1.Comparative Analysis of Exercise-induced Transcriptomic Responses in Human and Mouse Homologous Genes: Divergence and Convergence Based on The GEPREP Database
Qian SUN ; Wei-Chu TAO ; Ru WANG ; Bing-Xiang XU
Progress in Biochemistry and Biophysics 2025;52(6):1617-1630
		                        		
		                        			
		                        			Exercise, as a non-pharmacological intervention, holds a pivotal role in metabolic regulation, neuroplasticity, and immune homeostasis maintenance. However, human exercise studies are constrained by ethical limitations in tissue sampling, especially for key organs such as muscles and the brain. Meanwhile, rodent models like mice exhibit physiological differences in exercise patterns and metabolic rates from human. Despite these challenges, approximately 70% of human and mouse genes are conserved, providing a molecular basis for cross-species comparisons. This paper leverages the GEPREP database, which integrates human and mouse exercise transcriptomic data from multiple platforms, to conduct a comprehensive cross-species analysis of exercise-induced gene expression patterns. We employ a stringent data standardization process, including the conversion of orthologous genes and the filtering of low-expressing genes, to ensure the accuracy and reliability of the analysis. A mixed-effects model is utilized to assess differential gene expression across multiple cohorts, identifying genes that are significantly upregulated or downregulated in response to exercise. The analysis reveals a complex pattern of gene expression, with a significant number of genes showing conserved responses between humans and mice, particularly in acute aerobic exercise, where genes such as ATF3, PPARGC1A, and ANKRD1 are commonly upregulated. These genes are implicated in muscle stress response, metabolic regulation, and muscle adaptation, highlighting the shared molecular pathways activated by exercise across species. However, the study also uncovers substantial species-specific differences in gene expression, especially in chronic aerobic exercise, where the number of divergently regulated genes increases. These differences suggest that while some fundamental biological processes are conserved, the specific regulatory mechanisms and gene expression patterns can vary significantly between humans and mice. Functional enrichment analysis further reveals that conserved genes are involved in muscle development, inflammation regulation, and energy metabolism, while species-specific genes are associated with ion transport, extracellular matrix (ECM) organization, and muscle contraction, indicating the multifaceted impact of exercise on skeletal muscle function. The findings emphasize the importance of considering species-specific differences when interpreting results from animal models and translating them to human health applications. The study highlights the need for a more nuanced understanding of the molecular underpinnings of exercise-induced adaptations and underscores the value of cross-species comparative analyses in uncovering the evolutionary and functional basis of these responses. Future research should focus on integrating multi-omics data and expanding the analysis to include other tissues to provide a more comprehensive view of the systemic effects of exercise. Additionally, the development of species-specific gene editing models and the validation of key genes in exercise physiology will further enhance our understanding of the evolutionary logic behind exercise interventions. This study not only provides valuable insights into the molecular mechanisms of exercise-induced adaptations but also underscores the necessity of validating findings from animal models in human cohorts to ensure the reliability and applicability of translational research in exercise science. By addressing these aspects, the study aims to bridge the gap between basic research and clinical applications, ultimately contributing to the development of personalized exercise prescriptions and interventions that can effectively promote health and prevent diseases. 
		                        		
		                        		
		                        		
		                        	
2. 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. 
		                        		
		                        		
		                        		
		                        	
3.Urinary Metabolomics Aanlysis of Differences in Effect of Aconiti Coreani Radix and Typhonii Rhizoma on Gerbils with Stroke
Liting ZHOU ; Wanting ZENG ; Ru JIA ; Huiying XU ; Yihui DING ; Hao DONG ; Haowen MA ; Yang QU ; Qian CAI
Chinese Journal of Experimental Traditional Medical Formulae 2024;30(8):157-166
		                        		
		                        			
		                        			ObjectiveTo investigate the effects of Aconiti Coreani Radix and Typhonii Rhizoma on the urinary metabolites of gerbils with stroke by non-targeted metabolomics technique, and then to clarify the mechanism of the two, as well as their similarities and differences. MethodTwenty-four gerbils were randomly divided into control group(CG), model group(MG), Aconiti Coreani Radix group(RA) and Typhonii Rhizoma group(RT). Except for the CG, ischemic stroke model was constructed using right unilateral ligation of gerbil carotid artery in the remaining groups. Except for the CG and MG, rats in the other groups received whole powder suspension(0.586 mg·g-1) was administered for 14 days. The neurological deficit in each group was scored by Longa scoring on days 0, 3, 7 and 14. After the end of administration, the serum, brain tissue and urine of gerbils in each group were collected, and the rate of cerebral infarction was detected by 2,3,5-triphenyltetrazolium chloride(TTC), and the levels of interleukin(IL)-6, tumor necrosis factor(TNF)-α, malondialdehyde(MDA), superoxide dismutase(SOD), glutathione(GSH), and nitric oxide(NO) in serum and brain tissue were determined by enzyme-linked immunosorbent assay(ELISA). The urine metabolomics of gerbils in each group was studied by ultra performance liquid chromatography-quadrupole-electrostatic field orbitrap high resolution mass spectrometry(UPLC-Q-Orbitrap-MS), and the data were processed by multivariate statistical analysis, and differential metabolites were screened based on value of variable importance in the projection(VIP) of the first principal component>1 and t-test P<0.05. Metabolic pathway analysis of the screened differential metabolites was performed using Kyoto Encyclopedia of Genes and Genomes(KEGG) database and Metaboanalyst 5.0. ResultCompared with the CG, the neurological deficit score was significantly increased in the MG(P<0.05), compared with the MG, the neurological deficit scores in the RA and RT were significantly reduced after 7 d and 14 d(P<0.05). Compared with the CG, the rate of cerebral infarction was significantly increased in the MG(P<0.05), compared with the MG, the rates of cerebral infarction in the RA and RT were significantly reduced(P<0.05). Compared with the CG, the levels of IL-6, TNF-α, and MDA in the serum and brain tissue of gerbils from the MG were significantly increased(P<0.05), and the levels of SOD, GSH and NO were significantly reduced(P<0.05). Compared with the MG, Aconiti Coreani Radix and Typhonii Rhizoma could down-regulate the levels of IL-6, TNF-α and MDA, and up-regulated the levels of SOD, GSH and NO. A total of 112 endogenous differential metabolites were screened by urine metabolomics, of which 16 and 26 metabolites were called back by Aconiti Coreani Radix and Typhonii Rhizoma, and could be used as potential biomarkers for both treatments in stroke gerbils, respectively. The results of the pathway analysis showed that both Aconiti Coreani Radix and Typhonii Rhizoma had regulatory effects on arginine and proline metabolism, pyrimidine metabolism, and aminoacyl-tRNA biosynthesis. In addition, Aconiti Coreani Radix could also regulate riboflavin metabolism, Typhonii Rhizoma could also regulate purine metabolism, glycine, serine and threonine metabolism, arachidonic acid metabolism, biosynthesis of pantothenate and coenzyme A, and β-alanine metabolism. ConclusionBoth Aconiti Coreani Radix and Typhonii Rhizoma have better therapeutic effects on stroke, with Aconiti Coreani Radix having stronger effects. From the metabolomics results, the main metabolic pathways regulated by Aconiti Coreani Radix involve amino acid metabolism, oxidative stress and so on, while Typhonii Rhizoma mainly involve amino acid metabolism, lipid metabolism, energy metabolism, etc. 
		                        		
		                        		
		                        		
		                        	
4.A multicenter study of neonatal stroke in Shenzhen,China
Li-Xiu SHI ; Jin-Xing FENG ; Yan-Fang WEI ; Xin-Ru LU ; Yu-Xi ZHANG ; Lin-Ying YANG ; Sheng-Nan HE ; Pei-Juan CHEN ; Jing HAN ; Cheng CHEN ; Hui-Ying TU ; Zhang-Bin YU ; Jin-Jie HUANG ; Shu-Juan ZENG ; Wan-Ling CHEN ; Ying LIU ; Yan-Ping GUO ; Jiao-Yu MAO ; Xiao-Dong LI ; Qian-Shen ZHANG ; Zhi-Li XIE ; Mei-Ying HUANG ; Kun-Shan YAN ; Er-Ya YING ; Jun CHEN ; Yan-Rong WANG ; Ya-Ping LIU ; Bo SONG ; Hua-Yan LIU ; Xiao-Dong XIAO ; Hong TANG ; Yu-Na WANG ; Yin-Sha CAI ; Qi LONG ; Han-Qiang XU ; Hui-Zhan WANG ; Qian SUN ; Fang HAN ; Rui-Biao ZHANG ; Chuan-Zhong YANG ; Lei DOU ; Hui-Ju SHI ; Rui WANG ; Ping JIANG ; Shenzhen Neonatal Data Network
Chinese Journal of Contemporary Pediatrics 2024;26(5):450-455
		                        		
		                        			
		                        			Objective To investigate the incidence rate,clinical characteristics,and prognosis of neonatal stroke in Shenzhen,China.Methods Led by Shenzhen Children's Hospital,the Shenzhen Neonatal Data Collaboration Network organized 21 institutions to collect 36 cases of neonatal stroke from January 2020 to December 2022.The incidence,clinical characteristics,treatment,and prognosis of neonatal stroke in Shenzhen were analyzed.Results The incidence rate of neonatal stroke in 21 hospitals from 2020 to 2022 was 1/15 137,1/6 060,and 1/7 704,respectively.Ischemic stroke accounted for 75%(27/36);boys accounted for 64%(23/36).Among the 36 neonates,31(86%)had disease onset within 3 days after birth,and 19(53%)had convulsion as the initial presentation.Cerebral MRI showed that 22 neonates(61%)had left cerebral infarction and 13(36%)had basal ganglia infarction.Magnetic resonance angiography was performed for 12 neonates,among whom 9(75%)had involvement of the middle cerebral artery.Electroencephalography was performed for 29 neonates,with sharp waves in 21 neonates(72%)and seizures in 10 neonates(34%).Symptomatic/supportive treatment varied across different hospitals.Neonatal Behavioral Neurological Assessment was performed for 12 neonates(33%,12/36),with a mean score of(32±4)points.The prognosis of 27 neonates was followed up to around 12 months of age,with 44%(12/27)of the neonates having a good prognosis.Conclusions Ischemic stroke is the main type of neonatal stroke,often with convulsions as the initial presentation,involvement of the middle cerebral artery,sharp waves on electroencephalography,and a relatively low neurodevelopment score.Symptomatic/supportive treatment is the main treatment method,and some neonates tend to have a poor prognosis.
		                        		
		                        		
		                        		
		                        	
5.Treatment of refractory diffuse large B-cell lymphoma involving the central nervous system with polatuzumab vedotin-based regimen: a case report and literature review
Jiefei BAI ; Ru FENG ; Ting WANG ; Xu LI ; Long QIAN ; Jiangtao LI ; Chunli ZHANG ; Hui LIU
Chinese Journal of Hematology 2024;45(9):864-866
		                        		
		                        			
		                        			Polatuzumab vedotin (Pola) is a novel antibody-drug conjugate targeting CD79b, which has been shown to be effective in treating newly diagnosed and relapsed/refractory diffuse large B cell lymphoma (DLBCL) during clinical trials. This study aims to conduct a retrospective analysis of the clinical characteristics, diagnosis, and treatment of a patient with refractory secondary central nervous system lymphoma at Beijing Hospital, alongside a review of relevant literature. This study included a 79-year-old female patient who was diagnosed with DLBCL affecting the ilium, sacrum, spinal cord, and nerve roots and had an IPI score of 5 and a high-risk score according to MSKCC. She showed a geriatric comprehensive assessment (IACA) score of 2, which was categorized under the unfit group. Her initial treatment comprised chemo-free therapy and radiotherapy, followed by progression. In the second-line treatment, a Pola-based regimen was applied, and the patient achieved a complete response, suggesting that this regimen may be a therapeutic option for patients with DLBCL involving the central nervous system.
		                        		
		                        		
		                        		
		                        	
		                				6.Activity evaluation and mechanism study of antibacterial-anti-inflammatory bifunctional Dioscoreae Nipponicae  Rhizoma natural components targeting regulatory protein posttranslational modification
		                			
		                			Ru-xu SHEN ; Zi-chen YE ; Jia-qi ZHAO ; Qian ZHANG ; Hai-feng TANG ; Di QU
Acta Pharmaceutica Sinica 2024;59(11):2981-2989
		                        		
		                        			
		                        			 The phenomenon of bacterial drug resistance is becoming more and more serious. Natural products, as an important resource for drug discovery, can play a role by regulating protein post-translational modifications related to bacterial infection and inflammatory responses. This provides a valuable compound library for the research and development of new antibacterial drugs. In this present research, dioscin and diosgenin were isolated and identified from 
		                        		
		                        	
7.Effects of transcription factor SOX11 on the biological behavior of neuroblastoma cell and potential regulatory mechanism
Jing-Ru HUANG ; Yong LI ; Peng CHEN ; Ji-Xiu WEI ; Xia YANG ; Qiong-Qian XU ; Jia-Bo CHEN
Annals of Surgical Treatment and Research 2024;106(5):284-295
		                        		
		                        			 Purpose:
		                        			This study aimed to analyze the expression and prognosis of SRY-box transcription factor 11 (SOX11) in neuroblastoma (NB), as well as the biological function and potential regulatory mechanism of SOX11 in NB. 
		                        		
		                        			Methods:
		                        			Public RNA sequencing was used to detect the expression level of SOX11. The Kaplan-Meier curve and hazard ratios (HR) were used to determine the prognostic value of SOX11 in NB. Functional analyses were performed using CCK8, wound healing assay, and transwell invasion assay. Finally, the potential target genes of SOX11 were predicted by Harmonizonme (Ma'ayan Laboratory) and Cistrome Data Browser (Cistrome Project) database to explore the potential molecular mechanism of SOX11 in NB. 
		                        		
		                        			Results:
		                        			Compared with normal adrenal tissue, the expression of SOX11 in NB tissue was significantly upregulated. The Kaplan-Meier curve showed that high expression of SOX11 was associated with poor prognosis in children with NB (HR, 1.719; P = 0.049). SOX11 knockdown suppressed the migration capacity of SK-N-SH cells but did not affect proliferation and invasion capacity. Enhancer of zeste homolog 2 (EZH2) may be a potential downstream target gene for the transcription factor SOX11 to play a role in NB. 
		                        		
		                        			Conclusion
		                        			The transcription factor SOX11 was significantly upregulated in NB. SOX11 knockdown suppressed the migration capacity of NB cell SK-N-SH. SOX11 may promote the progression of NB by targeting EZH2. 
		                        		
		                        		
		                        		
		                        	
8.Diabetes Promotes Myocardial Fibrosis via AMPK/EZH2/PPAR-γ Signaling Pathway
Shan-Shan LI ; Lu PAN ; Zhen-Ye ZHANG ; Meng-Dan ZHOU ; Xu-Fei CHEN ; Ling-Ling QIAN ; Min DAI ; Juan LU ; Zhi-Ming YU ; Shipeng DANG ; Ru-Xing WANG
Diabetes & Metabolism Journal 2024;48(4):716-729
		                        		
		                        			 Background:
		                        			Diabetes-induced cardiac fibrosis is one of the main mechanisms of diabetic cardiomyopathy. As a common histone methyltransferase, enhancer of zeste homolog 2 (EZH2) has been implicated in fibrosis progression in multiple organs. However, the mechanism of EZH2 in diabetic myocardial fibrosis has not been clarified. 
		                        		
		                        			Methods:
		                        			In the current study, rat and mouse diabetic model were established, the left ventricular function of rat and mouse were evaluated by echocardiography and the fibrosis of rat ventricle was evaluated by Masson staining. Primary rat ventricular fibroblasts were cultured and stimulated with high glucose (HG) in vitro. The expression of histone H3 lysine 27 (H3K27) trimethylation, EZH2, and myocardial fibrosis proteins were assayed. 
		                        		
		                        			Results:
		                        			In STZ-induced diabetic ventricular tissues and HG-induced primary ventricular fibroblasts in vitro, H3K27 trimethylation was increased and the phosphorylation of EZH2 was reduced. Inhibition of EZH2 with GSK126 suppressed the activation, differentiation, and migration of cardiac fibroblasts as well as the overexpression of the fibrotic proteins induced by HG. Mechanical study demonstrated that HG reduced phosphorylation of EZH2 on Thr311 by inactivating AMP-activated protein kinase (AMPK), which transcriptionally inhibited peroxisome proliferator-activated receptor γ (PPAR-γ) expression to promote the fibroblasts activation and differentiation. 
		                        		
		                        			Conclusion
		                        			Our data revealed an AMPK/EZH2/PPAR-γ signal pathway is involved in HG-induced cardiac fibrosis. 
		                        		
		                        		
		                        		
		                        	
		                				9.A new macrocyclic flavonoid from Onychium japonicum 
		                			
		                			Guang-feng LIAO ; Liu-yan MO ; Ming-xue TENG ; Xiu-hong XU ; Qian-xi HUANG ; Ru-mei LU
Acta Pharmaceutica Sinica 2023;58(2):423-428
		                        		
		                        			
		                        			 Seven compounds were isolated from 
		                        		
		                        	
10.Postmortem Interval Estimation Using Protein Chip Technology Combined with Multivariate Analysis Methods.
Xu-Dong ZHANG ; Yao-Ru JIANG ; Xin-Rui LIANG ; Tian TIAN ; Qian-Qian JIN ; Xiao-Hong ZHANG ; Jie CAO ; Qiu-Xiang DU ; Jun-Hong SUN
Journal of Forensic Medicine 2023;39(2):115-120
		                        		
		                        			OBJECTIVES:
		                        			To estimate postmortem interval (PMI) by analyzing the protein changes in skeletal muscle tissues with the protein chip technology combined with multivariate analysis methods.
		                        		
		                        			METHODS:
		                        			Rats were sacrificed for cervical dislocation and placed at 16 ℃. Water-soluble proteins in skeletal muscles were extracted at 10 time points (0 d, 1 d, 2 d, 3 d, 4 d, 5 d, 6 d, 7 d, 8 d and 9 d) after death. Protein expression profile data with relative molecular mass of 14 000-230 000 were obtained. Principal component analysis (PCA) and orthogonal partial least squares (OPLS) were used for data analysis. Fisher discriminant model and back propagation (BP) neural network model were constructed to classify and preliminarily estimate the PMI. In addition, the protein expression profiles data of human skeletal muscles at different time points after death were collected, and the relationship between them and PMI was analyzed by heat map and cluster analysis.
		                        		
		                        			RESULTS:
		                        			The protein peak of rat skeletal muscle changed with PMI. The result of PCA combined with OPLS discriminant analysis showed statistical significance in groups with different time points (P<0.05) except 6 d, 7 d and 8 d after death. By Fisher discriminant analysis, the accuracy of internal cross-validation was 71.4% and the accuracy of external validation was 66.7%. The BP neural network model classification and preliminary estimation results showed the accuracy of internal cross-validation was 98.2%, and the accuracy of external validation was 95.8%. There was a significant difference in protein expression between 4 d and 25 h after death by the cluster analysis of the human skeletal muscle samples.
		                        		
		                        			CONCLUSIONS
		                        			The protein chip technology can quickly, accurately and repeatedly obtain water-soluble protein expression profiles in rats' and human skeletal muscles with the relative molecular mass of 14 000-230 000 at different time points postmortem. The establishment of multiple PMI estimation models based on multivariate analysis can provide a new idea and method for PMI estimation.
		                        		
		                        		
		                        		
		                        			Animals
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		                        			Humans
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		                        			Rats
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		                        			Multivariate Analysis
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		                        			Postmortem Changes
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		                        			Protein Array Analysis
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		                        			Technology
		                        			
		                        		
		                        	
            
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