1.Integrated Transcriptomic Landscape and Deep Learning Based Survival Prediction in Uterine Sarcomas
Yaolin SONG ; Guangqi LI ; Zhenqi ZHANG ; Yinbo LIU ; Huiqing JIA ; Chao ZHANG ; Jigang WANG ; Yanjiao HU ; Fengyun HAO ; Xianglan LIU ; Yunxia XIE ; Ding MA ; Ganghua LI ; Zaixian TAI ; Xiaoming XING
Cancer Research and Treatment 2025;57(1):250-266
Purpose:
The genomic characteristics of uterine sarcomas have not been fully elucidated. This study aimed to explore the genomic landscape of the uterine sarcomas (USs).
Materials and Methods:
Comprehensive genomic analysis through RNA-sequencing was conducted. Gene fusion, differentially expressed genes (DEGs), signaling pathway enrichment, immune cell infiltration, and prognosis were analyzed. A deep learning model was constructed to predict the survival of US patients.
Results:
A total of 71 US samples were examined, including 47 endometrial stromal sarcomas (ESS), 18 uterine leiomyosarcomas (uLMS), three adenosarcomas, two carcinosarcomas, and one uterine tumor resembling an ovarian sex-cord tumor. ESS (including high-grade ESS [HGESS] and low-grade ESS [LGESS]) and uLMS showed distinct gene fusion signatures; a novel gene fusion site, MRPS18A–PDC-AS1 could be a potential diagnostic marker for the pathology differential diagnosis of uLMS and ESS; 797 and 477 uterine sarcoma DEGs (uDEGs) were identified in the ESS vs. uLMS and HGESS vs. LGESS groups, respectively. The uDEGs were enriched in multiple pathways. Fifteen genes including LAMB4 were confirmed with prognostic value in USs; immune infiltration analysis revealed the prognositic value of myeloid dendritic cells, plasmacytoid dendritic cells, natural killer cells, macrophage M1, monocytes and hematopoietic stem cells in USs; the deep learning model named Max-Mean Non-Local multi-instance learning (MMN-MIL) showed satisfactory performance in predicting the survival of US patients, with the area under the receiver operating curve curve reached 0.909 and accuracy achieved 0.804.
Conclusion
USs harbored distinct gene fusion characteristics and gene expression features between HGESS, LGESS, and uLMS. The MMN-MIL model could effectively predict the survival of US patients.
2.Integrated Transcriptomic Landscape and Deep Learning Based Survival Prediction in Uterine Sarcomas
Yaolin SONG ; Guangqi LI ; Zhenqi ZHANG ; Yinbo LIU ; Huiqing JIA ; Chao ZHANG ; Jigang WANG ; Yanjiao HU ; Fengyun HAO ; Xianglan LIU ; Yunxia XIE ; Ding MA ; Ganghua LI ; Zaixian TAI ; Xiaoming XING
Cancer Research and Treatment 2025;57(1):250-266
Purpose:
The genomic characteristics of uterine sarcomas have not been fully elucidated. This study aimed to explore the genomic landscape of the uterine sarcomas (USs).
Materials and Methods:
Comprehensive genomic analysis through RNA-sequencing was conducted. Gene fusion, differentially expressed genes (DEGs), signaling pathway enrichment, immune cell infiltration, and prognosis were analyzed. A deep learning model was constructed to predict the survival of US patients.
Results:
A total of 71 US samples were examined, including 47 endometrial stromal sarcomas (ESS), 18 uterine leiomyosarcomas (uLMS), three adenosarcomas, two carcinosarcomas, and one uterine tumor resembling an ovarian sex-cord tumor. ESS (including high-grade ESS [HGESS] and low-grade ESS [LGESS]) and uLMS showed distinct gene fusion signatures; a novel gene fusion site, MRPS18A–PDC-AS1 could be a potential diagnostic marker for the pathology differential diagnosis of uLMS and ESS; 797 and 477 uterine sarcoma DEGs (uDEGs) were identified in the ESS vs. uLMS and HGESS vs. LGESS groups, respectively. The uDEGs were enriched in multiple pathways. Fifteen genes including LAMB4 were confirmed with prognostic value in USs; immune infiltration analysis revealed the prognositic value of myeloid dendritic cells, plasmacytoid dendritic cells, natural killer cells, macrophage M1, monocytes and hematopoietic stem cells in USs; the deep learning model named Max-Mean Non-Local multi-instance learning (MMN-MIL) showed satisfactory performance in predicting the survival of US patients, with the area under the receiver operating curve curve reached 0.909 and accuracy achieved 0.804.
Conclusion
USs harbored distinct gene fusion characteristics and gene expression features between HGESS, LGESS, and uLMS. The MMN-MIL model could effectively predict the survival of US patients.
3.Integrated Transcriptomic Landscape and Deep Learning Based Survival Prediction in Uterine Sarcomas
Yaolin SONG ; Guangqi LI ; Zhenqi ZHANG ; Yinbo LIU ; Huiqing JIA ; Chao ZHANG ; Jigang WANG ; Yanjiao HU ; Fengyun HAO ; Xianglan LIU ; Yunxia XIE ; Ding MA ; Ganghua LI ; Zaixian TAI ; Xiaoming XING
Cancer Research and Treatment 2025;57(1):250-266
Purpose:
The genomic characteristics of uterine sarcomas have not been fully elucidated. This study aimed to explore the genomic landscape of the uterine sarcomas (USs).
Materials and Methods:
Comprehensive genomic analysis through RNA-sequencing was conducted. Gene fusion, differentially expressed genes (DEGs), signaling pathway enrichment, immune cell infiltration, and prognosis were analyzed. A deep learning model was constructed to predict the survival of US patients.
Results:
A total of 71 US samples were examined, including 47 endometrial stromal sarcomas (ESS), 18 uterine leiomyosarcomas (uLMS), three adenosarcomas, two carcinosarcomas, and one uterine tumor resembling an ovarian sex-cord tumor. ESS (including high-grade ESS [HGESS] and low-grade ESS [LGESS]) and uLMS showed distinct gene fusion signatures; a novel gene fusion site, MRPS18A–PDC-AS1 could be a potential diagnostic marker for the pathology differential diagnosis of uLMS and ESS; 797 and 477 uterine sarcoma DEGs (uDEGs) were identified in the ESS vs. uLMS and HGESS vs. LGESS groups, respectively. The uDEGs were enriched in multiple pathways. Fifteen genes including LAMB4 were confirmed with prognostic value in USs; immune infiltration analysis revealed the prognositic value of myeloid dendritic cells, plasmacytoid dendritic cells, natural killer cells, macrophage M1, monocytes and hematopoietic stem cells in USs; the deep learning model named Max-Mean Non-Local multi-instance learning (MMN-MIL) showed satisfactory performance in predicting the survival of US patients, with the area under the receiver operating curve curve reached 0.909 and accuracy achieved 0.804.
Conclusion
USs harbored distinct gene fusion characteristics and gene expression features between HGESS, LGESS, and uLMS. The MMN-MIL model could effectively predict the survival of US patients.
4.Application Value of Organoid Technology in the Research of Traditional Chinese Medicine for the Prevention and Treatment of Digestive System Diseases
Yongtian WEN ; Xiangxue MA ; Beihua ZHANG ; Fengyun WANG ; Xudong TANG
Journal of Traditional Chinese Medicine 2025;66(14):1433-1438
Organoid technology, a rapidly advancing three-dimensional (3D) cell culture platform, can closely mimic the microarchitecture and functions of human digestive organs, effectively overcoming the limitations of conventional two-dimensional cell models and animal experiments. By systematically summarizing the distinctive strengths of organoid technology in simulating digestive physiological and pathological states, constructing digestive system disease models, enabling high-throughput drug screening, and facilitating personalized treatment, this review explored the potential applications of organoids in identifying active components of traditional Chinese medicine (TCM) formulas, evaluating in vitro pharmacokinetics and toxicological parameters, and investigating multi-target synergistic mechanisms. By integrating cutting-edge engineering technologies, organoids are expected to provide a more scientific research platform for TCM, accelerate the modernization of its mechanistic studies, and enhance its scientific value and global impact.
5.Efficacy and mechanism of Xiaoshuan enteric-coated capsule as an adjunctive treatment for ischemic stroke: A randomized clinical trial
Chunli Wen ; Zhixia Su ; Zhibin Ding ; Cungen Ma ; Fengyun Hu ; Lijuan Song ; Lingqun Zhu
Journal of Traditional Chinese Medical Sciences 2024;11(4):405-414
Objective:
To explore the clinical efficacy of Xiaoshuan enteric-coated capsule (XSECC) in treating cerebral infarction and its potential mechanism of action.
Methods:
Patients with acute ischemic stroke (AIS) of the qi deficiency and blood stasis type were randomly assigned to the control and observation groups. They were evaluated using the National Institutes of Health Stroke Scale (NIHSS), Activities of Daily Living (ADL), Hachinskilnchemic Scale (HIS), Barthel Index (BI), clinical efficacy scores, and TCM syndrome scores on days 0, 14, 30, and 90. Furthermore, VEGF and BDNF levels were measured on days 30 and 90. Finally, we analyzed the changes in each scale score and vascular neurological factor in both groups.
Results:
After 14 days of treatment, the difference values in NIHSS, ADL, and BI were higher, and TCM syndrome and clinical efficacy scores were increased in the observation group compared with those of the control group (all P < .05). After 30 days, the NIHSS, ADL, HIS, and TCM syndrome scores were decreased compared with those of the control group, while BI and clinical efficacy scores were increased (all P < .05). After 90 days, the difference value in ADL was higher, and TCM syndrome score was increased in the observation group compared with that of the control group (P = .047, P = .005, respectively). The levels of VEGF and BDNF were higher in the observation group than in the control group on days 14, 30, and 90 (all P < .05). VEGF and BDNF levels on day 0 were associated with prognosis of patients with AIS; therefore, they have a predictive value for the prognosis of acute cerebral infarction.
Conclusions
XSECC therapy can improve clinical outcomes in patients with acute and recurrent cerebral infarctions. Its mechanism of action may be associated with the secretion of VEGF and BDNF.
6.Meta-Analysis of the Placebo Effect of Chinese Herbal Medicine in Clinical Trials of Traditional Chinese Medicine for Functional Dyspepsia
Kaiyue HUANG ; Jinke HUANG ; Fengyun WANG ; Xiangxue MA ; Xudong TANG ; Lin LYU
Journal of Traditional Chinese Medicine 2024;65(5):479-488
ObjectiveTo analyse the current implementation status of Chinese herbal medicine (CHM) placebo and systematically evaluate the placebo effect in randomised controlled trials (RCTs) of traditional Chinese medicine (TCM) for the treatment of functional dyspepsia (FD). MethodsA combination of medical subject terms and free words was used to search six databases, including PubMed, EMBASE, Cochrane Library, Web of Science, China National Knowledge Infrastructure, and Wanfang, for RCTs with CHM placebo group for FD published from January 31st, 1994 to September 30th, 2023. The dosage forms, composition, and methodological quality were collected and evaluated. The quality of the included articles was evaluated by Cochrane risk of bias assessment tool, and meta-analysis was performed on the CHM placebo response rate of patients with FD, and subgroup analysis and meta-regression was performed according to diagnostic criteria, efficacy criteria, duration of treatment, type of placebo, whether it contained active ingredient, and whether it evaluated placebo effects. ResultsA total of 34 publications were included involving 5046 participants, of which 2221 FD patients received CHM placebo treatment. Granules were the predominant placebo preparation, accounting for 71% (24/34); 32.35% (11/34) of the studies added real CHM to the placebo, and only 12 (35%) of the studies described appearance, odour, and taste. The placebo response rate in FD patients in the placebo group was 41% (95% CI: 0.35 to 0.47; P<0.01, I2 = 87%); there was significant difference between groups with different diagnostic criteria and different treatment durations (P<0.05 or P<0.01), but there was no significant difference between the different efficacy evaluation criteria, the different placebo preparation, the presence of a low-dose active ingredient, and the presence or absence of placebo assessment (P>0.05). ConclusionThere was a significant CHM placebo effect in patients with FD, with granules as the main preparation of placebop. Different diagnostic criteria and different treatment times may affect the response rate of patients, and the addition of low-dose real medicine to the CHM placebos has not been seen to have an effect on the response rate. Clinical investigators have not paid enough attention to placebos, and there is a lack of uniform standards and norms for the preparation and evaluation of CHM placebos.
7.Discussion on the Scientific Connotation of Spleen Deficiency in Traditional Chinese Medicine
Lin LYU ; Fengyun WANG ; Xiangxue MA ; Beihua ZHANG ; Xudong TANG
World Science and Technology-Modernization of Traditional Chinese Medicine 2024;26(3):622-627
Spleen deficiency is an important part of the theoretical system of Traditional Chinese Medicine,which has experienced the process of origin,standardization,maturity,perfection and development in different historical periods.The physiological function of the spleen in Traditional Chinese Medicine involves"the spleen governs transportation and transformation,promotes blood circulation";The study of"spleen governing transportation and transformation"divided into"spleen governing transportation"and"spleen governing transformation"from the function of spleen,which is more conducive to explaining the scientific connotation of spleen governing transportation and transformation.Spleen governing transport and transformation is the basis of spleen governing clearing,and spleen governing clearing is the purpose of spleen governing transport and transformation.Spleen governing blood circulation is the outcome of spleen governing clearing,and there is a progressive logical hierarchy relationship between them.With the rise of proteomics,metabonomics and intestinal flora research,it provides technical support for the study of spleen deficiency syndrome;In addition,based on the correlation between spleen of Traditional Chinese Medicine and the functions of endoplasmic reticulum,the material basis of essence of spleen deficiency is discussed from the perspective of endoplasmic reticulum stress,which provides a new direction for the study of spleen deficiency.
8.Clinical value of matrix metalloproteinases-3 in rheumatoid arthritis
Yanyan SUN ; Li LIU ; Ye LI ; Jing WANG ; Fengyun MA ; Xuyan LI ; Hongyu DONG
Chinese Journal of Laboratory Medicine 2020;43(6):666-669
Objective:To analyze the relationship and clinical value between serum matrix metalloproteinases-3 (MMP-3) and rheumatoid arthritis (RA).Methods:By using retrospective study to collect 123 patients with RA diagnosed in our hospital from January 2019 to January 2020 as the RA group. Among the patients, there are 25 males and 98 females, the median age is 60 years old. During the same term, 53 healthy people were selected as the control group, with 12 males and 41 females, the median age is 55 years old. MMP-3, erythrocyte sedimentation rate (ESR), high sensitivity C-reactive protein (hs-CRP), rheumatoid facotrs (RF), anti-cyclocitrulline factor (ACCP) in peripheral blood of all subjects were detected. Disease activity score of 28 joints (DAS28) were collected. This research used T test, Spearman correlation analysis and receiver operating characteristic curve (ROC curve) to analyze the relationship between MMP-3 and other clinical biochemical indices, and the efficacy of MMP-3 in the diagnosis of RA.Results:Compared with the control group (26.30±14.83)ng/ml, the levels of serum MMP-3 in the RA group (79.71±123.54) ng/ml had significantly increased ( t=-4.95, P<0.001). The serum concentration of MMP-3 in RA patients was significantly correlated with ESR, hs-CRP and DAS28 ( r value were 0.521, 0.372, 0.405 respectively, P<0.001). The area under the curve (AUC) of MMP-3 to diagnose RA was 0.765, and the sensitivity was 64.44%, and the specificity was 75.76%, cut-off of MMP-3 were 32.50 ng/ml. Conclusions:The levels of serum MMP-3 in the RA group had significantly increased. MMP-3 and the disease activity were highly correlated. MMP-3 can be used as an indicator of RA disease activity, also can significantly improve the diagnostic efficacy, treatment and warning of early RA.
9.Study on correlation between ERα gene PvuⅡ ,XbaⅠ and Erβ gene RsaⅠ , AluⅠ digestion polymorphism with coronary heart disease
Qin WU ; Guifang MA ; Jinxia SUN ; Xianghe SONG ; Liucai YANG ; Shihong LI ; Fengyun DING
International Journal of Laboratory Medicine 2017;38(22):3116-3119
Objective To investigate the correlation of ERα gene PvuⅡ ,XbaⅠ and ERβ gene RsaⅠ ,AluⅠ digestion polymorphism with coronary atherosclerotic heart disease(CHD) risk factors in Yancheng area .Methods A total of 124 cases of CHD and 163 persons undergoing physical examination served as the CHD group and CON group .The enzyme method was adopted to detect TG and TC .The direction method was adopted to detect HDL and LDL .ERα gene PvuⅡ ,XbaⅠ and ERβ gene RsaⅠ ,AluⅠ digestion polymorphisms were detected by adopting RFLP-PCR .Results The ratios of smoking history ,family history ,complicating hypertension and diabetes ,and the level of body mass index ,TC ,TG and LDLC in the CHD group were significantly higher than those in the control group ,the difference was statistically significant (P<0 .05) .The various indicators had no statistically difference between male and female(P>0 .05) .The frequency distribution and geographic distribution of ERα gene PvuⅡ ,XbaⅠ and ERβ gene RsaⅠ ,Alu Ⅰ digestion polymorphisms had no difference between the two groups ,all conformed to Hardy-Weinberg genetic equilibrium and had the group representativeness .pp ,xx ,RR and AA genotypes in the CHD group were maximal ,while PP , XX ,rr and aa genotypes were minimal ;Pp ,xx ,RR and AA genotypes in the CON group were maximal ,while PP ,XX ,rr and aa genotypes were minimal .The distribution frequency of p and x genes in the CHD group was significantly higher than that in the control group ,the difference was statistically significant(P<0 .05) .Conclusion The estrogen gene polymorphism might be a target spot for effectively treating CHD ,and p and x gene distribution frequency may be related with CHD risk factors .
10.Efficacy Observation of Urinary Kallidinogenase in the Treatment of Acute Cerebral Watershed Infarct
Bin WANG ; Yang LIU ; Xiaoyuan LI ; Jing WANG ; Fengyun ZHANG ; Fulian MA ; Shuqin LIU
China Pharmacy 2016;27(5):650-652
OBJECTIVE:To observe clinical efficacy of urinary kallidinogenase in the treatment of acute cerebral watershed in-farct (WSI). METHODS:128 patients with WSI were randomly divided into control group and treatment group,each of the 64 cases. Control group was given Shuxuening 15 ml added into 0.9% Sodium chloride 250 ml,ivgtt,qd;treatment group received urinary kallidinogenase 0.15 PNA added into 0.9% Sodium chloride 100 ml,ivgtt,qd. Both groups were treated for consecutive 14 days. Neurologic impairment score(NIHSS)and clinical efficacy were observed in 2 groups before treatment and 3,7 and 14 days after treatment. The blood specimens were collected after 7 and 14 days treatment,to determine serum levels of TCC. RESULTS:After treatment,NIHSS and total effective rate of treatment group were significantly higher than those of control group,with statis-tical significance(P<0.01). There was no statistical significance in TCC between 2 groups before treatment(P>0.05);7 days af-ter treatment,TCC level of 2 groups increased significantly,to 14 days,and a declive;the treatment group was higher than the control group,with statistical significance (P<0.05). CONCLUSIONS:Urinary kallidinogenase can improve clinical efficacy of WSI significantly,and promote neurologic impairment symptom and TCC levels.


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