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.Differential analysis of biogas production in simulated experiments of aquitard layers in coal seam fire zones.
Daping XIA ; Yunxia NIU ; Jijun TIAN ; Haichao WANG ; Donglei JIA ; Dan HUANG ; Zhenzhi WANG ; Weizhong ZHAO
Chinese Journal of Biotechnology 2025;41(8):3064-3080
To explore the differences in biological gas production in the waterlogged zone of a coal seam fire-affected area, in this study the in-situ gas production experiment was conducted with the mine water from aquitard layers in coal seam fire zones in Xinjiang. The results showed that the biogas production first increased and then decreased with the increase in distance, and the highest gas production reached 216.55 mL. The changes in key metabolic pathways during the anaerobic fermentation of coal were analyzed, which showed that as the distance from the aquitard layer in the coal seam fire zone increased, the methanogenesis pathways gradually shifted from acetic acid decarboxylation and carbon dioxide reduction to acetic acid decarboxylation and methylamine methanogenesis. The significant variability in the in-situ mine water reservoir conditions contributed to the differences. In addition, the reservoir pressure and temperature increased as the distance from the fire zone became longer, and the salinity of the farthest mine water in the reverse fault was the highest due to the lack of groundwater supply. Pearson correlation analysis revealed significant correlations of microbial communities with key functional genes and the types and concentrations of ions. The ions significantly influencing microbial enzymatic metabolic activities included Al3+, Fe2+, Co2+, Ni2+, Cu2+, Zn2+, Mg2+, PO43-, and Mo6+. The differences in metabolic pathways were attributed to the integrated effects of a co-occurring environment with multiple ions. The gas production simulation experiments and metagenomic analyses provide data support for the practical application of in-situ biogas experiments, laying a foundation for engineering applications.
Biofuels
;
Coal
;
Methane/biosynthesis*
;
Fires
;
Groundwater
;
Coal Mining
;
Fermentation
;
China
;
Anaerobiosis
5.Maternal heterozygous mutation in CHEK1 leads to mitotic arrest in human zygotes.
Beili CHEN ; Jianying GUO ; Ting WANG ; Qianhui LEE ; Jia MING ; Fangfang DING ; Haitao LI ; Zhiguo ZHANG ; Lin LI ; Yunxia CAO ; Jie NA
Protein & Cell 2022;13(2):148-154
6.The value of colposcopy in referral of cervical high-risk HPV positive women
Xiaoping JIA ; Min JIANG ; Yunxia LI ; Yijiang A ; Cailing MA
Journal of Chinese Physician 2022;24(11):1620-1624
Objective:To investigate the clinical value of referral colposcopy in cervical high-risk human papillomavirus (HR-HPV) positive women in cervical cancer screening.Methods:Totally 2 445 cases, which were referred for colposcopic cervical biopsy for cervical HR-HPV positive in Karamay Central Hospital from January 2018 to November 2021 were collected. The status of cervical HR-HPV positive transferred colposcopy in different situations to identify high-grade squamous intraepithelial lesions (HSIL) and above (HISL+ ) was analyzed. The value of referral colposcopy in cervical HR-HPV positive women under different conditions was evaluated.Results:2 445 HR-HPV positive women were referred for colposcopic cervical biopsy, which confirmed 1 447 cases of negative for intraepithelial lesion or malignancy (NILM), 362 cases of low grade squamous intraepithelia lesion (LSIL), 510 cases of HSIL and 126 cases of squamous cell carcinoma (SCC); The complete coincidence rate between colposcopy diagnosis and pathological diagnosis was 67.08%(1 640/2 445), and the Kappa value of consistency test was 0.489. The sensitivity and specificity of colposcopy in the diagnosis of LSIL+ were 91.28% and 69.38%, and HSIL+ were 74.52% and 93.15%. The detection rates of HSIL+ in HPV16/18 positive and other 12 HPV positive patients with abnormal cervical liquid based cytology (TCT) were 64.78%(103/159) and 78.79%(364/462), respectively. The positive rates of HPV16/18 and 12 other HPV positive HSIL+ with normal TCT were 16.46%(82/498) and 6.56%(87/1 326), respectively. The rate of detecting HSIL+ in abnormal areas under colposcopy was 44.69%(534/1 195), and that in routine biopsy was 8.16%(102/1 250).Conclusions:Among the referred for colposcopic cases, the detection rate of HSIL+ was higher in cases with cervical HR-HPV positive and TCT abnormalities. Colposcopy has obvious value in identifying cervical lesions. The accurate diagnosis of cervical lesions is based on cervical biopsy under colposcopy.
7.Clinical study of linear scleroderma " en coup de sabre " with central nervous system involvement in children
Kaili XU ; Yao ZHANG ; Hui DONG ; Ye WU ; Jiangxi XIAO ; Yunxia JIA ; Hui XIONG
Chinese Journal of Applied Clinical Pediatrics 2021;36(3):210-213
Objective:To investigate the clinical features, imaging features, treatment options and prognosis of linear scleroderma with central nervous system involvement.Methods:One case of linear scleroderma " en coup de sabre" (LSES) school-age child suffering from dizziness, vomiting and blurred vision was admitted to the Department of Pediatrics, Peking University First Hospital on March 25, 2019.The curative effect was observed after treatment.The relevant literature was searched, and the characteristics of cases and therapeutic effects were reviewed.Results:The clinical features of this case included recurrent and transient dizziness, vomiting, and blurred vision.Cranial imaging indicated abnormal signals in the left frontotemporal lobe white matter, cingulate gyrus, basal ganglia region, and corpus callosum proximal pressure part, multiple soft meningeal line enhancement and abnormal brain substance enhancement on the brain surface in the lesion area.After 2 months of combined treatment with Methotrexate(MTX) and corticosteroids, some symptoms such as dizziness and vomiting disappeared.Three months after the treatment, in the primary cerebral hemisphere and multiple calcifications in the brain parenchyma, the lesions significantly reduced in cranial imaging.The child was followed up for 11 months and displayed no clinical symptoms.New hair was dense at the alopecia area, and skin color, texture and grain were close to normal at the damaged area.In the review of domestic literature, treatment and prognosis were not involved.Foreign literatures reported 5 cases of children, with the first choice of Methylprednisolone being combined with MTX treatment, significant effect was observed, and consistent with the treatment of this case.Conclusions:In order to detect and treat them as early as possible and improve the prognosis, LSES patients should undergo cranial integrity assessment and neurological imaging examination at an early stage, regardless of clinical manifestations of nervous system involvement.
8.N-methyl-D-aspartic receptor and major depressive disorder
Yunxia ZHU ; Shuming ZHONG ; Shunkai LAI ; Yanbin JIA
Chinese Journal of Behavioral Medicine and Brain Science 2021;30(3):284-288
Major depressive disorder(MDD) is a kind of mental disorder with depression and decreased interest as the main clinical manifestations. The pathogenesis of MDD is unclear, and MDD is characterized by high incidence, high recurrence rate and high suicide rate. At present, the hypothesis of monomamine mechanism can not fully clarify its pathological characteristics, and a considerable number of patients with depression do not respond well to existing antidepressants. N-methyl-D-aspartate receptor (NMDAR) antagonist and γ-aminobutyric acid A(GABAA) receptor positive allosteric regulator have a potential rapid antidepressant effect, which may be a breakthrough in the pathogenesis and clinical treatment of depression. NMDAR has bidirectional regulation, when proper activation of NMDAR can promote dendrite development, neuronal growth and long-term potentiation, but overstimulation of NMDAR can cause toxic reaction, leading to synaptic atrophy and neuronal death. In addition, inflammation can induce changes in NMDAR function and lead to depressive symptoms. At present, ketamine, a new antidepressant NMDAR antagonist, may plays a role in rapid antidepressant and delayed recurrence of depression by increasing the release of BDNF, activating the signal pathway of mammalian target of rapamycin complex 1(mTORC1), and promoting protein synthesis and synaptic plasticity. Thus, ketamine has the effect of rapid antidepressant and delaying the recurrence of depression. However, due to the large variability of NMDAR gene in patients with MDD, its potential functional polymorphism affects clinical symptoms and drug sensitivity. Therefore, by analyzing the latest research at home and abroad, this review comprehensively summarizes the pathogenesis of NMDAR dysfunction, the pathogenesis of MDD, antidepressant treatment and clinical application status, in order to provide theoretical basis for clinical accurate treatment of MDD patients in the future.
9.Expression of hsa_circ_0019413 in the peripheral blood of patients with primary Sj?gren's syndrome
Yunxia LUO ; Jinhai TIAN ; Yao CHEN ; Lijuan ZHAO ; Yan ZHOU ; Jia CAO ; Libin WANG ; Hong ZHU
Chinese Journal of Rheumatology 2020;24(5):302-305,C5-2
Objective:To investigate the expression of hsa_circ_0019413 in the peripheral blood of patients with primary Sj?gren's syndrome (pSS) and its role in the development of pSS disease.Methods:Microarray screening of circ ribonucleic acid (circRNA) changes was first performed in the peripheral blood of 4 pSS patients and 4 healthy controls. Real-time quantitative reverse transcription polymerase chain reaction (qPCR) was used to verify the difference in the expression of hsa_circ_0019413 in the peripheral blood of 30 pSS patients and 30 controls. By establishing the receiver operating characteristic (ROC) curve, the potential diagnostic value of hsa_circ_0019413 in peripheral blood was analyzed, and the expression level of hsa_circ_0019413 was correlated with the clinical presentations of patients with pSS.Results:① By microarray analysis, 437 circRNAs were differentially expressed between the two groups (FC≥2.0, P<0.05), of which 365 were up-regulated and 72 were down-regulated. ② The expression level of hsa_circ_0019413 in pSS patients was significantly higher than that in healthy controls by qPCR. The difference between the two groups was statistically significant ( P<0.05). It showed that hsa_circ_0019413 in peripheral blood of pSS patients had potential diagnostic value by ROC curve analysis [area under the curve (AUC)=0.883, 95% CI (0.782, 0.984), P<0.01]. ③ The expression level of hsa_circ_0019413 was positively correlated with the ESSDAI, ANA, titer of the pSS patients by correlation analysis ( r=0.721, P=0.012; r=0.625, P=0.040), but not with (immunoglobulin (Ig)G or erythrocyte sedimentation rate (ESR). Conclusion:Hsa_circ_0019413 in the peripheral blood may be involved in the development of pSS and may be a biomarker for the diagnosis of pSS.
10. Clinical analysis of 5 cases of dural arteriovenous fistulas complained of pulsatile tinnitus
Xiaodong JIA ; Weixing BAI ; Yunxia GENG ; Guangke WANG ; Shaoguang DING ; Hongjian LIU
Chinese Journal of Otorhinolaryngology Head and Neck Surgery 2020;55(1):56-59
Objective:
The clinical characteristics of dural arteriovenous fistula with pulsatile tinnitus were analyzed to deepen the understanding of the disease.
Methods:
The clinical data of five patients complained of pulsatile tinnitus and diagnosed dural arteriovenous fistula in Henan People's Hospital from May 2013 to June 2018 were retrospectively analyzed, including 3 males and 2 females, aged 27-65 years.
Results:
The main clinical symptoms of the five patients were continuous pulsatile tinnitus, accompanied/not accompanied by headache, memory decline, etc., with a course of three months to 20 years. They were diagnosed as dural arteriovenous fistula by digital subtraction angiography, and three cases of tinnitus disappeared and two cases of tinnitus were relieved after embolization.
Conclusions
The dural arteriovenous fistula is a rare and complicated disease. When the patient complain of the pulsatile tinnitus, the related etiology should be considered and managed properly.

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