1.Construction of an immune-related LncRNA prognostic risk model for gastric cancer based on bioinformatics
Huaji JIANG ; Wei DING ; Yulin TAN ; Lin ZHUANG ; Cheng XI ; Yixin XU ; Yibo WANG ; Xuezhong XU
Chinese Journal of Immunology 2024;40(6):1203-1209
Objective:Based on bioinformatics,new immune-related LncRNAs related to the prognosis of gastric cancer were screened,and a prognostic risk model of immune-related LncRNA was further constructed,in order to be used as a new indicator for early diagnosis and prognostic status of gastric cancer.Methods:The gastric cancer transcriptome data and corresponding clinical prog-nosis data were downloaded from multiple data platforms,and the immune-related LncRNAs of gastric cancer were screened by bioin-formatics methods.Cox regression analysis was used to screen LncRNAs related to immune prognosis in gastric cancer,and LncRNAs related to immune prognosis with independent prognostic significance were identified to construct a prognostic risk model,and the risk score of each patient was calculated.Patients were divided into low-risk and high-risk groups according to the cutpoint.Kaplan-Meier analysis was performed for survival analysis and survival curves were drawn,nomograms were drawn and internal validation was per-formed,and univariate and multivariate Cox regression analysis was performed to analyze the relationship between risk scores and clin-icopathological characteristics and survival prognosis of gastric cancer patients.Results:Three immune prognosis-related LncRNAs(UCA1,MIR4435-1HG,RP11-617F23.1)were identified by Cox regression analysis,and a predictive scoring model was constructed to divide the patients into high-risk group and low-risk group according to the prognosis score.There was a statistically significant dif-ference in the prognosis of patients between the two groups(P<0.05).The multivariate Cox regression analysis risk score was an inde-pendent risk factor for the prognosis of gastric cancer,and the internal verification of the nomogram showed good reliability.Conclu-sion:Three immune-related LncRNAs in gastric cancer are significantly correlated with the prognosis of gastric cancer patients,and the predictive scoring model constructed based on them can effectively predict the prognosis and can be used as their independent prog-nostic biomarkers.
2.Characteristics of brain network topological properties in schizophrenic patients based on machine learning
Lunpu AI ; Yangyang LIU ; Ningning DING ; Entu ZHANG ; Yibo GENG ; Qingjiang ZHAO ; Haisan ZHANG
Chinese Journal of Behavioral Medicine and Brain Science 2024;33(5):419-424
Objective:To analyze brain topological property data through machine learning methods and explore changes in brain network topological properties in patients with schizophrenia.Methods:From January 2022 to August 2023, functional magnetic resonance imaging data of 60 patients with schizophrenia and 56 healthy controls were collected , and the data were preprocessed to construct brain functional networks and extract global and nodal topological properties. All subjects were divided into a training group and a testing group.The data of training group were fitted based on support vector machine, and the predictive performance was evaluated through cross-validation.The model was optimized by recursive feature elimination algorithm, then the indicators that contributed the most to predictive performance were extrated.The classification performance of the testing group was calculated based on the trained model with optimal predictive performance.SPSS 20.0 software was used for data analysis, the independent t-test and χ2 test were used for comparing the differences between the two groups. Results:The support vector machine achieved an accuracy of 75.00% in predicting the test group of schizophrenia patients based on all indicators. After removing redundant features and combining with the recursive feature elimination algorithm, the accuracy of the SVM model in predicting the test group increased to 90.00%. The nodal global efficiency(Ne)of the left superior temporal gyrus, right dorsal agranular insula, bilateral dorsal granular insula, bilateral caudal cingulate gyrus, and left lateral orbitofrontal cortex in the model contributed the most to classification.Compared to the control group, patients with schizophrenia had abnormal Ne values in these brain regions.Conclusion:There are multiple brain regions with abnormal Ne values in patients with schizophrenia, indicating that the abnormalities in information integration and transmission functions may be related to the imbalance in the dynamic equilibrium of the patients' brain networks.
3.Vascularized tracheal substitutes constructed by exosome-load hydrogel-modified 3D printed scaffolds
Ziqing SHEN ; Tian XIA ; Yibo SHAN ; Ruijun ZHU ; Haoxin WAN ; Hao DING ; Shu PAN ; Jun ZHAO
Chinese Journal of Tissue Engineering Research 2024;28(5):697-705
BACKGROUND:For the replacement treatment of long-segment tracheal defects,although tissue engineering research has made some progress in recent years,it is still not perfect,and one of the biggest difficulties is that the hemodynamic reconstruction of the tracheal replacement cannot be achieved rapidly. OBJECTIVE:To preliminarily explore the potential of polycaprolactone scaffolds modified with exosome-loaded hydrogels to construct a rapidly vascularized tracheal substitute. METHODS:Exosomes were extracted from bone marrow mesenchymal stem cells of SD rats.After preparation of hyaluronic acid methacrylate solution,the exosome solution was mixed with hyaluronic acid methacrylate solution at a volume ratio of 1:1.Hyaluronic acid methacrylate hydrogels loaded with exosomes were prepared under ultraviolet irradiation for 5 minutes.The degradation of exosome-unloaded hydrogels and the controlled release of exosome-loaded hydrogels were detected.Polycaprolactone scaffolds were prepared by 3D printing.The pure hyaluronic acid methacrylate solution and the exosome-loaded hyaluronic acid methacrylate solution were respectively added to the surface of the scaffold.Hydrogel-modified scaffolds and exosome-modified scaffolds were obtained after ultraviolet irradiation.Thirty SD rats were randomly divided into three groups with 10 rats in each group and subcutaneously implanted with simple scaffolds,hydrogel-modified scaffolds and exosome-modified scaffolds,respectively.At 30 days after surgery,the scaffolds and surrounding tissues of each group were removed.Neovascularization was observed by hematoxylin-eosin staining and Masson staining and the expression of CD31 was detected by immunofluorescence. RESULTS AND CONCLUSION:(1)As time went by,the hydrogel degraded gradually,and the exosomes enclosed in the hydrogel were gradually released,which could be sustained for more than 30 days.The exosome release rate was faster than the degradation rate of the hydrogel itself,and nearly 20%of the exosomes were still not released after 30 days of soaking.(2)Under a scanning electron microscope,the surface of the simple polycaprolactone scaffold was rough.After hydrogel modification,a layer of gel was covered between the pores of the scaffold,and the scaffold surface became smooth and dense.(3)After 30 days of subcutaneous embedding,hematoxylin-eosin staining and Masson staining showed that more neovascularization was observed inside the scaffolds of the exosome-modified scaffold group compared with the hydrogel-modified scaffold group.The hydrogels on the scaffolds of the two groups were not completely degraded.Immunofluorescence staining showed that CD31 expression in the exosome-modified scaffold group was higher than that in the hydrogel-modified scaffold group(P<0.000 1).(4)These results indicate that hyaluronic acid methacrylate hydrogels can be used as controlled-release carriers for exosomes.The 3D-printed polycaprolactone scaffold modified by hyaluronic acid methacrylate hydrogel loaded with exosomes has good biocompatibility and has the potential to promote the formation of neovascularization.
4.Proteomics and Phosphoproteomics Analysis of Effect of Retinoic Acid-Induced Protein 16 Knockout on Human Colon Cancer Cells
Yibo CHEN ; Gen MIAO ; Wen WANG ; Cuiling DING ; Zhongtian QI
Cancer Research on Prevention and Treatment 2024;51(10):820-830
Objective To analyze the differences in the expressions of the total and phosphorylated proteins in human colon cancer HCT116 cells after the knockout(KO)of retinoic acid-induced protein 16(RAI16)and explore the possible mechanism and related signaling pathways affecting its protein function in HCT116 cells.Methods HCT116 KO and WT cell proteins were collected and extracted,and the protein extraction efficiency was detected via a sodium dodecyl sulfate-polyacrylamide gel electrophoresis(SDS-PAGE)experiment.After protein digestion,the peptides were labeled with TMT and analyzed via mass spectrometry.We used bioinformatics methods to analyze the identified differential proteins and differentially phosphory-lated proteins by using GO,KEGG,and STRING databases.Results The results of SDS-PAGE showed no evident protein degradation.In addition,some key bands were significantly different between the experi-mental and control groups.A total of 147 up-regulated and 230 down-regulated differential proteins were screened in accordance with the conditions of Foldchange≥1.5 or Foldchange≤1/1.5 and P<0.05.Meanwhile,106 up-regulated and 217 down-regulated phosphorylation sites were screened.GO enrichment analysis revealed that the differential proteins were mainly enriched in the composition of nucleoplasm,nucleus and cytoplasm,RNA binding,cadherin and chromatin,DNA repair,RNA splicing,and positive regulation of DNA as template transcription.The results of KEGG enrichment indicated that the differential proteins were mainly enriched in nucleocytoplasmic transport,spliceosomes,cell cycle,cell-cell tight junctions,viral carcinogenesis,microRNAs in cancer,etc.The protein interaction network mainly focused on DDX17,NCL,EEF2,CDK1,SSRP1,and SMARCC1.The statistical findings unveiled the up-regulated changes in the two omics of SKP1,ORC1,and BAD and the down-regulated changes in RBL1,RB1,CDK1,CDC6,MCM4,TFDP1,CHD4,and SNW1.Moreover,the phosphorylation differences were more significant than the protein differences.Conclusion RAI16 plays the possible crucial role in multiple biological functions and signaling pathways through key proteins,such as SKP1,ORC1,RB1,and CDK1,which affect the cell cycle and thereby the occurrence and development of cancer.
5.A panel study on the association of organophosphate ester flame retardant exposure with thyroid function related hormones in healthy older adults
Chenfeng LI ; Yibo XU ; Peijie SUN ; Enmin DING ; Chenlong LI ; Xiaojie GUO ; Jiran ZHANG ; Song TANG ; Xiaoming SHI
Chinese Journal of Preventive Medicine 2024;58(6):847-856
Objective:To explore the impact of whole blood organophosphate esters (OPEs) flame retardant exposure on thyroid function-related hormones in healthy older adults.Methods:In this panel study, five repeated population-based epidemiological surveys and biological sample collection were conducted from September 2018 to January 2019, with 76 healthy older adults aged 60-69 years in the Dianliu Community of Jinan, Shandong Province. Information on the sociodemographic characteristics, diet, and health status of the respondents was systematically gathered through questionnaires and physical examinations. Fasting venous blood was collected to determine the levels of OPEs, thyroid-stimulating hormone (TSH), triiodothyronine (T 3), and thyroxine (T 4). A linear mixed-effects model was used to analyze the impact of OPEs exposure on thyroid function-related hormones in healthy older adults. Results:Each of the 76 subjects participated in at least two follow-up visits, resulting in a total of 350 person visits. The age of the study participants was (65.07±2.76) years, with 38 participants of both sexes. A total of eight OPEs were included with a detection rate exceeding 50%, and the M ( Q 1, Q3) for ∑OPEs was 3.85 (2.33, 5.74) ng/ml, with alkyl-OPEs being the major type of OPEs with an M ( Q 1, Q3) of 1.27 (0.64, 2.50) ng/ml. The M ( Q 1, Q3) for TSH, T 3, and T 4 was 3.74 (2.55, 5.69) μIU/ml, 1.32 (1.10, 1.60) ng/ml, and 45.04 (36.96, 53.27) ng/ml, respectively. Linear mixed-effects model showed that TSH was significantly decreased by 9.93% (95% CI:-15.17%, -4.36%) and 11.14% (95% CI:-15.94%, -6.06%) in older adults for each quartile level increase in TnBP and TEHP exposures, respectively. Gender-stratified analysis indicated that TEHP exposure was negatively associated with TSH levels in male older adults, whereas a decrease in TSH levels among female older adults was associated with TnBP exposure. Conclusion:Exposure to whole blood OPEs is associated with decreased TSH levels among healthy older adults, with notable gender differences.
6.A panel study on the association of organophosphate ester flame retardant exposure with thyroid function related hormones in healthy older adults
Chenfeng LI ; Yibo XU ; Peijie SUN ; Enmin DING ; Chenlong LI ; Xiaojie GUO ; Jiran ZHANG ; Song TANG ; Xiaoming SHI
Chinese Journal of Preventive Medicine 2024;58(6):847-856
Objective:To explore the impact of whole blood organophosphate esters (OPEs) flame retardant exposure on thyroid function-related hormones in healthy older adults.Methods:In this panel study, five repeated population-based epidemiological surveys and biological sample collection were conducted from September 2018 to January 2019, with 76 healthy older adults aged 60-69 years in the Dianliu Community of Jinan, Shandong Province. Information on the sociodemographic characteristics, diet, and health status of the respondents was systematically gathered through questionnaires and physical examinations. Fasting venous blood was collected to determine the levels of OPEs, thyroid-stimulating hormone (TSH), triiodothyronine (T 3), and thyroxine (T 4). A linear mixed-effects model was used to analyze the impact of OPEs exposure on thyroid function-related hormones in healthy older adults. Results:Each of the 76 subjects participated in at least two follow-up visits, resulting in a total of 350 person visits. The age of the study participants was (65.07±2.76) years, with 38 participants of both sexes. A total of eight OPEs were included with a detection rate exceeding 50%, and the M ( Q 1, Q3) for ∑OPEs was 3.85 (2.33, 5.74) ng/ml, with alkyl-OPEs being the major type of OPEs with an M ( Q 1, Q3) of 1.27 (0.64, 2.50) ng/ml. The M ( Q 1, Q3) for TSH, T 3, and T 4 was 3.74 (2.55, 5.69) μIU/ml, 1.32 (1.10, 1.60) ng/ml, and 45.04 (36.96, 53.27) ng/ml, respectively. Linear mixed-effects model showed that TSH was significantly decreased by 9.93% (95% CI:-15.17%, -4.36%) and 11.14% (95% CI:-15.94%, -6.06%) in older adults for each quartile level increase in TnBP and TEHP exposures, respectively. Gender-stratified analysis indicated that TEHP exposure was negatively associated with TSH levels in male older adults, whereas a decrease in TSH levels among female older adults was associated with TnBP exposure. Conclusion:Exposure to whole blood OPEs is associated with decreased TSH levels among healthy older adults, with notable gender differences.
7.Research progress in site mutations of SARS-CoV-2 Omicron variants
Gen MIAO ; Zhiwei HE ; Yibo CHEN ; Cuiling DING ; Hao REN ; Ping ZHAO ; Zhongtian QI
Chinese Journal of Microbiology and Immunology 2023;43(3):173-181
SARS-CoV-2 Omicron variant (B.1.1.529) was first discovered in South Africa in November 2021 and has since become a mainstream strain worldwide. Omicron variant was defined as the fifth "variant of concern (VOC)" by World Health Organization on November 26, 2021. This paper illustrates the mutation trends of Omicron variants in terms of SARS-CoV-2 genome and protein structure as well as nucleic acid site mutations and amino acid site mutations, describes the features of Omicron mutation sites in terms of lineage comparison among the VOCs and Omicron sublineages, and further highlights the influences of Omicron site mutations from the aspects of immune escape, virulence and transmission ability. Moreover, this paper also reviews the development of direct antiviral agents, antibodies and vaccines, aiming to provide reference for further investigation.
8.Analysis on characteristics of virus isolation and unique recombinant forms from untreated HIV-1 infected patients in three provinces of China
Lijie WANG ; Yi FENG ; Lin HE ; Ruolei XIN ; Yan WANG ; Shu LIANG ; Yibo DING ; Shujia LIANG ; Yuanyuan ZHANG ; Caiqin HU ; Yuhua RUAN ; Hui XING ; Kunxue HONG ; Yiming SHAO ; Liying MA
Chinese Journal of Experimental and Clinical Virology 2022;36(3):263-269
Objective:To analyze the characteristics of viral isolation and unique recombinant from untreated HIV-1 patients infected through sexual transmission and injection drug use, so as to provide evidence for understanding the biological characteristics and precise prevention and control of HIV-1 infection in different transmission routes.Methods:In view of the different HIV-1 transmission risks, newly diagnosed untreated HIV-1 patients from Beijing, Guangxi and Sichuan were carefully selected. Venous blood was collected to detect the viral load and CD4 + T cell count, and peripheral blood lymphocytes were isolated for virus isolation. Viral RNAs were extracted from the virus supernatant, and the near full-length genome sequences were obtained using in-house method, then the recombination patterns were determined. Results:Among the 65 HIV-1 infection, 32(49.2%), 20(30.8%) and 13(20.0%) were infected via men who have sex with men (MSM), heterosexual and injection drug use (IDU), respectively; genotypes mainly included 26(40.0%) CRF07_ BC, 23(35.4%) CRF01_ AE, and 9(13.8%) unique recombinant types (URFs). A total of 46 HIV-1 clinical strains were isolated. The positive rate of HIV-1 isolation was significantly negatively correlated with CD4 + T cells ( X2=4.22, P=0.04), but positively correlated with viral load ( X2=22.4, P<0.001); the multi-variate generalized estimating equations(GEE) model analysis of HIV-1 P24 antigen content showed similar result. In addition, GEE model showed a positive correlation between viral P24 antigen content and virus-producing culture time (52.14, 95% CI: 9.42~94.87, P=0.017). Viral growth curve analysis showed that the level of viral P24 antigen in MSM Group was significantly higher than that in heterosexual group and IDU group (adjusted P values were p<0.01 and P<0.05, respectively), on the 14th day after culture. The proportion of URFs in MSM Group was higher than that in heterosexual group, and the recombinant breakpoints in MSM Group were more than that in heterosexual group. Conclusions:MSM population was more sensitive to HIV-1 virus isolation; there was unique diversity of recombinant forms of HIV-1 among those with sexually transmitted infections, especially in the MSM population.
9.Analysis of 43 cases of anti-NMDA receptor encephalitis misdiagnosed as mental disorder
Yanxia GAO ; Yang JING ; Yi LI ; Ding YUAN ; Changju ZHU ; Yibo WANG ; Linlin HOU ; Guoyu DUAN ; Pei SUN ; Jingjing WANG ; Wanwan JIN ; Zhigao XU
Chinese Journal of Emergency Medicine 2021;30(2):208-212
Objective:To investigate the clinical features of patients with anti-N-methyl-D-aspartate receptor (NMDAR) encephalitis misdiagnosed as mental disorder, improve the early diagnosis rate and reduce misdiagnosis.Methods:The clinical data of patients with anti-NMDA receptor encephalitis diagnosed at the First Affiliated Hospital of Zhengzhou University from 2012 to 2018 were collected. Patients misdiagnosed as mental disorders were screened out. Their psychiatric symptom characteristics, disease course characteristics, imaging and laboratory findings, treatment and prognosis were retrospectively analyzed.Results:A total of 121 cases of anti-NMDA receptor encephalitis were collected, and 43 cases of mental disorders were screened out. Sixteen of the 43 patients (37.2%) had prodromal symptoms, and all the patients had psychiatric behavioral abnormalities (100%), including 32 cases (74.4%) of seizures, 13 cases (30.2%) of decreased level of consciousness, 21 cases (48.8%) of involuntary movements, 15 cases (34.9%) of decreased memory, 8 cases (18.6%) of speech dysfunction, and 8 cases (18.6%) of other neurological symptoms (central hyperventilation, autonomic dysfunction). Memory loss was observed in 15 cases (34.9%), speech dysfunction in 8 cases (18.6%), other neurological symptoms (central hypoventilation, autonomic dysfunction) in 8 cases (18.6%), and various symptoms may appear simultaneously or successively in the same patient. Thirty-eight cases had complete resolution of symptoms or only minor physical impairment, and 5 cases had recurrent admissions with mental abnormalities and seizures. The recurrence rate accounted for 11.6% (5/43).Conclusions:The clinical manifestations of anti-NMDA receptor encephalitis are complex and varied. Most of them have mental behavior abnormalities as the first symptom, which is easily misdiagnosed as mental disorder and delayed treatment will lead to prolonged disease course and poor prognosis.
10.Analysis on characteristics of untreated 16-25 years old people living with HIV-1 at the China-Myanmar border from 2009 to 2017 based on molecular network method
Yibo DING ; Min CHEN ; Jibao WANG ; Yi FENG ; Mengze GAN ; Lijie WANG ; Qianru LIN ; Lin HE ; Yanling MA ; Mengjie HAN ; Liying MA
Chinese Journal of Experimental and Clinical Virology 2021;35(2):124-129
Objective:To analyze the epidemiological characteristics of untreated 16-25 years old people living with HIV-1 (PLWH) in Dehong on the China-Myanmar border during 2009 to 2017, by using molecular network method and to provide references for precise prevention and reduction of the spread of HIV-1 in Dehong.Methods:Screening people living with HIV-1, collecting blood sample and separating plasma, extracting RNA were performed to amplify HIV-1 pol sequence, construct molecular network by HIV-TRACE program and conduct statistical analysis. Results:Among the 573 infected persons in the group, 319 were Chinese (55.67%), 254 were Burmese (44.33%); 351 were males (61%), and 222 were females (39%); 404 had heterosexual transmission (HET, 70.51%), 110 people injected drugs (PWID, 19.20%), 51 men had sex with men (MSM, 8.9%); genotypes included 252 unique recombinant forms (43.98%), and 222 had circular recombinant forms (39.02%), 76 had HIV-1 C (13.26%) and 23 HIV-1 B (4.01%) infection. The 83 molecular networks constructed through HIV-TRACE involved 250 PLWH, 49% were the China-Myanmar mixed network (41/83). Myanmar citizens were at high risk of accessing the China-Myanmar mixed network ( AOR=2.676, p=0.002). Chinese male PWID network assortativity is 0.34, Myanmar male PWID was 0.14, MSM was 0.12. Conclusions:There is a continuous risk of cross-border transmission of HIV-1 in Dehong on the China-Myanmar border; attention should be paid to the mixed transmission of MSM and Myanmar male PWID populations with other transmission routes.

Result Analysis
Print
Save
E-mail