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Ren P, Lei W, Zhao C, Duan Z. HO-1-induced autophagy establishes a HO-1-p62-Nrf2 positive feedback loop to reduce gut permeability in cholestatic liver disease. Scand J Gastroenterol 2024:1-12. [PMID: 38745449 DOI: 10.1080/00365521.2024.2353108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 05/05/2024] [Indexed: 05/16/2024]
Abstract
OBJECTIVES The gut-liver axis disruption is a unified pathogenetic principle of cholestatic liver disease (CSLD). Increased gut permeability is the leading cause of gut-liver axis disruption. HO-1 is capable of protecting against gut-liver axis injury. However, it has rarely been reported whether autophagy is involved in HO-1 protecting gut-liver barrier integrity and the underlying mechanism. MATERIALS AND METHODS Mice underwent bile duct ligation (BDL) was established as CSLD model in vivo. Caco-2 cells with LPS treatment was established as in vitro cell model. Immunofluorescence, western blot and transepithelial electrical resistance (TER) assay were used to observe epithelial tight junction (TJ) and autophagy. Liver injury and fibrosis were evaluated as well through H&E staining, masson staining, sirius red staining and ELISA. RESULTS AND CONCLUSIONS Our study demonstrated that the epithelial TJ and TER were notably reduced both in BDL mice and in LPS treated intestinal epithelial cells. Increased HO-1 expression could significantly induce intestinal epithelial cell autophagy. Additionally, this increased autophagy level reversed the reduction effects of BDL or LPS on epithelial TJ and TER in vivo and in vitro, therefore decreased transaminase level in serum and relieved liver fibrosis in BDL mice. Besides, increased autophagy level in turn upregulated the expression of HO-1 by p62 degradation of Keap1 and subsequent activation of Nrf2 pathway. Collectively, these results indicate that HO-1 reduces gut permeability by enhancing autophagy level in CSLD, the increased autophagy establishes a HO-1-p62-Nrf2 positive feedback loop to further improve gut-liver axis disruption. Therefore, our study confirms the critical role of autophagy in HO-1 ameliorating gut-liver axis injury during CSLD, highlighting HO-1 as a promising therapeutic target.
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Affiliation(s)
- Pingping Ren
- Second Department of Gastroenterology, The First Affiliated Hospital of Dalian Medical University, Dalian, China
- Second Department of Gastroenterology, The Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Wei Lei
- Second Department of Gastroenterology, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Changcheng Zhao
- Second Department of Gastroenterology, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Zhijun Duan
- Second Department of Gastroenterology, The First Affiliated Hospital of Dalian Medical University, Dalian, China
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2
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Zhou T, Zhang R, Jia D, Doty RT, Munday AD, Gao D, Xin L, Abkowitz JL, Duan Z, Ma J. GAGE-seq concurrently profiles multiscale 3D genome organization and gene expression in single cells. Nat Genet 2024:10.1038/s41588-024-01745-3. [PMID: 38744973 DOI: 10.1038/s41588-024-01745-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 04/05/2024] [Indexed: 05/16/2024]
Abstract
The organization of mammalian genomes features a complex, multiscale three-dimensional (3D) architecture, whose functional significance remains elusive because of limited single-cell technologies that can concurrently profile genome organization and transcriptional activities. Here, we introduce genome architecture and gene expression by sequencing (GAGE-seq), a scalable, robust single-cell co-assay measuring 3D genome structure and transcriptome simultaneously within the same cell. Applied to mouse brain cortex and human bone marrow CD34+ cells, GAGE-seq characterized the intricate relationships between 3D genome and gene expression, showing that multiscale 3D genome features inform cell-type-specific gene expression and link regulatory elements to target genes. Integration with spatial transcriptomic data revealed in situ 3D genome variations in mouse cortex. Observations in human hematopoiesis unveiled discordant changes between 3D genome organization and gene expression, underscoring a complex, temporal interplay at the single-cell level. GAGE-seq provides a powerful, cost-effective approach for exploring genome structure and gene expression relationships at the single-cell level across diverse biological contexts.
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Affiliation(s)
- Tianming Zhou
- Ray and Stephanie Lane Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Ruochi Zhang
- Ray and Stephanie Lane Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
- Eric and Wendy Schmidt Center, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Deyong Jia
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Raymond T Doty
- Division of Hematology and Oncology, Department of Medicine/Fred Hutch Cancer Center, University of Washington, Seattle, WA, USA
| | - Adam D Munday
- Division of Hematology and Oncology, Department of Medicine/Fred Hutch Cancer Center, University of Washington, Seattle, WA, USA
| | - Daniel Gao
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
- Department of Chemistry, Pomona College, Claremont, CA, USA
| | - Li Xin
- Department of Urology, University of Washington, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Janis L Abkowitz
- Division of Hematology and Oncology, Department of Medicine/Fred Hutch Cancer Center, University of Washington, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Zhijun Duan
- Division of Hematology and Oncology, Department of Medicine/Fred Hutch Cancer Center, University of Washington, Seattle, WA, USA.
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA.
| | - Jian Ma
- Ray and Stephanie Lane Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA.
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3
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Cheng J, Guo J, Xu L, Shi Z, Xu F, Xu Y, Yan G, Li J, Yang Y, Duan Z, Yang J, Yin L, Liu D, Wei W, Wang M, Bu X, Sha W, Lv L, Wang J, Huang Y, Feng Q, Li X, Gong S, Mao H, Jin D, Lin L, Chen JDZ. The Overlap Subgroup of Functional Dyspepsia Exhibits More Severely Impaired Gastric and Autonomic Functions. J Clin Gastroenterol 2024; 58:31-38. [PMID: 36730560 DOI: 10.1097/mcg.0000000000001802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 10/17/2022] [Indexed: 02/04/2023]
Abstract
GOALS A combination of multiple tests was introduced to noninvasively investigate the differences in pathophysiologies among functional dyspepsia (FD) subgroups, including postprandial distress syndrome (PDS), epigastric pain syndrome (EPS), and overlap. BACKGROUND It has not been extensively evaluated whether different pathophysiologies are involved in FD subgroups. STUDY This multicenter study included 364 FD patients fulfilling Rome IV criteria and 47 healthy controls. A combined noninvasive gastric and autonomic function test was performed: The electrogastrogram and electrocardiogram were recorded simultaneously in the fasting state and after a drink test. Symptoms after drinking were recorded using visual analog scale. RESULTS (1) Compared with HC, FD patients showed a decreased maximum tolerable volume (MTV) ( P <0.01) and percentage of normal gastric slow waves [normal gastric slow waves (%NSW)] ( P <0.01), and increased postdrinking symptoms, anxiety ( P <0.01), and depression ( P <0.01). The drink reduced %NSW in both FD patients and HC; however, the effect was more potent in patients. (2) The PDS and overlap groups displayed a reduced MTV ( P <0.05). The overlap group exhibited a higher symptom score at 30 minutes after drinking, and higher anxiety and depression scores, and a higher sympathovagal ratio than the EPS ( P <0.05 for all) and PDS ( P <0.01 for all). (3) In the PDS subgroup, the MTV, postprandial sympathovagal ratio, and depression were associated with the overall dyspepsia symptom scale (DSS, P =0.034, 0.021, 0.043, respectively). No significant associations were found in the other 2 subgroups. CONCLUSIONS The combination of multiple tests can detect pathophysiological abnormities in FD patients. Overall, patients with overlap symptoms display more severe pathophysiologies.
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Affiliation(s)
- Jiafei Cheng
- Division of Gastroenterology, Jiangsu Province Hospital of Chinese Medicine (Affiliated Hospital of Nanjing University of Chinese Medicine)
- The First Affiliated Hospital of Nanjing Medical University, Nanjing
| | | | - Luzhou Xu
- Division of Gastroenterology, Jiangsu Province Hospital of Chinese Medicine (Affiliated Hospital of Nanjing University of Chinese Medicine)
| | | | - Feng Xu
- Ningbo Medical Center Lihuili Hospital
| | - Yuemei Xu
- The affiliated People's Hospital of Ningbo University, Ningbo
| | - Guangjun Yan
- Jingzhou Hospital of traditional Chinese Medicine, Jingzhou
| | - Jie Li
- Jingzhou Hospital of traditional Chinese Medicine, Jingzhou
| | - Yi Yang
- The First Affiliated Hospital of Dalian Medical University, Dalian
| | - Zhijun Duan
- The First Affiliated Hospital of Dalian Medical University, Dalian
| | - Jie Yang
- The First Affiliated Hospital of Guizhou Medical University, Guiyang
| | - Lu Yin
- Wangjing Hospital of China Academy of Chinese Medical Sciences, Beijing
| | - Dengke Liu
- Wangjing Hospital of China Academy of Chinese Medical Sciences, Beijing
| | - Wei Wei
- Wangjing Hospital of China Academy of Chinese Medical Sciences, Beijing
| | - Meifeng Wang
- The First Affiliated Hospital of Nanjing Medical University, Nanjing
| | - Xiaoling Bu
- Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Guangzhou
| | - Weihong Sha
- Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Guangzhou
| | - Litao Lv
- The 9th Hospital of Xingtai, Xingtai
| | | | - Yan Huang
- Shenzhen Guangming New Area Medical Group Digestive Disease Center, Shenzhen
| | - Qiaoqun Feng
- Shenzhen Guangming New Area Medical Group Digestive Disease Center, Shenzhen
| | - Xueliang Li
- Changzhou Wujin People's Hospital, Changzhou
| | - Shan Gong
- Changzhou Wujin People's Hospital, Changzhou
| | - Hua Mao
- Zhujiang Hospital of Southern Medical University, Guangzhou, China
| | - DanDan Jin
- Zhujiang Hospital of Southern Medical University, Guangzhou, China
| | - Lin Lin
- The First Affiliated Hospital of Nanjing Medical University, Nanjing
| | - Jiande D Z Chen
- Division of Gastroenterology and Hepatology, University of Michigan, Ann Arbor, MI
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Li D, Wang X, Zhou J, Duan Z, Yang R, Liu Y, Chen Y, Zhang L, Liu H, Li W, You J. Analysis of Efficacy and Safety of Small-Volume-Plasma Artificial Liver Model in the Treatment of Acute-On-Chronic Liver Failure. Physiol Res 2023; 72:767-782. [PMID: 38215063 PMCID: PMC10805255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 08/11/2023] [Indexed: 01/14/2024] Open
Abstract
To explore the efficacy and safety of a small-volume-plasma artificial liver support system (ALSS) in the treatment of acute-on-chronic liver failure (ACLF). A retrospective analysis was performed. All ACLF patients received ALSS of plasma exchange & double plasma molecular absorb system (PE+DPMAS) treatment, and successfully completed this treatment. Patients were divided into small-volume and half-volume plasma groups. We compared the changes of the indicators on liver function, kidney function, blood coagulation function, and blood ammonia level before and after PE+DPMAS treatment; we compared the short-term and long-term curative effects between small-volume and half-volume plasma groups; and the factors influencing Week 4 and Week 12 mortality of ACLF patients were analyzed. The Week 4 improvement rates were 63.96 % and 66.86 % in the small-volume and half-volume plasma groups, respectively. The Week 12 survival rates in the small-volume-plasma and half-volume plasma groups were 66.72 % and 64.61 %, respectively. We found several risk factors affecting Week 4 and Week 12 mortality. Kaplan-Meier survival curves suggested no significant difference in Week 4 and Week 12 survival rates between the small-volume and half-volume plasma groups (P=0.34). The small-volume-plasma PE+DPMAS treatment could effectively reduce bilirubin and bile acids, and this was an approach with high safety and few complications, similar to the half-volume-plasma PE+DPMAS treatment. The small-volume-plasma PE+DPMAS has the advantage of greatly reducing the need for intraoperative plasma, which is especially of importance in times of shortage of plasma.
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Affiliation(s)
- D Li
- The First Affiliated Hospital of Kunming Medical University, Yunnan, Kunming, China.
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5
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Ge Z, Fang Y, Chang J, Yu Z, Qiao Y, Zhang J, Yang X, Duan Z. Using deep learning to assess the function of gastroesophageal flap valve according to the Hill classification system. Ann Med 2023; 55:2279239. [PMID: 37949083 PMCID: PMC10653650 DOI: 10.1080/07853890.2023.2279239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 10/26/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND The endoscopic Hill classification of the gastroesophageal flap valve (GEFV) is of great importance for understanding the functional status of the esophagogastric junction (EGJ). Deep learning (DL) methods have been extensively employed in the area of digestive endoscopy. To improve the efficiency and accuracy of the endoscopist's Hill classification and assist in incorporating it into routine endoscopy reports and GERD assessment examinations, this study first employed DL to establish a four-category model based on the Hill classification. MATERIALS AND METHODS A dataset consisting of 3256 GEFV endoscopic images has been constructed for training and evaluation. Furthermore, a new attention mechanism module has been provided to improve the performance of the DL model. Combined with the attention mechanism module, numerous experiments were conducted on the GEFV endoscopic image dataset, and 12 mainstream DL models were tested and evaluated. The classification accuracy of the DL model and endoscopists with different experience levels was compared. RESULTS 12 mainstream backbone networks were trained and tested, and four outstanding feature extraction backbone networks (ResNet-50, VGG-16, VGG-19, and Xception) were selected for further DL model development. The ResNet-50 showed the best Hill classification performance; its area under the curve (AUC) reached 0.989, and the classification accuracy (93.39%) was significantly higher than that of junior (74.83%) and senior (78.00%) endoscopists. CONCLUSIONS The DL model combined with the attention mechanism module in this paper demonstrated outstanding classification performance based on the Hill grading and has great potential for improving the accuracy of the Hill classification by endoscopists.
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Affiliation(s)
- Zhenyang Ge
- Department of Gastroenterology, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
- Department of Digestive Endoscopy, Dalian Municipal Central Hospital, Dalian, Liaoning, China
| | - Youjiang Fang
- Department of Computer Science, Dalian University of Technology, Dalian, Liaoning, China
| | - Jiuyang Chang
- Department of Cardiology, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Zequn Yu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Yu Qiao
- Department of Computer Science, Dalian University of Technology, Dalian, Liaoning, China
| | - Jing Zhang
- Department of Digestive Endoscopy, Dalian Municipal Central Hospital, Dalian, Liaoning, China
| | - Xin Yang
- Department of Computer Science, Dalian University of Technology, Dalian, Liaoning, China
| | - Zhijun Duan
- Department of Gastroenterology, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
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6
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Fayn S, King AP, Gutsche NT, Duan Z, Buffington J, Olkowski CP, Fu Y, Hong J, Sail D, Baidoo KE, Swenson RE, Cheloha RW, Ho M, Choyke P, Escorcia FE. Nanobody-Based ImmunoPET for Hepatocellular Carcinoma. Int J Radiat Oncol Biol Phys 2023; 117:S44. [PMID: 37784500 DOI: 10.1016/j.ijrobp.2023.06.320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) HCC accounts for 75-90% of all primary liver cancers, the majority of which are treated with liver-directed therapy. Treatment response and recurrence are difficult to discern using conventional imaging with MR/CT. Tumor-selective PET imaging could help with clinical management in this setting. Here, we engineer HN3, a single-domain antibody (nanobody) specific to GPC3, a histopathologically-defining HCC marker, as an immunoPET agent. We compared both conventional and sortase-based site-specific modification methods for synthesizing HN3 immunoPET tracers. MATERIALS/METHODS Stochastic lysine conjugation with deferoxamine (DFO-NCS) was done to synthesize nHN3-DFO. ssHN3-DFO was engineered utilizing sortase-mediated conjugation of HN3 containing an LPETG C-terminal tag and a triglycine-DFO chelator. Biolayer interferometry (BLI) and radioligand saturation assays were done to determine binding affinity pre- and post-Zirconium-89 labeling. Following, PET/CT with a terminal 3-hour biodistribution was done in mice inoculated with isogenic A431 and A431-GPC3+ xenografts to determine conjugate specificity for GPC3. Finally, conjugates were evaluated in a HepG2 liver cancer model via ex vivo biodistribution studies and a comparative PET/CT study in mice bearing HepG2 tumors that were imaged with both [18F]FDG and 89Zr-ssHN3. RESULTS Both conjugates exhibited nanomolar binding affinity for GPC3 in vitro (11-30 nM for nHN3 and 10-15 nM for ssHN3). A431 and A431-GPC3+ PET/CT and biodistribution studies showed specificity to GPC3 by both probes, with more favorable tumor uptake by 89Zr-ssHN3 at 3 hours post-injection (14% IA/g vs. 7% IA/g for nHN3). Both tracers also displayed uptake in HepG2 (GPC3+) liver tumors, again with the site specifically conjugated probe having higher tumor accumulation and lower liver signal than the conventionally modified HN3 (7% IA/g vs. 5 % IA/g for tumor and 2% IA/g vs. 4% IA/g for liver at 1-hour post-injection). PET/CT studies in mice imaged with [18F]FDG and 89Zr-ssHN3 demonstrated more consistent tumor accumulation for the nanobody conjugate (4/4 mice had uptake by the tumor vs. 1/4 for FDG). CONCLUSION We successfully designed, synthesized, and characterized novel GPC3-selective nanobody PET probes that can image liver tumors in vivo. The site-specifically conjugated tracer showed more favorable biodistribution and pharmacokinetic properties, resulting in a much higher tumor: liver signal compared to 89Zr-nHN3. We also show the superiority of the 89Zr-ssHN3 imaging over conventional [18F]FDG, highlighting a clear advantage in using targeted tumor imaging for this cancer type. Successful translation of the site-specifically conjugated nanobody may ultimately aid in characterizing lesions following liver-directed therapy and allow for more comprehensive screening, early diagnosis, and post-treatment surveillance of HCC.
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Affiliation(s)
- S Fayn
- Molecular Imaging Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - A P King
- Molecular Imaging Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - N T Gutsche
- Molecular Imaging Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Z Duan
- Antibody Engineering Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - J Buffington
- Antibody Engineering Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - C P Olkowski
- Molecular Imaging Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Y Fu
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - J Hong
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - D Sail
- Chemistry and Synthesis Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Rockville, MD
| | - K E Baidoo
- Molecular Imaging Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - R E Swenson
- Chemistry and Synthesis Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Rockville, MD
| | - R W Cheloha
- Chemical Biology in Signaling Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD
| | - M Ho
- Antibody Engineering Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD; Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - P Choyke
- Molecular Imaging Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - F E Escorcia
- Molecular Imaging Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD; Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
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7
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Zhou T, Zhang R, Jia D, Doty RT, Munday AD, Gao D, Xin L, Abkowitz JL, Duan Z, Ma J. Concurrent profiling of multiscale 3D genome organization and gene expression in single mammalian cells. bioRxiv 2023:2023.07.20.549578. [PMID: 37546900 PMCID: PMC10401946 DOI: 10.1101/2023.07.20.549578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
The organization of mammalian genomes within the nucleus features a complex, multiscale three-dimensional (3D) architecture. The functional significance of these 3D genome features, however, remains largely elusive due to limited single-cell technologies that can concurrently profile genome organization and transcriptional activities. Here, we report GAGE-seq, a highly scalable, robust single-cell co-assay that simultaneously measures 3D genome structure and transcriptome within the same cell. Employing GAGE-seq on mouse brain cortex and human bone marrow CD34+ cells, we comprehensively characterized the intricate relationships between 3D genome and gene expression. We found that these multiscale 3D genome features collectively inform cell type-specific gene expressions, hence contributing to defining cell identity at the single-cell level. Integration of GAGE-seq data with spatial transcriptomic data revealed in situ variations of the 3D genome in mouse cortex. Moreover, our observations of lineage commitment in normal human hematopoiesis unveiled notable discordant changes between 3D genome organization and gene expression, underscoring a complex, temporal interplay at the single-cell level that is more nuanced than previously appreciated. Together, GAGE-seq provides a powerful, cost-effective approach for interrogating genome structure and gene expression relationships at the single-cell level across diverse biological contexts.
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Affiliation(s)
- Tianming Zhou
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Ruochi Zhang
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Present address: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Deyong Jia
- Department of Urology, University of Washington, Seattle, WA 98195, USA
| | - Raymond T. Doty
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Adam D. Munday
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Daniel Gao
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
- Present address: Department of Chemistry, Pomona College, Claremont, CA 91711, USA
| | - Li Xin
- Department of Urology, University of Washington, Seattle, WA 98195, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
| | - Janis L. Abkowitz
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA 98195, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
| | - Zhijun Duan
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA 98195, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
| | - Jian Ma
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
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8
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Xing Z, Li Y, Cortes-Gomez E, Jiang X, Gao S, Pao A, Shan J, Song Y, Perez A, Yu T, Highsmith MR, Boadu F, Conroy JM, Singh PK, Bakin AV, Cheng J, Duan Z, Wang J, Liu S, Tycko B, Yu YE. Dissection of a Down syndrome-associated trisomy to separate the gene dosage-dependent and -independent effects of an extra chromosome. Hum Mol Genet 2023; 32:2205-2218. [PMID: 37014740 PMCID: PMC10281752 DOI: 10.1093/hmg/ddad056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 02/13/2023] [Accepted: 03/27/2023] [Indexed: 04/05/2023] Open
Abstract
As an aneuploidy, trisomy is associated with mammalian embryonic and postnatal abnormalities. Understanding the underlying mechanisms involved in mutant phenotypes is broadly important and may lead to new strategies to treat clinical manifestations in individuals with trisomies, such as trisomy 21 [Down syndrome (DS)]. Although increased gene dosage effects because of a trisomy may account for the mutant phenotypes, there is also the possibility that phenotypic consequences of a trisomy can arise because of the presence of a freely segregating extra chromosome with its own centromere, i.e. a 'free trisomy' independent of gene dosage effects. Presently, there are no reports of attempts to functionally separate these two types of effects in mammals. To fill this gap, here we describe a strategy that employed two new mouse models of DS, Ts65Dn;Df(17)2Yey/+ and Dp(16)1Yey/Df(16)8Yey. Both models carry triplications of the same 103 human chromosome 21 gene orthologs; however, only Ts65Dn;Df(17)2Yey/+ mice carry a free trisomy. Comparison of these models revealed the gene dosage-independent impacts of an extra chromosome at the phenotypic and molecular levels for the first time. They are reflected by impairments of Ts65Dn;Df(17)2Yey/+ males in T-maze tests when compared with Dp(16)1Yey/Df(16)8Yey males. Results from the transcriptomic analysis suggest the extra chromosome plays a major role in trisomy-associated expression alterations of disomic genes beyond gene dosage effects. This model system can now be used to deepen our mechanistic understanding of this common human aneuploidy and obtain new insights into the effects of free trisomies in other human diseases such as cancers.
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Affiliation(s)
- Zhuo Xing
- The Children’s Guild Foundation Down Syndrome Research Program, Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Yichen Li
- The Children’s Guild Foundation Down Syndrome Research Program, Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Eduardo Cortes-Gomez
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Xiaoling Jiang
- The Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China
| | - Shuang Gao
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
- Bioinformatics, OmniSeq Inc., Buffalo, NY, USA
| | - Annie Pao
- The Children’s Guild Foundation Down Syndrome Research Program, Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Jidong Shan
- Molecular Cytogenetics Core, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Yinghui Song
- Molecular Cytogenetics Core, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Amanda Perez
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Tao Yu
- The Children’s Guild Foundation Down Syndrome Research Program, Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Max R Highsmith
- Department of Electric Engineering and Computer Science, University of Missouri, Columbia, MO, USA
| | - Frimpong Boadu
- Department of Electric Engineering and Computer Science, University of Missouri, Columbia, MO, USA
| | - Jeffrey M Conroy
- Research and Development, OmniSeq Inc., Buffalo, NY, USA
- Research Support Services, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Prashant K Singh
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Andrei V Bakin
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Jianlin Cheng
- Department of Electric Engineering and Computer Science, University of Missouri, Columbia, MO, USA
| | - Zhijun Duan
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Jianmin Wang
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Song Liu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Benjamin Tycko
- Hackensack-Meridian Health Center for Discovery and Innovation, Nutley, NJ, USA
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ, USA
| | - Y Eugene Yu
- The Children’s Guild Foundation Down Syndrome Research Program, Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
- Genetics, Genomics and Bioinformatics Program, State University of New York at Buffalo, Buffalo, NY, USA
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9
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Duan Z, Li D, Zeng D, Bian Z, Ma J. [A semi-supervised material quantitative intelligent imaging algorithm for spectral CT based on prior information perception learning]. Nan Fang Yi Ke Da Xue Xue Bao 2023; 43:620-630. [PMID: 37202199 DOI: 10.12122/j.issn.1673-4254.2023.04.16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
OBJECTIVE To propose a semi-supervised material quantitative intelligent imaging algorithm based on prior information perception learning (SLMD-Net) to improve the quality and precision of spectral CT imaging. METHODS The algorithm includes a supervised and a self- supervised submodule. In the supervised submodule, the mapping relationship between low and high signal-to-noise ratio (SNR) data was constructed through mean square error loss function learning based on a small labeled dataset. In the self- supervised sub-module, an image recovery model was utilized to construct the loss function incorporating the prior information from a large unlabeled low SNR basic material image dataset, and the total variation (TV) model was used to to characterize the prior information of the images. The two submodules were combined to form the SLMD-Net method, and pre-clinical simulation data were used to validate the feasibility and effectiveness of the algorithm. RESULTS Compared with the traditional model-driven quantitative imaging methods (FBP-DI, PWLS-PCG, and E3DTV), data-driven supervised-learning-based quantitative imaging methods (SUMD-Net and BFCNN), a material quantitative imaging method based on unsupervised learning (UNTV-Net) and semi-supervised learning-based cycle consistent generative adversarial network (Semi-CycleGAN), the proposed SLMD-Net method had better performance in both visual and quantitative assessments. For quantitative imaging of water and bone materials, the SLMD-Net method had the highest PSNR index (31.82 and 29.06), the highest FSIM index (0.95 and 0.90), and the lowest RMSE index (0.03 and 0.02), respectively) and achieved significantly higher image quality scores than the other 7 material decomposition methods (P < 0.05). The material quantitative imaging performance of SLMD-Net was close to that of the supervised network SUMD-Net trained with labeled data with a doubled size. CONCLUSIONS A small labeled dataset and a large unlabeled low SNR material image dataset can be fully used to suppress noise amplification and artifacts in basic material decomposition in spectral CT and reduce the dependence on labeled data-driven network, which considers more realistic scenario in clinics.
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Affiliation(s)
- Z Duan
- School of Biomedical Engineering, Southern Medical University, Guangzhou 510515, China
- Guangzhou Key Laboratory of Medical Radioimaging and Detection Technology, Guangzhou 510515, China
| | - D Li
- School of Biomedical Engineering, Southern Medical University, Guangzhou 510515, China
- Guangzhou Key Laboratory of Medical Radioimaging and Detection Technology, Guangzhou 510515, China
| | - D Zeng
- School of Biomedical Engineering, Southern Medical University, Guangzhou 510515, China
- Guangzhou Key Laboratory of Medical Radioimaging and Detection Technology, Guangzhou 510515, China
| | - Z Bian
- School of Biomedical Engineering, Southern Medical University, Guangzhou 510515, China
- Guangzhou Key Laboratory of Medical Radioimaging and Detection Technology, Guangzhou 510515, China
| | - J Ma
- School of Biomedical Engineering, Southern Medical University, Guangzhou 510515, China
- Guangzhou Key Laboratory of Medical Radioimaging and Detection Technology, Guangzhou 510515, China
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10
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Scheutz C, Duan Z, Møller J, Kjeldsen P. Environmental assessment of landfill gas mitigation using biocover and gas collection with energy utilisation at aging landfills. Waste Manag 2023; 165:40-50. [PMID: 37080016 DOI: 10.1016/j.wasman.2023.04.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 03/17/2023] [Accepted: 04/07/2023] [Indexed: 05/03/2023]
Abstract
A life cycle-based environmental assessment was conducted on the mitigation of landfill gas emissions, by implementing biocover and gas collection along with energy utilisation at aging landfills. Based on recent studies about gas generation at Danish landfills, the efficiency of the mitigation technologies involved and the composition of substituted energy production, 15 scenarios were modelled using the EASETECH life cycle assessment model, through which potential environmental impacts in the category "Climate change" were calculated. In all scenarios, biocover and gas collection systems with energy utilisation led to significant environmental improvements compared to the baseline scenario with no emission mitigation action. Scenarios representing biocovers with methane oxidation efficiencies between 70 and 90 % were environmentally superior in terms of climate change impact - in comparison to scenarios with 20-30 years of gas collection and energy utilisation (collection efficiencies between 40 and 80 %). Combining gas collection with energy utilisation and the subsequent installation of a biocover saw major improvements in comparison to where only gas collection and energy utilisation were in effect. Overall, it can be concluded that a biocover under the given assumptions is environmentally more appropriate than gas collection and utilisation at aging landfills, mainly due to methane emissions escaping through the landfill cover during and after the gas collection period playing a crucial role in the latter situation. Maintaining high methane oxidation efficiency for a biocover throughout the lifetime of a landfill is vital for reducing environmental impacts.
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Affiliation(s)
- C Scheutz
- Department of Environmental and Resource Engineering, Technical University of Denmark, Bygningstorvet, Building 115, 2800 Kgs. Lyngby, Denmark.
| | - Z Duan
- Department of Environmental and Resource Engineering, Technical University of Denmark, Bygningstorvet, Building 115, 2800 Kgs. Lyngby, Denmark
| | - J Møller
- Department of Environmental and Resource Engineering, Technical University of Denmark, Bygningstorvet, Building 115, 2800 Kgs. Lyngby, Denmark
| | - P Kjeldsen
- Department of Environmental and Resource Engineering, Technical University of Denmark, Bygningstorvet, Building 115, 2800 Kgs. Lyngby, Denmark
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11
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Li Y, Wang L, Yang D, Zhang Z, Sun X, Geng X, Lin J, Duan Z. Esophageal chemical clearance and mucosa integrity values in refractory gastroesophageal reflux disease patients with different esophageal dynamics. Scand J Gastroenterol 2023; 58:322-330. [PMID: 36259257 DOI: 10.1080/00365521.2022.2132534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
OBJECTIVES Esophageal post-reflux swallow-induced peristaltic wave index (PSPWI) and mean nocturnal baseline impedance (MNBI), novel impedance-based markers of reflux burden, are associated with esophageal dynamics. We aim to investigate the characteristics of PSPWI and MNBI in Chinese refractory gastroesophageal reflux disease (RGERD) patients with different esophageal dynamic changes. MATERIALS AND METHODS 201 RGERD and 76 functional heartburn patients, undergone off-PPI endoscopy, esophageal manometry and impedance-pH monitoring, were included. Comparisons of conventional and novel impedance-pH metrics were made among different esophageal dynamics groups. Receiver operating-characteristic analyses were utilized to evaluate the diagnostic efficacy of PSPWI and MNBI in differentiating abnormal esophageal dynamics. Correlations were used to investigate their associated factors. RESULTS PSPWI and MNBI of RGERD with esophagogastric junction (EGJ) injury and esophageal dysmotility were lower than EGJ injury alone or normal dynamics (p < 0.05 for both comparisons). PSPWI with esophageal peristalsis abnormality was lower than EGJ injury (p = 0.049), while MNBI showed no statistical difference. PSPWI, MNBI and their combination have auxiliary diagnostic values for esophageal peristalsis [area under the curves (AUCs): 0.683, 0.656, 0.708)] while only their combination for EGJ injury (AUC: 0.610). And they positively correlated with esophageal motility while negatively correlated with ineffective swallows and acid reflux events. CONCLUSIONS PSPWI and MNBI, indicating impairment of esophageal chemical clearance and mucosa integrity, were lower in RGERD patients with multiple esophageal dynamic injuries than single injuries or normal dynamics. Moreover, they provided useful contributing information for potential dynamic injuries if manometry has already been found normal or marginal.
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Affiliation(s)
- Yanqiu Li
- Second Gastroenterology Department, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Lixia Wang
- Second Gastroenterology Department, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Dong Yang
- Second Gastroenterology Department, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Zhifeng Zhang
- Second Gastroenterology Department, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Xiaoyu Sun
- Second Gastroenterology Department, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Xiaoling Geng
- Second Gastroenterology Department, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Jiarong Lin
- Second Gastroenterology Department, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Zhijun Duan
- Second Gastroenterology Department, The First Affiliated Hospital of Dalian Medical University, Dalian, China
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12
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Bozarth XL, Lopez J, Fang H, Lee-Eng J, Duan Z, Deng X. Phenotypes and Genotypes in Patients with SMC1A-Related Developmental and Epileptic Encephalopathy. Genes (Basel) 2023; 14:852. [PMID: 37107610 PMCID: PMC10138066 DOI: 10.3390/genes14040852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/27/2023] [Accepted: 03/29/2023] [Indexed: 04/05/2023] Open
Abstract
The X-linked SMC1A gene encodes a core subunit of the cohesin complex that plays a pivotal role in genome organization and gene regulation. Pathogenic variants in SMC1A are often dominant-negative and cause Cornelia de Lange syndrome (CdLS) with growth retardation and typical facial features; however, rare SMC1A variants cause a developmental and epileptic encephalopathy (DEE) with intractable early-onset epilepsy that is absent in CdLS. Unlike the male-to-female ratio of 1:2 in those with CdLS associated with dominant-negative SMC1A variants, SMC1A-DEE loss-of-function (LOF) variants are found exclusively in females due to presumed lethality in males. It is unclear how different SMC1A variants cause CdLS or DEE. Here, we report on phenotypes and genotypes of three females with DEE and de novo SMC1A variants, including a novel splice-site variant. We also summarize 41 known SMC1A-DEE variants to characterize common and patient-specific features. Interestingly, compared to 33 LOFs detected throughout the gene, 7/8 non-LOFs are specifically located in the N/C-terminal ATPase head or the central hinge domain, both of which are predicted to affect cohesin assembly, thus mimicking LOFs. Along with the characterization of X-chromosome inactivation (XCI) and SMC1A transcription, these variants strongly suggest that a differential SMC1A dosage effect of SMC1A-DEE variants is closely associated with the manifestation of DEE phenotypes.
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Affiliation(s)
- Xiuhua L. Bozarth
- Division of Neurology, Seattle Children’s Hospital, University of Washington, Seattle, WA 98105, USA
| | - Jonathan Lopez
- Division of Neurology, Seattle Children’s Hospital, University of Washington, Seattle, WA 98105, USA
| | - He Fang
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Jacqueline Lee-Eng
- Division of Neurology, Seattle Children’s Hospital, University of Washington, Seattle, WA 98105, USA
| | - Zhijun Duan
- Division of Hematology, University of Washington, Seattle, WA 98195, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98195, USA
| | - Xinxian Deng
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
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Ge Z, Wang B, Chang J, Yu Z, Zhou Z, Zhang J, Duan Z. Using deep learning and explainable artificial intelligence to assess the severity of gastroesophageal reflux disease according to the Los Angeles Classification System. Scand J Gastroenterol 2023; 58:596-604. [PMID: 36625026 DOI: 10.1080/00365521.2022.2163185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
OBJECTIVES Gastroesophageal reflux disease (GERD) is a complex disease with a high worldwide prevalence. The Los Angeles classification (LA-grade) system is meaningful for assessing the endoscopic severity of GERD. Deep learning (DL) methods have been widely used in the field of endoscopy. However, few DL-assisted researches have concentrated on the diagnosis of GERD. This study is the first to develop a five-category classification DL model based on the LA-grade using explainable artificial intelligence (XAI). MATERIALS AND METHODS A total of 2081 endoscopic images were used for the development of a DL model, and the classification accuracy of the models and endoscopists with different levels of experience was compared. RESULTS Some mainstream DL models were utilized, of which DenseNet-121 outperformed. The area under the curve (AUC) of the DenseNet-121 was 0.968, and its classification accuracy (86.7%) was significantly higher than that of junior (71.5%) and experienced (77.4%) endoscopists. An XAI evaluation was also performed to explore the perception consistency between the DL model and endoscopists, which showed meaningful results for real-world applications. CONCLUSIONS The DL model showed a potential in improving the accuracy of endoscopists in LA-grading of GERD, and it has noticeable clinical application prospects and is worthy of further promotion.
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Affiliation(s)
- Zhenyang Ge
- Department of Gastroenterology, The First Affiliated Hospital of Dalian Medical University, Dalian, China.,Department of Digestive Endoscopy, Dalian Municipal Central Hospital, Dalian, China
| | - Bowen Wang
- Science and Technology, Graduate School of Information, Osaka University, Yamadaoka, Osaka, Japan
| | - Jiuyang Chang
- Department of Cardiology, The First Affiliated Hospital of Dalian Medical University, Dalian, China.,Department of Cardiovascular Medicine, Graduate School of Medicine, Osaka University, Yamadaoka, Osaka, Japan
| | - Zequn Yu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Zhenyuan Zhou
- Information Management Department, Dalian Municipal Central Hospital, Dalian, China
| | - Jing Zhang
- Department of Digestive Endoscopy, Dalian Municipal Central Hospital, Dalian, China
| | - Zhijun Duan
- Department of Gastroenterology, The First Affiliated Hospital of Dalian Medical University, Dalian, China
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Li Y, Duan Z. Updates in interaction of gastroesophageal reflux disease and extragastroesophageal digestive diseases. Expert Rev Gastroenterol Hepatol 2022; 16:1053-1063. [PMID: 35860994 DOI: 10.1080/17474124.2022.2056018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
INTRODUCTION Gastroesophageal reflux disease (GERD) is one of the common chronic diseases with prevalence increasing in the last decades. Because of its prevalence and chronicity, GERD affects the quality of life and increases health-care costs. Gastroesophageal diseases leading to GERD have been thoroughly studied, while extragastroesophageal digestive diseases (EGEDDs) may coexist with GERD and affect the occurrence and persistence of GERD symptoms and therapeutic effect. AREAS COVERED In this review, we aim to summarize the EGEDDs correlated with GERD and explore the potential mechanisms of this interaction. EXPERT OPINION Individuals with troublesome GERD symptoms may have some common gastroesophageal etiologies, but EGEDDs may also overlap and impact on the progression of GERD, which are often ignored in clinic. The lesions in the small intestine, colon, and hepatobiliary tract as well as functional bowel disorders had positive or negative associations with GERD through potential mechanisms. These diseases aggravate GERD symptoms, increase the esophageal acid burden, cause esophageal hypersensitivity, and finally affect the response to therapy in GERD patients. Therefore, it is necessary to clear the interaction between GERD and EGEDDs and their mechanisms.
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Affiliation(s)
- Yanqiu Li
- Second Gastroenterology Department, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Zhijun Duan
- Second Gastroenterology Department, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
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15
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Lei W, Zhao C, Sun J, Jin Y, Duan Z. Activation of α7nAChR preserves intestinal barrier integrity by enhancing the HO-1 / STAT3 signaling to inhibit NF-κB activation in mice. Biomed Pharmacother 2022; 149:112733. [DOI: 10.1016/j.biopha.2022.112733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 02/10/2022] [Accepted: 02/15/2022] [Indexed: 11/02/2022] Open
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16
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Reilly A, Philip Creamer J, Stewart S, Stolla MC, Wang Y, Du J, Wellington R, Busch S, Estey EH, Becker PS, Fang M, Keel SB, Abkowitz JL, Soma LA, Ma J, Duan Z, Doulatov S. Lamin B1 deletion in myeloid neoplasms causes nuclear anomaly and altered hematopoietic stem cell function. Cell Stem Cell 2022; 29:577-592.e8. [PMID: 35278369 PMCID: PMC9018112 DOI: 10.1016/j.stem.2022.02.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 01/05/2022] [Accepted: 02/15/2022] [Indexed: 11/19/2022]
Abstract
Abnormal nuclear morphology is a hallmark of malignant cells widely used in cancer diagnosis. Pelger-Huët anomaly (PHA) is a common abnormality of neutrophil nuclear morphology of unknown molecular etiology in myeloid neoplasms (MNs). We show that loss of nuclear lamin B1 (LMNB1) encoded on chromosome 5q, which is frequently deleted in MNs, induces defects in nuclear morphology and human hematopoietic stem cell (HSC) function associated with malignancy. LMNB1 deficiency alters genome organization inducing in vitro and in vivo expansion of HSCs, myeloid-biased differentiation with impaired lymphoid commitment, and genome instability due to defective DNA damage repair. Nuclear dysmorphology of neutrophils in patients with MNs is associated with 5q deletions spanning the LMNB1 locus, and lamin B1 loss is both necessary and sufficient to cause PHA in normal and 5q-deleted neutrophils. LMNB1 loss thus causes acquired PHA and links abnormal nuclear morphology with HSCs and progenitor cell fate determination via genome organization.
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Affiliation(s)
- Andreea Reilly
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - J Philip Creamer
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Sintra Stewart
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Massiel C Stolla
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Yuchuan Wang
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Jing Du
- Division of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA
| | - Rachel Wellington
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA 98195, USA; Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Stephanie Busch
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Elihu H Estey
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA 98195, USA; Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Pamela S Becker
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA 98195, USA; Division of Hematology/Oncology, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA 92617, USA; Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Min Fang
- Department of Clinical Transplant Research, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Siobán B Keel
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Janis L Abkowitz
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA 98195, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Lorinda A Soma
- Division of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA
| | - Jian Ma
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Zhijun Duan
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA 98195, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98195, USA
| | - Sergei Doulatov
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA 98195, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98195, USA.
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17
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Lei W, Zhao C, Sun J, Jin Y, Duan Z. Electroacupuncture Ameliorates Intestinal Barrier Destruction in Mice With Bile Duct Ligation-Induced Liver Injury by Activating the Cholinergic Anti-Inflammatory Pathway. Neuromodulation 2022; 25:1122-1133. [PMID: 35300921 DOI: 10.1016/j.neurom.2022.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 01/19/2022] [Accepted: 01/31/2022] [Indexed: 02/07/2023]
Abstract
OBJECTIVES Electroacupuncture (EA) at Zusanli (ST36) can attenuate inflammation in different rodent models. However, the therapeutic mechanisms underlying its action in inhibiting intestinal barrier destruction and liver injury in cholestasis mice have not been clarified. This study aimed at investigating whether EA at ST36 could activate the cholinergic anti-inflammatory pathway to inhibit intestinal barrier destruction and liver injury in cholestasis mice. MATERIALS AND METHODS Male Hmox1floxp/floxp C57BL/6 mice were randomized and subjected to a sham or bile duct ligation (BDL) surgery. The BDL mice were randomized and treated with, or without (BDL group), sham EA at ST36 (BDL+sham-ST36) or EA at ST36 (BDL+ST36), or received α-bungarotoxin (α-BGT), a specific inhibitor of nicotinic acetylcholine receptor α7 subunit (α7nAChR), before stimulation (BDL+ST36+α-BGT). These mice, together with a group of intestine-specific heme oxygenase-1 (HO-1) knockout (KO) Villin-Cre-HO-1-/- mice, were monitored for their body weights before and 14 days after BDL. The levels of plasma cytokines and liver injury-related alanine aminotransferase (ALT) and aspartate aminotransferase (AST) were measured by enzyme-linked immunoassay, and pathological changes in the intestinal mucosa and liver fibrosis as well as intestinal barrier permeability in individual mice were examined by histology and immunohistochemistry. The levels of α7nAChR, HO-1, ZO-1, Occludin, Claudin-1, and NF-κBp65 expression and NF-κBp65 phosphorylation in intestinal tissues were quantified. RESULTS Compared with the sham group, BDL significantly increased the levels of plasma interleukin (IL)-1β, IL-6, IL-10, tumor necrosis factor α, ALT, and AST and caused intestinal mucosal damages, high permeability, and liver fibrosis in mice, which were remarkably mitigated, except for further increased levels of plasma IL-10 in the BDL+ST36 group of mice. Similarly, EA at ST36 significantly up-regulated α7nAChR and HO-1 expression; mitigated the BDL-decreased ZO-1, Occludin, and Claudin-1 expression; and attenuated the BDL-increased NF-κBp65 phosphorylation in intestinal tissues of mice. The therapeutic effects of EA at ST36 were significantly abrogated by pretreatment with α-BGT or HO-1 KO. CONCLUSION EA at ST36 inhibits the BDL-induced intestinal mucosal damage and liver fibrosis by activating the HO-1 cholinergic anti-inflammatory pathway in intestinal tissues of mice.
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Affiliation(s)
- Wei Lei
- Second Department of Gastroenterology, the First Affiliated Hospital of Dalian Medical University, Dalian, China; Laboratory of Integrated Chinese and Western Medicine, the First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Changcheng Zhao
- Second Department of Gastroenterology, the First Affiliated Hospital of Dalian Medical University, Dalian, China; Laboratory of Integrated Chinese and Western Medicine, the First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Jiasen Sun
- Second Department of Gastroenterology, the First Affiliated Hospital of Dalian Medical University, Dalian, China; Laboratory of Integrated Chinese and Western Medicine, the First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Yanling Jin
- Pathology Department, the First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Zhijun Duan
- Second Department of Gastroenterology, the First Affiliated Hospital of Dalian Medical University, Dalian, China; Laboratory of Integrated Chinese and Western Medicine, the First Affiliated Hospital of Dalian Medical University, Dalian, China.
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18
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Yu SS, Ma MY, Zhou R, Liang R, Duan Z, Wang J, Tian Y, Jiang J, He X, Zhou Q. Methotrexate/mifepristone-combined with embryo removal in the treatment of caesarean scar pregnancy. Eur Rev Med Pharmacol Sci 2022; 26:1984-1993. [PMID: 35363349 DOI: 10.26355/eurrev_202203_28347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
OBJECTIVE The aim of this study was to compare the effect of different administration modalities of methotrexate (MTX)/mifepristone in the initial medication stage, followed by embryo transfer in the treatment of caesarean scar pregnancy (CSP). PATIENTS AND METHODS A retrospective analysis of 66 CSP patients who received treatment in our hospital from January 2015 to July 2021 was performed, and participants were divided into three groups: Group one (n=14) received mifepristone followed by embryo removal treatment, Group two (n=29) received MTX followed by embryo removal, and Group three (n=23) received a methotrexate/mifepristone combined treatment followed by embryo removal. The basic findings were analysed, along with the curative effects between the three groups. Risk factors predicting additional treatment after initial intervention failure were analysed. RESULTS There were statistically significant differences in gestational age, hospitalization days, costs, myometrial thickness, cardiac activity, and mean sac diameter between groups (p<0.05) after grouping by eight weeks. The initial intervention success rates were 92.86%, 89.66%, and 65.22% in Group one, two, and three, respectively (p<0.05), while the complication rates were 14.29%, 6.90%, and 26.87%, respectively (p>0.05). After grouping according to eight weeks of gestational age, the difference in initial serum β-hCG between Group two and three was statistically significant (p<0.05). Mean sac diameter was a risk factor for additional treatment after initial intervention failure, with an odds ratio of 1.113 (p<0.05). A cut-off of 22.75 mm was a preferable indicator. CONCLUSIONS MTX/mifepristone followed by embryo removal is a reliable way to treat CSP. Mean sac diameter was a risk factor for additional treatment after initial intervention failure.
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Affiliation(s)
- S-S Yu
- Department of Ultrasound, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.
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Yang Q, Mao Y, Wang J, Yu H, Zhang X, Pei X, Duan Z, Xiao C, Ma M. Gestational bisphenol A exposure impairs hepatic lipid metabolism by altering mTOR/CRTC2/SREBP1 in male rat offspring. Hum Exp Toxicol 2022; 41:9603271221129852. [PMID: 36137816 DOI: 10.1177/09603271221129852] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Lipid metabolism is an important biochemical process in the body. Recent studies have found that environmental endocrine disruptors play an important role in the regulation of lipid metabolism. Bisphenol A (BPA), a common environmental endocrine disruptor, has adverse effects on lipid metabolism, but the mechanism is still unclear. This study aimed to investigate the effects of gestational BPA exposure on hepatic lipid metabolism and its possible mechanism in male offspring. The pregnant Sprague-Dawley rats were exposed to BPA (0, 0.05, 0.5, 5 mg/kg/day) from day 5 to day 19 of gestation to investigate the levels of triglyceride (TG) and total cholesterol (TC), and the expression of liver lipid metabolism-related genes in male offspring rats. The results showed that compared with the control group, the TG and TC levels in serum and liver in BPA-exposed groups was increased. And the expressions of liver fatty acid oxidation related genes, such as peroxisome proliferators-activated receptor α (PPARα) and carnitine palmitoyl transferase 1α (CPT1α), were down-regulated. However, the expressions of fatty acid synthesis related genes, such as sterol regulatory element binding proteins 1 (SREBP-1), acetyl-CoA carboxylase 1 (ACC1), fatty acid synthase (FAS) and stearoyl-CoA desaturase 1 (SCD-1), were up-regulated. The increased protein levels of mTOR and p-CRTC2 suggested that CREB-regulated transcription coactivator 2 (CRTC2) might be an important mediator in the mTOR/SREBP-1 pathway. In conclusion, these results demonstrated that mTOR/CRTC2/SREBP-1 could be affected by gestational BPA exposure, which may involve in the lipid metabolic disorders in later life.
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Affiliation(s)
- Q Yang
- Department of Toxicology, School of Public Heath, 70577Shenyang Medical College, Shenyang, China
| | - Y Mao
- Department of Toxicology, School of Public Heath, 70577Shenyang Medical College, Shenyang, China
| | - J Wang
- Department of Toxicology, School of Public Heath, 70577Shenyang Medical College, Shenyang, China
| | - H Yu
- Department of Toxicology, School of Public Heath, 70577Shenyang Medical College, Shenyang, China
| | - X Zhang
- Department of Toxicology, School of Public Heath, 70577Shenyang Medical College, Shenyang, China
| | - X Pei
- Department of Toxicology, School of Public Heath, 70577Shenyang Medical College, Shenyang, China
| | - Z Duan
- Department of Toxicology, School of Public Heath, 70577Shenyang Medical College, Shenyang, China
| | - C Xiao
- Department of Key Laboratory of Environmental Pollution and Microecology, 70577Shenyang Medical College, Shenyang, China
| | - M Ma
- Department of Toxicology, School of Public Heath, 70577Shenyang Medical College, Shenyang, China.,Department of Key Laboratory of Environmental Pollution and Microecology, 70577Shenyang Medical College, Shenyang, China
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20
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Bonora G, Ramani V, Singh R, Fang H, Jackson DL, Srivatsan S, Qiu R, Lee C, Trapnell C, Shendure J, Duan Z, Deng X, Noble WS, Disteche CM. Single-cell landscape of nuclear configuration and gene expression during stem cell differentiation and X inactivation. Genome Biol 2021; 22:279. [PMID: 34579774 PMCID: PMC8474932 DOI: 10.1186/s13059-021-02432-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 07/07/2021] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Mammalian development is associated with extensive changes in gene expression, chromatin accessibility, and nuclear structure. Here, we follow such changes associated with mouse embryonic stem cell differentiation and X inactivation by integrating, for the first time, allele-specific data from these three modalities obtained by high-throughput single-cell RNA-seq, ATAC-seq, and Hi-C. RESULTS Allele-specific contact decay profiles obtained by single-cell Hi-C clearly show that the inactive X chromosome has a unique profile in differentiated cells that have undergone X inactivation. Loss of this inactive X-specific structure at mitosis is followed by its reappearance during the cell cycle, suggesting a "bookmark" mechanism. Differentiation of embryonic stem cells to follow the onset of X inactivation is associated with changes in contact decay profiles that occur in parallel on both the X chromosomes and autosomes. Single-cell RNA-seq and ATAC-seq show evidence of a delay in female versus male cells, due to the presence of two active X chromosomes at early stages of differentiation. The onset of the inactive X-specific structure in single cells occurs later than gene silencing, consistent with the idea that chromatin compaction is a late event of X inactivation. Single-cell Hi-C highlights evidence of discrete changes in nuclear structure characterized by the acquisition of very long-range contacts throughout the nucleus. Novel computational approaches allow for the effective alignment of single-cell gene expression, chromatin accessibility, and 3D chromosome structure. CONCLUSIONS Based on trajectory analyses, three distinct nuclear structure states are detected reflecting discrete and profound simultaneous changes not only to the structure of the X chromosomes, but also to that of autosomes during differentiation. Our study reveals that long-range structural changes to chromosomes appear as discrete events, unlike progressive changes in gene expression and chromatin accessibility.
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Affiliation(s)
- Giancarlo Bonora
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Vijay Ramani
- Department of Biochemistry & Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Ritambhara Singh
- Department of Computer Science, Brown University, Providence, RI, USA
- Center for Computational Molecular Biology, Brown University, Providence, RI, USA
| | - He Fang
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Dana L Jackson
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Sanjay Srivatsan
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Ruolan Qiu
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Choli Lee
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
| | - Zhijun Duan
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, USA
- Division of Hematology, Department of Medicine, University of Washington, Seattle, USA
| | - Xinxian Deng
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA.
| | - William S Noble
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA.
| | - Christine M Disteche
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA.
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.
- Department of Medicine, University of Washington, Seattle, WA, USA.
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21
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Lei W, Duan Z. Advances in the Treatment of Cholinergic Anti-Inflammatory Pathways in Gastrointestinal Diseases by Electrical Stimulation of Vagus Nerve. Digestion 2021; 102:128-138. [PMID: 31786570 DOI: 10.1159/000504474] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 10/31/2019] [Indexed: 02/04/2023]
Abstract
BACKGROUND The cholinergic anti-inflammatory pathway (CAIP) has been proposed as a key mechanism by which the brain, through the vagus nerve (VN), modulates the immune system in the body. Recent studies of VN stimulation (VNS) in vivo systems have shown that it plays an anti-inflammatory role through CAIP. Inflammatory diseases in the gastrointestinal tract are frequent and difficult to treat. SUMMARY The mechanism of the anti-inflammatory effect of VNS through CAIP is not fully known. The current review covers anatomy, molecular mechanisms, and the application in gastrointestinal diseases of the vagal CAIP. Key Messages: CAIP bridges immune and nervous systems and plays pleiotropic roles in modulating inflammation in animal models by targeting different immune, proinflammatory, epithelial and endothelial cells, and signaling pathways. Numerous animal studies have shown beneficial effects of stimulation of this pathway in models of inflammatory diseases, either through (electrical) stimulation of the VN or pharmacological approaches. In this review, we focus on the anti-inflammatory benefits of VNS as a means of providing new insights into treating inflammation-related gastrointestinal diseases, as exemplified by those described herein.
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Affiliation(s)
- Wei Lei
- Second Department of Gastroenterology, The First Affiliated Hospital of Dalian Medical University, Dalian, China.,Laboratory of Integrated Chinese and Western Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Zhijun Duan
- Second Department of Gastroenterology, The First Affiliated Hospital of Dalian Medical University, Dalian, China, .,Laboratory of Integrated Chinese and Western Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, China,
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22
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Abstract
Introduction: Esophagus dysmotility is a crucial risk factor of gastroesophageal reflux disease (GERD), which is one of the most common diseases in digestive medicine globally. This review emphasizes the mechanisms of esophagus dysmotility in diabetes and summarizes more targeted treatments for these patients to avoid the overuse of proton pump inhibitors (PPIs).Areas covered: Diabetes mellitus (DM) is a clear factor that must not be neglected in the development of GERD. Previous studies have preliminarily researched the esophagus deterioration in diabetes. However, the multi-faceted mechanisms of esophagus dysmotility in diabetes need more studies. Besides, targeted treatments for these patients rather than conventional PPIs are urgently needed.Expert opinion: The treatments for GERD patients with diabetes should be further explored. Pharmacological approaches such as prokinetic agents, psychotherapy can be adopted. Meanwhile, it's feasible to explore non-drug treatments. For example, Electroacupuncture (EA) at Zusanli (ST-36) may be effective to protect the networks of intestinal cells of Cajal (ICCs) in diabetes. More effective approaches should be explored to achieve individualized treatment for these patients.
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Affiliation(s)
- Jiarong Lin
- The Second Department of Gastroenterology, The First Affiliated Hospital of Dalian Medical University, Dalian, China.,Laboratory of Integrated Chinese and Western Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Gongkai Liu
- School of Medicine, Nova Southeastern University, Davie, FL, USA
| | - Zhijun Duan
- The Second Department of Gastroenterology, The First Affiliated Hospital of Dalian Medical University, Dalian, China.,Laboratory of Integrated Chinese and Western Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, China
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23
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Zhang Z, Zhang Q, Li F, Xin Y, Duan Z. Contributions of HO-1-Dependent MAPK to Regulating Intestinal Barrier Disruption. Biomol Ther (Seoul) 2021; 29:175-183. [PMID: 33093265 PMCID: PMC7921856 DOI: 10.4062/biomolther.2020.112] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 08/08/2020] [Accepted: 08/14/2020] [Indexed: 12/13/2022] Open
Abstract
The mitogen-activated protein kinase (MAPK) pathway controls intestinal epithelial barrier permeability by regulating tight junctions (TJs) and epithelial cells damage. Heme oxygenase-1 (HO-1) and carbon monoxide (CO) protect the intestinal epithelial barrier function, but the molecular mechanism is not yet clarified. MAPK activation and barrier permeability were studied using monolayers of Caco-2 cells treated with tissue necrosis factor α (TNF-α) transfected with FUGW-HO-1 or pLKO.1-sh-HO-1 plasmid. Intestinal mucosal barrier permeability and MAPK activation were also investigated using carbon tetrachloride (CCl4) administration with CoPP (a HO-1 inducer), ZnPP (a HO-1 inhibitor), CO releasing molecule 2 (CORM-2), or inactived-CORM-2-treated wild-type mice and mice with HO-1 deficiency in intestinal epithelial cells. TNF-α increased epithelial TJ disruption and cleaved caspase-3 expression, induced ERK, p38, and JNK phosphorylation. In addition, HO-1 blocked TNF-α-induced increase in epithelial TJs disruption, cleaved caspase-3 expression, as well as ERK, p38, and JNK phosphorylation in an HO-1-dependent manner. CoPP and CORM-2 directly ameliorated intestinal mucosal injury, attenuated TJ disruption and cleaved caspase-3 expression, and inhibited epithelial ERK, p38, and JNK phosphorylation after chronic CCl4 injection. Conversely, ZnPP completely reversed these effects. Furthermore, mice with intestinal epithelial HO-1 deficient exhibited a robust increase in mucosal TJs disruption, cleaved caspase-3 expression, and MAPKs activation as compared to the control group mice. These data demonstrated that HO-1-dependent MAPK signaling inhibition preserves the intestinal mucosal barrier integrity by abrogating TJ dysregulation and epithelial cell damage. The differential targeting of gut HO-1-MAPK axis leads to improved intestinal disease therapy.
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Affiliation(s)
- Zhenling Zhang
- Department of Gastroenterology, the First Affiliated Hospital of Dalian Medical University, Dalian116011, China
| | - Qiuping Zhang
- Department of Pathology, the First Affiliated Hospital of Dalian Medical University, Dalian 116011, China
| | - Fang Li
- Department of Immunology, Dalian Medical University, Dalian 116044, China
| | - Yi Xin
- Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian 116044, China
| | - Zhijun Duan
- Department of Gastroenterology, the First Affiliated Hospital of Dalian Medical University, Dalian116011, China
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24
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Sun X, Tang S, Hou B, Duan Z, Liu Z, Li Y, He S, Wang Q, Chang Q. Overexpression of P-glycoprotein, MRP2, and CYP3A4 impairs intestinal absorption of octreotide in rats with portal hypertension. BMC Gastroenterol 2021; 21:2. [PMID: 33407159 PMCID: PMC7789354 DOI: 10.1186/s12876-020-01532-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 11/09/2020] [Indexed: 02/08/2023] Open
Abstract
Background Portal hypertension (PH) is the main cause of complications and death in liver cirrhosis. The effect of oral administration of octreotide (OCT), a drug that reduces PH by the constriction of mesenteric arteries, is limited by a remarkable intestinal first-pass elimination.
Methods The bile duct ligation (BDL) was used in rats to induce liver cirrhosis with PH to examine the kinetics and molecular factors such as P-glycoprotein (P-gp), multidrug resistance-associated protein 2 (MRP2) and cytochrome P450 3A4 (CYP3A4) influencing the intestinal OCT absorption via in situ and in vitro experiments on jejunal segments, transportation experiments on Caco-2 cells and experiments using intestinal microsomes and recombinant human CYP3A4. Moreover, RT-PCR, western blot, and immunohistochemistry were performed. Results Both in situ and in vitro experiments in jejunal segments showed that intestinal OCT absorption in both control and PH rats was largely controlled by P-gp and, to a lesser extent, by MRP2. OCT transport mediated by P-gp and MRP2 was demonstrated on Caco-2 cells. The results of RT-PCR, western blot, and immunohistochemistry suggested that impaired OCT absorption in PH was in part due to the jejunal upregulation of these two transporters. The use of intestinal microsomes and recombinant human CYP3A4 revealed that CYP3A4 metabolized OCT, and its upregulation in PH likely contributed to impaired drug absorption. Conclusions Inhibition of P-gp, MRP2, and CYP3A4 might represent a valid option for decreasing intestinal first-pass effects on orally administered OCT, thereby increasing its bioavailability to alleviate PH in patients with cirrhosis.
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Affiliation(s)
- Xiaoyu Sun
- Department of Gastroenterology, First Affiliated Hospital of Dalian Medical University, Dalian, 0086-116011, China
| | - Shunxiong Tang
- Department of Invasive Technology, Affiliated Zhongshan Hospital of Dalian University, Dalian, China
| | - Binbin Hou
- Department of Dermatology, Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Zhijun Duan
- Department of Gastroenterology, First Affiliated Hospital of Dalian Medical University, Dalian, 0086-116011, China.
| | - Zhen Liu
- Department of Gastroenterology, First Affiliated Hospital of Dalian Medical University, Dalian, 0086-116011, China
| | - Yang Li
- Department of Clinical Pharmacology, College of Pharmacy, Dalian Medical University, Dalian, China.,Department of Breast Surgery, Hospital of Chinese Medical University, Liaoning Provincial Cancer Institute and Hospital, Shenyang, China
| | - Shoucheng He
- Department of Gastroenterology, First Affiliated Hospital of Dalian Medical University, Dalian, 0086-116011, China
| | - Qiuming Wang
- Department of Gastroenterology, First Affiliated Hospital of Dalian Medical University, Dalian, 0086-116011, China
| | - Qingyong Chang
- Department of Neurosurgery, Affiliated Zhongshan Hospital of Dalian University, Dalian, China.
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25
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Liu W, Duan Z, Zhang C, Hu XX, Cao JB, Liu LJ., Lin L. Experimental observations and density functional simulations on the structural transition behavior of a two-dimensional transition-metal dichalcogenide. Sci Rep 2020; 10:18255. [PMID: 33106537 PMCID: PMC7588463 DOI: 10.1038/s41598-020-75240-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 09/15/2020] [Indexed: 11/29/2022] Open
Abstract
In this work, we show an obvious evidence of nondestructive Raman spectra for the structural transition, i.e., the existence of a charge density wave (CDW) in monolayer 2H-TaS2, which can exhibit a much higher transition temperature than bulk and results in additional vibrational modes, indicating strong interactions with light. Furthermore, we reveal that the degenerate breath and wiggle modes of 2H-TaS2 originated from the periodic lattice distortion can be probed using the optical methods. Since recently several light-tunable devices have been proposed based on the CDW phase transition of 1 T-TaS2, our study and in particular, the theoretical results will be very helpful for understanding and designing electronic devices based on the CDW of 2H-TaS2.
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26
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Duan Z. [The exploration of Hujia Pasture wooden slip medicine prescription]. Zhonghua Yi Shi Za Zhi 2020; 50:307-310. [PMID: 33287499 DOI: 10.3760/cma.j.cn112155-20200804-00125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Some features in the medical prescriptions of western Han dynasty on the wooden slips unearthed in Hujia Pasture were interpreted, and the words were annotated and translated. The study found that this recipe with male magpie excrement treatment epileptic disease is the first moxibustion combined with drugs to treat epilepsy. This is the earliest recorded treatment. The drug is still administered to lactate children by applying it to the mother's nipple and making the child to suck, and it is the earliest recorded of its kind.
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Affiliation(s)
- Z Duan
- School of Humanities and Foreign Languages, Gansu University of Traditional Chinese Medicine, Lanzhou 730000, China
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27
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Kim HJ, Yardımcı GG, Bonora G, Ramani V, Liu J, Qiu R, Lee C, Hesson J, Ware CB, Shendure J, Duan Z, Noble WS. Capturing cell type-specific chromatin compartment patterns by applying topic modeling to single-cell Hi-C data. PLoS Comput Biol 2020; 16:e1008173. [PMID: 32946435 PMCID: PMC7526900 DOI: 10.1371/journal.pcbi.1008173] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 09/30/2020] [Accepted: 07/21/2020] [Indexed: 01/01/2023] Open
Abstract
Single-cell Hi-C (scHi-C) interrogates genome-wide chromatin interaction in individual cells, allowing us to gain insights into 3D genome organization. However, the extremely sparse nature of scHi-C data poses a significant barrier to analysis, limiting our ability to tease out hidden biological information. In this work, we approach this problem by applying topic modeling to scHi-C data. Topic modeling is well-suited for discovering latent topics in a collection of discrete data. For our analysis, we generate nine different single-cell combinatorial indexed Hi-C (sci-Hi-C) libraries from five human cell lines (GM12878, H1Esc, HFF, IMR90, and HAP1), consisting over 19,000 cells. We demonstrate that topic modeling is able to successfully capture cell type differences from sci-Hi-C data in the form of “chromatin topics.” We further show enrichment of particular compartment structures associated with locus pairs in these topics. The genomes of higher organisms are intricately folded and organized in a dynamic manner that has strong implications for many biological processes. Each chromosome undergoes dramatic changes to their three dimensional conformation during the cell cycle, whereas the positioning of chromosomes within the nucleus plays an important role in controlling the activation of specific genes. Recently, it has become possible to investigate the 3D conformations of the genomes of individual cells using a high throughput sequencing assay called single cell Hi-C (scHi-C). However, data from these assays are sparse and noisy, making analysis and interpretation of scHi-C data challenging. In this work, we generated a scHi-C dataset of over 19,000 cells from five human cell lines and applied a natural language processing method called topic modeling to discover cell type-specific “chromatin” topics. We show that these topics can be used to distinguish between cells at different stages of the cell cycle and cells from different tissues based on the 3D conformation of their genomes, despite the sparsity of the data. We further show that the 3D conformations of single cells are linked to the expression of cell type-specific genes and to cell cycle-associated conformational patterns.
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Affiliation(s)
- Hyeon-Jin Kim
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Galip Gürkan Yardımcı
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Giancarlo Bonora
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Vijay Ramani
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
| | - Jie Liu
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Ruolan Qiu
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Choli Lee
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Jennifer Hesson
- Department of Comparative Medicine, University of Washington, Seattle, Washington, United States of America
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, United States of America
| | - Carol B. Ware
- Department of Comparative Medicine, University of Washington, Seattle, Washington, United States of America
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, United States of America
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Zhijun Duan
- Division of Hematology, Department of Medicine, University of Washington, Seattle, Washington, United States of America
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, United States of America
- * E-mail: (Z. Duan); (W.S. Noble)
| | - William Stafford Noble
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, Washington, United States of America
- * E-mail: (Z. Duan); (W.S. Noble)
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28
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Singh R, Demetci P, Bonora G, Ramani V, Lee C, Fang H, Duan Z, Deng X, Shendure J, Disteche C, Noble WS. Unsupervised manifold alignment for single-cell multi-omics data. ACM BCB 2020; 2020:1-10. [PMID: 33954299 PMCID: PMC8095090 DOI: 10.1145/3388440.3412410] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Integrating single-cell measurements that capture different properties of the genome is vital to extending our understanding of genome biology. This task is challenging due to the lack of a shared axis across datasets obtained from different types of single-cell experiments. For most such datasets, we lack corresponding information among the cells (samples) and the measurements (features). In this scenario, unsupervised algorithms that are capable of aligning single-cell experiments are critical to learning an in silico co-assay that can help draw correspondences among the cells. Maximum mean discrepancy-based manifold alignment (MMD-MA) is such an unsupervised algorithm. Without requiring correspondence information, it can align single-cell datasets from different modalities in a common shared latent space, showing promising results on simulations and a small-scale single-cell experiment with 61 cells. However, it is essential to explore the applicability of this method to larger single-cell experiments with thousands of cells so that it can be of practical interest to the community. In this paper, we apply MMD-MA to two recent datasets that measure transcriptome and chromatin accessibility in ~2000 single cells. To scale the runtime of MMD-MA to a more substantial number of cells, we extend the original implementation to run on GPUs. We also introduce a method to automatically select one of the user-defined parameters, thus reducing the hyperparameter search space. We demonstrate that the proposed extensions allow MMD-MA to accurately align state-of-the-art single-cell experiments.
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Affiliation(s)
- Ritambhara Singh
- Department of Computer Science, Center for Computational Molecular Biology, Brown University
| | - Pinar Demetci
- Center for Computational Molecular Biology, Brown University
| | | | | | - Choli Lee
- Department of Genome Sciences, University of Washington
| | - He Fang
- Department of Pathology, University of Washington
| | - Zhijun Duan
- Division of Hematology, University of Washington
| | - Xinxian Deng
- Department of Pathology, University of Washington
| | - Jay Shendure
- Howard Hughes Medical Institute, Department of Genome Sciences, University of Washington
| | | | - William Stafford Noble
- Department of Genome Sciences, University of Washington, Paul G. Allen School of Computer Science and Engineering, University of Washington
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29
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Yang H, Yang H, Wang L, Shi H, Liu B, Lin X, Chang Q, Chen JDZ, Duan Z. Transcutaneous Neuromodulation improved inflammation and sympathovagal ratio in patients with primary biliary ssscholangitis and inadequate response to Ursodeoxycholic acid: a pilot study. BMC Complement Med Ther 2020; 20:242. [PMID: 32738911 PMCID: PMC7395375 DOI: 10.1186/s12906-020-03036-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 07/24/2020] [Indexed: 02/08/2023] Open
Abstract
Background At present, ursodeoxycholic acid (UDCA) is internationally recognized as a therapeutic drug in clinic. However, about 40% Primary Biliary Cholangitis (PBC) patients are poor responders to UDCA. It has been demonstrated that Transcutaneous Neuromodulation (TN) can be involved in gut motility, metabolism of bile acids, immune inflammation, and autonomic nerve. Therefore, this study aimed to explore the effect of TN combined with UDCA on PBC and related mechanisms. Methods According to inclusion and exclusion criteria, 10 healthy volunteers and 15 PBC patients were recruited to control group and TN group, respectively. PBC patients were alternately but blindly assigned to group A (TN combined with UDCA) and group B (sham-TN combined with UDCA), and a crossover design was used. The TN treatment was performed via the posterior tibial nerve and acupoint ST36 (Zusanli) 1 h twice/day for 2 weeks. T test and nonparametric test were used to analyze the data. Results 1. TN combined with UDCA improved the liver function of PBC patients shown by a significant decrease of alkaline phosphatase and gamma-glutamyltransferase (γ-GT) (P < 0.05). 2. The treatment also decreased serum IL-6 levels (P < 0.05), but not the level of Tumor Necrosis Factor-α, IL-1β or IL-10. 3. TN combined with UDCA regulated autonomic function, enhanced vagal activity, and decreased the sympathovagal ratio assessed by the spectral analysis of heart rate variability (P < 0.05). 4. There was no change in 13 bile acids in serum or stool after TN or sham-TN. Conclusions TN cssombined with UDCA can significantly improve the liver function of PBC patients. It is possibly via the cholinergic anti-inflammatory pathway. TN might be a new non-drug therapy for PBC. Further studies are required. Trial registration The study protocol was registered in Chinese Clinical Trial Registry (number ChiCTR1800014633) on 25 January 2018.
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Affiliation(s)
- Hui Yang
- The Second Department of Gastroenterology, The First Affiliated Hospital of Dalian Medical University, No. 222 Zhongshan Road, Dalian, 116011, Liaoning, China
| | - Hang Yang
- Department of Gastroenterology, West China Hospital, Sichuan University, No. 37, Guo Xue Xiang, Wu Hou District, Chengdu, 610041, China
| | - Lixia Wang
- The Second Department of Gastroenterology, The First Affiliated Hospital of Dalian Medical University, No. 222 Zhongshan Road, Dalian, 116011, Liaoning, China
| | - Honggang Shi
- The Second Department of Gastroenterology, The First Affiliated Hospital of Dalian Medical University, No. 222 Zhongshan Road, Dalian, 116011, Liaoning, China
| | - Bojia Liu
- The Second Department of Gastroenterology, The First Affiliated Hospital of Dalian Medical University, No. 222 Zhongshan Road, Dalian, 116011, Liaoning, China
| | - Xue Lin
- The Second Department of Gastroenterology, The First Affiliated Hospital of Dalian Medical University, No. 222 Zhongshan Road, Dalian, 116011, Liaoning, China
| | - Qingyong Chang
- The Second Department of Neurosurgery, Affiliated Zhongshan Hospital of Dalian University, No. 6 Jiefang Street, Dalian, 116001, Liaoning, China.
| | - Jiande D Z Chen
- Division of Gastroenterology and Hepatology, Johns Hopkins Center for Neurogastroenterology, Baltimore, MD, 21224, USA.
| | - Zhijun Duan
- The Second Department of Gastroenterology, The First Affiliated Hospital of Dalian Medical University, No. 222 Zhongshan Road, Dalian, 116011, Liaoning, China.
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Zhang X, Nan D, Zha C, He G, Zhang W, Duan Z. Long-term intervention of taurocholic acid over-expressing in cholestatic liver disease inhibits the growth of hepatoma cells. Cell Mol Biol (Noisy-le-grand) 2020. [DOI: 10.14715/cmb/2020.66.2.10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Bile acids usually build up in patients with cholestatic liver disease. It was found that the concentration of taurocholic acid (TCA), one of the taurine conjugates of primary bile acids in serum, was elevated the most. While the role played by TCA in the disease is unclear, there is concern whether TCA contributes to the development of hepatocarcinoma from cholestasis. In the present study, the cell viability, flow cytometry, real-time polymerase chain reaction, intracellular ROS measurement, and intracellular Ca2+ measurement were used to investigate the effects of TCA on THLE-2 and HepG2 cells. The results showed that TCA is capable of inhibiting HepG2 cell growth whereas it has relatively little or no impact on that of THLE-2 cells until later stages of 16-day treatment. The growth inhibition is a result of cell apoptosis induced by the increase of Ca2+ and ROS level, and also associated with the increased expression of c-Myc, CEBPα, TNF-α, ICAM-1, VCAM-1, CXCL-2, Egr-1. HepG2 growth inhibition could contribute to the research on the treatment methods of patients already with hepatocarcinoma.
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Zhang X, Nan D, Zha C, He G, Zhang W, Duan Z. Long-term intervention of taurocholic acid over-expressing in cholestatic liver disease inhibits the growth of hepatoma cells. Cell Mol Biol (Noisy-le-grand) 2020; 66:65-70. [PMID: 32415929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 05/03/2020] [Accepted: 05/03/2020] [Indexed: 06/11/2023]
Abstract
Bile acids usually build up in patients with cholestatic liver disease. It was found that the concentration of taurocholic acid (TCA), one of the taurine conjugates of primary bile acids in serum, was elevated the most. While the role played by TCA in the disease is unclear, there is concern whether TCA contributes to the development of hepatocarcinoma from cholestasis. In the present study, the cell viability, flow cytometry, real-time polymerase chain reaction, intracellular ROS measurement, and intracellular Ca2+ measurement were used to investigate the effects of TCA on THLE-2 and HepG2 cells. The results showed that TCA is capable of inhibiting HepG2 cell growth whereas it has relatively little or no impact on that of THLE-2 cells until later stages of 16-day treatment. The growth inhibition is a result of cell apoptosis induced by the increase of Ca2+ and ROS level, and also associated with the increased expression of c-Myc, CEBPα, TNF-α, ICAM-1, VCAM-1, CXCL-2, Egr-1. HepG2 growth inhibition could contribute to the research on the treatment methods of patients already with hepatocarcinoma.
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Affiliation(s)
- Xiujuan Zhang
- State Key Laboratory of Fine Chemicals, School of Chemical Engineering, Panjin Campus, Dalian University of Technology, 124221, China
| | - De Nan
- State Key Laboratory of Fine Chemicals, School of Chemical Engineering, Panjin Campus, Dalian University of Technology, 124221, China
| | - Chunting Zha
- State Key Laboratory of Fine Chemicals, School of Chemical Engineering, Panjin Campus, Dalian University of Technology, 124221, China
| | - Gaohong He
- State Key Laboratory of Fine Chemicals, School of Chemical Engineering, Panjin Campus, Dalian University of Technology, 124221, China
| | - Wenjun Zhang
- State Key Laboratory of Fine Chemicals, School of Chemical Engineering, Panjin Campus, Dalian University of Technology, 124221, China
| | - Zhijun Duan
- Department of Gastroenterology, The First Affiliated Hospital of Dalian Medical University, Dalian, 116011, China
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Duan Z, Yuan Y, Lu JC, Wang JL, Li Y, Svanberg S, Zhao GY. Underwater spatially, spectrally, and temporally resolved optical monitoring of aquatic fauna. Opt Express 2020; 28:2600-2610. [PMID: 32121945 DOI: 10.1364/oe.383061] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 01/06/2020] [Indexed: 06/10/2023]
Abstract
A continuous-wave (CW) Scheimpflug underwater multi-spectral lidar system was constructed to monitor aquatic fauna with spatial, spectral, and temporal resolution. Utilizing a 1 W 414 nm diode laser and a detection set-up with a reflective grating, measurements of shrimp pleopod movements at fixed range, and the swimming of small fish trapped in a clear tube were performed in a 5 m ×0.6 m ×0.6 m water tank. The spatial resolution is about 5 mm, the spectral resolution is 10 nm (from 400 nm to 700 nm), and with proper binning of the CCD, a read-out repetition rate up to 150 Hz can be reached. The experimental results demonstrate that the underwater Scheimpflug lidar system has great potential for detailed monitoring of the small aquatic fauna in oceanic environments.
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Ramani V, Deng X, Qiu R, Lee C, Disteche CM, Noble WS, Shendure J, Duan Z. Sci-Hi-C: A single-cell Hi-C method for mapping 3D genome organization in large number of single cells. Methods 2020; 170:61-68. [PMID: 31536770 PMCID: PMC6949367 DOI: 10.1016/j.ymeth.2019.09.012] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 09/13/2019] [Indexed: 12/31/2022] Open
Abstract
The highly dynamic nature of chromosome conformation and three-dimensional (3D) genome organization leads to cell-to-cell variability in chromatin interactions within a cell population, even if the cells of the population appear to be functionally homogeneous. Hence, although Hi-C is a powerful tool for mapping 3D genome organization, this heterogeneity of chromosome higher order structure among individual cells limits the interpretive power of population based bulk Hi-C assays. Moreover, single-cell studies have the potential to enable the identification and characterization of rare cell populations or cell subtypes in a heterogeneous population. However, it may require surveying relatively large numbers of single cells to achieve statistically meaningful observations in single-cell studies. By applying combinatorial cellular indexing to chromosome conformation capture, we developed single-cell combinatorial indexed Hi-C (sci-Hi-C), a high throughput method that enables mapping chromatin interactomes in large number of single cells. We demonstrated the use of sci-Hi-C data to separate cells by karytoypic and cell-cycle state differences and to identify cellular variability in mammalian chromosomal conformation. Here, we provide a detailed description of method design and step-by-step working protocols for sci-Hi-C.
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Affiliation(s)
- Vijay Ramani
- Department of Genome Sciences, University of Washington, Seattle, WA, United States.
| | - Xinxian Deng
- Department of Pathology, University of Washington, Seattle, WA, United States
| | - Ruolan Qiu
- Department of Genome Sciences, University of Washington, Seattle, WA, United States
| | - Choli Lee
- Department of Genome Sciences, University of Washington, Seattle, WA, United States
| | - Christine M Disteche
- Department of Pathology, University of Washington, Seattle, WA, United States; Department of Medicine, University of Washington, Seattle, WA, United States
| | - William S Noble
- Department of Genome Sciences, University of Washington, Seattle, WA, United States
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, United States; Howard Hughes Medical Institute, Seattle, WA, United States.
| | - Zhijun Duan
- Division of Hematology, University of Washington School of Medicine, Seattle, WA, United States; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, United States.
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He Y, Li C, Xu H, Duan Z, Liu Y, Zeng R, Li M, Wang B. AKT‐dependent hyperproliferation of keratinocytes in familial hidradenitis suppurativa with a
NCSTN
mutation: a potential role of defective miR‐100‐5p. Br J Dermatol 2019; 182:500-502. [DOI: 10.1111/bjd.18460] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Y. He
- Institute of Dermatology Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs Chinese Academy of Medical Sciences and Peking Union Medical College Nanjing Jiangsu 210042 China
| | - C. Li
- Institute of Dermatology Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs Chinese Academy of Medical Sciences and Peking Union Medical College Nanjing Jiangsu 210042 China
| | - H. Xu
- Institute of Dermatology Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs Chinese Academy of Medical Sciences and Peking Union Medical College Nanjing Jiangsu 210042 China
| | - Z. Duan
- Institute of Dermatology Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs Chinese Academy of Medical Sciences and Peking Union Medical College Nanjing Jiangsu 210042 China
| | - Y. Liu
- Institute of Dermatology Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs Chinese Academy of Medical Sciences and Peking Union Medical College Nanjing Jiangsu 210042 China
| | - R. Zeng
- Institute of Dermatology Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs Chinese Academy of Medical Sciences and Peking Union Medical College Nanjing Jiangsu 210042 China
| | - M. Li
- Institute of Dermatology Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs Chinese Academy of Medical Sciences and Peking Union Medical College Nanjing Jiangsu 210042 China
| | - B. Wang
- Institute of Dermatology Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs Chinese Academy of Medical Sciences and Peking Union Medical College Nanjing Jiangsu 210042 China
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Sarin SK, Choudhury A, Sharma MK, Maiwall R, Al Mahtab M, Rahman S, Saigal S, Saraf N, Soin AS, Devarbhavi H, Kim DJ, Dhiman RK, Duseja A, Taneja S, Eapen CE, Goel A, Ning Q, Chen T, Ma K, Duan Z, Yu C, Treeprasertsuk S, Hamid SS, Butt AS, Jafri W, Shukla A, Saraswat V, Tan SS, Sood A, Midha V, Goyal O, Ghazinyan H, Arora A, Hu J, Sahu M, Rao PN, Lee GH, Lim SG, Lesmana LA, Lesmana CR, Shah S, Prasad VGM, Payawal DA, Abbas Z, Dokmeci AK, Sollano JD, Carpio G, Shresta A, Lau GK, Fazal Karim M, Shiha G, Gani R, Kalista KF, Yuen MF, Alam S, Khanna R, Sood V, Lal BB, Pamecha V, Jindal A, Rajan V, Arora V, Yokosuka O, Niriella MA, Li H, Qi X, Tanaka A, Mochida S, Chaudhuri DR, Gane E, Win KM, Chen WT, Rela M, Kapoor D, Rastogi A, Kale P, Rastogi A, Sharma CB, Bajpai M, Singh V, Premkumar M, Maharashi S, Olithselvan A, Philips CA, Srivastava A, Yachha SK, Wani ZA, Thapa BR, Saraya A, Kumar A, Wadhawan M, Gupta S, Madan K, Sakhuja P, Vij V, Sharma BC, Garg H, Garg V, Kalal C, Anand L, Vyas T, Mathur RP, Kumar G, Jain P, Pasupuleti SSR, Chawla YK, Chowdhury A, Alam S, Song DS, Yang JM, Yoon EL. Correction to: Acute-on-chronic liver failure: consensus recommendations of the Asian Pacific association for the study of the liver (APASL): an update. Hepatol Int 2019; 13:826-828. [PMID: 31595462 PMCID: PMC6861344 DOI: 10.1007/s12072-019-09980-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 08/16/2019] [Indexed: 12/18/2022]
Abstract
The article Acute-on-chronic liver failure: consensus recommendations of the Asian Pacific association for the study of the liver (APASL): an update, written by [Shiv Sarin], was originally published electronically on the publisher's internet portal (currently SpringerLink) on June 06, 2019 without open access.
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Affiliation(s)
- Shiv Kumar Sarin
- Department of Hepatology, Institute of Liver and Biliary Sciences, New Delhi, 110070, India.
| | - Ashok Choudhury
- Department of Hepatology, Institute of Liver and Biliary Sciences, New Delhi, 110070, India
| | - Manoj K Sharma
- Department of Hepatology, Institute of Liver and Biliary Sciences, New Delhi, 110070, India
| | - Rakhi Maiwall
- Department of Hepatology, Institute of Liver and Biliary Sciences, New Delhi, 110070, India
| | - Mamun Al Mahtab
- Department of Hepatology, Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh
| | - Salimur Rahman
- Department of Hepatology, Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh
| | - Sanjiv Saigal
- Department of Hepatology, Medanta The Medicity, Gurgaon, India
| | - Neeraj Saraf
- Department of Hepatology, Medanta The Medicity, Gurgaon, India
| | - A S Soin
- Department of Hepatology, Medanta The Medicity, Gurgaon, India
| | | | - Dong Joon Kim
- Department of Internal Medicine, Hallym University College of Medicine, Seoul, South Korea
| | - R K Dhiman
- Department of Hepatology, PGIMER, Chandigarh, India
| | - Ajay Duseja
- Department of Hepatology, PGIMER, Chandigarh, India
| | - Sunil Taneja
- Department of Hepatology, PGIMER, Chandigarh, India
| | - C E Eapen
- Department of Hepatology, CMC, Vellore, India
| | - Ashish Goel
- Department of Hepatology, CMC, Vellore, India
| | - Q Ning
- Institute and Department of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tao Chen
- Translational Hepatology Institute Capital Medical University, Beijing You'an Hospital, Beijing, China
| | - Ke Ma
- Institute and Department of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Z Duan
- Translational Hepatology Institute Capital Medical University, Beijing You'an Hospital, Beijing, China
| | - Chen Yu
- Translational Hepatology Institute Capital Medical University, Beijing You'an Hospital, Beijing, China
| | | | - S S Hamid
- Department of Medicine, Aga Khan University Hospital, Karachi, Pakistan
| | - Amna S Butt
- Department of Medicine, Aga Khan University Hospital, Karachi, Pakistan
| | - Wasim Jafri
- Department of Medicine, Aga Khan University Hospital, Karachi, Pakistan
| | - Akash Shukla
- Department of Gastroenterology, Lokmanya Tilak Municipal General Hospital and Lokmanya Tilak Municipal Medical College, Sion, Mumbai, India
| | | | - Soek Siam Tan
- Department of Medicine, Hospital Selayang, Bata Caves, Selangor, Malaysia
| | - Ajit Sood
- Department of Gastroenterology, DMC, Ludhiana, India
| | - Vandana Midha
- Department of Gastroenterology, DMC, Ludhiana, India
| | - Omesh Goyal
- Department of Gastroenterology, DMC, Ludhiana, India
| | - Hasmik Ghazinyan
- Department of Hepatology, Nork Clinical Hospital of Infectious Disease, Yerevan, Armenia
| | - Anil Arora
- Department of Gastroenterology and Hepatology, Sir Ganga Ram Hospital and GRIPMER, New Delhi, Delhi, India
| | - Jinhua Hu
- Department of Medicine, 302 Millitary Hospital, Beijing, China
| | - Manoj Sahu
- Department of Gastroenterology and Hepatology Sciences, IMS & SUM Hospital, Bhubaneswar, Odisha, India
| | - P N Rao
- Asian Institute of Gastroenterology, Hyderabad, India
| | - Guan H Lee
- Division of Gastroenterology and Hepatology, Department of Medicine, National University Health System, Singapore, Singapore
| | - Seng G Lim
- Division of Gastroenterology and Hepatology, Department of Medicine, National University Health System, Singapore, Singapore
| | | | | | - Samir Shah
- Department of Hepatology, Global Hospitals, Mumbai, India
| | | | - Diana A Payawal
- Fatima University Medical Center Manila, Manila, Philippines
| | - Zaigham Abbas
- Department of Medicine, Ziauddin University Hospital, Karachi, Pakistan
| | - A Kadir Dokmeci
- Department of Medicine, Ankara University School of Medicine, Ankara, Turkey
| | - Jose D Sollano
- Department of Medicine, University of Santo Tomas, Manila, Philippines
| | - Gian Carpio
- Department of Medicine, University of Santo Tomas, Manila, Philippines
| | - Ananta Shresta
- Department of Hepatology, Foundation Nepal Sitapaila Height, Kathmandu, Nepal
| | - G K Lau
- Department of Medicine, Humanity and Health Medical Group, New Kowloon, Hong Kong, China
| | - Md Fazal Karim
- Department of Hepatology, Sir Salimullah Medical College, Dhaka, Bangladesh
| | - Gamal Shiha
- Egyptian Liver Research Institute And Hospital, Cairo, Egypt
| | - Rino Gani
- Division of Hepatobiliary, Department of Internal Medicine, Faculty of Medicine, Cipto Mangunkusumo Hospital, Universitas Indonesia, Jakarta, Indonesia
| | - Kemal Fariz Kalista
- Division of Hepatobiliary, Department of Internal Medicine, Faculty of Medicine, Cipto Mangunkusumo Hospital, Universitas Indonesia, Jakarta, Indonesia
| | - Man-Fung Yuen
- Department of Medicine, Queen Mary Hospital Hong Kong, The University of Hong Kong, Hong Kong, China
| | - Seema Alam
- Department of Pediatric Hepatology, Institute of Liver and Biliary Sciences, New Delhi, Delhi, India
| | - Rajeev Khanna
- Department of Pediatric Hepatology, Institute of Liver and Biliary Sciences, New Delhi, Delhi, India
| | - Vikrant Sood
- Department of Pediatric Hepatology, Institute of Liver and Biliary Sciences, New Delhi, Delhi, India
| | - Bikrant Bihari Lal
- Department of Pediatric Hepatology, Institute of Liver and Biliary Sciences, New Delhi, Delhi, India
| | - Viniyendra Pamecha
- Department of Hepatobilliary Pancreatic Surgery and Liver Transplant, Institute of Liver and Biliary Sciences, New Delhi, Delhi, India
| | - Ankur Jindal
- Department of Hepatology, Institute of Liver and Biliary Sciences, New Delhi, 110070, India
| | - V Rajan
- Department of Hepatology, Institute of Liver and Biliary Sciences, New Delhi, 110070, India
| | - Vinod Arora
- Department of Hepatology, Institute of Liver and Biliary Sciences, New Delhi, 110070, India
| | | | | | - Hai Li
- Department of Gastroenterology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaolong Qi
- CHESS Frontier Center, The First Hospital of Lanzhou University, Lanzhou University, Lanzhou, China
| | - Atsushi Tanaka
- Department of Medicine, Tokyo University School of Medicine, Tokyo, Japan
| | - Satoshi Mochida
- Department of Gastroenterology and Hepatology, Faculty of Medicine, Saitama Medical University, Saitama, Japan
| | | | - Ed Gane
- New Zealand Liver Transplant Unit, Auckland Hospital, Auckland, New Zealand
| | | | - Wei Ting Chen
- Division of Hepatology, Department of Gastroenterology and Hepatology, Chang Gung Medical Foundation, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Mohd Rela
- Department of Liver Transplant Surgery, Dr. Rela Institute and Medical Centre, Chennai, India
| | | | - Amit Rastogi
- Department of Hepatology, Medanta The Medicity, Gurgaon, India
| | - Pratibha Kale
- Department of Microbiology, Institute of Liver and Biliary Sciences, New Delhi, Delhi, India
| | - Archana Rastogi
- Department of Pathology, Institute of Liver and Biliary Sciences, New Delhi, Delhi, India
| | - Chhagan Bihari Sharma
- Department of Pathology, Institute of Liver and Biliary Sciences, New Delhi, Delhi, India
| | - Meenu Bajpai
- Department of Immunohematology and Transfusion Medicine, Institute of Liver and Biliary Sciences, New Delhi, Delhi, India
| | | | | | | | - A Olithselvan
- Division of Liver Transplantation and Hepatology, Manipal Hospitals, Bangalore, India
| | - Cyriac Abby Philips
- The Liver Unit, Cochin Gastroenterology Group, Ernakulam Medical Centre, Kochi, India
| | - Anshu Srivastava
- Department of Pediatric Gastroenterology, SGPGIMS, Lucknow, India
| | | | | | - B R Thapa
- Department of Gastroenterology and Pediatric Gastroenterology, PGIMER, Chandigarh, India
| | - Anoop Saraya
- Department of Gastroenterology and Human Nutrition, AIIMS, New Delhi, India
| | - Ashish Kumar
- Department of Gastroenterology and Hepatology, Sir Ganga Ram Hospital and GRIPMER, New Delhi, Delhi, India
| | - Manav Wadhawan
- Department of Gastroenterology, Hepatology and Liver Transplant, B L K Hospital, New Delhi, India
| | - Subash Gupta
- Centre for Liver and Biliary Science, Max Hospital, New Delhi, India
| | - Kaushal Madan
- Department of Gastroenterology, Hepatology and Liver Transplant, Max Hospital, New Delhi, India
| | - Puja Sakhuja
- Department of Pathology, GB Pant Hospital, New Delhi, India
| | - Vivek Vij
- Department of Liver Transplant and Hepatobilliary Surgery, Fortis Hospital, New Delhi, India
| | - Barjesh C Sharma
- Department of Gastroenterology, GB Pant Hospital, New Delhi, India
| | - Hitendra Garg
- Department of Gastroenterology, Hepatology and Liver Transplant, Apollo Hospital, New Delhi, India
| | - Vishal Garg
- Department of Gastroenterology, Hepatology and Liver Transplant, Apollo Hospital, New Delhi, India
| | - Chetan Kalal
- Department of Hepatology, Sir H N Reliance Hospital and Research Centre, Mumbai, India
| | - Lovkesh Anand
- Department of Gastroenterology and Hepatology, Narayana Hospital, Gurugram, India
| | - Tanmay Vyas
- Department of Hepatology, Parimal Multi-Speciality Hospital, Ahmedabad, India
| | - Rajan P Mathur
- Department of Nephrology, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Guresh Kumar
- Department of Statistics and Clinical Research, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Priyanka Jain
- Department of Statistics and Clinical Research, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Samba Siva Rao Pasupuleti
- Department of Statistics and Clinical Research, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Yogesh K Chawla
- Department of Hepatology and Gastroenterology, Kalinga Institute of Med Sciences, KIIT University, Bhubaneswar, India
| | - Abhijit Chowdhury
- Department of Hepatology, Institute of Post Graduate Medical Education and Research, Kolkata, India
| | - Shahinul Alam
- Department of Hepatology, Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh
| | - Do Seon Song
- Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Jin Mo Yang
- Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Eileen L Yoon
- Department Of Internal Medicine, Inje University College of Medicine, Busan, South Korea
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Abstract
Abstract
Along with the urbanization process, large amount of construction and demolition (C&D) waste during the construction, reconstruction, expansion or demolition of buildings is generated. Meanwhile, the impact on environment due to natural aggregate mining has become increasingly significant. These factors have driven the building industry to look for environmentally friendly materials and focusing on sustainable construction. Through nearly a decade of research, recycled concrete (RC) made with recycled aggregates manufactured from construction and demolition (C&D) waste has shown a competitive performance compared to natural materials and has already achieved industrial application. Researches on sustainably recycled concrete have become an essential part of sustainable development and continue to play a vital role for future research.
This paper engages in the discussion and the overview of research done by the Research Group for Recycled Concrete Structures and Construction at Tongji University, Shanghai. The first part discusses the necessary mechanical and durability properties of recycled concrete with recycled aggregate as well as recycled powder focusing on workability, strength, Poisson’s ratio, stress-strain behaviour along with carbonation, chloride penetration shrinkage and creep. The second part throws light on the elements and structures made with recycled aggregate concrete (RAC), discussing the behaviours of RAC components and structures.
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Xue Y, Zhang J, Bai Y, Jing C, Zhang Z, Sun X, Yang D, Duan Z. Establishment and validation of a prognostic model for hepatocellular carcinoma after radical liver resection. J BUON 2019; 24:1420-1428. [PMID: 31646786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
PURPOSE The prognostic factors related to survival of primary hepatocellular carcinoma (HCC) after radical resection were analyzed in order to establish a new prognostic model for HCC patients and to shed light on personalized treatments. METHODS 141 patients pathologically diagnosed with HCC were enrolled. The independent prognostic factors affecting overall survival were identified, and a prognostic mathematical model was established. Independent samples of 21 cases were used to validate the model's ability to predict prognosis of HCC patients. RESULTS The median survival time was 34 months, and the 1-, 3-, and 5-year overall survival rates were 93.2%, 80%, and 68.9%, respectively. Univariate analysis showed that alpha fetoprotein (AFP) serum level, tumor size, tumor capsule, liver cirrhosis, neutrophil-to-lymphocyte ratio (NLR), and total bilirubin (TBIL) were significantly correlated with overall survival (p<0.05). Cox multivariate analysis indicated that the independent prognostic factors were AFP serum level, liver cirrhosis, tumor size, tumor capsule, and NLR. The prognostic mathematical model was: Prognostic Index (PI)=1.725 * liver cirrhosis + 0.783 * NLR + 1.046 * AFP + 0.595 * tumor size - 0.811 * tumor capsule. Based on the PI quartiles, 3.933 (25%), 4.716 (50%), and 5.195 (75%), the patients were divided into 4 groups: low risk (PI﹤3.933), moderate-risk (3.933 ≤ PI < 4.716), high-risk (4.761 ≤ PI < 5.195), and very high-risk (PI ≥ 5.195) group. The median survival times were 60, 34, 32, and 20 months, respectively. The 1-, 2-, 3-, and 5-year cumulative survival rates were 100%, 96%, 96%, 86%; 89%, 75%, 68%, 68%; 77%, 68%, 57%, 44%; 50%, 34%, 29%, 29%, separately. The predictions of the prognostic model demonstrated good consistency with the actual results. The total accuracy rate was 80.9%, and the Kappa consistency coefficient was 0.571 (p=0.009). CONCLUSIONS The higher the PI, the lower the postoperative cumulative survival rate and the worse the prognosis. This model can be used as an effective method to assess the prognosis of HCC patients after resection.
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Affiliation(s)
- Yan Xue
- Department of Gastroenterology, The Second People's Hospital of Liaocheng, Liaocheng 252600, China
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Sarin SK, Choudhury A, Sharma MK, Maiwall R, Al Mahtab M, Rahman S, Saigal S, Saraf N, Soin AS, Devarbhavi H, Kim DJ, Dhiman RK, Duseja A, Taneja S, Eapen CE, Goel A, Ning Q, Chen T, Ma K, Duan Z, Yu C, Treeprasertsuk S, Hamid SS, Butt AS, Jafri W, Shukla A, Saraswat V, Tan SS, Sood A, Midha V, Goyal O, Ghazinyan H, Arora A, Hu J, Sahu M, Rao PN, Lee GH, Lim SG, Lesmana LA, Lesmana CR, Shah S, Prasad VGM, Payawal DA, Abbas Z, Dokmeci AK, Sollano JD, Carpio G, Shresta A, Lau GK, Fazal Karim M, Shiha G, Gani R, Kalista KF, Yuen MF, Alam S, Khanna R, Sood V, Lal BB, Pamecha V, Jindal A, Rajan V, Arora V, Yokosuka O, Niriella MA, Li H, Qi X, Tanaka A, Mochida S, Chaudhuri DR, Gane E, Win KM, Chen WT, Rela M, Kapoor D, Rastogi A, Kale P, Rastogi A, Sharma CB, Bajpai M, Singh V, Premkumar M, Maharashi S, Olithselvan A, Philips CA, Srivastava A, Yachha SK, Wani ZA, Thapa BR, Saraya A, Shalimar, Kumar A, Wadhawan M, Gupta S, Madan K, Sakhuja P, Vij V, Sharma BC, Garg H, Garg V, Kalal C, Anand L, Vyas T, Mathur RP, Kumar G, Jain P, Pasupuleti SSR, Chawla YK, Chowdhury A, Alam S, Song DS, Yang JM, Yoon EL. Acute-on-chronic liver failure: consensus recommendations of the Asian Pacific association for the study of the liver (APASL): an update. Hepatol Int 2019; 13:353-390. [PMID: 31172417 PMCID: PMC6728300 DOI: 10.1007/s12072-019-09946-3] [Citation(s) in RCA: 413] [Impact Index Per Article: 82.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Accepted: 04/03/2019] [Indexed: 02/07/2023]
Abstract
The first consensus report of the working party of the Asian Pacific Association for the Study of the Liver (APASL) set up in 2004 on acute-on-chronic liver failure (ACLF) was published in 2009. With international groups volunteering to join, the "APASL ACLF Research Consortium (AARC)" was formed in 2012, which continued to collect prospective ACLF patient data. Based on the prospective data analysis of nearly 1400 patients, the AARC consensus was published in 2014. In the past nearly four-and-a-half years, the AARC database has been enriched to about 5200 cases by major hepatology centers across Asia. The data published during the interim period were carefully analyzed and areas of contention and new developments in the field of ACLF were prioritized in a systematic manner. The AARC database was also approached for answering some of the issues where published data were limited, such as liver failure grading, its impact on the 'Golden Therapeutic Window', extrahepatic organ dysfunction and failure, development of sepsis, distinctive features of acute decompensation from ACLF and pediatric ACLF and the issues were analyzed. These initiatives concluded in a two-day meeting in October 2018 at New Delhi with finalization of the new AARC consensus. Only those statements, which were based on evidence using the Grade System and were unanimously recommended, were accepted. Finalized statements were again circulated to all the experts and subsequently presented at the AARC investigators meeting at the AASLD in November 2018. The suggestions from the experts were used to revise and finalize the consensus. After detailed deliberations and data analysis, the original definition of ACLF was found to withstand the test of time and be able to identify a homogenous group of patients presenting with liver failure. New management options including the algorithms for the management of coagulation disorders, renal replacement therapy, sepsis, variceal bleed, antivirals and criteria for liver transplantation for ACLF patients were proposed. The final consensus statements along with the relevant background information and areas requiring future studies are presented here.
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Affiliation(s)
- Shiv Kumar Sarin
- Department of Hepatology, Institute of Liver and Biliary Sciences, New Delhi, 110070, India.
| | - Ashok Choudhury
- Department of Hepatology, Institute of Liver and Biliary Sciences, New Delhi, 110070, India
| | - Manoj K Sharma
- Department of Hepatology, Institute of Liver and Biliary Sciences, New Delhi, 110070, India
| | - Rakhi Maiwall
- Department of Hepatology, Institute of Liver and Biliary Sciences, New Delhi, 110070, India
| | - Mamun Al Mahtab
- Department of Hepatology, Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh
| | - Salimur Rahman
- Department of Hepatology, Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh
| | - Sanjiv Saigal
- Department of Hepatology, Medanta The Medicity, Gurgaon, India
| | - Neeraj Saraf
- Department of Hepatology, Medanta The Medicity, Gurgaon, India
| | - A S Soin
- Department of Hepatology, Medanta The Medicity, Gurgaon, India
| | | | - Dong Joon Kim
- Department of Internal Medicine, Hallym University College of Medicine, Seoul, South Korea
| | - R K Dhiman
- Department of Hepatology, PGIMER, Chandigarh, India
| | - Ajay Duseja
- Department of Hepatology, PGIMER, Chandigarh, India
| | - Sunil Taneja
- Department of Hepatology, PGIMER, Chandigarh, India
| | - C E Eapen
- Department of Hepatology, CMC, Vellore, India
| | - Ashish Goel
- Department of Hepatology, CMC, Vellore, India
| | - Q Ning
- Institute and Department of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tao Chen
- Translational Hepatology Institute Capital Medical University, Beijing You'an Hospital, Beijing, China
| | - Ke Ma
- Institute and Department of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Z Duan
- Translational Hepatology Institute Capital Medical University, Beijing You'an Hospital, Beijing, China
| | - Chen Yu
- Translational Hepatology Institute Capital Medical University, Beijing You'an Hospital, Beijing, China
| | | | - S S Hamid
- Department of Medicine, Aga Khan University Hospital, Karachi, Pakistan
| | - Amna S Butt
- Department of Medicine, Aga Khan University Hospital, Karachi, Pakistan
| | - Wasim Jafri
- Department of Medicine, Aga Khan University Hospital, Karachi, Pakistan
| | - Akash Shukla
- Department of Gastroenterology, Lokmanya Tilak Municipal General Hospital and Lokmanya Tilak Municipal Medical College, Sion, Mumbai, India
| | | | - Soek Siam Tan
- Department of Medicine, Hospital Selayang, Bata Caves, Selangor, Malaysia
| | - Ajit Sood
- Department of Gastroenterology, DMC, Ludhiana, India
| | - Vandana Midha
- Department of Gastroenterology, DMC, Ludhiana, India
| | - Omesh Goyal
- Department of Gastroenterology, DMC, Ludhiana, India
| | - Hasmik Ghazinyan
- Department of Hepatology, Nork Clinical Hospital of Infectious Disease, Yerevan, Armenia
| | - Anil Arora
- Department of Gastroenterology and Hepatology, Sir Ganga Ram Hospital and GRIPMER, New Delhi, Delhi, India
| | - Jinhua Hu
- Department of Medicine, 302 Millitary Hospital, Beijing, China
| | - Manoj Sahu
- Department of Gastroenterology and Hepatology Sciences, IMS & SUM Hospital, Bhubaneswar, Odisha, India
| | - P N Rao
- Asian Institute of Gastroenterology, Hyderabad, India
| | - Guan H Lee
- Division of Gastroenterology and Hepatology, Department of Medicine, National University Health System, Singapore, Singapore
| | - Seng G Lim
- Division of Gastroenterology and Hepatology, Department of Medicine, National University Health System, Singapore, Singapore
| | | | | | - Samir Shah
- Department of Hepatology, Global Hospitals, Mumbai, India
| | | | - Diana A Payawal
- Fatima University Medical Center Manila, Manila, Philippines
| | - Zaigham Abbas
- Department of Medicine, Ziauddin University Hospital, Karachi, Pakistan
| | - A Kadir Dokmeci
- Department of Medicine, Ankara University School of Medicine, Ankara, Turkey
| | - Jose D Sollano
- Department of Medicine, University of Santo Tomas, Manila, Philippines
| | - Gian Carpio
- Department of Medicine, University of Santo Tomas, Manila, Philippines
| | - Ananta Shresta
- Department of Hepatology, Foundation Nepal Sitapaila Height, Kathmandu, Nepal
| | - G K Lau
- Department of Medicine, Humanity and Health Medical Group, New Kowloon, Hong Kong, China
| | - Md Fazal Karim
- Department of Hepatology, Sir Salimullah Medical College, Dhaka, Bangladesh
| | - Gamal Shiha
- Egyptian Liver Research Institute And Hospital, Cairo, Egypt
| | - Rino Gani
- Division of Hepatobiliary, Department of Internal Medicine, Faculty of Medicine, Cipto Mangunkusumo Hospital, Universitas Indonesia, Jakarta, Indonesia
| | - Kemal Fariz Kalista
- Division of Hepatobiliary, Department of Internal Medicine, Faculty of Medicine, Cipto Mangunkusumo Hospital, Universitas Indonesia, Jakarta, Indonesia
| | - Man-Fung Yuen
- Department of Medicine, Queen Mary Hospital Hong Kong, The University of Hong Kong, Hong Kong, China
| | - Seema Alam
- Department of Pediatric Hepatology, Institute of Liver and Biliary Sciences, New Delhi, Delhi, India
| | - Rajeev Khanna
- Department of Pediatric Hepatology, Institute of Liver and Biliary Sciences, New Delhi, Delhi, India
| | - Vikrant Sood
- Department of Pediatric Hepatology, Institute of Liver and Biliary Sciences, New Delhi, Delhi, India
| | - Bikrant Bihari Lal
- Department of Pediatric Hepatology, Institute of Liver and Biliary Sciences, New Delhi, Delhi, India
| | - Viniyendra Pamecha
- Department of Hepatobilliary Pancreatic Surgery and Liver Transplant, Institute of Liver and Biliary Sciences, New Delhi, Delhi, India
| | - Ankur Jindal
- Department of Hepatology, Institute of Liver and Biliary Sciences, New Delhi, 110070, India
| | - V Rajan
- Department of Hepatology, Institute of Liver and Biliary Sciences, New Delhi, 110070, India
| | - Vinod Arora
- Department of Hepatology, Institute of Liver and Biliary Sciences, New Delhi, 110070, India
| | | | | | - Hai Li
- Department of Gastroenterology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaolong Qi
- CHESS Frontier Center, The First Hospital of Lanzhou University, Lanzhou University, Lanzhou, China
| | - Atsushi Tanaka
- Department of Medicine, Tokyo University School of Medicine, Tokyo, Japan
| | - Satoshi Mochida
- Department of Gastroenterology and Hepatology, Faculty of Medicine, Saitama Medical University, Saitama, Japan
| | | | - Ed Gane
- New Zealand Liver Transplant Unit, Auckland Hospital, Auckland, New Zealand
| | | | - Wei Ting Chen
- Division of Hepatology, Department of Gastroenterology and Hepatology, Chang Gung Medical Foundation, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Mohd Rela
- Department of Liver Transplant Surgery, Dr. Rela Institute and Medical Centre, Chennai, India
| | | | - Amit Rastogi
- Department of Hepatology, Medanta The Medicity, Gurgaon, India
| | - Pratibha Kale
- Department of Microbiology, Institute of Liver and Biliary Sciences, New Delhi, Delhi, India
| | - Archana Rastogi
- Department of Pathology, Institute of Liver and Biliary Sciences, New Delhi, Delhi, India
| | - Chhagan Bihari Sharma
- Department of Pathology, Institute of Liver and Biliary Sciences, New Delhi, Delhi, India
| | - Meenu Bajpai
- Department of Immunohematology and Transfusion Medicine, Institute of Liver and Biliary Sciences, New Delhi, Delhi, India
| | | | | | | | - A Olithselvan
- Division of Liver Transplantation and Hepatology, Manipal Hospitals, Bangalore, India
| | - Cyriac Abby Philips
- The Liver Unit, Cochin Gastroenterology Group, Ernakulam Medical Centre, Kochi, India
| | - Anshu Srivastava
- Department of Pediatric Gastroenterology, SGPGIMS, Lucknow, India
| | | | | | - B R Thapa
- Department of Gastroenterology and Pediatric Gastroenterology, PGIMER, Chandigarh, India
| | - Anoop Saraya
- Department of Gastroenterology and Human Nutrition, AIIMS, New Delhi, India
| | - Shalimar
- Department of Gastroenterology and Human Nutrition, AIIMS, New Delhi, India
| | - Ashish Kumar
- Department of Gastroenterology and Hepatology, Sir Ganga Ram Hospital and GRIPMER, New Delhi, Delhi, India
| | - Manav Wadhawan
- Department of Gastroenterology, Hepatology and Liver Transplant, B L K Hospital, New Delhi, India
| | - Subash Gupta
- Centre for Liver and Biliary Science, Max Hospital, New Delhi, India
| | - Kaushal Madan
- Department of Gastroenterology, Hepatology and Liver Transplant, Max Hospital, New Delhi, India
| | - Puja Sakhuja
- Department of Pathology, GB Pant Hospital, New Delhi, India
| | - Vivek Vij
- Department of Liver Transplant and Hepatobilliary Surgery, Fortis Hospital, New Delhi, India
| | - Barjesh C Sharma
- Department of Gastroenterology, GB Pant Hospital, New Delhi, India
| | - Hitendra Garg
- Department of Gastroenterology, Hepatology and Liver Transplant, Apollo Hospital, New Delhi, India
| | - Vishal Garg
- Department of Gastroenterology, Hepatology and Liver Transplant, Apollo Hospital, New Delhi, India
| | - Chetan Kalal
- Department of Hepatology, Sir H N Reliance Hospital and Research Centre, Mumbai, India
| | - Lovkesh Anand
- Department of Gastroenterology and Hepatology, Narayana Hospital, Gurugram, India
| | - Tanmay Vyas
- Department of Hepatology, Parimal Multi-Speciality Hospital, Ahmedabad, India
| | - Rajan P Mathur
- Department of Nephrology, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Guresh Kumar
- Department of Statistics and Clinical Research, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Priyanka Jain
- Department of Statistics and Clinical Research, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Samba Siva Rao Pasupuleti
- Department of Statistics and Clinical Research, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Yogesh K Chawla
- Department of Hepatology and Gastroenterology, Kalinga Institute of Med Sciences, KIIT University, Bhubaneswar, India
| | - Abhijit Chowdhury
- Department of Hepatology, Institute of Post Graduate Medical Education and Research, Kolkata, India
| | - Shahinul Alam
- Department of Hepatology, Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh
| | - Do Seon Song
- Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Jin Mo Yang
- Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Eileen L Yoon
- Department Of Internal Medicine, Inje University College of Medicine, Busan, South Korea
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Timoshenko J, Duan Z, Henkelman G, Crooks RM, Frenkel AI. Solving the Structure and Dynamics of Metal Nanoparticles by Combining X-Ray Absorption Fine Structure Spectroscopy and Atomistic Structure Simulations. Annu Rev Anal Chem (Palo Alto Calif) 2019; 12:501-522. [PMID: 30699037 DOI: 10.1146/annurev-anchem-061318-114929] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Extended X-ray absorption fine structure (EXAFS) spectroscopy is a premiere method for analysis of the structure and structural transformation of nanoparticles. Extraction of analytical information about the three-dimensional structure and dynamics of metal-metal bonds from EXAFS spectra requires special care due to their markedly non-bulk-like character. In recent decades, significant progress has been made in the first-principles modeling of structure and properties of nanoparticles. In this review, we summarize new approaches for EXAFS data analysis that incorporate particle structure modeling into the process of structural refinement.
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Affiliation(s)
- J Timoshenko
- Department of Materials Science and Chemical Engineering, Stony Brook University, Stony Brook, New York 11794, USA;
| | - Z Duan
- Department of Chemistry and Texas Materials Institute, University of Texas at Austin, Austin, Texas 78712, USA
- Institute for Computational and Engineering Sciences, University of Texas at Austin, Austin, Texas 78712, USA
| | - G Henkelman
- Department of Chemistry and Texas Materials Institute, University of Texas at Austin, Austin, Texas 78712, USA
- Institute for Computational and Engineering Sciences, University of Texas at Austin, Austin, Texas 78712, USA
| | - R M Crooks
- Department of Chemistry and Texas Materials Institute, University of Texas at Austin, Austin, Texas 78712, USA
| | - A I Frenkel
- Department of Materials Science and Chemical Engineering, Stony Brook University, Stony Brook, New York 11794, USA;
- Division of Chemistry, Brookhaven National Laboratory, Upton, New York 11973, USA
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Abstract
Recent burst of new technologies that allow for quantitatively delineating chromatin structure has greatly expanded our understanding of how the genome is organized in the three-dimensional (3D) space of the nucleus. It is now clear that the hierarchical organization of the eukaryotic genome critically impacts nuclear activities such as transcription, replication, as well as cellular and developmental events such as cell cycle, cell fate decision and embryonic development. In this review, we discuss new insights into how the structural features of the 3D genome hierarchy are established and maintained, how this hierarchy undergoes dynamic rearrangement during normal development and how its perturbation will lead to human disease, highlighting the accumulating evidence that links the diverse 3D genome architecture components to a multitude of human diseases and the emerging mechanisms by which 3D genome derangement causes disease phenotypes.
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Affiliation(s)
- Anton Krumm
- Department of Microbiology, University of Washington, USA.
| | - Zhijun Duan
- Institute for Stem Cell and Regenerative Medicine, University of Washington, USA; Division of Hematology, Department of Medicine, University of Washington, USA.
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Kim JS, He X, Liu J, Duan Z, Kim T, Gerard J, Kim B, Pillai MM, Lane WS, Noble WS, Budnik B, Waldman T. Systematic proteomics of endogenous human cohesin reveals an interaction with diverse splicing factors and RNA-binding proteins required for mitotic progression. J Biol Chem 2019; 294:8760-8772. [PMID: 31010829 PMCID: PMC6552432 DOI: 10.1074/jbc.ra119.007832] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 04/18/2019] [Indexed: 12/23/2022] Open
Abstract
The cohesin complex regulates sister chromatid cohesion, chromosome organization, gene expression, and DNA repair. Cohesin is a ring complex composed of four core subunits and seven regulatory subunits. In an effort to comprehensively identify additional cohesin-interacting proteins, we used gene editing to introduce a dual epitope tag into the endogenous allele of each of 11 known components of cohesin in cultured human cells, and we performed MS analyses on dual-affinity purifications. In addition to reciprocally identifying all known components of cohesin, we found that cohesin interacts with a panoply of splicing factors and RNA-binding proteins (RBPs). These included diverse components of the U4/U6.U5 tri-small nuclear ribonucleoprotein complex and several splicing factors that are commonly mutated in cancer. The interaction between cohesin and splicing factors/RBPs was RNA- and DNA-independent, occurred in chromatin, was enhanced during mitosis, and required RAD21. Furthermore, cohesin-interacting splicing factors and RBPs followed the cohesin cycle and prophase pathway of cell cycle-regulated interactions with chromatin. Depletion of cohesin-interacting splicing factors and RBPs resulted in aberrant mitotic progression. These results provide a comprehensive view of the endogenous human cohesin interactome and identify splicing factors and RBPs as functionally significant cohesin-interacting proteins.
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Affiliation(s)
- Jung-Sik Kim
- From the Departments of Oncology and Biochemistry & Molecular Biology, Georgetown University School of Medicine, Washington, D. C. 20057
| | - Xiaoyuan He
- From the Departments of Oncology and Biochemistry & Molecular Biology, Georgetown University School of Medicine, Washington, D. C. 20057
| | - Jie Liu
- the Department of Genome Sciences
| | - Zhijun Duan
- Institute for Stem Cell and Regenerative Medicine, and
- Division of Hematology, University of Washington, Seattle, Washington 98195
| | - Taeyeon Kim
- From the Departments of Oncology and Biochemistry & Molecular Biology, Georgetown University School of Medicine, Washington, D. C. 20057
| | - Julia Gerard
- From the Departments of Oncology and Biochemistry & Molecular Biology, Georgetown University School of Medicine, Washington, D. C. 20057
| | - Brian Kim
- From the Departments of Oncology and Biochemistry & Molecular Biology, Georgetown University School of Medicine, Washington, D. C. 20057
| | - Manoj M Pillai
- the Section of Hematology, Yale Cancer Center, Yale University School of Medicine, New Haven, Connecticut 06510, and
| | - William S Lane
- the Mass Spectrometry and Proteomics Resource Laboratory, Harvard University, Cambridge, Massachusetts 02138
| | | | - Bogdan Budnik
- the Mass Spectrometry and Proteomics Resource Laboratory, Harvard University, Cambridge, Massachusetts 02138
| | - Todd Waldman
- From the Departments of Oncology and Biochemistry & Molecular Biology, Georgetown University School of Medicine, Washington, D. C. 20057,
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Lang J, Lan M, Feng M, Xu P, Fu B, Duan Z, Zhang S, Qin Y, Peng X, Liu J, Li F, Lu S. Validation of the 8th Edition of the UICC/AJCC Staging System for Nasopharyngeal Carcinoma From non-Endemic Areas in the Era of Intensity-Modulated Radiation Therapy. Int J Radiat Oncol Biol Phys 2018. [DOI: 10.1016/j.ijrobp.2018.07.890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Giordano S, Duan Z, Zhao H, Hwang J, Chavez MacGregor M. Hepatitis B virus (HBV), hepatitis C virus (HCV) and human immunodeficiency virus (HIV) screening prior to chemotherapy initiation among patients with solid tumors. Ann Oncol 2018. [DOI: 10.1093/annonc/mdy300.098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Abstract
BACKGROUND The gut microbiome has been developing and making adaption all the time, which is consistent with their host from the initial colonization at birth or earlier. Emerging evidence is showing that dysbiosis is involved in various diseases associated with immune, metabolism, infection, nervous system, social behaviors, and psychopathology, etc., maybe via modulating gut barrier, microbiome-gut-brain axis, or some metabolites like short-chain fatty acids (SCFAs). SUMMARY In the review, we will conclude the recent researches related to the influence of microbiome on local structure, function, regulation, metabolism of gut, and systematic modulation to the host, as well as some affective factors such as diet or antibiotics. Key Messages: It is a reasonable hypothesis that the balance of bioactive factors or cells and the opposites such as the regulatory T/helper T17 balance and interleukin (IL)-10/IL-17 balance plays a vital role in homeostasis of immunity system. Meanwhile, the link between gut microbiome and immune system via microbiota-derived metabolite SCFAs involved in multi-function of the host locally and systematically has been revealed. We hope to contribute to the microbiome-targeted treatment and prevention of some diseases.
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Liu Z, Zhang Z, Huang M, Sun X, Liu B, Guo Q, Chang Q, Duan Z. Taurocholic acid is an active promoting factor, not just a biomarker of progression of liver cirrhosis: evidence from a human metabolomic study and in vitro experiments. BMC Gastroenterol 2018; 18:112. [PMID: 29996772 PMCID: PMC6042259 DOI: 10.1186/s12876-018-0842-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 07/02/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Previous studies have indicated that bile acid is associated with progression of liver cirrhosis. However, the particular role of specific bile acid in the development of liver cirrhosis is not definite. The present study aims to identify the specific bile acid and explore its possible mechanisms in promoting liver cirrhosis. METHODS Thirty two cirrhotic patients and 27 healthy volunteers were enrolled. Age, gender, Child-Pugh classification and serum of patients and volunteers were collected. Liquid chromatography tandem mass spectrometry (LC-MS) was utilized to determine concentrations of 12 bile acids in serum. Principal component analysis, fold change analysis and heatmap analysis were used to identify the most changed bile acid. And pathway analysis was used to identify the most affected pathway in bile acid metabolism. Spearman rank correlation analysis was employed to assess correlation between concentrations of bile acids and Child-Pugh classification. Hepatic stellate cells (LX-2) were cultured in DMEM. LX-2 cells were also co-cultured with HepG2 cells in the transwell chambers. LX-2 cells were treated with Na+/taurocholate in different concentrations. Western blot was used to evaluate the expression of alpha smooth muscle actin (α-SMA), type I collagen, and Toll-like receptor 4 (TLR4) in LX-2 cells. RESULTS Concentrations of 12 bile acids in serum of patients and healthy volunteers were determined with LC-MS successively. Principal component analysis, fold change analysis and heatmap analysis identified taurocholic acid (TCA) to be the most changed bile acid. Pathway analysis showed that TCA biosynthesis increased significantly. Spearman rank correlation analysis showed that concentration of TCA in serum of cirrhotic patients was positively associated with Child-Pugh classification. TCA increased the expression of α-SMA, type I collagen, and TLR4 in LX-2 cells. Moreover, the above effect was strengthened when LX-2 cells were co-cultured with HepG2 cells. CONCLUSIONS Increased TCA concentration in serum of liver cirrhotic patients is mainly due to increased bile acid biosynthesis. TCA is an active promoter of the progression of liver cirrhosis. TCA promoting liver cirrhosis is likely through activating hepatic stellate cells via upregulating TLR4 expression. TCA is a potential therapeutic target for the prevention and treatment of liver cirrhosis.
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Affiliation(s)
- Zhimin Liu
- Second department of Gastroenterology, First Affiliated Hospital of Dalian Medical University, Dalian, 116011, China
| | - Zhifeng Zhang
- Second department of Gastroenterology, First Affiliated Hospital of Dalian Medical University, Dalian, 116011, China
| | - Mei Huang
- Second department of Gastroenterology, First Affiliated Hospital of Dalian Medical University, Dalian, 116011, China
| | - Xiaoping Sun
- The Sixth People's Hospital of Dalian, Dalian, 116021, China
| | - Bojia Liu
- Second department of Gastroenterology, First Affiliated Hospital of Dalian Medical University, Dalian, 116011, China
| | - Qiyang Guo
- Second department of Gastroenterology, First Affiliated Hospital of Dalian Medical University, Dalian, 116011, China
| | - Qingshan Chang
- The Sixth People's Hospital of Dalian, Dalian, 116021, China
| | - Zhijun Duan
- Second department of Gastroenterology, First Affiliated Hospital of Dalian Medical University, Dalian, 116011, China.
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Li X, Yang H, Duan Z, Chang Q, Wei X, Li C, Ba Y, Du J. A case series study of hypopituitarism in older patients with and without gastrointestinal symptoms. Postgrad Med 2018; 130:501-506. [PMID: 29863435 DOI: 10.1080/00325481.2018.1479612] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 05/18/2018] [Indexed: 12/17/2022]
Abstract
OBJECTIVES Some older individuals who present with gastrointestinal symptoms as their chief complaint were ultimately diagnosed with hypopituitarism instead of gastrointestinal diseases. The aim of this study was to find the characteristics of biochemical indicators in these patients so as to reduce early misdiagnosis. METHODS We conducted a retrospective review of 45 patients with hypopituitarism who were at least 60 years of age. Two groups were included: group of hypopituitarism patients with gastrointestinal symptoms (Group G) included 23 patients with gastrointestinal symptoms and group of hypopituitarism patients without gastrointestinal symptoms (Group N) included 22 patients without these symptoms. In Group G, we investigated the prevalence of different gastrointestinal symptoms, the response of these symptoms to treatment, the occurrence of electrolyte disorders, and target gland dysfunction. Then, we compared the electrolyte and target gland function indices between the two groups. RESULTS Nausea and vomiting were the most common complaints, accounting for 69.57% of the gastrointestinal symptoms in Group G. Hyponatremia was the most common electrolyte disorder, occurring in 72.86% (n = 18) of patients in Group G. Hypoadrenalism and hypothyroidism were reported by 69.57% and 60.78% of patients, respectively, in Group G. None of the gastrointestinal symptoms were relieved by 4 weeks of treatment with antacid and motility drugs. As mentioned, 18 patients also experienced refractory hyponatremia during early treatment including regular sodium supplements; however, their gastrointestinal symptoms and hyponatremia improved after only a week of treatment for hypopituitarism. Regarding the biochemical indicators, only serum sodium and cortisol in Group G were statistically lower compared with those in Group N (P < .05). CONCLUSION Nausea and vomiting were the most common gastrointestinal symptoms in older patients with hypopituitarism, which were associated with lower serum sodium and cortisol. In addition, we hope to share the research to our gastroenterologists that serum sodium and cortisol should be tested when meeting elder patients with unexplained gastrointestinal symptoms.
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Affiliation(s)
- Xiaowei Li
- a Second Department of Gastroenterology , First Affiliated Hospital of Dalian Medical University , Dalian , China
| | - Hang Yang
- a Second Department of Gastroenterology , First Affiliated Hospital of Dalian Medical University , Dalian , China
| | - Zhijun Duan
- a Second Department of Gastroenterology , First Affiliated Hospital of Dalian Medical University , Dalian , China
| | - Qingyong Chang
- b Second Department of Neurosurgery , Affiliated Zhongshan Hospital of Dalian University , Dalian , China
| | - Xiaoting Wei
- a Second Department of Gastroenterology , First Affiliated Hospital of Dalian Medical University , Dalian , China
| | - Changjin Li
- a Second Department of Gastroenterology , First Affiliated Hospital of Dalian Medical University , Dalian , China
| | - Ying Ba
- c Department of Endocrinology , First Affiliated Hospital of Dalian Medical University , Dalian , China
| | - Jianling Du
- c Department of Endocrinology , First Affiliated Hospital of Dalian Medical University , Dalian , China
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48
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Zhang H, Chang Z, Mehmood K, Yang MK, Liu Z, Duan Z, Yuan F, Ali MM, Adnan M, Qasim MU, Shaheen S, Abbas RZ, Tian Y, Guo R. Tetramethylpyrazine inhibited hypoxia-induced expression of calcium-sensing receptors in pulmonary artery smooth muscle cells in chickens. J BIOL REG HOMEOS AG 2018; 32:489-495. [PMID: 29921373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Tetramethylpyrazine (TMP) is a biologically active ingredient, which is isolated from a popularChinese medicinal plant. It has been used effectively to treat ischemic heart problems, cerebrovascular and thrombotic vascular diseases. This study was designed to evaluate the effect of TMP on calciumsensing receptors in pulmonary artery smooth muscle in chickens. For this purpose forty day-old chicks were distributed into five groups: the control group, the hypoxia group (kept under low Oxygen treatment), and TMP groups (kept under low Oxygen treatment along with treatment of different concentrations of TMP). The pulmonary artery smooth muscle cells were also cultured on 6-well plates in high glucose culture medium and divided into the same five groups. We used in vivo and in vitro study models by applying immunohistochemistry, RT-qPCR assay and Western blotting analysis. Our results showed that pre-incubation with hypoxia markedly stimulated the activation of calcium-sensing receptor (CaSR) in pulmonary artery smooth muscle cells (PASMCs). The TMP decreased the mRNA and protein levels of CaSR. Treatment with TMP clearly inhibited the activation of all CaSR in a dose-dependent manner. Our data demonstrated that TMP can down-regulate the expression of CaSR. Therefore, these findings provide a new target to treat pulmonary arterial hypertension (PAH) under hypoxic conditions.
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Affiliation(s)
- H Zhang
- Animal Husbandry and Veterinary Institute, Hubei Academy of Agricultural Science, Wuhan, China
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture) Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Z Chang
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - K Mehmood
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- University College of Veterinary and Animal Sciences, Islamia University of Bahawalpur, Pakistan
| | - M K Yang
- Animal Husbandry and Veterinary Institute, Hubei Academy of Agricultural Science, Wuhan, China
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture) Wuhan, China
| | - Z Liu
- Animal Husbandry and Veterinary Institute, Hubei Academy of Agricultural Science, Wuhan, China
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture) Wuhan, China
| | - Z Duan
- Animal Husbandry and Veterinary Institute, Hubei Academy of Agricultural Science, Wuhan, China
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture) Wuhan, China
| | - F Yuan
- Animal Husbandry and Veterinary Institute, Hubei Academy of Agricultural Science, Wuhan, China
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture) Wuhan, China
| | - M M Ali
- University of Veterinary and Animal Sciences Lahore, Pakistan
| | - M Adnan
- College of Plant Science, Huazhong Agricultural University, Wuhan, P. R. China
| | - M U Qasim
- College of Plant Science, Huazhong Agricultural University, Wuhan, P. R. China
| | - S Shaheen
- Bahauddin Zakariya University Multan, Pakistan
| | - R Z Abbas
- Department of Parasitology, University of Agriculture Faisalabad, Pakistan
| | - Y Tian
- Animal Husbandry and Veterinary Institute, Hubei Academy of Agricultural Science, Wuhan, China
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture) Wuhan, China
| | - R Guo
- Animal Husbandry and Veterinary Institute, Hubei Academy of Agricultural Science, Wuhan, China
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture) Wuhan, China
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49
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Wu C, Pan W, Feng C, Su Z, Duan Z, Zheng Q, Hua C, Li C. Grafting materials for alveolar cleft reconstruction: a systematic review and best-evidence synthesis. Int J Oral Maxillofac Surg 2018; 47:345-356. [DOI: 10.1016/j.ijom.2017.08.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Revised: 05/30/2017] [Accepted: 08/09/2017] [Indexed: 10/18/2022]
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50
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Lan M, Chen C, Huang Y, Mao M, Han F, Liao J, Deng M, Duan Z, Zheng L, Wu S, Lu T, Jian Y. Elevated plasma fibrinogen level shows superior prognostic value than Epstein-Barr virus DNA load for stage IVA/B nasopharyngeal carcinoma patients in the intensity-modulated radiotherapy era. Oncotarget 2018; 7:46242-46252. [PMID: 27323828 PMCID: PMC5216794 DOI: 10.18632/oncotarget.10083] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 05/29/2016] [Indexed: 11/25/2022] Open
Abstract
Purpose Effective prognostic factors for patients with stage IVA/B nasopharyngeal carcinoma (NPC) who are susceptible to distant metastases are limited. We aim to investigate the prognostic value of pretreatment plasma fibrinogen (FIB) level and Epstein–Barr virus DNA (EBV-DNA) load in these patients in the era of intensity-modulated radiotherapy (IMRT). Results The 5-year DSS, DFS and DMFS rates of the entire cohort were 72.7%, 66.8%, 80.0%, respectively. High FIB level was identified as a negative prognostic factor for survival: the 5-year DSS, DFS and DMFS rates for patients with high FIB (> 4.0 g/L) and normal FIB (≤ 4.0 g/L) were 60.3% vs. 76.0%, 56.0% vs. 69.9%, and 59.4% vs. 85.5%, respectively (all P < 0.001). Subgroup analysis demonstrated that DSS, DFS and DMFS decreased as FIB gradually increased, even within the normal range. The risk of distant metastasis in patients with high FIB was over 3-fold than patients with normal FIB. EBV-DNA was not an independent prognostic factor for any survival outcomes in multivariate analysis. Conclusion High pretreatment FIB level shows superior prognostic value than EBV-DNA load for stage IVA/B NPC patients in the era of IMRT. Materials and Methods A total of 755 patients with newly-diagnosed stage IVA/B NPC treated with definitive IMRT between January 2007 and December 2011 were enrolled. Plasma FIB and EBV-DNA were measured before treatment. Disease-specific survival (DSS), disease-free survival (DFS) and distant metastasis-free survival (DMFS) were calculated using the Kaplan-Meier method; differences were compared using the log-rank test.
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Affiliation(s)
- Mei Lan
- Department of Radiation Oncology, State Key Laboratory of Oncology in Southern China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Chunyan Chen
- Department of Radiation Oncology, State Key Laboratory of Oncology in Southern China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Ying Huang
- Department of Radiation Oncology, State Key Laboratory of Oncology in Southern China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Minjie Mao
- Department of Clinical Laboratory, State Key Laboratory of Oncology in Southern China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Fei Han
- Department of Radiation Oncology, State Key Laboratory of Oncology in Southern China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Junfang Liao
- Department of Radiation Oncology, State Key Laboratory of Oncology in Southern China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Meiling Deng
- Department of Radiation Oncology, State Key Laboratory of Oncology in Southern China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Zhijun Duan
- Department of Radiation Diagnosis and Interventional Center, Chengdu Military General Hospital, Chengdu, China
| | - Lie Zheng
- Department of Imaging Diagnosis and Interventional Center, State Key Laboratory of Oncology in Southern China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Shaoxiong Wu
- Department of Radiation Oncology, State Key Laboratory of Oncology in Southern China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Taixiang Lu
- Department of Radiation Oncology, State Key Laboratory of Oncology in Southern China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Yutao Jian
- Institute of Stomatological Research, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China
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