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.Mechanism of Treatment of Hepatocellular Carcinoma with Traditional Chinese Medicine Based on Epigenetic Regulation: A Review
Xianyu XU ; Yongping ZHU ; Yanqing LIU ; Liwei GU ; Junzhe ZHANG ; Shengnan SHEN ; Jigang WANG
Chinese Journal of Experimental Traditional Medical Formulae 2024;30(23):281-291
Hepatocellular carcinoma (HCC) is the sixth most common cancer in the world. In recent years, the clinical early diagnosis and treatment protocols of HCC have been improved, whereas the prognosis of patients is still not satisfactory, which is due to the fact that the mechanism of HCC development has not been fully elucidated. Therefore, it is of great significance to explore the molecular mechanisms and key regulatory links of hepatocellular carcinoma development to further improve the diagnosis and treatment of HCC in China. Epigenetics has become a research hotspot because of its reversibility and easy regulation. According to relevant studies, HCC involves the accumulation of multiple genetic and epigenetic changes during the initiation, promotion, and progression stages. HCC is categorized as infantile malnutrition with accumulation, hypochondriac pain, tympan ites, and abdominal mass in traditional Chinese medicine (TCM). In the treatment of HCC, TCM with low toxicity, multi-targets, and multi-mechanisms can inhibit tumor growth, alleviate the clinical symptoms, and enhance the quality of life of the patients. Chinese medicines and their active ingredients exert anti-HCC effects through epigenetic regulation of DNA methylation, histone modification, and non-coding RNA. Abnormal gene expression due to epigenetic regulation disorders is involved in all stages of HCC development. There are few studies on epigenetic regulation in TCM treatment of HCC, and there is still much room for development in basic and clinical trials. This paper reviews the mechanism of epigenetic regulation in HCC and summarizes the experimental results of TCM research on the related mechanism, with a view to providing a theoretical basis for future research on the mechanism of HCC development and clinical diagnosis and treatment of hepatocellular carcinoma with TCM.
5.The application of CT angiography and global biomimetic three-dimensional model reconstruction technology in the diagnosis of erectile dysfunction
Jigang GENG ; Xiaoshi LI ; Wei NIU ; Liyao LIU ; Yue QIN ; Yinhu ZHU
Journal of Practical Radiology 2024;40(8):1354-1357
Objective To investigate the diagnostic potential of low-dose computed tomography angiography(CTA)and global biomimetic three-dimensional model reconstruction technology in patients with arterial erectile dysfunction(ED).Methods A total of 136 patients with ED were selected.Digital subtraction angiography(DSA)was performed on all patients as per their treatment requirements and conditions,following ultrasound and CTA examination,and 75 patients finally completed DSA examination.All patients with International Index for Erectile Function(IIEF5)score ranged from 1 to 20.All patients received immediate ultrasound monitoring after injection of alprostadil 10 μg and underwent CTA examination.DSA was conducted at a minimum interval of 72 h.The global biomimetic three-dimensional model tool was used to reconstruct the CTA data and evaluate the stenosis of the pudendal vessels.The diagnostic efficacy of CTA examination,ultrasound and DSA examination were compared and calculated.Results A total of 1 632 vessels were evaluated in 136 patients,including 155 stenoses.DSA was performed in 75 patients.A total of 900 vessels were evaluated,of which 88 were stenoses.Compared with the results of CTA,ultrasound and DSA,the average stenosis scores of all measured vessels were not statistically significant(P<0.05).The correlation between CTA and ultrasound(r2=0.939 9,P<0.000 1)and DSA(r2=0.944 0,P<0.000 1)in the evaluation of vascular stenosis were good,and the diagnostic consistency was consistent.Conclusion Low-dose CTA and global biomimetic three-dimensional model reconstruction technology can effectively diagnose pudendal artery stenosis,and can perform all-round reconstruction observation,which is worthy of further clinical application.
6.Correlation between SWE parameters and histopathological features and immunohistochemical biomarkers in invasive breast cancer.
Xu LIU ; Jigang LI ; Ying HE ; Zhiyuan WANG
Journal of Central South University(Medical Sciences) 2024;49(12):1941-1952
OBJECTIVES:
Shear wave elastography (SWE) is a novel quantitative elastography technique that can assess the hardness of different tissues. This study introduces a novel shear wave parameter-frequency of mass characteristic (fmass)-and investigates its correlation, along with other shear wave parameters, with the histopathological features and immunohistochemical (IHC) biomarkers of invasive breast cancer (IBC). The study aims to explore whether SWE can provide useful information for IBC treatment and prognosis.
METHODS:
With the pathological results as the gold standard, 258 malignant breast lesions were collected, and all patients underwent conventional ultrasound and SWE examinations. The SWE parameters [maximum elastic value (Emax), minimum elastic value (Emin), mean elastic value (Emean), standard deviation of elastic value of the whole lesion (Esd)] and fmass] in the transverse and longitudinal orthogonal sections were measured, and their correlations with the prognostic factors of IBC [including tumor diameters, axillary lymph node (ALN) metastasis, lymphatic vessel invasion (LVI), calcification, histological type, histological grade, and IHC biomarkers (ER, PR, HER-2, Ki-67), and molecular subtypes] were analyzed. The correlations between the SWE parameters of the transverse and longitudinal sections of the tumors with different prognostic factors and the above indicators were analyzed. At the same time, the receiver operating characteristic (ROC) curve was used to analyze the efficacy of fmass in predicting ER and PR expression.
RESULTS:
Emean, Emax, Esd, and fmass were correlated with tumor diameters; Emean, Emax and Esd were correlated with histological types and histological grades. Emax and Esd were correlated with ALN metastasis, LVI and pathological types. In the IHC biomarker-labeled masses, fmass was correlated with ER and PR (both P<0.05), and Emean, Emax, and Esd were correlated with HER-2 and Ki-67 (all P<0.05). Emean, Emax, and fmass were all correlated with breast cancer subtypes (all P<0.05), and Emean and Emax were higher in Luminal B [HER-2(+)] breast cancer, while fmass was lower in HER-2(+) and triple-negative breast cancer. Among the statistically significant prognostic factors, the P values of the transverse sections of the masses were all less than or equal to those of the longitudinal sections. The AUC of fmass in the transverse sections of the masses for predicting ER and PR expression were 0.73 (95% CI 0.65 to 0.80) and 0.67 (95% CI 0.60 to 0.74), respectively, with the optimal cut-off values being 76.50 and 60.66, the sensitivities being 72.45% and 81.98%, the specificities being 66.13% and 45.35%, and the accuracies being 70.93% and 69.77%, respectively. The AUC of fmass in the longitudinal sections of the masses for predicting ER and PR expression were 0.74 (95% CI 0.67 to 0.81) and 0.65 (95% CI 0.58 to 0.72), respectively, with the optimal cut-off values being 131.8 and 137.5, the sensitivities being 69.90% and 66.28%, the specificities being 72.58% and 60.47%, and the accuracies being 70.54% and 64.34%, respectively. The fmass in the transverse sections of the masses was more statistically significant.
CONCLUSIONS
The poor prognosis factors of IBC are related to high Emean, Emin, Emax, Esd, and low fmass. The fmass can predict the expression of ER and PR, and the transverse cut data are more meaningful. SWE is helpful for predicting the invasiveness of IBC.
Humans
;
Breast Neoplasms/metabolism*
;
Female
;
Elasticity Imaging Techniques/methods*
;
Biomarkers, Tumor/metabolism*
;
Middle Aged
;
Adult
;
Prognosis
;
Immunohistochemistry
;
Neoplasm Invasiveness
;
Receptor, ErbB-2/metabolism*
;
Aged
;
Lymphatic Metastasis
;
Receptors, Estrogen/metabolism*
;
Receptors, Progesterone/metabolism*
;
Ki-67 Antigen/metabolism*
7.Single-cell transcriptome analysis reveals the regulatory effects of artesunate on splenic immune cells in polymicrobial sepsis
Jiayun CHEN ; Xueling HE ; Yunmeng BAI ; Jing LIU ; Kwan-Yin WONG ; Lulin XIE ; Qian ZHANG ; Piao LUO ; Peng GAO ; Liwei GU ; Qiuyan GUO ; Guangqing CHENG ; Chen WANG ; Jigang WANG
Journal of Pharmaceutical Analysis 2023;13(7):817-829
Sepsis is characterized by a severe and life-threatening host immune response to polymicrobial infection accompanied by organ dysfunction.Studies on the therapeutic effect and mechanism of immunomod-ulatory drugs on the sepsis-induced hyperinflammatory or immunosuppression states of various im-mune cells remain limited.This study aimed to investigate the protective effects and underlying mechanism of artesunate(ART)on the splenic microenvironment of cecal ligation and puncture-induced sepsis model mice using single-cell RNA sequencing(scRNA-seq)and experimental validations.The scRNA-seq analysis revealed that ART inhibited the activation of pro-inflammatory macrophages recruited during sepsis.ART could restore neutrophils'chemotaxis and immune function in the septic spleen.It inhibited the activation of T regulatory cells but promoted the cytotoxic function of natural killer cells during sepsis.ART also promoted the differentiation and activity of splenic B cells in mice with sepsis.These results indicated that ART could alleviate the inflammatory and/or immunosuppressive states of various immune cells involved in sepsis to balance the immune homeostasis within the host.Overall,this study provided a comprehensive investigation of the regulatory effect of ART on the splenic microenvironment in sepsis,thus contributing to the application of ART as adjunctive therapy for the clinical treatment of sepsis.
8.Clinicopathologic and molecular genetic featuresof metastatic follicular thyroid carcinoma:analyses of 22 cases
Wenwen RAN ; Yixuan LIU ; Weimao KONG ; Qianqian QIAO ; Guangqi LI ; Jigang WANG
Chinese Journal of Clinical and Experimental Pathology 2023;39(12):1453-1459
ABSTARCT Purpose To investigate the clinicopathologic characteristics and genetic mutations of metastatic follicular thy-roid carcinoma(FTC).Methods A total of 22 cases of meta-static FTC were collected,including previous medical history,imaging,treatments and outcomes,and next-generation sequen-cing study and Sanger sequencing were performed in 12 cases.Results There were 16 women and 6 men.Sixteen cases were older than 50 years.Seven cases presented with metastases as the first symptom.Fourteen cases developed metastases 3 to 12 years after thyroid surgery.Sixteen cases developed bone metas-tasis,10 cases had lung metastasis,and 3 cases had brain me-tastasis.Those patients with multiple bone metastases progressed during the follow-up period.The common gene mutations in me-tastases were NRAS p.Q61R(6 cases),HRAS p.Q61R(2 ca-ses)and KRAS p.Q61R(1 case),followed by TERT promoter mutation(8 cases).Other mutated genes included KEL,BRCA1/2,ALK,ROS1,ErbB4,etc.Conclusion FTC has a high misdiagnosis rate.Those diagnosed with FTC should under-go regular systemic examinations to detect potential metastasis,especially in bone,lung,and brain.Further research on the sig-nificance of NRAS and other molecular indicators in FTC metas-tasis will help to better predict its biological behaviors.
9.Shenling Baizhusan Improves Spermatogenesis in Hyperuricemia Oligoasthenospermia Mice by Regulating Nrf2/ARE Pathway
Xiaocui JIANG ; Daizhi TIAN ; Qi LIU ; Xingyu JIANG ; He YU ; Wenyao YU ; Min XIAO ; Jigang CAO
Chinese Journal of Experimental Traditional Medical Formulae 2023;29(15):22-30
ObjectiveTo investigate the effect and mechanism of Shenling Baizhusan on the treatment of oligoasthenospermia with hyperuricemia (HUA). MethodThirty-two male Kunming (KM) mice were randomly divided into blank group (n=6), model group (n=6), high-dose Shenling Baizhusan group (n=7), low-dose Shenling Baizhusan group (n=7), and febuxostat group (n=6). Except for the blank group, all other groups received intraperitoneal injection of potassium oxazinate suspension (600 mg·kg-1) for 7 days. After modeling, the high-dose Shenling Baizhusan group and the low-dose Shenling Baizhusan group were orally administered with 20.14 g·kg-1 and 10.07 g·kg-1 of Shenling Baizhusan, respectively. The Febuxostat group was orally administered with 0.25 g·kg-1 of Febuxostat, while the blank group and model group were orally administered with the same volume of physiological saline. Oral administration was performed once a day for 14 consecutive days, after which samples were collected. Biochemical methods were used to measure serum uric acid (UA), superoxide dismutase (SOD) and malondialdehyde (MDA) in testicular tissue. Hematoxylin-eosin (HE) staining was used to observe the histopathological changes in testicular tissue and evaluate the spermatogenesis function. Automated sperm analyzer was used to measure sperm density and motility. Single-cell gel electrophoresis (SCGE) was used to assess sperm DNA integrity. Terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling (TUNEL) was used to detect testicular cell apoptosis rate. Western blot analysis was performed to measure the protein expression levels of Kelch-like ECH-associated protein 1 (Keap1), nuclear factor E2-related factor 2 (Nrf2), heme oxygenase-1 (HO-1), B-cell lymphoma-2 (Bcl-2), Bcl-2-associated X protein (Bax), and Caspase-3 in testicular tissue. Real-time polymerase chain reaction (PCR) was conducted to evaluate the mRNA expression levels of Keap1, Nrf2, and HO-1 in testicular tissue. ResultCompared with the blank group, the model group showed elevated serum UA level (P<0.01), decreased testicular spermatogenesis function, sperm density, and motility (P<0.01), and increased sperm trailing rate and testicular cell apoptosis rate (P<0.01). Compared with the model group, the high-dose Shenling Baizhusan group showed significant improvements in the above-mentioned indicators (P<0.05, P<0.01). Additionally, the expression levels of Keap1, Bax, and Caspase-3 in testicular tissue were reduced, while the expression levels of Nrf2, HO-1, and Bcl-2 increased (P<0.05, P<0.01). The mRNA level of Keap1 decreased (P<0.05, P<0.01), while the mRNA levels of Nrf2 and HO-1 increased (P<0.05, P<0.01). ConclusionShenling Baizhusan can significantly improve HUA oligoasthenospermia, and its mechanism may be related to the Nrf2/antioxidant response element (ARE) signaling pathway.
10.Hepatic COX1 loss leads to impaired autophagic flux and exacerbates nonalcoholic steatohepatitis.
Qian YU ; Chang LI ; Qinghui NIU ; Jigang WANG ; Zhaodi CHE ; Ke LEI ; He REN ; Boyi MA ; Yixing REN ; Pingping LUO ; Zhuming FAN ; Huan ZHANG ; Zhaohui LIU ; George L TIPOE ; Jia XIAO
Acta Pharmaceutica Sinica B 2023;13(6):2628-2644
The mechanisms underlying autophagic defects in nonalcoholic steatohepatitis (NASH) remain largely unknown. We aimed to elucidate the roles of hepatic cyclooxygenase 1 (COX1) in autophagy and the pathogenesis of diet-induced steatohepatitis in mice. Human nonalcoholic fatty liver disease (NAFLD) liver samples were used to examine the protein expression of COX1 and the level of autophagy. Cox1Δhepa mice and their wildtype littermates were generated and fed with 3 different NASH models. We found that hepatic COX1 expression was increased in patients with NASH and diet-induced NASH mice models accompanied by impaired autophagy. COX1 was required for basal autophagy in hepatocytes and liver specific COX1 deletion exacerbated steatohepatitis by inhibiting autophagy. Mechanistically, COX1 directly interacted with WD repeat domain, phosphoinositide interacting 2 (WIPI2), which was crucial for autophagosome maturation. Adeno-associated virus (AAV)-mediated rescue of WIPI2 reversed the impaired autophagic flux and improved NASH phenotypes in Cox1Δhepa mice, indicating that COX1 deletion-mediated steatohepatitis was partially dependent on WIPI2-mediated autophagy. In conclusion, we demonstrated a novel role of COX1 in hepatic autophagy that protected against NASH by interacting with WIPI2. Targeting the COX1-WIPI2 axis may be a novel therapeutic strategy for NASH.

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