-3 fish oil fat emulsion can enhance immune function,reduce inflammatory response,abdominal drainage volume and promote postoperative rehabilitation in patients with gastric cancer.
8.Effects of ultra-filtration extract from Angelica Sinensis Radix and Hedysari Radix improves the kidney injury in diabetic kidney disease rats
Qing-Quan XU ; Xiao-Lin ZHANG ; Ting GAO ; Rong-Ke LI ; Lei ZHANG ; Sheng-Fang WAN
The Chinese Journal of Clinical Pharmacology 2024;40(20):3023-3027
Objective To explore the improve mechanism of ultra-filtration extract from Angelica Sinensis Radix and Hedysari Radix on kidney injury in diabetic kidney disease(DKD)rats.Methods The diabetes model was prepared by intraperitoneal injection of streptozotocin,and then fed with high sugar and high fat diet.The rats with successful DKD were randomly divided into model group,positive control group and experimental-L,-M,-H groups with 8 cases per group.Additionally,selected 8 Wistar rats as the blank group.The experimental-L,-M,-H groups were given 1.5,3.0 and 6.0 g·kg-1 ultra-filtration extract from Angelica Sinensis Radix and Hedysari Radix by gavage,respectively.The positive control group was given 1.75 × 10-3 g·kg-1irbesartan suspension by gavage.The blank and model groups were given equal volume of pure water by gavage.Six groups were administrated once a day for 12 consecutive weeks.The 24 h-urinary total protein were detected by coomassie brilliant blue method.The protein expression levels of nuclear factor erythroid 2-related factor 2(Nrf2),heme oxygenase-1(HO-1)and andacyl-CoA synthetase long chain family member 4(ACSL4)in kidney tissue were detected by Western blot.Results The 24 h-UTP in the experimental-M,-H groups,positive control group,model group and blank group were(47.70±3.85),(43.57±6.38),(36.80±6.52),(64.34±13.38)and(7.58±3.71)mg;the relative expression levels of Nrf2 protein were 0.86±0.08,0.75±0.06,0.64±0.08,1.09±0.06 and 0.60±0.07;the relative expression levels of HO-1 protein were 0.77±0.04,0.63±0.07,0.47±0.05,1.04±0.06 and 0.34±0.07;the relative expression levels of ACSL4 protein were 0.62±0.07,0.55±0.07,0.46±0.06,1.08±0.07 and 0.30±0.01,respectively.Compared with the model group,the above indexes in the experimental-M,-H groups and positive control group were significantly different(P<0.05,P<0.01).Conclusion Ultra-filtration extract from Angelica Sinensis Radix and Hedysari Radix can improve the damage of kidney tissue in DKD rats,and the mechanism may be related to ferroptosis caused by excessive activation of Nrf2/HO-1 signaling pathway.
9.Linarin inhibits microglia activation-mediated neuroinflammation and neuronal apoptosis in mouse spinal cord injury by inhibiting the TLR4/NF-κB pathway
Linyu XIAO ; Ting DUAN ; Yongsheng XIA ; Yue CHEN ; Yang SUN ; Yibo XU ; Lei XU ; Xingzhou YAN ; Jianguo HU
Journal of Southern Medical University 2024;44(8):1589-1598
Objective To investigate the mechanism underlying the neuroprotective effect of linarin(LIN)against microglia activation-mediated inflammation and neuronal apoptosis following spinal cord injury(SCI).Methods Fifty C57BL/6J mice(8-10 weeks old)were randomized to receive sham operation,SCI and linarin treatment at 12.5,25,and 50 mg/kg following SCI(n=10).Locomotor function recovery of the SCI mice was assessed using the Basso Mouse Scale,inclined plane test,and footprint analysis,and spinal cord tissue damage and myelination were evaluated using HE and LFB staining.Nissl staining,immunofluorescence assay and Western blotting were used to observe surviving anterior horn motor neurons in injured spinal cord tissue.In cultured BV2 cells,the effects of linarin against lipopolysaccharide(LPS)-induced microglia activation,inflammatory factor release and signaling pathway changes were assessed with immunofluorescence staining,Western blotting,RT-qPCR,and ELISA.In a BV2 and HT22 cell co-culture system,Western blotting was performed to examine the effect of linarin against HT22 cell apoptosis mediated by LPS-induced microglia activation.Results Linarin treatment significantly improved locomotor function(P<0.05),reduced spinal cord damage area,increased spinal cord myelination,and increased the number of motor neurons in the anterior horn of the SCI mice(P<0.05).In both SCI mice and cultured BV2 cells,linarin effectively inhibited glial cell activation and suppressed the release of iNOS,COX-2,TNF-α,IL-6,and IL-1β,resulting also in reduced neuronal apoptosis in SCI mice(P<0.05).Western blotting suggested that linarin-induced microglial activation inhibition was mediated by inhibition of the TLR4/NF-κB signaling pathway.In the cell co-culture experiments,linarin treatment significantly decreased inflammation-mediated apoptosis of HT22 cells(P<0.05).Conclusion The neuroprotective effect of linarin is medicated by inhibition of microglia activation via suppressing the TLR4/NF-κB signaling pathway,which mitigates neural inflammation and reduce neuronal apoptosis to enhance motor function of the SCI mice.
10.Correlation between Combined Urinary Metal Exposure and Grip Strength under Three Statistical Models: A Cross-sectional Study in Rural Guangxi
Jian Yu LIANG ; Hui Jia RONG ; Xiu Xue WANG ; Sheng Jian CAI ; Dong Li QIN ; Mei Qiu LIU ; Xu TANG ; Ting Xiao MO ; Fei Yan WEI ; Xia Yin LIN ; Xiang Shen HUANG ; Yu Ting LUO ; Yu Ruo GOU ; Jing Jie CAO ; Wu Chu HUANG ; Fu Yu LU ; Jian QIN ; Yong Zhi ZHANG
Biomedical and Environmental Sciences 2024;37(1):3-18
Objective This study aimed to investigate the potential relationship between urinary metals copper (Cu), arsenic (As), strontium (Sr), barium (Ba), iron (Fe), lead (Pb) and manganese (Mn) and grip strength. Methods We used linear regression models, quantile g-computation and Bayesian kernel machine regression (BKMR) to assess the relationship between metals and grip strength.Results In the multimetal linear regression, Cu (β=-2.119), As (β=-1.318), Sr (β=-2.480), Ba (β=0.781), Fe (β= 1.130) and Mn (β=-0.404) were significantly correlated with grip strength (P < 0.05). The results of the quantile g-computation showed that the risk of occurrence of grip strength reduction was -1.007 (95% confidence interval:-1.362, -0.652; P < 0.001) when each quartile of the mixture of the seven metals was increased. Bayesian kernel function regression model analysis showed that mixtures of the seven metals had a negative overall effect on grip strength, with Cu, As and Sr being negatively associated with grip strength levels. In the total population, potential interactions were observed between As and Mn and between Cu and Mn (Pinteractions of 0.003 and 0.018, respectively).Conclusion In summary, this study suggests that combined exposure to metal mixtures is negatively associated with grip strength. Cu, Sr and As were negatively correlated with grip strength levels, and there were potential interactions between As and Mn and between Cu and Mn.

Result Analysis
Print
Save
E-mail