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.
3.Generalized Functional Linear Models: Efficient Modeling for High-dimensional Correlated Mixture Exposures.
Bing Song ZHANG ; Hai Bin YU ; Xin PENG ; Hai Yi YAN ; Si Ran LI ; Shutong LUO ; Hui Zi WEIREN ; Zhu Jiang ZHOU ; Ya Lin KUANG ; Yi Huan ZHENG ; Chu Lan OU ; Lin Hua LIU ; Yuehua HU ; Jin Dong NI
Biomedical and Environmental Sciences 2025;38(8):961-976
OBJECTIVE:
Humans are exposed to complex mixtures of environmental chemicals and other factors that can affect their health. Analysis of these mixture exposures presents several key challenges for environmental epidemiology and risk assessment, including high dimensionality, correlated exposure, and subtle individual effects.
METHODS:
We proposed a novel statistical approach, the generalized functional linear model (GFLM), to analyze the health effects of exposure mixtures. GFLM treats the effect of mixture exposures as a smooth function by reordering exposures based on specific mechanisms and capturing internal correlations to provide a meaningful estimation and interpretation. The robustness and efficiency was evaluated under various scenarios through extensive simulation studies.
RESULTS:
We applied the GFLM to two datasets from the National Health and Nutrition Examination Survey (NHANES). In the first application, we examined the effects of 37 nutrients on BMI (2011-2016 cycles). The GFLM identified a significant mixture effect, with fiber and fat emerging as the nutrients with the greatest negative and positive effects on BMI, respectively. For the second application, we investigated the association between four pre- and perfluoroalkyl substances (PFAS) and gout risk (2007-2018 cycles). Unlike traditional methods, the GFLM indicated no significant association, demonstrating its robustness to multicollinearity.
CONCLUSION
GFLM framework is a powerful tool for mixture exposure analysis, offering improved handling of correlated exposures and interpretable results. It demonstrates robust performance across various scenarios and real-world applications, advancing our understanding of complex environmental exposures and their health impacts on environmental epidemiology and toxicology.
Humans
;
Environmental Exposure/analysis*
;
Linear Models
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Nutrition Surveys
;
Environmental Pollutants
;
Body Mass Index
4.Epidemiological characteristics of human parainfluenza virus in Pudong New Area, Shanghai, 2017‒2022
Rongxin WU ; Li ZHANG ; Chuchu YE ; Bing ZHAO ; Ge ZHANG ; Qiang CHU
Shanghai Journal of Preventive Medicine 2025;37(9):746-751
ObjectiveTo investigate the epidemiological characteristics of human parainfluenza virus (HPIV) in Pudong New Area, Shanghai, and to provide a basis for the prevention and control of HPIV infections in this area. MethodsA total of 8 180 cases with acute respiratory infection (ARI)/influenza-like illness (ILI) attending the fever outpatient clinics, pediatric outpatient clinics, respiratory outpatient clinics, pediatric wards, emergency departments, respiratory wards, and intensive care units (ICUs) and other monitoring departments in 9 sentinel hospitals in Pudong New Area from 2017 to 2022 were selected as the research subjects, and their nasopharyngeal/ throat swabs were collected. Polymerase chain reaction (PCR) method was performed for testing the respiratory virus such as influenza virus, human adenovirus, human parainfluenza virus, respiratory syncytial virus (RSV), human enterovirus, rhinovirus, et al. HPIV serotypes were analyzed, and the detection rates of HPIV were compared between different times, seasons, and population groups. ResultsThe overall HPIV detection rate of ARI/ILI cases in Pudong New Area was 3.73% (305/8 180) in 2017‒2022, with HPIV-3 being the predominant serotype. The detection rate of HPIV decreased significantly in 2017‒2022, peaking at 7.66% (99/1 293) in 2017 and falling to 0.80% (13/1 617) in 2021. Statistically significant differences were observed in HPIV detection rates across different years (χ2trend=80.037, Ptrend<0.001). The detection rate was higher in 2017‒2019 than that in 2020‒2022 (χ2trend=38.990, Ptrend<0.001). HPIV exhibited seasonal patterns in 2017‒2019, with higher detection rates in summer and autumn and lower in spring and winter, whereas no seasonal patterns were observed in 2020‒2022. Children aged <6 years had the highest detection rate (7.07%, 139/1 967), followed by adults aged ≥60 years (4.78%, 85/1 779). Statistically significant differences were observed in the detection rates of HPIV among different age groups (χ2=111.210, P<0.001). Symptoms of HPIV infection were predominantly cough, fever, and runny nose in pre-school children, fever, cough, and sore throat in school-age children, and adults, and cough, expectoration, and fever in the elderly. ConclusionThe HPIV detection rate in Pudong New Area was low in 2017‒2022. The seasonal pattern of HPIV circulation in Pudong New Area disappeared in 2020‒2022 due to the influence of infectious disease epidemics. Young children and the elderly should be prioritized in HPIV prevention and control efforts.
5.Chemical constituents from the leaves of Cyclocarya paliurus and their α-glucosidase inhibitory activities
Yong YANG ; Ting-Si GUO ; Min XIE ; Li-Hong TAN ; Wen-Chu LI ; Hao ZHENG ; Fei-Bing HUANG ; Yu-Pei YANG ; Wei WANG ; Yu-Qing JIAN
Chinese Traditional Patent Medicine 2024;46(3):834-842
AIM To study the chemical constituents from the leaves of Cyanocarya paliurus(Batalin)Iljinskaja and their α-glucosidase inhibitory activities.METHODS The 95%ethanol extract from the leaves of C.paliurus was isolated and purified by macroporous resin,silica gel,Sephadex LH-20,polyamide,C18 reversed-phase silica gel and semi-preparative HPLC,then the structures of obtained compounds were identified by physicochemical properties and spectral data.Their α-glucosidase inhibitory activities were evaluated by PNPG.RESULTS Fifteen compounds were isolated and identified as cyclopaloside C(1),cyclopaloside A(2),juglanosides E(3),vaccinin A(4),ent-murin A(5),kaempferol 3-O-α-L-rhamnopyranoside(6),kaempferol-3-O-β-D-glucopyranoside(7),kaempferol-3-O-β-D-glucuronide methyl ester(8),kaempferol-3-O-β-D-glucuronide ethyl ester(9),kaempferol-3-O-β-D-glucuronide butyl ester(10),quercetin-3-O-α-L-rhamnopyranoside(11)quercetin-3-O-β-D-glucopyranoside(12),quercetin-3-O-β-D-galactopyranoside(13),quercetin-3-O-β-D-glucuronide butyl ester(14),dihydrokaempferol(15).The IC50 value of total extracts ihibited α-glucosidase was(1.83±0.04)μg/mL,and the IC50 values of compounds 1,4-5 were(29.48±1.86),(0.50±0.07),(0.71±0.07)μmol/L,respectively.CONCLUSION Compound 1 is a new tetrahydronaphthalene glycoside.Compounds 4-5,8-10 and 14 are isolated from the leaves of C.paliurus for the first time.Compounds 4-5 are relatively rare flavonoid lignans with potential inhibitory activities against α-glucosidase.
6.Environmental hygiene and healthcare-associated infection:a time-series study based on generalized additive model
Kai LIN ; Kun CHEN ; Jian-Bing WANG ; Fang-Hua FAN ; Hui LIANG ; Fang CHEN ; Kai-Ling JIN ; Wen-Jie CHU ; Wei-Guo CHEN ; Huan SHAN
Chinese Journal of Infection Control 2024;23(7):798-805
Objective To quantitatively analyze the impact of environmental hygiene on the occurrence of health-care-associated infections(HAI).Methods Monitoring data of HAI and environmental hygiene from a tertiary first-class hospital from January 2018 to December 2022 were collected,and the impact of environmental bacterial colony forming unit(CFU)on the occurrence of HAI was analyzed by a time-series generalized additive model.Results The single-contamination model showed a significant positive correlation between HAI and staff's hand bacterial CFU(β1=0.009,P=0.012).For an increase of 1 interquartile range(IQR)in the monthly mean CFU per dish(MCFU/Dish)of staffs'hand,the incidence of HAI increased by 13.28%(95%CI:2.82%-24.81%).Subgroup and lag effect analysis showed that when the monthly MCFU/Dish(after hand disinfection)of staffs'hand in-creased by one IQR,the excess risk(ER)of HAI for the month(lag0)was 16.26%(95%CI:15.45%-17.09%).In the multi-contamination model,the correlation between surface contamination and HAI was also statistically sig-nificant.Conclusion There is a significant correlation between hospital environmental hygiene and the occurrence of HAI.
7.A consistency comparison between next-generation sequencing and the FISH method for gene rearrangement detection in B-cell lymphomas
Zheng YAN ; Zhihua YAO ; Shuna YAO ; Shuang ZHAO ; Haiying WANG ; Junfeng CHU ; Yuanlin XU ; Jiuyang ZHANG ; Bing WEI ; Jiawen ZHENG ; Qingxin XIA ; Daoyuan WU ; Xufeng LUO ; Wenping ZHOU ; Yanyan LIU
Chinese Journal of Hematology 2024;45(6):561-565
Objective:To compare the consistency of lymphoma multigene detection panels based on next-generation sequencing (NGS) with FISH detection of B-cell lymphoma gene rearrangement.Methods:From January 2019 to May 2023, fusion genes detected by lymphoma-related 413 genes that targeted capture sequencing of 489 B-cell lymphoma tissues embedded in paraffin were collected from Henan Cancer Hospital, and the results were compared with simultaneous FISH detection of four break/fusion genes: BCL2, BCL6, MYC, and CCND1. Consistency was defined as both methods yielding positive or negative results for the same sample. The relationship between fusion mutation abundance in NGS and the positivity rate of cells in FISH was also analyzed.Results:Kappa consistency analysis revealed high consistency between NGS and FISH in detecting the four B-cell lymphoma-related gene rearrangement ( P<0.001 for all) ; however, the detection rates of positive individuals differed for the four genes. Compared with FISH, NGS demonstrated a higher detection rate for BCL2 rearrangement, a lower detection rate for BCL6 and MYC rearrangement, and a similar detection rate for CCND1 rearrangement. No correlation was found between fusion mutation abundance in NGS and the positivity rate of cells in FISH. Conclusions:NGS and FISH detection of B-cell lymphoma gene rearrangement demonstrate overall good consistency. NGS is superior to FISH in detecting BCL2 rearrangement, inferior in detecting MYC rearrangement, and comparable in detecting CCND1 rearrangement.
8.Clinical and molecular genetic analysis of 18 cases of cerebrotendinous xanthomatosis
Cong TIAN ; Zhifei CHU ; Tongxia ZHANG ; Bing ZHAO ; Xiuhe ZHAO ; Cuiping ZHAO ; Chuanzhu YAN ; Yuying ZHAO
Chinese Journal of Neurology 2024;57(11):1217-1226
Objective:To analyze the clinical and molecular genetic characteristics of patients with cerebrotendinous xanthomatosis (CTX) to increase the awareness of the disease among clinicians.Methods:The clinical data, including the age of onset and diagnosis, clinical manifestations, neuroimaging and neuroelectrophysiology and the genetic data of patients diagnosed with CTX in the Department of Neurology, Qilu Hospital of Shandong University from March 2017 to December 2023 were retrospectively collected and analyzed.Results:A total of 18 patients were enrolled in this study, including 12 males and 6 females.The onset age was 10 (6, 29) years, with a minimum onset age of 3 years and a maximum onset age of 32 years; the period from onset to diagnosis was 19.00 (8.75, 24.25) years, with the shortest being 6 months and the longest being 35 years. Among the 18 patients, 16 patients had symptoms and signs of spastic paralysis, 9 patients had cognitive impairment and peripheral neuropathy, 8 patients had cerebellar ataxia, 3 patients had mental disorders, 3 patients had autonomic nervous dysfunction, and only 2 patients had seizures. Among the non-neurological symptoms, 9 patients had Achilles tendon xanthoma, of whom 1 patient was accompanied by patellar tendon xanthoma; 8 patients had adolescent cataracts, 6 patients had chronic diarrhea since childhood. All patients underwent brain MRI examination, among whom 15 patients had cerebellar dentate nucleus involvement, 10 patients had corticospinal tract involvement and 2 patients had normal brain MRI. Fourteen patients underwent nerve conduction and electromyography examinations, among whom 9 patients presented with multiple peripheral neuropathy characterized by motor or motor sensory demyelination. A total of 17 CYP27A1 gene variants were detected in 18 patients. The c.1420C>T and c.1263+1G>A were the hot-spot mutations in this cohort. Conclusions:Spastic paralysis, cerebellar ataxia, tendon xanthoma and adolescent cataracts are typical manifestations of CTX. The cerebellar dentate nucleus and corticospinal tract are mainly involved on the neuroimaging. It should be noted that some patients lack the typical characteristics mentioned above. The c.1420C>T and c.1263+1G>A are the hot-spot mutations in this cohort.
9.Zero-profile intervertebral fusion with cage-titanium plate for the treatment of multilevel cervical spondylotic myelopathy.
Jian-Bin ZHONG ; Yong HU ; Zhen-Tao CHU ; Wei-Xin DONG ; Zhen-Shan YUAN ; Xiao-Yang SUN ; Bing-Ke ZHU ; Ou-Jie LAI
China Journal of Orthopaedics and Traumatology 2024;37(12):1188-1195
OBJECTIVE:
To explore clinical effect of Zero-profile intervertebral fusion with cage-titanium plate in treating multilevel cervical spondylotic myelopathy.
METHODS:
From January 2016 to January 2020, 107 patients with multisegmental cervical spondylotic myelopathy treated by surgery were retrospectively analyzed and divided into Hybrid group and control group according to different surgical methods. There were 54 patients in Hybrid group, including 42 males and 12 females, aged from 33 to 77 years old with an average of (57.3±9.5) years old;20 patients with C3-C6, 27 patients with C4-C7 and 7 patients with C3-C7;Zero-profile intervertebral fusion with cage-titanium plate internal fixation was performed. There were 53 patients in control group, including 34 males and 19 females;aged from 36 to 79 years old with an average of (57.8±8.9) years old;17 patients with C3-C6, 27 patients with C4-C7, and 9 patients with C3-C7;titanium plate interbody fusion fixation was performed. Operation time, blood loss and complications between two groups were compared, visual analogue scale (VAS), Japanese Orthopedic Association (JOA) scores and neck disability index (NDI) were used to assess recovery of clinical symptoms;cervical lordosis (CL), cervical sagittal vertical axis (C-SVA), and T1 slope (T1S) were measured and compared to evaluate cervical sagittal plane parameters.
RESULTS:
All patients were followed up, Hybrid group was followed up for 24 to 64 months with an average of (31.7±18.4) months, and control group was followed up for 24 to 65 months with an average of (32.6±15.8) months. There was no significant difference in follow-up time between two groups (P>0.05). Operation time and blood loss in Hybrid group were less than those in control group (P<0.05). VAS, JOA score and NDI were significantly improved between two groups at the lastest follow-up (P<0.05). There were no significant difference in VAS, JOA and NDI scores between two groups before and after operation (P>0.05). CL in both two groups at 3 months and the latest follow-up after operation were significantly improved than those before operation (P<0.05), there were no significant difference between two groups in T1S and C-SVA before and after operation (P>0.05). Postoperative dysphagia occurred in 2 patients in Hybrid group and 9 patients in control group, and had statistically difference in the incidence of dysphagia between two groups (χ2=5.112, P=0.024). During the follow-up, there were no complications such as loosening, displacement or fracture of internal fixation between two groups.
CONCLUSION
Compared with titanium plate interbody fusion, Zero-profile intervertebral fusion combined with cage-titanium plate for the treatment of multilevel cervical spondylotic myelopathy could shorten surgical time and blood loss, reduce surgical trauma and postoperative swallowing difficulties, and is conducive to early and rapid recovery.
Humans
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Male
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Female
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Middle Aged
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Spinal Fusion/instrumentation*
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Bone Plates
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Titanium
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Aged
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Spondylosis/surgery*
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Adult
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Cervical Vertebrae/surgery*
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Retrospective Studies
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Spinal Cord Diseases/surgery*
10. Roscovitine rescuing neuronal loss and neuroinflammation in brain regions associated with Parkinson’s disease mice
Ye LIU ; Ya-Nan CHU ; Cen-Lu XU ; Jia-Cheng HE ; Bing-Yin SU ; Hao-Ran TAI ; Ya-Nan CHU ; Bing-Yin SU ; Hao-Ran TAI
Acta Anatomica Sinica 2023;54(6):635-643
[Abstract] Objective To investigate the effect and possible mechanism of cell cycle-dependent kinase (Cdk)5 inhibitor Roscovitine on 1-methyl4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-induced pathological changes in brain regions associated with Parkinson’ s disease (PD) model mice. Methods The effect of Roscovitine on the relative expression levels of P25 and Cdk5 proteins was detected by Western blotting in MPP

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