39 results on '"Zhi-Xuan Li"'
Search Results
2. Interferon-α stimulates DExH-box helicase 58 to prevent hepatocyte ferroptosis
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Kai-Wei Jia, Ren-Qi Yao, Yi-Wen Fan, Ding-Ji Zhang, Ye Zhou, Min-Jun Wang, Li-Yuan Zhang, Yue Dong, Zhi-Xuan Li, Su-Yuan Wang, Mu Wang, Yun-Hui Li, Lu-Xin Zhang, Ting Lei, Liang-Chen Gui, Shan Lu, Ying-Yun Yang, Si-Xian Wang, Yi-Zhi Yu, Yong-Ming Yao, and Jin Hou
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Ischemia/reperfusion (I/R) ,DExH-box helicase 58 (DHX58) ,Glutathione peroxidase 4 (GPX4) ,m6A modification ,YT521-B homology domain containing 2 (YTHDC2) ,Medicine (General) ,R5-920 ,Military Science - Abstract
Abstract Background Liver ischemia/reperfusion (I/R) injury is usually caused by hepatic inflow occlusion during liver surgery, and is frequently observed during war wounds and trauma. Hepatocyte ferroptosis plays a critical role in liver I/R injury, however, it remains unclear whether this process is controlled or regulated by members of the DEAD/DExH-box helicase (DDX/DHX) family. Methods The expression of DDX/DHX family members during liver I/R injury was screened using transcriptome analysis. Hepatocyte-specific Dhx58 knockout mice were constructed, and a partial liver I/R operation was performed. Single-cell RNA sequencing (scRNA-seq) in the liver post I/R suggested enhanced ferroptosis by Dhx58 hep−/− . The mRNAs and proteins associated with DExH-box helicase 58 (DHX58) were screened using RNA immunoprecipitation-sequencing (RIP-seq) and IP-mass spectrometry (IP-MS). Results Excessive production of reactive oxygen species (ROS) decreased the expression of the IFN-stimulated gene Dhx58 in hepatocytes and promoted hepatic ferroptosis, while treatment using IFN-α increased DHX58 expression and prevented ferroptosis during liver I/R injury. Mechanistically, DHX58 with RNA-binding activity constitutively associates with the mRNA of glutathione peroxidase 4 (GPX4), a central ferroptosis suppressor, and recruits the m6A reader YT521-B homology domain containing 2 (YTHDC2) to promote the translation of Gpx4 mRNA in an m6A-dependent manner, thus enhancing GPX4 protein levels and preventing hepatic ferroptosis. Conclusions This study provides mechanistic evidence that IFN-α stimulates DHX58 to promote the translation of m6A-modified Gpx4 mRNA, suggesting the potential clinical application of IFN-α in the prevention of hepatic ferroptosis during liver I/R injury.
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- 2024
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3. METTL14 downregulation drives S100A4+ monocyte-derived macrophages via MyD88/NF-κB pathway to promote MAFLD progression
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Yue-fan Wang, Wen-li Zhang, Zhi-xuan Li, Yue Liu, Jian Tan, Hao-zan Yin, Zhi-chao Zhang, Xian-jie Piao, Min-hao Ruan, Zhi-hui Dai, Si-jie Wang, Chen-yang Mu, Ji-hang Yuan, Shu-han Sun, Hui Liu, and Fu Yang
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Medicine ,Biology (General) ,QH301-705.5 - Abstract
Abstract Without intervention, a considerable proportion of patients with metabolism‐associated fatty liver disease (MAFLD) will progress from simple steatosis to metabolism‐associated steatohepatitis (MASH), liver fibrosis, and even hepatocellular carcinoma. However, the molecular mechanisms that control progressive MAFLD have yet to be fully determined. Here, we unraveled that the expression of the N6-methyladenosine (m6A) methyltransferase METTL14 is remarkably downregulated in the livers of both patients and several murine models of MAFLD, whereas hepatocyte-specific depletion of this methyltransferase aggravated lipid accumulation, liver injury, and fibrosis. Conversely, hepatic Mettl14 overexpression alleviated the above pathophysiological changes in mice fed on a high-fat diet (HFD). Notably, in vivo and in vitro mechanistic studies indicated that METTL14 downregulation decreased the level of GLS2 by affecting the translation efficiency mediated by YTHDF1 in an m6A-depedent manner, which might help to form an oxidative stress microenvironment and accordingly recruit Cx3cr1 + Ccr2 + monocyte-derived macrophages (Mo-macs). In detail, Cx3cr1 + Ccr2 + Mo-macs can be categorized into M1-like macrophages and S100A4-positive macrophages and then further activate hepatic stellate cells (HSCs) to promote liver fibrosis. Further experiments revealed that CX3CR1 can activate the transcription of S100A4 via CX3CR1/MyD88/NF-κB signaling pathway in Cx3cr1 + Ccr2 + Mo-macs. Restoration of METTL14 or GLS2, or interfering with this signal transduction pathway such as inhibiting MyD88 could ameliorate liver injuries and fibrosis. Taken together, these findings indicate potential therapies for the treatment of MAFLD progression.
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- 2024
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4. Single-cell transcriptome profiling of sepsis identifies HLA-DR low S100A high monocytes with immunosuppressive function
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Ren-Qi Yao, Peng-Yue Zhao, Zhi-Xuan Li, Yu-Yang Liu, Li-Yu Zheng, Yu Duan, Lu Wang, Rong-Li Yang, Hong-Jun Kang, Ji-Wei Hao, Jing-Yan Li, Ning Dong, Yao Wu, Xiao-Hui Du, Feng Zhu, Chao Ren, Guo-Sheng Wu, Zhao-Fan Xia, and Yong-Ming Yao
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Single-cell analysis ,Sepsis ,Immunosuppression ,S100A ,Human leukocyte antigen DR (HLA-DR) ,Monocytes ,Medicine (General) ,R5-920 ,Military Science - Abstract
Abstract Background Sustained yet intractable immunosuppression is commonly observed in septic patients, resulting in aggravated clinical outcomes. However, due to the substantial heterogeneity within septic patients, precise indicators in deciphering clinical trajectories and immunological alterations for septic patients remain largely lacking. Methods We adopted cross-species, single-cell RNA sequencing (scRNA-seq) analysis based on two published datasets containing circulating immune cell profile of septic patients as well as immune cell atlas of murine model of sepsis. Flow cytometry, laser scanning confocal microscopy (LSCM) imaging and Western blotting were applied to identify the presence of S100A9+ monocytes at protein level. To interrogate the immunosuppressive function of this subset, splenic monocytes isolated from septic wild-type or S100a9 −/− mice were co-cultured with naïve CD4+ T cells, followed by proliferative assay. Pharmacological inhibition of S100A9 was implemented using Paquinimod via oral gavage. Results ScRNA-seq analysis of human sepsis revealed substantial heterogeneity in monocyte compartments following the onset of sepsis, for which distinct monocyte subsets were enriched in disparate subclusters of septic patients. We identified a unique monocyte subset characterized by high expression of S100A family genes and low expression of human leukocyte antigen DR (HLA-DR), which were prominently enriched in septic patients and might exert immunosuppressive function. By combining single-cell transcriptomics of murine model of sepsis with in vivo experiments, we uncovered a similar subtype of monocyte significantly associated with late sepsis and immunocompromised status of septic mice, corresponding to HLA-DR low S100A high monocytes in human sepsis. Moreover, we found that S100A9+ monocytes exhibited profound immunosuppressive function on CD4+ T cell immune response and blockade of S100A9 using Paquinimod could partially reverse sepsis-induced immunosuppression. Conclusions This study identifies HLA-DR low S100A high monocytes correlated with immunosuppressive state upon septic challenge, inhibition of which can markedly mitigate sepsis-induced immune depression, thereby providing a novel therapeutic strategy for the management of sepsis.
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- 2023
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5. A lncRNA signature associated with tumor immune heterogeneity predicts distant metastasis in locoregionally advanced nasopharyngeal carcinoma
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Ye-Lin Liang, Yuan Zhang, Xi-Rong Tan, Han Qiao, Song-Ran Liu, Ling-Long Tang, Yan-Ping Mao, Lei Chen, Wen-Fei Li, Guan-Qun Zhou, Yin Zhao, Jun-Yan Li, Qian Li, Sheng-Yan Huang, Sha Gong, Zi-Qi Zheng, Zhi-Xuan Li, Ying Sun, Wei Jiang, Jun Ma, Ying-Qin Li, and Na Liu
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Science - Abstract
Long noncoding RNAs (lncRNAs) can be used for the development of prognostic signatures to predict tumour metastasis. Here the authors identify an immune-associated nine-lncRNA signature for predicting metastasis in a multicentre cohort of locoregionally advanced nasopharyngeal cancer patients.
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- 2022
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6. Terpenoid Glucosides from Gentiana macrophylla That Attenuate TNF-α Induced Pulmonary Inflammation in A549 Cells
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Pei-Qi Huang, Yong-Xin Luo, Yu-Jia Zhang, Zhi-Xuan Li, Yan Wen, Kun Zhang, Dong-Li Li, Jing-Wei Jin, Ri-Hui Wu, and Li-She Gan
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Gentiana macrophylla (Gentianaceae) ,terpenoid glucosides ,pulmonary inflammation ,ELISA ,Organic chemistry ,QD241-441 - Abstract
Four previously undescribed terpenoid glucosides, including one sesquiterpenoid di-glucoside (1), two new iridoid glucosides (2, 3), and a new triterpenoid tri-glucoside (4), were isolated from a 70% ethanol extract of the root of Gentiana macrophylla (Gentianaceae), along with eight known terpenoids. Their structures were determined by spectroscopic techniques, including 1D, 2D NMR, and HRMS (ESI), as well as chemical methods. The absolute configuration of compound 1 was determined by quantum chemical calculation of its theoretical electronic circular dichroism (ECD) spectrum. The sugar moieties of all the new compounds were confirmed to be D-glucose by GC analysis after acid hydrolysis and acetylation. Anti-pulmonary inflammation activity of the iridoids were evaluated on a TNF-α induced inflammation model in A549 cells. Compound 2 could significantly alleviate the release of proinflammatory cytokines IL-1β and IL-8 and increase the expression of anti-inflammatory cytokine IL-10.
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- 2023
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7. Distinct Immune Signatures in Peripheral Blood Predict Chemosensitivity in Intrahepatic Cholangiocarcinoma Patients
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Tong Wu, Ying-Cheng Yang, Bo Zheng, Xue-Bing Shi, Wei Li, Wen-Cong Ma, Shan Wang, Zhi-Xuan Li, Yan-Jing Zhu, Jian-Min Wu, Kai-Ting Wang, Yan Zhao, Rui Wu, Cheng-Jun Sui, Si-Yun Shen, Xuan Wu, Lei Chen, Zhen-Gang Yuan, and Hong-Yang Wang
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Intrahepatic cholangiocarcinoma ,Gemcitabine ,Chemosensitivity ,Peripheral blood mononuclear cells ,Engineering (General). Civil engineering (General) ,TA1-2040 - Abstract
Intrahepatic cholangiocarcinoma (ICC) is the second most common liver cancer. Chemotherapy remains the main therapeutic strategy for advanced ICC patients, but chemosensitivity varies individually. Here, we applied cytometry by time-of-flight (CyTOF) to establish the immune profile of peripheral blood mononuclear cells (PBMCs) on the single-cell level at indicated time points before, during, and after chemotherapy. Multiplex immunofluorescence staining was applied to examine the spatial distribution of certain immune clusters. Tissue microarrays (TMAs) were used for prognostic evaluation. A total of 20 ICC patients treated with gemcitabine (GEM) were enrolled in our study, including eight cases with good response (R) and 12 cases with non-response (NR). Tremendous changes in PBMC composition, including an increased level of CD4/CD8 double-positive T cells (DPT), were observed after chemotherapy. Patients with higher level of CD4+CD45RO+CXCR3+ T cells before treatment had a favorable response to chemotherapy. Our study identified a positive correlation between the percentage of T cell subpopulations and clinical response after chemotherapy, which suggests that it is practical to predict the potential response before treatment by evaluating the proportions of the cell population in PBMCs.
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- 2021
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8. Three-dimensional electroanatomical mapping guidelines for the selection of pacing site to achieve cardiac resynchronization therapy
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Bao-Tong Hua, Li-Jin Pu, Xin Tian, Wen-Juan Song, Hao Li, Chao Wang, Xiao-Xia Shao, Rui Li, Shu-Min Li, Zhi-Xuan Li, Jun-Hua Zou, Ling Zhao, and Jing Wang
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three-dimensional electroanatomical mapping ,left bundle branch area pacing ,coronary venous pacing ,cardiac resynchronization therapy (CRT) ,heart failure ,Diseases of the circulatory (Cardiovascular) system ,RC666-701 - Abstract
ObjectivesWe aimed to evaluate the feasibility of left ventricular electroanatomical mapping to choose between left bundle branch area pacing (LBBAP) or coronary venous pacing (CVP).BackgroundThere are several ways to achieve left ventricular activation in cardiac resynchronization therapy (CRT): LBBAP and CVP are two possible methods of delivering CRT. However, the criteria for choosing the best approach remains unknown.MethodsA total of 71 patients with heart failure, reduced ejection fraction, and left bundle branch block (LBBB) were recruited, of which 38 patients underwent the three-dimensional electroanatomical mapping of the left ventricle to accurately assess whether the left bundle branch was blocked and the block level, while the remaining 33 patients were not mapped. Patients with true LBBB achieved CRT by LBBAP, while patients with pseudo-LBBB achieved CRT by CVP. After a mean follow-up of 6 months and 1 year, the QRS duration and transthoracic echocardiography, including mechanical synchrony indices, were evaluated.ResultsTwenty-five patients with true LBBB received LBBAP, while 13 without true LBBB received CVP. Seventeen patients received LBBAP, and 16 patients received CVP without mapping. Paced QRS duration after the implantation of LBBAP and CVP was significantly narrower in the mapping subgroup compared to the non-mapping subgroup. A significant increase in post-implantation left ventricular ejection fraction was observed in patients with LBBAP or CVP, and the mapping subgroup were better than the non-mapping subgroup. After a 12-month follow-up, atrioventricular, intraventricular, and biventricular synchronization were significantly improved in the mapping subgroup compared to non-mapping groups in both LBBAP and CVP.ConclusionIn our study, three-dimensional electroanatomical mapping was used to choose LBBAP or CVP for heart failure patients, which proved feasible, with better cardiac resynchronization in the long-term follow-up. Therefore, three-dimensional electroanatomical mapping before CRT appears to be a reliable method for heart failure patients with LBBB who are indicated for CRT.
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- 2022
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9. Effects of ER-resident and secreted AGR2 on cell proliferation, migration, invasion, and survival in PANC-1 pancreatic cancer cells
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Xian Hong, Zhi-Xuan Li, Jie Hou, Hui-Yu Zhang, Chun-Yan Zhang, Jian Zhang, He Sun, Li-Hong Pang, Tao Wang, and Zhi-Hui Deng
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AGR2 ,Drug sensitivity ,ER stress ,Pancreatic cancer ,Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Abstract
Abstract Background Anterior gradient-2 (AGR2) is a proto-oncogene involved in tumorigenesis and cancer progression. AGR2, predominantly localized in the endoplasmic reticulum (ER), is also a secreted protein detected in the extracellular compartment in multiple cancers. However, the biological functions of intracellular and extracellular AGR2 remain to be elucidated. Methods Based on the biochemical structure of AGR2 protein, PANC-1 pancreatic cancer cells stably expressing ER-resident or secreted AGR2 were generated by a lentivirus-mediated stable overexpression system. The capacities of cell proliferation, migration, invasion and survival were assessed in PANC-1 stable cells. Moreover, EGFR expression and activation were determined to explore the possible mechanism of AGR2 roles in pancreatic cancer tumorigenesis. Results It was discovered that secreted AGR2, but not ER-resident AGR2, promotes cell proliferation, migration and invasion of PANC-1 cells. Moreover, the data indicated that both the ER-resident and the secreted AGR2 enhance the survival capacity of PANC-1 cells after tunicamycin-induced ER stress and gemcitabine treatment. However, EGFR expression and activation were not found to be involved in AGR2-dependent oncogenic phenotypes in PANC-1 cells. Conclusions Secreted AGR2 is predominantly involved in cell proliferation, migration and invasion in PANC-1 pancreatic cancer cells. Both secreted and ER-resident AGR2 contribute to the survival of PANC-1 cells under the challenging conditions. These findings provide insight into how different localizations of AGR2 have contributed to pancreatic cancer growth, metastasis, and drug sensitivity.
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- 2021
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10. Single‐Cell Transcriptome Analysis Uncovers Intratumoral Heterogeneity and Underlying Mechanisms for Drug Resistance in Hepatobiliary Tumor Organoids
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Yan Zhao, Zhi‐Xuan Li, Yan‐Jing Zhu, Jing Fu, Xiao‐Fang Zhao, Ya‐Ni Zhang, Shan Wang, Jian‐Min Wu, Kai‐Ting Wang, Rui Wu, Cheng‐Jun Sui, Si‐Yun Shen, Xuan Wu, Hong‐Yang Wang, Dong Gao, and Lei Chen
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drug resistance ,hepatobiliary tumor organoid ,single‐cell analysis ,tumor ecosystem ,tumor heterogeneity ,Science - Abstract
Abstract Molecular heterogeneity of hepatobiliary tumor including intertumoral and intratumoral disparity always leads to drug resistance. Here, seven hepatobiliary tumor organoids are generated to explore heterogeneity and evolution via single‐cell RNA sequencing. HCC272 with high status of epithelia‐mesenchymal transition proves broad‐spectrum drug resistance. By examining the expression pattern of cancer stem cells markers (e.g., PROM1, CD44, and EPCAM), it is found that CD44 positive population may render drug resistance in HCC272. UMAP and pseudo‐time analysis identify the intratumoral heterogeneity and distinct evolutionary trajectories, of which catenin beta‐1 (CTNNB1), glyceraldehyde‐3‐phosphate dehydrogenase (GAPDH), and nuclear paraspeckle assembly transcript 1 (NEAT1) advantage expression clusters are commonly shared across hepatobiliary organoids. CellphoneDB analysis further implies that metabolism advantage organoids with enrichment of hypoxia signal upregulate NEAT1 expression in CD44 subgroup and mediate drug resistance that relies on Jak‐STAT pathway. Moreover, metabolism advantage clusters shared in several organoids have similar characteristic genes (GAPDH, NDRG1 (N‐Myc downstream regulated 1), ALDOA, and CA9). The combination of GAPDH and NDRG1 is an independent risk factor and predictor for patient survival. This study delineates heterogeneity of hepatobiliary tumor organoids and proposes that the collaboration of intratumoral heterogenic subpopulations renders malignant phenotypes and drug resistance.
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- 2021
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11. Supplementary Table S9 from Long Noncoding RNA FAM225A Promotes Nasopharyngeal Carcinoma Tumorigenesis and Metastasis by Acting as ceRNA to Sponge miR-590-3p/miR-1275 and Upregulate ITGB3
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Ying Sun, Na Liu, Jun Ma, Ying-Qin Li, Xin Wen, Jian Zhang, Jia Kou, Xiao-Jun He, FoPing Chen, Rui-Qi Liu, Xiao-Dan Huang, Jia-Wei Lv, Lu-Lu Zhang, Li Lin, Guan-Qun Zhou, Zhi-Xuan Li, and Zi-Qi Zheng
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Supplementary Table S9. The predicted miRNAs that bind with FAM225A according to DIANA Tools
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- 2023
12. Supplemental Tables from Long Noncoding RNA TINCR-Mediated Regulation of Acetyl-CoA Metabolism Promotes Nasopharyngeal Carcinoma Progression and Chemoresistance
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Ying Sun, Na Liu, Jun Ma, Si-Si Xu, Feng Li, Ying-Qin Li, Xiao-Jun He, FoPing Chen, Rui-Qi Liu, Guan-Qun Zhou, Lu-Lu Zhang, Jia-Wei Lv, Jia Kou, Li Lin, Yue Chen, Jun-Yan Li, Xu Liu, Jia-Li Guan, Zhi-Xuan Li, and Zi-Qi Zheng
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Supplemental Table S1. qRT-PCR primers used in this study Supplemental Table S2. siRNA sequence used in this study Supplemental Table S3. Primers used for shRNA plasmid construction Supplemental Table S4. Primers used for truncation variants plasmid construction Supplemental Table S5. Primers sequence used for ChIP-PCR assay Supplemental Table S6. Probe sequence of TINCR in situ hybridization (ISH) Supplemental Table S7. Clinical characteristics of nasopharyngeal carcinoma patients according to the high and low expression of TINCR Supplemental Table S8. Univariate and multivariable Cox regression analysis of TINCR expression level and survival Supplemental Table S9. The top10 proteins found by mass spectrometry analysis in the antisense-TINCR group (negative control). Supplemental Table S10. The top10 proteins found by mass spectrometry analysis in the TINCR group. The bold portion shows the proteins that overlap antisense-TINCR
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- 2023
13. Data from Long Noncoding RNA TINCR-Mediated Regulation of Acetyl-CoA Metabolism Promotes Nasopharyngeal Carcinoma Progression and Chemoresistance
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Ying Sun, Na Liu, Jun Ma, Si-Si Xu, Feng Li, Ying-Qin Li, Xiao-Jun He, FoPing Chen, Rui-Qi Liu, Guan-Qun Zhou, Lu-Lu Zhang, Jia-Wei Lv, Jia Kou, Li Lin, Yue Chen, Jun-Yan Li, Xu Liu, Jia-Li Guan, Zhi-Xuan Li, and Zi-Qi Zheng
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Frontier evidence suggests that dysregulation of long noncoding RNAs (lncRNA) is ubiquitous in all human tumors, indicating that lncRNAs might have essential roles in tumorigenesis. Therefore, an in-depth study of the roles of lncRNA in nasopharyngeal carcinoma (NPC) carcinogenesis might be helpful to provide novel therapeutic targets. Here we report that lncRNA TINCR was significantly upregulated in NPC and was associated positively with poor survival. Silencing TINCR inhibited NPC progression and cisplatin resistance. Mechanistically, TINCR bound ACLY and protected it from ubiquitin degradation to maintain total cellular acetyl-CoA levels. Accumulation of cellular acetyl-CoA promoted de novo lipid biosynthesis and histone H3K27 acetylation, which ultimately regulated the peptidyl arginine deiminase 1 (PADI1)–MAPK–MMP2/9 pathway. In addition, insulin-like growth factor 2 mRNA-binding protein 3 interacted with TINCR and slowed its decay, which partially accounted for TINCR upregulation in NPC. These findings demonstrate that TINCR acts as a crucial driver of NPC progression and chemoresistance and highlights the newly identified TINCR–ACLY–PADI1–MAPK–MMP2/9 axis as a potential therapeutic target in NPC.Significance:TINCR-mediated regulation of a PADI1–MAPK–MMP2/9 signaling pathway plays a critical role in NPC progression and chemoresistance, marking TINCR as a viable therapeutic target in this disease.
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- 2023
14. Data from Long Noncoding RNA FAM225A Promotes Nasopharyngeal Carcinoma Tumorigenesis and Metastasis by Acting as ceRNA to Sponge miR-590-3p/miR-1275 and Upregulate ITGB3
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Ying Sun, Na Liu, Jun Ma, Ying-Qin Li, Xin Wen, Jian Zhang, Jia Kou, Xiao-Jun He, FoPing Chen, Rui-Qi Liu, Xiao-Dan Huang, Jia-Wei Lv, Lu-Lu Zhang, Li Lin, Guan-Qun Zhou, Zhi-Xuan Li, and Zi-Qi Zheng
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Long noncoding RNAs (lncRNA) play important roles in the tumorigenesis and progression of cancers. However, the clinical significance of lncRNAs and their regulatory mechanisms in nasopharyngeal carcinogenesis (NPC) are largely unknown. Here, based on a microarray analysis, we identified 384 dysregulated lncRNAs, of which, FAM225A was one of the most upregulated lncRNAs in NPC. FAM225A significantly associated with poor survival in NPC. N(6)-Methyladenosine (m6A) was highly enriched within FAM225A and enhanced its RNA stability. FAM225A functioned as an oncogenic lncRNA that promoted NPC cell proliferation, migration, invasion, tumor growth, and metastasis. Mechanistically, FAM225A functioned as a competing endogenous RNA (ceRNA) for sponging miR-590-3p and miR-1275, leading to the upregulation of their target integrin β3 (ITGB3), and the activation of FAK/PI3K/Akt signaling to promote NPC cell proliferation and invasion. In summary, our study reveals a potential ceRNA regulatory pathway in which FAM225A modulates ITGB3 expression by binding to miR-590-3p and miR-1275, ultimately promoting tumorigenesis and metastasis in NPC.Significance:These findings demonstrate the clinical significance of the lncRNA FAM225A in nasopharyngeal carcinoma (NPC) and the regulatory mechanism involved in NPC development and progression, providing a novel prognostic indicator and promising therapeutic target.
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- 2023
15. Supplementary Tables S1-S5, S7-S8, S10 from Long Noncoding RNA FAM225A Promotes Nasopharyngeal Carcinoma Tumorigenesis and Metastasis by Acting as ceRNA to Sponge miR-590-3p/miR-1275 and Upregulate ITGB3
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Ying Sun, Na Liu, Jun Ma, Ying-Qin Li, Xin Wen, Jian Zhang, Jia Kou, Xiao-Jun He, FoPing Chen, Rui-Qi Liu, Xiao-Dan Huang, Jia-Wei Lv, Lu-Lu Zhang, Li Lin, Guan-Qun Zhou, Zhi-Xuan Li, and Zi-Qi Zheng
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Supplementary Table S1. qPCR primers used in this study Supplementary Table S2. The FAM225A expression level and grouping of samples based on GEO dataset (GSE12452) Supplementary Table S3. Primers used for shRNA plasmid construction Supplementary Table S4. Sequence of miRNA mimic or inhibitor used in this study Supplementary Table S5. Probe sequence of FAM225A in situ hybridization (ISH) Supplementary Table S7. Clinical characteristics of nasopharyngeal carcinoma patients according to the high and low expression of FAM225A. Supplementary Table S8. Univariate and multivariable Cox regression analysis of FAM225A expression level and survival. Supplementary Table S10. Inguinal lymph node metastasis in vivo.
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- 2023
16. Supplementary Figures from Long Noncoding RNA TINCR-Mediated Regulation of Acetyl-CoA Metabolism Promotes Nasopharyngeal Carcinoma Progression and Chemoresistance
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Ying Sun, Na Liu, Jun Ma, Si-Si Xu, Feng Li, Ying-Qin Li, Xiao-Jun He, FoPing Chen, Rui-Qi Liu, Guan-Qun Zhou, Lu-Lu Zhang, Jia-Wei Lv, Jia Kou, Li Lin, Yue Chen, Jun-Yan Li, Xu Liu, Jia-Li Guan, Zhi-Xuan Li, and Zi-Qi Zheng
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Supplemental Figure S1. TINCR is upregulated in six other cancer types. Supplemental Figure S2. GSEA analyses results of TINCR silencing. Supplemental Figure S3. Overexpression of TINCR promotes NPC cell proliferation, metastasis and cisplatin resistance in vitro. Supplemental Figure S4. Overexpression of TINCR reverses the suppressive effects of TINCR knockdown on cell proliferation, cisplatin resistance and metastasis. Supplemental Figure S5. TINCR targets ACLY and impairs its ubiquitination degradation. Supplemental Figure S6. Silencing TINCR has no effects on the expressions of KAT3A and KAT3B. Supplemental Figure S7. The ACLY-binding motif CUGKR is critical for the role of TINCR in maintaining ACLY protein stability and lipid synthesis levels. Supplemental Figure S8. Acetyl-CoA is responsible for TINCR-mediated NPC progression and chemoresistance. Supplemental Figure S9. Correlation between TINCR and PADI1 expression in 16 other cancer types from the TCGA database. Supplemental Figure S10. Silencing TINCR decreases the proteolytic activities of MMP2/9, but had no effects on H3K27ac levels at MMP2/9 promoters. Supplemental Figure S11. IGFBP3 is overexpressed in NPC
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- 2023
17. Supplementary Figures S1-S11 from Long Noncoding RNA FAM225A Promotes Nasopharyngeal Carcinoma Tumorigenesis and Metastasis by Acting as ceRNA to Sponge miR-590-3p/miR-1275 and Upregulate ITGB3
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Ying Sun, Na Liu, Jun Ma, Ying-Qin Li, Xin Wen, Jian Zhang, Jia Kou, Xiao-Jun He, FoPing Chen, Rui-Qi Liu, Xiao-Dan Huang, Jia-Wei Lv, Lu-Lu Zhang, Li Lin, Guan-Qun Zhou, Zhi-Xuan Li, and Zi-Qi Zheng
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Supplementary Figure S1. FAM225A is overexpressed in NPC and other tumor types. Supplementary Figure S2. Silencing METTL3 resulted in the decreased m6A level of total RNA. Supplementary Figure S3. FAM225A promotes NPC cell proliferation, migration and invasion in vitro. Supplementary Figure S4. FISH assay showed that FAM225A was mainly located in cytoplasmic. Supplementary Figure S5. FAM225A acts as a ceRNA for miR-590-3p and miR-1275. Supplementary Figure S6. The expression of FAM225A is negatively correlated with miR-590-3p and miR-1275 expression. Supplementary Figure S7. Silencing of miR-590-3p and miR-1275 endows NP69 and N2Tert cells with carcinogenicity in vitro. Supplementary Figure S8. miR-590-3p/miR-1275 are responsible for FAM225A-mediated proliferation, migration and invasion. Supplementary Figure S9. Correlation between FAM225A and ITGB3 expression in 12 other cancer types from the TCGA database. Supplementary Figure S10. FAM225A promotes NPC cell metastasis in vivo. Supplementary Figure S11. ITGB3 is responsible for FAM225A-meidated tumorigenesis and metastasis in vivo.
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- 2023
18. Spatial maps of hepatocellular carcinoma transcriptomes reveal spatial expression patterns in tumor immune microenvironment
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Yue-fan Wang, Sheng-xian Yuan, Hui Jiang, Zhi-xuan Li, Hao-zan Yin, Jian Tan, Zhi-hui Dai, Chun-mei Ge, Shu-han Sun, and Fu Yang
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Carcinoma, Hepatocellular ,Liver Neoplasms ,Biomarkers, Tumor ,Tumor Microenvironment ,Humans ,Medicine (miscellaneous) ,Transcriptome ,Pharmacology, Toxicology and Pharmaceutics (miscellaneous) - Published
- 2022
19. Sustainable Operation of Fine-Dining Restaurants: Antecedents and Consequences of Customers’ Self-Image Congruity at a Cantonese Michelin-Starred Restaurant Based on the Value-Attitude-Behavior Model
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Si-Fan Liu, Zhi-Xuan Li, and Yang Zhang
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self-congruity theory ,willingness to pay a price premium ,Renewable Energy, Sustainability and the Environment ,Geography, Planning and Development ,value-attitude-behavior framework ,Building and Construction ,perceived quality ,Management, Monitoring, Policy and Law ,fine-dining restaurant ,generational theory - Abstract
With the current rapid economic development, restaurant practitioners need to pay attention to the issue of how fine-dining restaurants can achieve sustainable operations in the presence of fierce competition. Fine-dining restaurants have gradually become a reflection of consumers’ self-image; therefore, this study combines the VAB framework, self-congruity theory, and generational theory to investigate the relationships among perceived quality, customers’ self-image congruity, and their willingness to pay a price premium (WTP-PP). Current research uses generation as a moderator to explore the intergenerational differences between Gen X and Gen Y. We adopted Smart-PLS to conduct SEM and MGA. The results of this study showed that the quality of the atmosphere and food induced actual, ideal, and ideal social self-image congruity, while the quality of the service could not only induce the above three aspects of self-consistency but also induce social self-image congruity and have a significant positive impact on WTP-PP. Meanwhile, WTP-PP was also significantly affected by actual self-image congruity and ideal self-image congruity. Furthermore, Gen Yers cared more about the atmosphere quality than Gen X. Contrarily, Gen Xers valued food quality more than Gen Y.
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- 2023
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20. VIRMA promotes nasopharyngeal carcinoma, tumorigenesis, and metastasis by upregulation of E2F7 in an m6A-dependent manner
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Zi-Qi Zheng, Zhuo-Hui Huang, Ye-Lin Liang, Wei-Hong Zheng, Cheng Xu, Zhi-Xuan Li, Na Liu, Pan-Yang Yang, Ying-Qin Li, Jun Ma, Ying Sun, Ling-Long Tang, and Denghui Wei
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Cell Biology ,Molecular Biology ,Biochemistry - Abstract
The N6-methyladenosine (m6A) modification possesses new and essential roles in tumor initiation and progression by regulating mRNA biology. However, the role of aberrant m6A regulation in nasopharyngeal carcinoma (NPC) remains unclear. Here, through comprehensive analyses of NPC cohorts from the GEO database (GES12452, GSE12349, and GSE61218) and our internal cohort, we identified that VIRMA, an m6A writer, is significantly upregulated in NPC and plays an essential role in tumorigenesis and metastasis of NPC, both in vitro and in vivo. High VIRMA expression served as a prognostic biomarker and was associated with poor outcomes in patients with NPC. Mechanistically, VIRMA mediated the m6A methylation of E2F7 3′-UTR, then IGF2BP2 bound and maintained the stability of E2F7 mRNA. An integrative high-throughput sequencing approach revealed that E2F7 drives a unique transcriptome distinct from the classical E2F family in NPC, which functioned as an oncogenic transcriptional activator. E2F7 cooperated with CBFB-recruited RUNX1 in a non-canonical manner to transactivate ITGA2, ITGA5, and NTRK1, strengthening Akt signaling-induced tumor-promoting effect. These results together demonstrate the role of VIRMA as an m6A writer that modulates E2F7 expression to control the transcription program of NPC, unveiling an m6A modulator that is essential for NPC tumorigenesis and metastasis.
- Published
- 2023
21. m6A-enriched lncRNA LINC00839 promotes tumor progression by enhancing TAF15-mediated transcription of amine oxidase AOC1 in nasopharyngeal carcinoma
- Author
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Wei-Hong Zheng, Zhi-Qing Long, Zi-Qi Zheng, Lu-Lu Zhang, Ye-Lin Liang, Zhi-Xuan Li, Jia-Wei Lv, Jia Kou, Xiao-Hong Hong, Shi-Wei He, Rui Xu, Guan-Qun Zhou, Na Liu, Jun Ma, Ying Sun, Li Lin, and Denghui Wei
- Subjects
Cell Biology ,Molecular Biology ,Biochemistry - Published
- 2023
22. Effects of ER-resident and secreted AGR2 on cell proliferation, migration, invasion, and survival in PANC-1 pancreatic cancer cells
- Author
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Chun-Yan Zhang, Zhi-Xuan Li, Hui-Yu Zhang, Jie Hou, Xian Hong, Jian Zhang, Zhi-Hui Deng, He Sun, Li-Hong Pang, and Tao Wang
- Subjects
0301 basic medicine ,Cancer Research ,Antimetabolites, Antineoplastic ,AGR2 ,Biology ,medicine.disease_cause ,Endoplasmic Reticulum ,Deoxycytidine ,Proto-Oncogene Mas ,lcsh:RC254-282 ,Metastasis ,03 medical and health sciences ,0302 clinical medicine ,Mucoproteins ,Cell Movement ,Pancreatic cancer ,Genetics ,medicine ,Extracellular ,Biomarkers, Tumor ,Tumor Cells, Cultured ,Humans ,Neoplasm Invasiveness ,Cell Proliferation ,Oncogene Proteins ,Cell growth ,Cancer ,medicine.disease ,Endoplasmic Reticulum Stress ,lcsh:Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,Gemcitabine ,Gene Expression Regulation, Neoplastic ,Pancreatic Neoplasms ,030104 developmental biology ,Oncology ,Drug Resistance, Neoplasm ,030220 oncology & carcinogenesis ,Cancer research ,Unfolded protein response ,Carcinogenesis ,ER stress ,Research Article ,Drug sensitivity - Abstract
Background Anterior gradient-2 (AGR2) is a proto-oncogene involved in tumorigenesis and cancer progression. AGR2, predominantly localized in the endoplasmic reticulum (ER), is also a secreted protein detected in the extracellular compartment in multiple cancers. However, the biological functions of intracellular and extracellular AGR2 remain to be elucidated. Methods Based on the biochemical structure of AGR2 protein, PANC-1 pancreatic cancer cells stably expressing ER-resident or secreted AGR2 were generated by a lentivirus-mediated stable overexpression system. The capacities of cell proliferation, migration, invasion and survival were assessed in PANC-1 stable cells. Moreover, EGFR expression and activation were determined to explore the possible mechanism of AGR2 roles in pancreatic cancer tumorigenesis. Results It was discovered that secreted AGR2, but not ER-resident AGR2, promotes cell proliferation, migration and invasion of PANC-1 cells. Moreover, the data indicated that both the ER-resident and the secreted AGR2 enhance the survival capacity of PANC-1 cells after tunicamycin-induced ER stress and gemcitabine treatment. However, EGFR expression and activation were not found to be involved in AGR2-dependent oncogenic phenotypes in PANC-1 cells. Conclusions Secreted AGR2 is predominantly involved in cell proliferation, migration and invasion in PANC-1 pancreatic cancer cells. Both secreted and ER-resident AGR2 contribute to the survival of PANC-1 cells under the challenging conditions. These findings provide insight into how different localizations of AGR2 have contributed to pancreatic cancer growth, metastasis, and drug sensitivity.
- Published
- 2021
23. Seasonal and spatiotemporal differences in the public transport-based mobility of elderly population: A case study of Wuhu City in Anhui Province
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Feng Zhen, Zhi-xuan Li, Shanqi Zhang, and Yu Yang
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Geography ,Ecology ,business.industry ,Public transport ,Elderly population ,Geography, Planning and Development ,Earth and Planetary Sciences (miscellaneous) ,business ,Socioeconomics ,Nature and Landscape Conservation - Published
- 2021
24. Development and validation of a web‐based calculator to predict individualized conditional risk of site‐specific recurrence in nasopharyngeal carcinoma: Analysis of 10,058 endemic cases
- Author
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Si-Si Xu, Zhi-Xuan Li, Yan Ping Mao, Fo-Ping Chen, Xing-Li Yang, Wei-Hong Zheng, Jia Kou, Bin Deng, Zi-Qi Zheng, Jia-Wei Lv, Chen-Fei Wu, Ying Sun, Yue Chen, Li Lin, Dan-Wan Wen, and Jun Ma
- Subjects
0301 basic medicine ,Oncology ,Conditional risk ,Cancer Research ,medicine.medical_specialty ,medicine.medical_treatment ,endemic nasopharyngeal carcinoma ,03 medical and health sciences ,0302 clinical medicine ,Conditional survival ,big data ,Internal medicine ,medicine ,Humans ,web‐based, individualized prediction model, overall survival, disease‐free survival, locoregional relapse‐free survival, distant metastasis‐free survival, NPC‐specific survival ,Stage (cooking) ,Neoplasm Staging ,Retrospective Studies ,Web-based calculator ,Internet ,conditional survival ,Nasopharyngeal Carcinoma ,business.industry ,Inverse probability weighting ,Nasopharyngeal Neoplasms ,Original Articles ,medicine.disease ,Radiation therapy ,030104 developmental biology ,Nasopharyngeal carcinoma ,030220 oncology & carcinogenesis ,Cohort ,Original Article ,Neoplasm Recurrence, Local ,business - Abstract
Background Conditional survival (CS) provides dynamic prognostic estimates by considering the patients existing survival time. Since CS for endemic nasopharyngeal carcinoma (NPC) is lacking, we aimed to assess the CS of endemic NPC and establish a web‐based calculator to predict individualized, conditional site‐specific recurrence risk. Methods Using an NPC‐specific database with a big‐data intelligence platform, 10,058 endemic patients with non‐metastatic stage I–IVA NPC receiving intensity‐modulated radiotherapy with or without chemotherapy between April 2009 and December 2015 were investigated. Crude CS estimates of conditional overall survival (COS), conditional disease‐free survival (CDFS), conditional locoregional relapse‐free survival (CLRRFS), conditional distant metastasis‐free survival (CDMFS), and conditional NPC‐specific survival (CNPC‐SS) were calculated. Covariate‐adjusted CS estimates were generated using inverse probability weighting. A prediction model was established using competing risk models and was externally validated with an independent, non‐metastatic stage I–IVA NPC cohort undergoing intensity‐modulated radiotherapy with or without chemotherapy (n = 601) at another institution. Results The median follow‐up of the primary cohort was 67.2 months. The 5‐year COS, CDFS, CLRRFS, CDMFS, and CNPC‐SS increased from 86.2%, 78.1%, 89.8%, 87.3%, and 87.6% at diagnosis to 87.3%, 87.7%, 94.4%, 96.0%, and 90.1%, respectively, for an existing survival time of 3 years since diagnosis. Differences in CS estimates between prognostic factor subgroups of each endpoint were noticeable at diagnosis but diminished with time, whereas an ever‐increasing disparity in CS between different age subgroups was observed over time. Notably, the prognoses of patients that were poor at diagnosis improved greatly as patients survived longer. For individualized CS predictions, we developed a web‐based model to estimate the conditional risk of local (C‐index, 0.656), regional (0.667), bone (0.742), lung (0.681), and liver (0.711) recurrence, which significantly outperformed the current staging system (P < 0.001). The performance of this web‐based model was further validated using an external validation cohort (median follow‐up, 61.3 months), with C‐indices of 0.672, 0.736, 0.754, 0.663, and 0.721, respectively. Conclusions We characterized the CS of endemic NPC in the largest cohort to date. Moreover, we established a web‐based calculator to predict the CS of site‐specific recurrence, which may help to tailor individualized, risk‐based, time‐adapted follow‐up strategies.
- Published
- 2020
25. Long Noncoding RNA TINCR-Mediated Regulation of Acetyl-CoA Metabolism Promotes Nasopharyngeal Carcinoma Progression and Chemoresistance
- Author
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Ying Sun, Ying-Qin Li, Jun Ma, Jia-Li Guan, Rui-Qi Liu, Zhi-Xuan Li, Na Liu, Jia Kou, Fo-Ping Chen, Guan-Qun Zhou, Si-Si Xu, Jun-Yan Li, Jia-Wei Lv, Li Lin, Yue Chen, Xiao-Jun He, Lu-Lu Zhang, Feng Li, Zi-Qi Zheng, and Xu Liu
- Subjects
0301 basic medicine ,Cancer Research ,RNA Stability ,Antineoplastic Agents ,medicine.disease_cause ,03 medical and health sciences ,0302 clinical medicine ,Downregulation and upregulation ,Acetyl Coenzyme A ,Cell Movement ,Protein-Arginine Deiminase Type 1 ,Cell Line, Tumor ,Lipid biosynthesis ,medicine ,Animals ,Humans ,Gene silencing ,Regulation of gene expression ,Mice, Inbred BALB C ,Nasopharyngeal Carcinoma ,biology ,Ubiquitination ,RNA-Binding Proteins ,Prognosis ,medicine.disease ,Xenograft Model Antitumor Assays ,Long non-coding RNA ,Gene Expression Regulation, Neoplastic ,030104 developmental biology ,Histone ,Oncology ,Nasopharyngeal carcinoma ,Drug Resistance, Neoplasm ,030220 oncology & carcinogenesis ,ATP Citrate (pro-S)-Lyase ,biology.protein ,Cancer research ,RNA, Long Noncoding ,Cisplatin ,Carcinogenesis - Abstract
Frontier evidence suggests that dysregulation of long noncoding RNAs (lncRNA) is ubiquitous in all human tumors, indicating that lncRNAs might have essential roles in tumorigenesis. Therefore, an in-depth study of the roles of lncRNA in nasopharyngeal carcinoma (NPC) carcinogenesis might be helpful to provide novel therapeutic targets. Here we report that lncRNA TINCR was significantly upregulated in NPC and was associated positively with poor survival. Silencing TINCR inhibited NPC progression and cisplatin resistance. Mechanistically, TINCR bound ACLY and protected it from ubiquitin degradation to maintain total cellular acetyl-CoA levels. Accumulation of cellular acetyl-CoA promoted de novo lipid biosynthesis and histone H3K27 acetylation, which ultimately regulated the peptidyl arginine deiminase 1 (PADI1)–MAPK–MMP2/9 pathway. In addition, insulin-like growth factor 2 mRNA-binding protein 3 interacted with TINCR and slowed its decay, which partially accounted for TINCR upregulation in NPC. These findings demonstrate that TINCR acts as a crucial driver of NPC progression and chemoresistance and highlights the newly identified TINCR–ACLY–PADI1–MAPK–MMP2/9 axis as a potential therapeutic target in NPC. Significance: TINCR-mediated regulation of a PADI1–MAPK–MMP2/9 signaling pathway plays a critical role in NPC progression and chemoresistance, marking TINCR as a viable therapeutic target in this disease.
- Published
- 2020
26. Single-cell transcriptome profiling of the immune space-time landscape reveals dendritic cell regulatory program in polymicrobial sepsis
- Author
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Ren-qi Yao, Zhi-xuan Li, Li-xue Wang, Yu-xuan Li, Li-yu Zheng, Ning Dong, Yao Wu, Zhao-fan Xia, Timothy R. Billiar, Chao Ren, and Yong-ming Yao
- Subjects
Mice ,Gene Expression Profiling ,Sepsis ,Medicine (miscellaneous) ,Animals ,COVID-19 ,Humans ,Dendritic Cells ,Pharmacology, Toxicology and Pharmaceutics (miscellaneous) ,T-Lymphocytes, Regulatory - Published
- 2022
27. WTAP-mediated m(6)A modification of lncRNA DIAPH1-AS1 enhances its stability to facilitate nasopharyngeal carcinoma growth and metastasis
- Author
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Zhi-Xuan Li, Zi-Qi Zheng, Pan-Yang Yang, Li Lin, Guan-Qun Zhou, Jia-Wei Lv, Lu-Lu Zhang, FoPing Chen, Ying-Qin Li, Chen-Fei Wu, Feng Li, Jun Ma, Na Liu, and Ying Sun
- Subjects
Adenosine ,Nasopharyngeal Carcinoma ,Carcinogenesis ,Formins ,Membrane Proteins ,RNA-Binding Proteins ,Cell Cycle Proteins ,Nasopharyngeal Neoplasms ,Cell Biology ,LIM Domain Proteins ,Article ,Epigenesis, Genetic ,Cytoskeletal Proteins ,Cell Line, Tumor ,Humans ,RNA, Long Noncoding ,RNA Splicing Factors ,Neoplasm Metastasis ,Molecular Biology ,Adaptor Proteins, Signal Transducing ,Cell Proliferation - Abstract
As the most predominant RNA epigenetic regulation in eukaryotic cells, N(6)-methyladenosine (m(6)A) plays a critical role in human tumorigenesis and cancer progression. However, the biological function and molecular mechanism of m(6)A regulation in naso-pharyngeal carcinoma (NPC) remain elusive. Here, we showed that Wilms’ tumor 1-associating protein (WTAP) expression was apparently upregulated in NPC, and increased WTAP was associated with poor prognosis. WTAP upregulated in NPC was fine-tuned by KAT3A-mediated H3K27 acetylation. Functionally, WTAP was required for the growth and metastasis of NPC. Mechanistically, lncRNA DIAPH1-AS1 was identified as a bona fide m(6)A target of WTAP. WTAP-mediated m(6)A modification of DIAPH1-AS1 enhanced its stability relying on the m(6)A reader IGF2BP2-dependent pathway. Furthermore, DIAPH1-AS1 acted as a molecular adaptor that promoted MTDH-LASP1 complex formation and upregulated LASP1 expression, ultimately facilitating NPC growth and metastasis. Thus, WTAP-mediated DIAPH1-AS1 m(6)A methylation is required for NPC tumorigenesis and metastasis.
- Published
- 2022
28. Efficient Computation of Map-scale Continuous Mutual Information on Chip in Real Time
- Author
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Keshav Gupta, Peter Zhi Xuan Li, Sertac Karaman, and Vivienne Sze
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FOS: Computer and information sciences ,Computer Science - Robotics ,Hardware Architecture (cs.AR) ,Computer Science - Hardware Architecture ,Robotics (cs.RO) - Abstract
Exploration tasks are essential to many emerging robotics applications, ranging from search and rescue to space exploration. The planning problem for exploration requires determining the best locations for future measurements that will enhance the fidelity of the map, for example, by reducing its total entropy. A widely-studied technique involves computing the Mutual Information (MI) between the current map and future measurements, and utilizing this MI metric to decide the locations for future measurements. However, computing MI for reasonably-sized maps is slow and power hungry, which has been a bottleneck towards fast and efficient robotic exploration. In this paper, we introduce a new hardware accelerator architecture for MI computation that features a low-latency, energy-efficient MI compute core and an optimized memory subsystem that provides sufficient bandwidth to keep the cores fully utilized. The core employs interleaving to counter the recursive algorithm, and workload balancing and numerical approximations to reduce latency and energy consumption. We demonstrate this optimized architecture with a Field-Programmable Gate Array (FPGA) implementation, which can compute MI for all cells in an entire 201-by-201 occupancy grid ({\em e.g.}, representing a 20.1m-by-20.1m map at 0.1m resolution) in 1.55 ms while consuming 1.7 mJ of energy, thus finally rendering MI computation for the whole map real time and at a fraction of the energy cost of traditional compute platforms. For comparison, this particular FPGA implementation running on the Xilinx Zynq-7000 platform is two orders of magnitude faster and consumes three orders of magnitude less energy per MI map compute, when compared to a baseline GPU implementation running on an NVIDIA GeForce GTX 980 platform. The improvements are more pronounced when compared to CPU implementations of equivalent algorithms.
- Published
- 2021
29. Treatment and bioresources utilization of traditional Chinese medicinal herb residues: Recent technological advances and industrial prospect
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Jing Gao, Yong Hu, Chao Huang, Yi Wu, Zhi-Xuan Li, and Zhong-Ying Huang
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Solid waste management ,China ,Environmental Engineering ,Plants, Medicinal ,Environmental pollution ,General Medicine ,Management, Monitoring, Policy and Law ,Environmentally friendly ,Sustainability ,Medicinal herbs ,Business ,Biochemical engineering ,Medicine, Chinese Traditional ,Waste Management and Disposal - Abstract
Traditional Chinese medicine (TCM) has wide application and important functions in curing many diseases, but a great number of herb residues are usually generated after its manufacture and usage. Without proper and timely treatment, these traditional Chinese medicinal herb (TCMH) residues will cause some environmental pollution. In addition to treatment, bioresources utilization of TCMH residues is also important for its great potential as a suitable feedstock for the production of energy, materials, and chemicals. In this situation, advanced and well-designed solid waste management is important to make the TCM industry environmentally friendly and economically attractive. In this review article, the recent progress focusing on various methods for TCMH residues treatment and bioresources utilization are introduced in detail. In particular, the technologies for thermochemical conversion and biochemical conversion of TCMH residues are mainly focused on in order to show how to fulfill effective and efficient bioresources utilization. Besides, some other technologies which are suitable for the treatment and bioresources utilization of TCMH residues are presented as well. Finally, some industrial prospects are given from the economic, operational, and environmental aspects for the further development of treatment and bioresources utilization of TCMH residues. Overall, this work can provide some systematical and comprehensive information for the development of technologies that help sustainably manage the herb residues generated in the TCM industry.
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- 2021
30. High-Throughput Computation of Shannon Mutual Information on Chip
- Author
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Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology. Department of Aeronautics and Astronautics, Zhi Xuan Li, Peter, Zhang, Zhengdong, Karaman, Sertac, Sze, Vivienne, Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology. Department of Aeronautics and Astronautics, Zhi Xuan Li, Peter, Zhang, Zhengdong, Karaman, Sertac, and Sze, Vivienne
- Published
- 2021
31. Prognostic potential of liquid biopsy tracking in the posttreatment surveillance of patients with nonmetastatic nasopharyngeal carcinoma
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Guan-Qun Zhou, Chen-Fei Wu, Zi-Qi Zheng, Xiao-Dan Huang, Dan-Wan Wen, Zhi-Xuan Li, Jia-Wei Lv, Fo-Ping Chen, Yue Chen, Jia Kou, Ying Sun, Xiao-Jun He, and Li Lin
- Subjects
Adult ,Male ,Cancer Research ,medicine.medical_specialty ,Epstein-Barr Virus Infections ,Herpesvirus 4, Human ,Databases, Factual ,medicine.medical_treatment ,Disease ,Gastroenterology ,Sensitivity and Specificity ,Virus ,03 medical and health sciences ,0302 clinical medicine ,Interquartile range ,Internal medicine ,medicine ,Humans ,030212 general & internal medicine ,Liquid biopsy ,Neoplasm Metastasis ,Pathological ,Nasopharyngeal Carcinoma ,business.industry ,Incidence ,Liquid Biopsy ,Distant metastasis ,Reproducibility of Results ,Nasopharyngeal Neoplasms ,medicine.disease ,Prognosis ,Radiation therapy ,Oncology ,Nasopharyngeal carcinoma ,030220 oncology & carcinogenesis ,Population Surveillance ,DNA, Viral ,Female ,Neoplasm Recurrence, Local ,business - Abstract
BACKGROUND The current study was performed to investigate whether circulating cell-free Epstein-Barr virus DNA (cfEBV DNA) would be useful for posttreatment surveillance in patients with nasopharyngeal carcinoma (NPC). METHODS The authors identified a total of 1984 nondisseminated NPC patients from an institutional big-data research platform. Blood samples were collected within 3 months of the completion of radiotherapy and every 3 to 12 months thereafter for cfEBV DNA analysis. Patients were followed until disease recurrence was detected or for a median of 60 months. Diagnostic performance was assessed by calculating the sensitivity, specificity, and accuracy based on the clinical detection of disease recurrence by conventional surveillance modalities (imaging scans and pathological examination). RESULTS During follow-up, a total of 767 patients (38.7%) had detectable cfEBV DNA. The recurrence rate among these patients was 63.8% (489 of 767 patients), which was significantly higher than that in patients with undetectable cfEBV DNA (8.6%; 105 of 1217 patients). cfEBV DNA sensitivity, specificity, and accuracy were 68.8%, 80.0%, and 78.2%, respectively, for local recurrence; 80.2%, 80.0%, and 85.9%, respectively, for regional recurrence; and 91.1%, 80.0%, and 92.8%, respectively, for distant metastasis. cfEBV DNA was found to have higher sensitivity for the detection of extrapulmonary metastases (94.9%-96.5%) compared with pulmonary metastases (78.4%). It is interesting to note that among the patients with disease recurrence with detectable cfEBV DNA, positive cfEBV DNA results preceded radiological and/or clinical evidence of disease recurrence by a median of 2.3 months (interquartile range, 0.1-9.5 months). In addition, of the 278 cfEBV DNA-positive patients who did not develop disease recurrence, 227 (81.7%) had transiently positive cfEBV DNA that fell to undetectable levels during long-term monitoring. CONCLUSIONS Plasma cfEBV DNA in patients with NPC appears to be an early sign of tumor recurrence, especially extrapulmonary metastases.
- Published
- 2019
32. Comprehensive characterization of the alternative splicing landscape in head and neck squamous cell carcinoma reveals novel events associated with tumorigenesis and the immune microenvironment
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Jia Kou, Guan-Qun Zhou, Jun Ma, Jia-Li Guan, Feng Li, Zi-Qi Zheng, Fo-Ping Chen, Xiao-Jun He, Rui-Qi Liu, Ying Sun, Jia-Wei Lv, Zhi-Xuan Li, Zhuo-Hui Wei, Li Lin, Lu-Lu Zhang, and Xiao-Dan Huang
- Subjects
0301 basic medicine ,Male ,Chemokine ,Carcinogenesis ,Medicine (miscellaneous) ,medicine.disease_cause ,head and neck squamous cell carcinoma ,Disease-Free Survival ,Cohort Studies ,03 medical and health sciences ,Splicing factor ,alternative splicing ,0302 clinical medicine ,Immune system ,medicine ,Biomarkers, Tumor ,Tumor Microenvironment ,Humans ,immune microenvironment ,Pharmacology, Toxicology and Pharmaceutics (miscellaneous) ,Viral Carcinogenesis ,biology ,Squamous Cell Carcinoma of Head and Neck ,Gene Expression Profiling ,Alternative splicing ,Papillomavirus Infections ,medicine.disease ,Prognosis ,Head and neck squamous-cell carcinoma ,tumorigenesis ,030104 developmental biology ,Head and Neck Neoplasms ,030220 oncology & carcinogenesis ,RNA splicing ,Cancer research ,biology.protein ,Female ,Research Paper ,genome-wide analysis - Abstract
Alternative splicing (AS) has emerged as a key event in tumor development and microenvironment formation. However, comprehensive analysis of AS and its clinical significance in head and neck squamous cell carcinoma (HNSC) is urgently required. Methods: Genome-wide profiling of AS events using RNA-Seq data from The Cancer Genome Atlas (TCGA) program was performed in a cohort of 464 patients with HNSC. Cancer-associated AS events (CASEs) were identified between paired HNSC and adjacent normal tissues and evaluated in functional enrichment analysis. Splicing networks and prognostic models were constructed using bioinformatics tools. Unsupervised clustering of the CASEs identified was conducted and associations with clinical, molecular and immune features were analyzed. Results: We detected a total of 32,309 AS events and identified 473 CASEs in HNSC; among these, 91 were validated in an independent cohort (n = 15). Functional protein domains were frequently altered, especially by CASEs affecting cancer drivers, such as PCSK5. CASE parent genes were significantly enriched in pathways related to HNSC and the tumor immune microenvironment, such as the viral carcinogenesis (FDR < 0.001), Human Papillomavirus infection (FDR < 0.001), chemokine (FDR < 0.001) and T cell receptor (FDR
- Published
- 2019
33. Long Noncoding RNA FAM225A Promotes Nasopharyngeal Carcinoma Tumorigenesis and Metastasis by Acting as ceRNA to Sponge miR-590-3p/miR-1275 and Upregulate ITGB3
- Author
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Zi-Qi Zheng, Lu-Lu Zhang, Jun Ma, Na Liu, Ying-Qin Li, Li Lin, Rui-Qi Liu, Zhi-Xuan Li, Xiao-Jun He, Ying Sun, Xin Wen, Guan-Qun Zhou, Jia-Wei Lv, Xiao-Dan Huang, Fo-Ping Chen, Jian Zhang, and Jia Kou
- Subjects
0301 basic medicine ,Cancer Research ,Lung Neoplasms ,Carcinogenesis ,Mice, Nude ,Apoptosis ,Biology ,medicine.disease_cause ,03 medical and health sciences ,Mice ,0302 clinical medicine ,Downregulation and upregulation ,Cell Movement ,otorhinolaryngologic diseases ,medicine ,Tumor Cells, Cultured ,Animals ,Humans ,PI3K/AKT/mTOR pathway ,Cell Proliferation ,Regulation of gene expression ,Mice, Inbred BALB C ,Nasopharyngeal Carcinoma ,Microarray analysis techniques ,Competing endogenous RNA ,Integrin beta3 ,Nasopharyngeal Neoplasms ,medicine.disease ,Prognosis ,Xenograft Model Antitumor Assays ,Long non-coding RNA ,Gene Expression Regulation, Neoplastic ,stomatognathic diseases ,MicroRNAs ,030104 developmental biology ,Oncology ,Nasopharyngeal carcinoma ,030220 oncology & carcinogenesis ,Cancer research ,Female ,RNA, Long Noncoding ,Transcriptome - Abstract
Long noncoding RNAs (lncRNA) play important roles in the tumorigenesis and progression of cancers. However, the clinical significance of lncRNAs and their regulatory mechanisms in nasopharyngeal carcinogenesis (NPC) are largely unknown. Here, based on a microarray analysis, we identified 384 dysregulated lncRNAs, of which, FAM225A was one of the most upregulated lncRNAs in NPC. FAM225A significantly associated with poor survival in NPC. N(6)-Methyladenosine (m6A) was highly enriched within FAM225A and enhanced its RNA stability. FAM225A functioned as an oncogenic lncRNA that promoted NPC cell proliferation, migration, invasion, tumor growth, and metastasis. Mechanistically, FAM225A functioned as a competing endogenous RNA (ceRNA) for sponging miR-590-3p and miR-1275, leading to the upregulation of their target integrin β3 (ITGB3), and the activation of FAK/PI3K/Akt signaling to promote NPC cell proliferation and invasion. In summary, our study reveals a potential ceRNA regulatory pathway in which FAM225A modulates ITGB3 expression by binding to miR-590-3p and miR-1275, ultimately promoting tumorigenesis and metastasis in NPC. Significance: These findings demonstrate the clinical significance of the lncRNA FAM225A in nasopharyngeal carcinoma (NPC) and the regulatory mechanism involved in NPC development and progression, providing a novel prognostic indicator and promising therapeutic target.
- Published
- 2019
34. Treatment of wastewater generated from traditional Chinese medicine processing and utilization: Recent advances and future outlook
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Yi Wu, Zhi-Xuan Li, Yong Hu, Zhong-Ying Huang, Chao Huang, and Jing Gao
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Engineering ,Renewable Energy, Sustainability and the Environment ,business.industry ,020209 energy ,Strategy and Management ,05 social sciences ,02 engineering and technology ,Building and Construction ,Traditional Chinese medicine ,Industrial and Manufacturing Engineering ,Wastewater ,Risk analysis (engineering) ,050501 criminology ,0202 electrical engineering, electronic engineering, information engineering ,business ,0505 law ,General Environmental Science - Abstract
Nowadays, traditional Chinese medicine plays an important role in curing many diseases, and its market expands quickly due to the potential great profits it can bring. To be an attractive industry, both economic and environmental aspects should be considered. As wastewater is usually generated from traditional Chinese medicine processing and utilization, its treatment is one of the hot research topics in environmental engineering currently. Many technologies can be applied for the treatment of this wastewater, but the technical background and performance vary greatly especially for different kinds of wastewater. In this situation, a systematical and comprehensive summary for the development of these technologies is necessary. In this review article, the sources of wastewater from the processing and utilization of traditional Chinese medicine are introduced firstly to show where this wastewater comes from. And then, the recent advances on the technologies for the treatment of this wastewater are introduced in detail to show what technologies can be applied. At last, the future outlook for the development of these treatment technologies is given to discuss how to fulfill their industrial application. Overall, this review article can present some important information for building a clean and sustainable traditional Chinese medicine industry.
- Published
- 2021
35. Hypoxia triggers the outbreak of infectious spleen and kidney necrosis virus disease through viral hypoxia response elements
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Jian He, Yang Yu, Zhi-Min Li, Zhi-Xuan Liu, Shao-Ping Weng, Chang-Jun Guo, and Jian-Guo He
- Subjects
Iridovirus ,ISKNV ,hypoxia ,hypoxia response elements ,HIF pathway ,Infectious and parasitic diseases ,RC109-216 - Abstract
Hypoxia frequently occurs in aquatic environments, especially in aquaculture areas. However, research on the relationship between hypoxic aquatic environments with viral diseases outbreak is limited, and its underlying mechanisms remain elusive. Herein, we demonstrated that hypoxia directly triggers the outbreak of infectious spleen and kidney necrosis virus (ISKNV) disease. Hypoxia or activated hypoxia-inducible factor (HIF) pathway could remarkably increase the levels of viral genomic DNA, titers, and gene expression, indicating that ISKNV can response to hypoxia and HIF pathway. To reveal the mechanism of ISKNV respond to HIF pathway, we identified the viral hypoxia response elements (HREs) in ISKNV genome. Fifteen viral HREs were identified, and four related viral genes responded to the HIF pathway, in which the hre-orf077r promoter remarkably responded to the HIF pathway. The level of orf077r mRNA dramatically increased after the infected cells were treated with dimethyloxalylglycine (DMOG) or the infected cells/fish subjected to hypoxic conditions, and overexpressed orf077r could remarkably increase the ISKNV replication. These finding shows that hypoxic aquatic environments induce the expression of viral genes through the viral HREs to promote ISKNV replication, indicating that viral HREs might be important biomarkers for the evaluation of the sensitivity of aquatic animal viral response to hypoxia stress. Furthermore, the frequencies of viral HREs in 43 species aquatic viral genomes from 16 families were predicted and the results indicate that some aquatic animal viruses, such as Picornavirdea, Dicistronviridae, and Herpesviridae, may have a high risk to outbreak when the aquatic environment encounters hypoxic stress.
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- 2022
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36. Three-dimensional numerical simulation of electromagnetic diffusion problem and magnetization effects
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Ming-Xin Yue, Zhi-Xuan Li, and Guan-Qun Zhou
- Subjects
Physics ,Magnetization ,Computer simulation ,Diffusion problem ,General Physics and Astronomy ,Mechanics - Abstract
We present a newly developed algorithm for three-dimensional (3D) magnetotelluric model based on the vector finite element method. In this paper, unstructured grids which are composed of irregular tetrahedrons are used in our finite element model, which can be refined locally and adaptively according to the complex geometry of computational domain or subsurface structure. For obtaining more accurate solutions, secondary field rather than total field is numerically computed, which makes the errors limited to relatively small secondary field. Traditional node-based finite element method does not satisfy the condition that the normal electrical field is discontinuous at the interface of electric separatrix and the electrical current density is divergence-free throughout the regions without source, which obviously violates Maxwell equations. In order to overcome these drawbacks of node-based finite element, vector finite element method is employed to solve the secondary field-based partial differential equation. Moreover, in this study, the heterogeneous permeability is taken into consideration in our algorithm, as a consequence, which can deal with heterogeneous permeability model. The accuracy of our approach is verified by comparing with previously published numerical simulations of a COMMEMI-3D model. The advantages of our approach are also illustrated by the numerical simulations of model with arbitrary topography and complicated anomalous body. In addition, the simulation results of the irregular anomaly and the complex model of arbitrary terrain are both ideal results. It proves that the effect of 3D terrain is more serious and complex than that of two-dimensional (2D) terrain, and dealing with 3D models or data with 2D algorithm may bring in large errors. In the area where the magnetic permeability is abnormal, the magnetic permeability has an important influence on the numerical simulation results, and the magnetic permeability must be treated as an independent parameter in the magnetotellurics survey.
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- 2019
37. Comparative Genomics Analysis and Outer Membrane Vesicle-Mediated Horizontal Antibiotic-Resistance Gene Transfer in Avibacterium paragallinarum
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Jie Xu, Chen Mei, Yan Zhi, Zhi-xuan Liang, Xue Zhang, and Hong-jun Wang
- Subjects
A. paragallinarum ,outer membrane vesicles ,whole genome ,antibiotic resistance gene ,horizontal gene transfer ,Microbiology ,QR1-502 - Abstract
ABSTRACT Avibacterium paragallinarum is the etiological agent of infectious coryza, an acute respiratory disease of chickens that is globally distributed and causes serious economic losses for chicken production. A. paragallinarum is a Gram-negative bacterium that releases outer membrane vesicles (OMVs). In this study, a comparative genomic analysis of A. paragallinarum isolate P4chr1 and its OMVs was carried out, and the ability to transfer antibiotic resistance genes (ARGs) via the OMVs was studied. Sequencing and data analyses demonstrated that the genomic size of A. paragallinarum P4chr1 was approximately 2.77 Mb with a 25 kb tolerance island that covered six types of antibiotics and 11 ARGs. The genomic size of its OMVs was approximately 2.69 Mb, covering 97% of the genomic length and almost all the gene sequences of P4chr1. Purified and DNase-treated A. paragallinarum P4chr1 OMVs were cocultured with the antibiotic-sensitive A. paragallinarum Modesto strain on an antibiotic (chloramphenicol, erythromycin, tetracycline, or streptomycin)-containing plate, and the corresponding ARGs were detected in the colonies grown on the plates. However, using an antimicrobial susceptibility test, we found that ARGs delivered by OMVs were not persistent but only appeared transiently on the antibiotic-containing plates. Antibiotic resistance and ARGs were lost by the second bacterial passage. IMPORTANCE The functions and roles of OMVs on ARG and virulent gene transfer and dissemination have been reported in numerous Gram-negative bacteria. However, the role of OMVs in mediating antibiotic resistance in A. paragallinarum has not been reported. This study is the first report to compare the genomic characteristics of OMVs with its parent A. paragallinarum strain and to study A. paragallinarum ARG transfer via OMVs. This work has provided useful data for further studies focusing on nonplasmid ARG transfer mediated by A. paragallinarum OMVs.
- Published
- 2022
- Full Text
- View/download PDF
38. Three antinematodal diterpenes from Euphorbia kansui
- Author
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Zhi Xuan Li, Shuhei Nakajima, Hiroshi Kanzaki, Naomichi Baba, Minoru Izumi, Jian Xiao Shi, Kazuyoshi Kawazu, and Teruhiko Nitoda
- Subjects
Models, Molecular ,Spectrometry, Mass, Electrospray Ionization ,Magnetic Resonance Spectroscopy ,Spectrophotometry, Infrared ,diterpenoid ,Bursaphelenchus xylophilus ,ingenane ,Spectrometry, Mass, Fast Atom Bombardment ,Applied Microbiology and Biotechnology ,Biochemistry ,Plant Roots ,Analytical Chemistry ,Euphorbia ,Botany ,Molecular Biology ,Traditional medicine ,biology ,antinematodal activity ,Antinematodal Agents ,Organic Chemistry ,General Medicine ,biology.organism_classification ,Euphorbia kansui ,Nematode ,Indicators and Reagents ,Spectrophotometry, Ultraviolet ,Chromatography, Thin Layer ,Diterpenes ,Biotechnology - Abstract
Three compounds, 20-O-acetyl-[3-O-(2'E,4'Z)-decadienoyl]-ingenol (1), 20-O-acetyl-[5-O-(2'E,4'Z)-decadienoyl]-ingenol (2) and 3-O-(2'E,4'Z)-decadienoylingenol (3), were isolated from Euphorbia kansui under the bioassay-guided method. Each compound showed the same antinematodal activity against the nematode, Bursaphelenchus xylophilus, at a minimum effective dose (MED) of 5 microg/cotton ball.
- Published
- 2007
39. Three Antinematodal Diterpenes from Euphorbia kansui.
- Author
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Jian-Xiao Shi, Zhi-Xuan Li, Nitoda, Teruhiko, Izumi, Minoru, Kanzaki, Hiroshi, Baba, Naomichi, Kawazu, Kazuyoshi, and Nakajima, Shuhei
- Subjects
- *
EUPHORBIA , *NEMATODES , *PINEWOOD nematode , *ALCOHOL , *EUPHORBIACEAE - Abstract
The article describes the isolation and structural characterization of three antinematodal compounds from Euphorbia kansui against the nematode, Bursaphelenchus xylophilus. The compounds include 20-O-acetyl-[3-O-(2'E,4'Z)-decadienoyl]-ingenol, 20-O-acetyl-[5-O-(2'E,4'Z)-decadienoyl]-ingenol and 3-O-(2'E,4'Z)-decadienoylingenol. According to the authors, each compound showed the same antinematodal activity against the nematode at a minimum effective dose of 5µg/cotton ball.
- Published
- 2007
- Full Text
- View/download PDF
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