1
|
Li ZW, Ruan B, Yang PJ, Liu JJ, Song P, Duan JL, Wang L. Oit3, a promising hallmark gene for targeting liver sinusoidal endothelial cells. Signal Transduct Target Ther 2023; 8:344. [PMID: 37696816 PMCID: PMC10495338 DOI: 10.1038/s41392-023-01621-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 08/22/2023] [Accepted: 08/22/2023] [Indexed: 09/13/2023] Open
Abstract
Liver sinusoidal endothelial cells (LSECs) play a pivotal role in maintaining liver homeostasis and influencing the pathological processes of various liver diseases. However, neither LSEC-specific hallmark genes nor a LSEC promoter-driven Cre mouse line has been introduced before, which largely restricts the study of liver diseases with vascular disorders. To explore LSEC-specific hallmark genes, we compared the top 50 marker genes between liver endothelial cells (ECs) and liver capillary ECs and identified 18 overlapping genes. After excluding globally expressed genes and those with low expression percentages, we narrowed our focus to two final candidates: Oit3 and Dnase1l3. Through single-cell RNA sequencing (scRNA-seq) and analysis of the NCBI database, we confirmed the extrahepatic expression of Dnase1l3. The paired-cell sequencing data further demonstrated that Oit3 was predominantly expressed in the midlobular liver ECs. Subsequently, we constructed inducible Oit3-CreERT2 transgenic mice, which were further crossed with ROSA26-tdTomato mice. Microscopy validated that the established Oit3-CreERT2-tdTomato mice exhibited significant fluorescence in the liver rather than in other organs. The staining analysis confirmed the colocalization of tdTomato and EC markers. Ex-vivo experiments further confirmed that isolated tdTomato+ cells exhibited well-differentiated fenestrae and highly expressed EC markers, confirming their identity as LSECs. Overall, Oit3 is a promising hallmark gene for tracing LSECs. The establishment of Oit3-CreERT2-tdTomato mice provides a valuable model for studying the complexities of LSECs in liver diseases.
Collapse
Affiliation(s)
- Zhi-Wen Li
- Department of Hepatobiliary Surgery, Xi-Jing Hospital, Fourth Military Medical University, 710032, Xi'an, China
| | - Bai Ruan
- Department of Hepatobiliary Surgery, Xi-Jing Hospital, Fourth Military Medical University, 710032, Xi'an, China
- Center of Clinical Aerospace Medicine & Department of Aviation Medicine, Fourth Military Medical University, 710032, Xi'an, China
| | - Pei-Jun Yang
- Department of Hepatobiliary Surgery, Xi-Jing Hospital, Fourth Military Medical University, 710032, Xi'an, China
| | - Jing-Jing Liu
- Department of Hepatobiliary Surgery, Xi-Jing Hospital, Fourth Military Medical University, 710032, Xi'an, China
| | - Ping Song
- Department of Hepatobiliary Surgery, Xi-Jing Hospital, Fourth Military Medical University, 710032, Xi'an, China
| | - Juan-Li Duan
- Department of Hepatobiliary Surgery, Xi-Jing Hospital, Fourth Military Medical University, 710032, Xi'an, China
| | - Lin Wang
- Department of Hepatobiliary Surgery, Xi-Jing Hospital, Fourth Military Medical University, 710032, Xi'an, China.
| |
Collapse
|
2
|
Wen J, Yang S, Yan G, Lei J, Liu X, Zhang N, Zhang J, Deng H, Wu L, Li Y. Increased OIT3 in macrophage promotes PD-L1 expression and hepatocellular carcinogenesis via NF-κB signaling. Exp Cell Res 2023; 428:113651. [PMID: 37201744 DOI: 10.1016/j.yexcr.2023.113651] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/25/2023] [Accepted: 05/15/2023] [Indexed: 05/20/2023]
Abstract
Oncoprotein-induced transcript 3 (OIT3) facilitates macrophage M2 polarization and hepatocellular carcinoma (HCC) progression, however, whether OIT3 regulates tumor immunity remains largely unknown. Here we found that OIT3 was upregulated in HCC-associated macrophages, which inhibited CD4+ and CD8+ T-cell infiltration in the tumor microenvironment (TME). Mechanistically, OIT3 increased the expression of PD-L1 on tumor-associated macrophages (TAMs) by activating NF-κB signaling, blockade of NF-κB reversed the immunosuppressive activity of TAMs and dampens HCC tumorigenesis. Our findings provide the molecular basis for OIT3 enhancing tumor immunosuppression and highlighted a potential therapeutic strategy for targeting the TAMs of HCC.
Collapse
Affiliation(s)
- Jiaqi Wen
- The Second Affiliated Hospital & Yuying Children's Hospital/The Second School of Medicine, Wenzhou Medical University, Wenzhou, China
| | - Shuai Yang
- Department of Pathology, The 958th Hospital, Southwest Hospital, Army Medical University, Chongqing 400038, China
| | - Guifang Yan
- Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing 400030, China
| | - Juan Lei
- Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing 400030, China
| | - Xudong Liu
- Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing 400030, China
| | - Nan Zhang
- Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing 400030, China
| | - Jiangang Zhang
- Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing 400030, China
| | - Huan Deng
- Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing 400030, China
| | - Lei Wu
- Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing 400030, China.
| | - Yongsheng Li
- The Second Affiliated Hospital & Yuying Children's Hospital/The Second School of Medicine, Wenzhou Medical University, Wenzhou, China; Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing 400030, China.
| |
Collapse
|
3
|
Wen J, Aili A, Yan YX, Lai Y, Niu S, He S, Zhang X, Zhang G, Li J. OIT3 serves as a novel biomarker of hepatocellular carcinoma by mediating ferroptosis via regulating the arachidonic acid metabolism. Front Oncol 2022; 12:977348. [PMID: 36132142 PMCID: PMC9483180 DOI: 10.3389/fonc.2022.977348] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 08/18/2022] [Indexed: 11/21/2022] Open
Abstract
Background Oncoprotein-Induced Transcript 3 Protein (OIT3) was identified as a liver-specific gene with abnormal expression in hepatocellular carcinoma (HCC). Herein, we aimed to examine the function and specific mechanism of OIT3 in HCC. Methods Bioinformatic analyses and tissue microarray via immunohistochemistry were used to validate the expression of OIT3 in HCC. The biofunctions of OIT3 in HCC were determined in vitro and in vivo. The mechanism was confirmed by RNA-Sequence and Western blotting. The uni- and multivariate analyses were used to identify the independent predictors for HCC. Results Low expression of OIT3 was observed in HCC and predicted a poor clinical outcome. Ectopic expression of OIT3 could inhibit the proliferation, migration, and invasion abilities of HCC cells. Mechanistically, OIT3 upregulated the expression of ALOX15 and CYP4F3, thus inducing arachidonic acid increase, ROS accumulation, and lipid peroxidation, and eventually causing ferroptosis. OIT3 was validated as a prognostic predictor for HCC patients. Conclusions Our findings revealed a novel role of OIT3 in the process of tumorigenesis of HCC. OIT3 inhibited reproliferation, migration, and invasion of HCC cells by triggering ferroptosis, which indicates that OIT3 could serve as a potential biomarker in HCC.
Collapse
Affiliation(s)
- Jie Wen
- Department of Interventional Oncology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China and Department of Medical Oncology and Radiation Sickness, Peking University Third Hospital, Beijing, China
- *Correspondence: Jie Wen, ; Jiaping Li,
| | - Abudureyimujiang Aili
- Department of Medical Oncology and Radiation Sickness, Peking University Third Hospital, Beijing, China
| | - Yao Xue Yan
- Department of Dermatology, Peking University People’s Hospital, Beijing, China
| | - YuLin Lai
- Deparment of Radiotherapy, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Shaoqing Niu
- Deparment of Radiotherapy, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Shasha He
- Deparment of Radiotherapy, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Xiaokai Zhang
- Department of Interventional Oncology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Guixiong Zhang
- Department of Interventional Oncology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Jiaping Li
- Department of Interventional Oncology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
- *Correspondence: Jie Wen, ; Jiaping Li,
| |
Collapse
|
4
|
Characterization of Extracellular vesicles isolated from different Liquid biopsies of uveal melanoma patients. J Circ Biomark 2022; 11:36-47. [PMID: 35784590 PMCID: PMC9238429 DOI: 10.33393/jcb.2022.2370] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 05/27/2022] [Indexed: 11/24/2022] Open
Abstract
Purpose: Uveal melanoma (UM) is the most common intraocular malignant tumor in adults. Extracellular vesicles (EVs) have been extensively studied as a biomarker to monitor disease in patients. The study of new biomarkers in melanoma patients could prevent metastasis by earlier diagnosis. In this study, we determined the proteomic profile of EVs isolated from aqueous humor (AH), vitreous humor (VH), and plasma from UM patients in comparison with cancer-free control patients. Methods: AH, VH and plasma were collected from seven patients with UM after enucleation; AH and plasma were collected from seven cancer-free patients with cataract (CAT; control group). EVs were isolated using the membrane-based affinity binding column method. Nanoparticle tracking analysis (NTA) was performed to determine the size and concentration of EVs. EV markers, CD63 and TSG101, were assessed by immunoblotting, and the EV proteome was characterized by mass spectrometry. Results: Mean EV concentration was higher in all analytes of UM patients compared to those in the CAT group. In the UM cohort, the mean concentration of EVs was significantly lower in AH and plasma than in VH. In contrast, the mean size and size distribution of EVs was invariably identical in all analyzed analytes and in both studied groups (UM vs. CAT). Mass spectrometry analyses from the different analytes from UM patients showed the presence of EV markers. Conclusion: EVs isolated from AH, VH, and plasma from patients with UM showed consistent profiles and support the use of blood to monitor UM patients as a noninvasive liquid biopsy.
Collapse
|
5
|
Yang S, Zhang J, Xu Y, Wang J, Zhao H, Lei J, Zhou Y, Chen Y, Wu L, Zhou M, Zheng L, Ji X, Li Y. OIT3 mediates macrophage polarization and facilitates hepatocellular carcinoma progression. Cancer Immunol Immunother 2022; 71:2677-2689. [PMID: 35353239 DOI: 10.1007/s00262-022-03188-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 03/08/2022] [Indexed: 12/12/2022]
Abstract
Hepatocellular carcinoma (HCC) is one of the most common causes of cancer-related mortality; however, effective immunotherapy strategies are limited because of the immunosuppressive tumor microenvironment. Macrophages are essential components of the HCC microenvironment and are related to poor prognosis. Here, we evaluated the attributes of paracancer tissues in tumor immunity and progression using public databases. Based on the abundance of immune cells estimated by CIBERSORT, we performed weighted gene co-expression network analysis and found a specific module associated with M2 macrophages. Through analyzing interaction networks using Cytoscape and public datasets, we identified oncoprotein-induced transcript 3 (OIT3) as a novel marker of M2 macrophages. Overexpression of OIT3 remodeled immune features and reprogrammed the metabolism of M2 macrophages. Moreover, compared with wildtype macrophages, OIT3-overexpressing macrophages further enhanced the migration and invasion of co-cultured cancer cells. Additionally, OIT3-overexpressing macrophages promoted tumorigenesis and cancer development in vivo. Taken together, the findings demonstrate that OIT3 is a novel biomarker of alternatively activated macrophages and facilitates HCC metastasis.
Collapse
Affiliation(s)
- Shuai Yang
- Clinical Medicine Research Center, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China
- Department of Pathology, the 958th Hospital, Southwest Hospital, Army Medical University, Chongqing, 400038, China
| | - Jiangang Zhang
- Clinical Medicine Research Center, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China
| | - Yanquan Xu
- Clinical Medicine Research Center, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China
| | - Jingchun Wang
- Clinical Medicine Research Center, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China
| | - Huakan Zhao
- Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing, 400030, China
- Chongqing Key Laboratory for Tumor Metastasis and the Translational Research of Individualized Diagnosis and Treatment, Chongqing University Cancer Hospital, Chongqing, 400030, China
| | - Juan Lei
- Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing, 400030, China
- Chongqing Key Laboratory for Tumor Metastasis and the Translational Research of Individualized Diagnosis and Treatment, Chongqing University Cancer Hospital, Chongqing, 400030, China
| | - Yu Zhou
- Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing, 400030, China
- Chongqing Key Laboratory for Tumor Metastasis and the Translational Research of Individualized Diagnosis and Treatment, Chongqing University Cancer Hospital, Chongqing, 400030, China
| | - Yu Chen
- Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing, 400030, China
- Chongqing Key Laboratory for Tumor Metastasis and the Translational Research of Individualized Diagnosis and Treatment, Chongqing University Cancer Hospital, Chongqing, 400030, China
| | - Lei Wu
- Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing, 400030, China
- Chongqing Key Laboratory for Tumor Metastasis and the Translational Research of Individualized Diagnosis and Treatment, Chongqing University Cancer Hospital, Chongqing, 400030, China
| | - Mingyue Zhou
- Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing, 400030, China
- Chongqing Key Laboratory for Tumor Metastasis and the Translational Research of Individualized Diagnosis and Treatment, Chongqing University Cancer Hospital, Chongqing, 400030, China
| | - Lu Zheng
- Department of Hepatobiliary Surgery, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China.
| | - Xiaohui Ji
- Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing, 400030, China.
- Chongqing Key Laboratory for Tumor Metastasis and the Translational Research of Individualized Diagnosis and Treatment, Chongqing University Cancer Hospital, Chongqing, 400030, China.
| | - Yongsheng Li
- Clinical Medicine Research Center, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China.
- Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing, 400030, China.
- Chongqing Key Laboratory for Tumor Metastasis and the Translational Research of Individualized Diagnosis and Treatment, Chongqing University Cancer Hospital, Chongqing, 400030, China.
| |
Collapse
|
6
|
Pedersen S, Jensen KP, Honoré B, Kristensen SR, Pedersen CH, Szejniuk WM, Maltesen RG, Falkmer U. Circulating microvesicles and exosomes in small cell lung cancer by quantitative proteomics. Clin Proteomics 2022; 19:2. [PMID: 34996345 PMCID: PMC8903681 DOI: 10.1186/s12014-021-09339-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 12/29/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Early detection of small cell lung cancer (SCLC) crucially demands highly reliable markers. Growing evidence suggests that extracellular vesicles carry tumor cell-specific cargo suitable as protein markers in cancer. Quantitative proteomic profiling of circulating microvesicles and exosomes can be a high-throughput platform for discovery of novel molecular insights and putative markers. Hence, this study aimed to investigate proteome dynamics of plasma-derived microvesicles and exosomes in newly diagnosed SCLC patients to improve early detection. METHODS Plasma-derived microvesicles and exosomes from 24 healthy controls and 24 SCLC patients were isolated from plasma by either high-speed- or ultracentrifugation. Proteins derived from these extracellular vesicles were quantified using label-free mass spectrometry and statistical analysis was carried out aiming at identifying significantly altered protein expressions between SCLC patients and healthy controls. Furthermore, significantly expressed proteins were subjected to functional enrichment analysis to identify biological pathways implicated in SCLC pathogenesis. RESULTS Based on fold change (FC) ≥ 2 or ≤ 0.5 and AUC ≥ 0.70 (p < 0.05), we identified 10 common and 16 and 17 unique proteins for microvesicles and exosomes, respectively. Among these proteins, we found dysregulation of coagulation factor XIII A (Log2 FC = - 1.1, p = 0.0003, AUC = 0.82, 95% CI: 0.69-0.96) and complement factor H-related protein 4 (Log2 FC = 1.2, p = 0.0005, AUC = 0.82, 95% CI; 0.67-0.97) in SCLC patients compared to healthy individuals. Our data may indicate a novel tumor-suppressing role of blood coagulation and involvement of complement activation in SCLC pathogenesis. CONCLUSIONS In comparing SCLC patients and healthy individuals, several differentially expressed proteins were identified. This is the first study showing that circulating extracellular vesicles may encompass specific proteins with potential diagnostic attributes for SCLC, thereby opening new opportunities as novel non-invasive markers.
Collapse
Affiliation(s)
- Shona Pedersen
- Department of Basic Medical Sciences, College of Medicine, QU Health, Qatar University, 2713, Doha, Qatar.
| | - Katrine Papendick Jensen
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark.,Department of Clinical Biochemistry, Aalborg University Hospital, Aalborg, Denmark
| | - Bent Honoré
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark.,Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Søren Risom Kristensen
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark.,Department of Clinical Biochemistry, Aalborg University Hospital, Aalborg, Denmark
| | | | - Weronika Maria Szejniuk
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark.,Department of Oncology, Aalborg University Hospital, Aalborg, Denmark
| | - Raluca Georgiana Maltesen
- Translational Radiation Biology and Oncology Laboratory, Centre for Cancer Research, Westmead Institute of Medical Research, Westmead, 2145, Australia
| | - Ursula Falkmer
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark.,Department of Oncology, Aalborg University Hospital, Aalborg, Denmark
| |
Collapse
|
7
|
Wu JX, He KY, Zhang ZZ, Qu YL, Su XB, Shi Y, Wang N, Wang L, Han ZG. LZP is required for hepatic triacylglycerol transportation through maintaining apolipoprotein B stability. PLoS Genet 2021; 17:e1009357. [PMID: 33591966 PMCID: PMC7909667 DOI: 10.1371/journal.pgen.1009357] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 02/26/2021] [Accepted: 01/12/2021] [Indexed: 12/12/2022] Open
Abstract
The conserved zona pellucida (ZP) domain is found in hundreds of extracellular proteins that are expressed in various organs and play a variety of roles as structural components, receptors and tumor suppressors. A liver-specific zona pellucida domain-containing protein (LZP), also named OIT3, has been shown to be mainly expressed in human and mouse hepatocytes; however, the physiological function of LZP in the liver remains unclear. Here, we show that Lzp deletion inhibited very low-density lipoprotein (VLDL) secretion, leading to hepatic TG accumulation and lower serum TG levels in mice. The apolipoprotein B (apoB) levels were significantly decreased in the liver, serum, and VLDL particles of LZP-deficient mice. In the presence of LZP, which is localized to the endoplasmic reticulum (ER) and Golgi apparatus, the ER-associated degradation (ERAD) of apoB was attenuated; in contrast, in the absence of LZP, apoB was ubiquitinated by AMFR, a known E3 ubiquitin ligase specific for apoB, and was subsequently degraded, leading to lower hepatic apoB levels and inhibited VLDL secretion. Interestingly, hepatic LZP levels were elevated in mice challenged with a high-fat diet and humans with simple hepatic steatosis, suggesting that LZP contributes to the physiological regulation of hepatic TG homeostasis. In general, our data establish an essential role for LZP in hepatic TG transportation and VLDL secretion by preventing the AMFR-mediated ubiquitination and degradation of apoB and therefore provide insight into the molecular function of LZP in hepatic lipid metabolism.
Collapse
Affiliation(s)
- Jiao-Xiang Wu
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine of Rui-Jin Hospital, Hongqiao International Institute of Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai-MOST Key Laboratory for Disease and Health Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
| | - Kun-Yan He
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Zhuang-Zhuang Zhang
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine of Rui-Jin Hospital, Hongqiao International Institute of Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yu-Lan Qu
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xian-Bin Su
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yi Shi
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Na Wang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Lan Wang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ze-Guang Han
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine of Rui-Jin Hospital, Hongqiao International Institute of Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai-MOST Key Laboratory for Disease and Health Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
| |
Collapse
|
8
|
Tomic A, Tomic I, Waldron L, Geistlinger L, Kuhn M, Spreng RL, Dahora LC, Seaton KE, Tomaras G, Hill J, Duggal NA, Pollock RD, Lazarus NR, Harridge SD, Lord JM, Khatri P, Pollard AJ, Davis MM. SIMON: Open-Source Knowledge Discovery Platform. PATTERNS (NEW YORK, N.Y.) 2021; 2:100178. [PMID: 33511368 PMCID: PMC7815964 DOI: 10.1016/j.patter.2020.100178] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 10/27/2020] [Accepted: 12/04/2020] [Indexed: 02/06/2023]
Abstract
Data analysis and knowledge discovery has become more and more important in biology and medicine with the increasing complexity of biological datasets, but the necessarily sophisticated programming skills and in-depth understanding of algorithms needed pose barriers to most biologists and clinicians to perform such research. We have developed a modular open-source software, SIMON, to facilitate the application of 180+ state-of-the-art machine-learning algorithms to high-dimensional biomedical data. With an easy-to-use graphical user interface, standardized pipelines, and automated approach for machine learning and other statistical analysis methods, SIMON helps to identify optimal algorithms and provides a resource that empowers non-technical and technical researchers to identify crucial patterns in biomedical data.
Collapse
Affiliation(s)
- Adriana Tomic
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK,Institute of Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA, USA,Corresponding author
| | - Ivan Tomic
- Deep Medicine, Nuffield Department of Women's and Reproductive Health, University of Oxford, Oxford, UK,Corresponding author
| | - Levi Waldron
- Graduate School of Public Health and Health Policy, City University of New York, New York, NY, USA,Institute for Implementation Science and Population Health, City University of New York, New York, NY, USA
| | - Ludwig Geistlinger
- Graduate School of Public Health and Health Policy, City University of New York, New York, NY, USA,Institute for Implementation Science and Population Health, City University of New York, New York, NY, USA
| | | | | | | | - Kelly E. Seaton
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
| | - Georgia Tomaras
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
| | - Jennifer Hill
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Niharika A. Duggal
- MRC-Versus Arthritis Centre for Musculoskeletal Ageing Research, Institute of Inflammation and Ageing, University of Birmingham Research Labs, Birmingham, UK
| | - Ross D. Pollock
- Centre for Human and Applied Physiological Sciences, King's College London, UK
| | - Norman R. Lazarus
- Centre for Human and Applied Physiological Sciences, King's College London, UK
| | | | - Janet M. Lord
- MRC-Versus Arthritis Centre for Musculoskeletal Ageing Research, Institute of Inflammation and Ageing, University of Birmingham Research Labs, Birmingham, UK,NIHR Birmingham Biomedical Research Centre, University Hospital Birmingham NHS Foundation Trust and University of Birmingham, Birmingham, UK
| | - Purvesh Khatri
- Institute of Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA, USA,Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Andrew J. Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Mark M. Davis
- Institute of Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA, USA,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA,Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA,Corresponding author
| |
Collapse
|
9
|
Yang P, Pi X, Marion TN, Wang J, Wang G, Xie Y, Xie D, Liu Y. Gout inheritance in an extended Chinese family analyzed by whole-exome sequencing: A case-report. Medicine (Baltimore) 2020; 99:e20057. [PMID: 32569156 PMCID: PMC7310917 DOI: 10.1097/md.0000000000020057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Revised: 02/06/2020] [Accepted: 03/26/2020] [Indexed: 11/25/2022] Open
Abstract
INTRODUCTION Gout is a worldwide chronic disease generally caused by high serum levels of uric acid. Using whole exome sequencing, we aimed to explore genetic alterations in hereditary gout. PATIENTS' CONCERNS There were 9 direct descendants diagnosed with gout in total in this family. The patients concerned about the high incidence and inheritance of gout. DIAGNOSIS The youngest propositus was diagnosed as gout in our hospital. Diagnoses of other patients in this family were made on the foundation of history and clinical tests. INTERVENTIONS Six direct descendants and 3 healthy spouses in 1 family were recruited in our study. Whole-exome sequencing was conducted in all participants. OUTCOMES Whole-exome sequencing and genetic analysis revealed 2 putative rare inherited deleterious variants, which were detected only in direct descendants. Twelve gout and uric acid (UC)-related nucleotide sequence variants previously reported by GWAS were detected among all subjects. CONCLUSIONS In the case of this family, the GWAS identified gout and UC-related nucleotide sequence variants may increase the risk of developing gout, but penetrance was not complete. The rare sequence variants in low-density lipoprotein receptor-related protein 1 (LRP1) and oncoprotein induced transcript 3 (OIT3) may have contributed to inheritance of gout within the 5 generations of family members in this study.
Collapse
Affiliation(s)
| | - Xuenan Pi
- Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Tony N. Marion
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee
| | | | - Gang Wang
- Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan, P.R. China
| | | | - Dan Xie
- Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Yi Liu
- Department of Rheumatology
| |
Collapse
|
10
|
Gao X, Santhanam RK, Xue Z, Jia Y, Wang Y, Lu Y, Phisalaphong M, Chen H. Antioxidant, α-amylase and α-glucosidase activity of various solvent fractions of I. obliquus and the preventive role of active fraction against H 2 O 2 induced damage in hepatic L02 cells as fungisome. J Food Sci 2020; 85:1060-1069. [PMID: 32147838 DOI: 10.1111/1750-3841.15084] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 12/23/2019] [Accepted: 01/25/2020] [Indexed: 11/30/2022]
Abstract
Inonotus obliquus is a traditional mushroom well known for its therapeutic value. In this study, various solvent fractions of I. obliquus were preliminarily screened for their antioxidant, α-amylase and α-glucosidase inhibition properties. To improve the drug delivery, the active fraction (ethyl acetate fraction) of I. obliquus was synthesized into fungisome (ethyl acetate phophotidyl choline complex, EAPC) and its physical parameters were assessed using Fourier transform infrared spectroscopy (FTIR), High performance liquid chromatography (HPLC), Scanning electron microscope (SEM), and ς potential analysis. Then normal human hepatic L02 cells was used to evaluate the cytotoxicity of EAPC. The results showed that EA fraction possesses significant free radical scavenging, α-amylase and α-glucosidase inhibition properties. FTIR, SEM, and HPLC analysis confirmed the fungisome formation. The particle size of EAPC was 102.80 ± 0.42 nm and the ς potential was -54.30 ± 0.61 mV. The percentage of drug entrapment efficiency was 97.13% and the drug release rates of EAPC in simulated gastric fluid and simulated intestinal fluid were 75.04 ± 0.29% and 93.03 ± 0.36%, respectively. EAPC was nontoxic to L02 cells, however it could selectively fight against the H2 O2 induced oxidative damage in L02 cells. This is the first study to provide scientific information to utilize the active fraction of I. obliquus as fungisome. PRACTICAL APPLICATIONS: Inonotus obliquus (IO) is a traditional medicinal fungus. The extracts of IO have obvious antioxidant and hypoglycemic activities. Ethyl acetate (EA) fraction of IO was encapsulated in liposomes to form EAPC. EAPC has a sustained-release effect. It has nontoxic to L02 cells and could protect L02 cells from oxidative damage caused by hydrogen peroxide. This study could provide new ideas for the treatment of diabetes.
Collapse
Affiliation(s)
- Xudong Gao
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, P.R. China
| | - Ramesh Kumar Santhanam
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, P.R. China.,School of Fundamental Science, University Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia
| | - Zihan Xue
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, P.R. China
| | - Yanan Jia
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, P.R. China
| | - Yajie Wang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, P.R. China
| | - Yangpeng Lu
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, P.R. China
| | - Muenduen Phisalaphong
- Department of Chemical Engineering, Chulalongkorn University, Phayathai Road, Bangkok, 10330, Pathum Wan, Thailand
| | - Haixia Chen
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, P.R. China
| |
Collapse
|
11
|
Humenik F, Cizkova D, Cikos S, Luptakova L, Madari A, Mudronova D, Kuricova M, Farbakova J, Spirkova A, Petrovova E, Cente M, Mojzisova Z, Aboulouard S, Murgoci AN, Fournier I, Salzet M. Canine Bone Marrow-derived Mesenchymal Stem Cells: Genomics, Proteomics and Functional Analyses of Paracrine Factors. Mol Cell Proteomics 2019; 18:1824-1835. [PMID: 31285283 PMCID: PMC6731083 DOI: 10.1074/mcp.ra119.001507] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 06/28/2019] [Indexed: 12/11/2022] Open
Abstract
Adult stem cells have become prominent candidates for treating various diseases in veterinary practice. The main goal of our study was therefore to provide a comprehensive study of canine bone marrow-derived mesenchymal stem cells (BMMSC) and conditioned media, isolated from healthy adult dogs of different breeds. Under well-defined standardized isolation protocols, the multipotent differentiation and specific surface markers of BMMSC were supplemented with their gene expression, proteomic profile, and their biological function. The presented data confirm that canine BMMSC express important genes for differentiation toward osteo-, chondro-, and tendo-genic directions, but also genes associated with angiogenic, neurotrophic, and immunomodulatory properties. Furthermore, using proteome profiling, we identify for the first time the dynamic release of various bioactive molecules, such as transcription and translation factors and osteogenic, growth, angiogenic, and neurotrophic factors from canine BMMSC conditioned medium. Importantly, the relevant genes were linked to their proteins as detected in the conditioned medium and further associated with angiogenic activity in chorioallantoic membrane (CAM) assay. In this way, we show that the canine BMMSC release a variety of bioactive molecules, revealing a strong paracrine component that may possess therapeutic potential in various pathologies. However, extensive experimental or preclinical trials testing canine sources need to be performed in order to better understand their paracrine action, which may lead to novel therapeutic strategies in veterinary medicine.
Collapse
Affiliation(s)
- Filip Humenik
- ‡University of Veterinary Medicine and Pharmacy in Košice, Komenského 73, Košice 041 81, Slovakia
| | - Dasa Cizkova
- ‡University of Veterinary Medicine and Pharmacy in Košice, Komenského 73, Košice 041 81, Slovakia; §Institute of Neuroimmunology, Slovak Academy of Sciences, Dúbravská cesta 9, Bratislava 845 10, Slovakia; ¶Université Lille, INSERM, U1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, F-59000 Lille, France.
| | - Stefan Cikos
- ‖Institute of Animal Physiology, Centre of Biosciences of the Slovak Academy of Sciences, Šoltésovej 4-6, Košice 04001, Slovakia
| | - Lenka Luptakova
- ‡University of Veterinary Medicine and Pharmacy in Košice, Komenského 73, Košice 041 81, Slovakia
| | - Aladar Madari
- ‡University of Veterinary Medicine and Pharmacy in Košice, Komenského 73, Košice 041 81, Slovakia
| | - Dagmar Mudronova
- ‡University of Veterinary Medicine and Pharmacy in Košice, Komenského 73, Košice 041 81, Slovakia
| | - Maria Kuricova
- ‡University of Veterinary Medicine and Pharmacy in Košice, Komenského 73, Košice 041 81, Slovakia
| | - Jana Farbakova
- ‡University of Veterinary Medicine and Pharmacy in Košice, Komenského 73, Košice 041 81, Slovakia
| | - Alexandra Spirkova
- ‖Institute of Animal Physiology, Centre of Biosciences of the Slovak Academy of Sciences, Šoltésovej 4-6, Košice 04001, Slovakia
| | - Eva Petrovova
- ‡University of Veterinary Medicine and Pharmacy in Košice, Komenského 73, Košice 041 81, Slovakia
| | - Martin Cente
- §Institute of Neuroimmunology, Slovak Academy of Sciences, Dúbravská cesta 9, Bratislava 845 10, Slovakia
| | - Zuzana Mojzisova
- ‡University of Veterinary Medicine and Pharmacy in Košice, Komenského 73, Košice 041 81, Slovakia
| | - Soulaimane Aboulouard
- ¶Université Lille, INSERM, U1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, F-59000 Lille, France
| | - Adriana-Natalia Murgoci
- §Institute of Neuroimmunology, Slovak Academy of Sciences, Dúbravská cesta 9, Bratislava 845 10, Slovakia; ¶Université Lille, INSERM, U1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, F-59000 Lille, France
| | - Isabelle Fournier
- ¶Université Lille, INSERM, U1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, F-59000 Lille, France
| | - Michel Salzet
- ¶Université Lille, INSERM, U1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, F-59000 Lille, France.
| |
Collapse
|
12
|
Bauzá-Martinez J, Aletti F, Pinto BB, Ribas V, Odena MA, Díaz R, Romay E, Ferrer R, Kistler EB, Tedeschi G, Schmid-Schönbein GW, Herpain A, Bendjelid K, de Oliveira E. Proteolysis in septic shock patients: plasma peptidomic patterns are associated with mortality. Br J Anaesth 2018; 121:1065-1074. [PMID: 30336851 DOI: 10.1016/j.bja.2018.05.072] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Revised: 04/25/2018] [Accepted: 06/13/2018] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Uncontrolled proteolysis contributes to cell injury and organ dysfunction in animal models of circulatory shock. We investigated in humans the relationship between septic shock, proteolysis, and outcome. METHODS Intensive care patients with septic shock (n=29) or sepsis (n=6) and non-hospitalised subjects (n=9) were recruited as part of the prospective observational trial 'ShockOmics' (ClinicalTrials.gov Identifier NCT02141607). A mass spectrometry-based approach was used to analyse the plasma peptidomes and the origin of circulating peptides from proteolysis in the enrolled subjects. RESULTS Evidence of systemic proteolysis was indicated by a larger number of circulating peptides in septic shock patients, compared with septic patients and non-hospitalised healthy subjects. The peptide count and abundance in the septic shock patients were greater in patients who died (n=6) than in survivors (n=23), suggesting an association between magnitude of proteolysis and outcome. In silico analysis of the peptide sequences and of the sites of cleavage on the proteins of origin indicated a predominant role for serine proteases, such as chymotrypsin, and matrix metalloproteases in causing the observed proteolytic degradation. CONCLUSIONS Systemic proteolysis is a novel fundamental pathological mechanism in septic shock. Plasma peptidomics is proposed as a new tool to monitor clinical trajectory in septic shock patients. CLINICAL TRIAL REGISTRATION NCT02141607.
Collapse
Affiliation(s)
| | - F Aletti
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - B B Pinto
- Geneva University Hospital, Geneva, Switzerland
| | - V Ribas
- Eurecat, Technology Centre of Catalonia, Barcelona, Spain
| | - M A Odena
- Proteomics Platform, Barcelona Science Park, Barcelona, Spain
| | - R Díaz
- Proteomics Platform, Barcelona Science Park, Barcelona, Spain
| | - E Romay
- University Hospital Mútua Terrassa, Barcelona, Spain
| | - R Ferrer
- Intensive Care Department, Vall d'Hebron University Hospital, Barcelona, Spain
| | - E B Kistler
- Department of Anesthesiology and Critical Care, VA San Diego Healthcare System, San Diego, CA, USA
| | - G Tedeschi
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milan, Italy; Fondazione Filarete Milano, Milan, Italy
| | - G W Schmid-Schönbein
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - A Herpain
- Université Libre de Bruxelles, Brussels, Belgium
| | - K Bendjelid
- Geneva University Hospital, Geneva, Switzerland.
| | - E de Oliveira
- Proteomics Platform, Barcelona Science Park, Barcelona, Spain.
| |
Collapse
|
13
|
Lui KY, Zhao H, Qiu C, Li C, Zhang Z, Peng H, Fu R, Chen HA, Lu MQ. Integrator complex subunit 6 (INTS6) inhibits hepatocellular carcinoma growth by Wnt pathway and serve as a prognostic marker. BMC Cancer 2017; 17:644. [PMID: 28899352 PMCID: PMC5596937 DOI: 10.1186/s12885-017-3628-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Accepted: 08/28/2017] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Integrator complex subunit 6 (INTS6) was found to play a tumour suppressing role in certain types of solid tumours. In this study, we wanted to determine the expression level of INTS6 in hepatocellular carcinoma (HCC) and evaluate its clinical characteristics and mechanisms in HCC patients (Lui and Lu, European Journal of Cancer, 51:S94, 2015). METHODS First, we used a microarray analysis to explore the mRNA expression levels in HCC and paired normal liver tissues; second, we used qRT-PCR to measure the INTS6 mRNA levels in a cohort of 50 HCC tissues and adjacent normal liver tissues; third, we used Western blot analyses to detect the INTS6 protein levels in 20 paired HCC and normal liver tissues; fourth, we used immunohistochemistry to determine the INTS6 expression levels in 70 archived paraffin-embedded HCC samples. Finally, we investigated the suppressive function of INTS6 in the Wnt pathway. RESULTS Herein, according to the microarray data analysis, the expression levels of INTS6 were dramatically down-regulated in HCC tissues vs. those in normal liver tissues (p<0.05). qRT-PCR and Western blot analyses showed that the INTS6 mRNA and protein expression was significantly down-regulated in tumour tissues compared to the adjacent normal liver tissues (p<0.05). Immunohistochemical assays revealed that decreased INTS6 expression was present in 62.9% (44/70) of HCC patients. Correlation analyses showed that INTS6 expression was significantly correlated with serum alpha-fetoprotein levels (AFP, p =0.004), pathology grade (p =0.005), and tumour recurrence (p =0.04). Kaplan-Meier analysis revealed that patients with low INTS6 expression levels had shorter overall and disease-free survival rates than patients with high INTS6 expression levels (p =0.001 and p =0.001). Multivariate regression analysis indicated that INTS6 was an independent predictor of overall survival and disease-free survival rates. Mechanistically, INTS6 increased WIF-1 expression and then inhibited the Wnt/β-catenin signalling pathway. CONCLUSION The results of our study show that down-regulated INTS6 expression is associated with a poorer prognosis in HCC patients. This newly identified INTS6/WIF-1 axis indicates the molecular mechanism of HCC and may represent a therapeutic target in HCC patients.
Collapse
Affiliation(s)
- Ka Yin Lui
- Department of Critical Care Medicine, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
| | - Hui Zhao
- Department of Hepatic Surgery, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Chunhui Qiu
- Department of Hepatic Surgery, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Chuo Li
- Obstetric Laboratory, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Zhigang Zhang
- Department of Pathology, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Haoran Peng
- Transitional Year, Gwinnentt Medical Center, Lawrenceville, GA, USA
| | - Rongdang Fu
- Department of Hepatic Surgery, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Hu-An Chen
- Department of Hepatic Surgery, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China.
| | - Min-Qiang Lu
- Department of Hepatobiliary Surgery, Guangzhou First People's Hospital, Guangzhou, 510180, China.
| |
Collapse
|
14
|
Salvatore M, Warholm P, Shu N, Basile W, Elofsson A. SubCons: a new ensemble method for improved human subcellular localization predictions. Bioinformatics 2017; 33:2464-2470. [DOI: 10.1093/bioinformatics/btx219] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 04/11/2017] [Indexed: 12/24/2022] Open
Affiliation(s)
- M Salvatore
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - P Warholm
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - N Shu
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, Sweden
- Sweden Bioinformatics Infrastructure for Life Sciences (BILS), Stockholm University, Solna, Stockholm, Sweden
| | - W Basile
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - A Elofsson
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, Sweden
| |
Collapse
|
15
|
Abstract
BACKGROUND Crohn's disease (CD) is a form of inflammatory bowel disease with different described behaviors, including stricture. At present, there are no laboratory studies that can differentiate stricturing CD from other phenotypes of inflammatory bowel disease. We performed a pilot study to examine differences in the proteome among patients with stricturing CD, nonstricturing CD, and ulcerative colitis. METHODS Serum samples were selected from the Ocean State Crohn's and Colitis Area Registry, an established cohort of patients with inflammatory bowel disease. Patients with CD with surgically resected stricture were matched with similar patients with CD without known stricture and with ulcerative colitis. Serum samples from each patient were digested and analyzed using liquid chromatography-mass spectrometry to characterize the proteome. Statistical analyses were performed to identify peptides and proteins that can differentiate CD with stricture. RESULTS Samples from 9 patients in each group (27 total patients) were analyzed. Baseline demographic characteristics were similar among the 3 groups. We quantified 7668 peptides and 897 proteins for analysis. Receiver operating characteristic analysis identified a subset of peptides with an area under the curve greater than 0.9, indicating greater separation potential. Partial least squares discriminant analysis was able to distinguish among the three groups with up to 70% accuracy by peptides and up to 80% accuracy by proteins. We identified the significantly different proteins and peptides and determined their function based on previously published literature. CONCLUSIONS The serum of patients with stricturing CD, nonstricturing CD, and ulcerative colitis is distinguishable through proteomic analysis. Some of the proteins that differentiate the stricturing phenotype have been implicated in complement activation, fibrinolytic pathways, and lymphocyte adhesion.
Collapse
|
16
|
OIT3 deficiency impairs uric acid reabsorption in renal tubule. FEBS Lett 2012; 586:760-5. [DOI: 10.1016/j.febslet.2012.01.038] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Revised: 01/20/2012] [Accepted: 01/21/2012] [Indexed: 11/20/2022]
|
17
|
Chu JH, Wang H, Ye Y, Chan PK, Pan SY, Fong WF, Yu ZL. Inhibitory effect of schisandrin B on free fatty acid-induced steatosis in L-02 cells. World J Gastroenterol 2011; 17:2379-88. [PMID: 21633637 PMCID: PMC3103790 DOI: 10.3748/wjg.v17.i19.2379] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2010] [Revised: 08/13/2010] [Accepted: 08/20/2010] [Indexed: 02/06/2023] Open
Abstract
AIM: To investigate the effects of schisandrin B (Sch B) on free fatty acid (FFA)-induced steatosis in L-02 cells.
METHODS: Cellular steatosis was induced by incubating L-02 cells with a FFA mixture (oleate and palmitate at the ratio of 2:1) for 24 h. Cytotoxicity and apoptosis were evaluated by 3-(4, 5-dmethylthiazol-2-yl)-2, 5-diphenyl tetrazolium bromide assay and Annexin V/propidium iodide staining, respectively. Cellular total lipid was determined using a photocolorimetric method after Nile red staining, and triglyceride content was measured using an enzymatic kit. To study the effects of Sch B on steatosis, L-02 cells were treated with Sch B (1-100 μmol/L) in the absence or presence of 1 mmol/L FFA for 24 h, and cellular total lipid and triglyceride levels were measured. To explore the mechanisms of action of Sch B in the steatotic L-02 cells, mRNA levels of several regulators of hepatic lipid metabolism including adipose differentiation related protein (ADRP), sterol regulatory element binding protein 1 (SREBP-1), peroxisome proliferator-activated receptor (PPAR)-α and PPAR-γ were measured by quantitative real-time polymerase chain reaction (PCR), and protein levels of ADRP and SREBP-1 were measured by immunoblotting.
RESULTS: Treatment with 1 mmol/L FFA for 24 h induced intracellular lipid accumulation in L-02 cells comparable to that in human steatotic livers without causing apparent apoptosis and cytotoxicity. Sch B mitigated cellular total lipid and triglyceride accumulations in the steatotic L-02 cells in a dose-dependent manner. Quantitative real-time PCR and Western blot analyses revealed that treatment of L-02 cells with 100 μmol/L Sch B reverted the FFA-stimulated up-regulation of ADRP and SREBP-1.
CONCLUSION: Sch B inhibits FFA-induced steatosis in L-02 cells by, at least in part, reversing the up-regulation of ADRP and SREBP-1.
Collapse
|
18
|
Wang H, Chan PK, Pan SY, Kwon KH, Ye Y, Chu JH, Fong WF, Tsui WMS, Yu ZL. ERp57 is up-regulated in free fatty acids-induced steatotic L-02 cells and human nonalcoholic fatty livers. J Cell Biochem 2010; 110:1447-56. [PMID: 20506389 DOI: 10.1002/jcb.22696] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Pathogenesis of nonalcoholic fatty liver disease (NAFLD) is not clear. In this study we aimed to identify proteins involved in NAFLD development in free fatty acids (FFA)-induced hepatosteatotic cells and in human liver biopsies. Steatosis was induced by incubating a normal human hepatocyte-derived cell line L-02 with FFA. Differentially expressed proteins in the steatotic cells were analyzed by two-dimensional gel electrophoresis-based proteomics. Involvement of one of the up-regulated proteins in steatosis was characterized using the RNA interference approach with the steatotic cells. Protein expression levels in liver biopsies of patients with NAFLD were assessed by immunohistochemistry. Proteomic analysis of L-02 steatotic cells revealed the up-regulation of ERp57, a condition not previously implicated in NAFLD. Knockdown of ERp57 expression with siRNA significantly reduced fat accumulation in the steatotic cells. ERp57 expression was detected in 16 out of 17 patient biopsies and correlated with inflammation grades or fibrosis stages, while in 5 normal biopsies ERp57 expression was not detectable in hepatocytes. In conclusion, ERp57 was up-regulated in FFA-induced steatotic hepatic cells and in NAFLD patient livers and demonstrated steatotic properties in cultured cells. Further investigations are warranted to verify the involvement of ERp57 in NAFLD development.
Collapse
Affiliation(s)
- Hui Wang
- Center for Cancer and Inflammation Research, School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China
| | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Yoshida T, Kobayashi T, Itoda M, Muto T, Miyaguchi K, Mogushi K, Shoji S, Shimokawa K, Iida S, Uetake H, Ishikawa T, Sugihara K, Mizushima H, Tanaka H. Clinical omics analysis of colorectal cancer incorporating copy number aberrations and gene expression data. Cancer Inform 2010; 9:147-61. [PMID: 20706620 PMCID: PMC2918356 DOI: 10.4137/cin.s3851] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Background: Colorectal cancer (CRC) is one of the most frequently occurring cancers in Japan, and thus a wide range of methods have been deployed to study the molecular mechanisms of CRC. In this study, we performed a comprehensive analysis of CRC, incorporating copy number aberration (CRC) and gene expression data. For the last four years, we have been collecting data from CRC cases and organizing the information as an “omics” study by integrating many kinds of analysis into a single comprehensive investigation. In our previous studies, we had experienced difficulty in finding genes related to CRC, as we observed higher noise levels in the expression data than in the data for other cancers. Because chromosomal aberrations are often observed in CRC, here, we have performed a combination of CNA analysis and expression analysis in order to identify some new genes responsible for CRC. This study was performed as part of the Clinical Omics Database Project at Tokyo Medical and Dental University. The purpose of this study was to investigate the mechanism of genetic instability in CRC by this combination of expression analysis and CNA, and to establish a new method for the diagnosis and treatment of CRC. Materials and methods: Comprehensive gene expression analysis was performed on 79 CRC cases using an Affymetrix Gene Chip, and comprehensive CNA analysis was performed using an Affymetrix DNA Sty array. To avoid the contamination of cancer tissue with normal cells, laser micro-dissection was performed before DNA/RNA extraction. Data analysis was performed using original software written in the R language. Result: We observed a high percentage of CNA in colorectal cancer, including copy number gains at 7, 8q, 13 and 20q, and copy number losses at 8p, 17p and 18. Gene expression analysis provided many candidates for CRC-related genes, but their association with CRC did not reach the level of statistical significance. The combination of CNA and gene expression analysis, together with the clinical information, suggested UGT2B28, LOC440995, CXCL6, SULT1B1, RALBP1, TYMS, RAB12, RNMT, ARHGDIB, S1000A2, ABHD2, OIT3 and ABHD12 as genes that are possibly associated with CRC. Some of these genes have already been reported as being related to CRC. TYMS has been reported as being associated with resistance to the anti-cancer drug 5-fluorouracil, and we observed a copy number increase for this gene. RALBP1, ARHGDIB and S100A2 have been reported as oncogenes, and we observed copy number increases in each. ARHGDIB has been reported as a metastasis-related gene, and our data also showed copy number increases of this gene in cases with metastasis. Conclusion: The combination of CNA analysis and gene expression analysis was a more effective method for finding genes associated with the clinicopathological classification of CRC than either analysis alone. Using this combination of methods, we were able to detect genes that have already been associated with CRC. We also identified additional candidate genes that may be new markers or targets for this form of cancer.
Collapse
Affiliation(s)
- Tsuyoshi Yoshida
- Information Center for Medical Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
20
|
Xu ZG, Du JJ, Cui SJ, Wang ZQ, Huo KK, Li YY, Han ZG. Identification ofLZPGene fromMus musculusandRattus norvegicusCoding for a Novel Liver-specific ZP Domain-Containing Secretory Protein. ACTA ACUST UNITED AC 2009; 15:81-7. [PMID: 15346761 DOI: 10.1080/10425170310001652200] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Zona pellucida (ZP) domain has been recognized in a number of receptor-like eukaryotic glycoproteins, which involved in many important biological processes, such as signal transduction, development, differentiation and so on. Here we report the identification of Mus musculus and Rattus norvegicus orthologues of Homo sapiens LZP gene which codes for a novel ZP domain-containing protein. Sequence analysis revealed that human, rat and mouse LZP proteins are highly conserved. Mouse LZP gene has two transcripts, 2.4 and 2.8 KB long respectively, coding for identical protein. Mouse LZP mRNA is expressed specifically in hepatocytes. Our data also showed that mouse LZP localizes mostly on nuclear envelope, and at the same time, it can be secreted into blood in a truncated form.
Collapse
Affiliation(s)
- Zhi-Gang Xu
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, 220 Han Dan Road, Shanghai, 200433, China
| | | | | | | | | | | | | |
Collapse
|
21
|
Ding ZB, Shi YH, Zhou J, Qiu SJ, Xu Y, Dai Z, Shi GM, Wang XY, Ke AW, Wu B, Fan J. Association of autophagy defect with a malignant phenotype and poor prognosis of hepatocellular carcinoma. Cancer Res 2008; 68:9167-75. [PMID: 19010888 DOI: 10.1158/0008-5472.can-08-1573] [Citation(s) in RCA: 218] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Hepatocellular carcinoma (HCC) is an aggressive cancer with a poor prognosis. The role of autophagy and the prognostic value of autophagic genes are largely unknown in HCC. Here, we showed decreased expression of autophagic genes and their corresponding autophagic activity and increased expression of the antiapoptotic gene Bcl-xL in HCC cell lines compared with a normal hepatic cell line. We also found decreased expression of the autophagic gene Beclin 1 in 44 HCC tissue samples compared with adjacent nontumor tissues. In addition, we found that the most aggressive malignant HCC cell lines and HCC tissues with recurrent disease displayed much lower autophagic levels, especially when Bcl-xL was overexpressed. Interestingly, in a tissue microarray study consisting of 300 HCC patients who underwent curative resection, the expression of Beclin 1 was only significantly correlated with disease-free survival (DFS; P < 0.0001) and overall survival (OS; P < 0.0001) in the Bcl-xL(+) group. Multivariate and univariate analyses also revealed that Beclin 1 expression was an independent predictor for DFS and OS in Bcl-xL(+) patients. In addition, we found a significant correlation between Beclin 1 expression and tumor differentiation in Bcl-xL(+) but not in Bcl-xL(-) HCC patients. In conclusion, our data showed expression of autophagic genes and their corresponding autophagic activities were suppressed in HCC. The autophagy defects synergized with altered apoptotic activity might facilitate tumor malignant differentiation, which results in a more aggressive cancer cell phenotype and poor prognosis of HCC.
Collapse
Affiliation(s)
- Zhen-Bin Ding
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Shanghai 200032, China
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
22
|
Shen Y, Xu Q, Han Z, Liu H, Zhou GB. Analysis of phenotype-genotype connection: the story of dissecting disease pathogenesis in genomic era in China, and beyond. Philos Trans R Soc Lond B Biol Sci 2007; 362:1043-61. [PMID: 17327209 PMCID: PMC2435570 DOI: 10.1098/rstb.2007.2033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
DNA is the ultimate depository of biological complexity. Thus, in order to understand life and gain insights into disease pathogenesis, genetic information embedded in the sequence of DNA base pairs comprising chromosomes should be deciphered. The stories of investigating the association between phenotype and genotype in China and other countries further demonstrate that genomics can serve as a probe for disease biology. We now know that in Mendelian disorders, one gene is not only a dictator of one phenotype but also a dictator of two or more distinct disorders. Dissecting genetic abnormalities of complex diseases, including diabetes, hypertension, mental diseases, coronary heart disease and cancer, may unravel the complicated networks and crosstalks, and help to simplify the complexity of the disease. The transcriptome and proteomic analysis for medicine not only deepen our understanding of disease pathogenesis, but also provide novel diagnostic and therapeutic strategies. Taken together, genomic research offers a new opportunity for determining how diseases occur, by taking advantage of experiments of nature and a growing array of sophisticated research tools to identify the molecular abnormalities underlying disease processes. We should be ready for the advent of genomic medicine, and put the genome into the doctors' bag, so that we can help patients to conquer diseases.
Collapse
Affiliation(s)
- Yan Shen
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Peking Union Medical College & Chinese Academy of Medical Sciences100005 Beijing, People's Republic of China
- Chinese National Human Genome Center at Beijing100176 Beijing, People's Republic of China
- Authors for correspondence () ()
| | - Qi Xu
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Peking Union Medical College & Chinese Academy of Medical Sciences100005 Beijing, People's Republic of China
| | - Zeguang Han
- Chinese National Human Genome Center at Shanghai201203 Shanghai, People's Republic of China
| | - Han Liu
- State Key Laboratory for Medical Genomics, Shanghai Institute of Hematology200025 Shanghai, People's Republic of China
| | - Guang-Biao Zhou
- Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences510663 Guangzhou, People's Republic of China
- Authors for correspondence () ()
| |
Collapse
|
23
|
Ren XW, Liang M, Meng X, Ye X, Ma H, Zhao Y, Guo J, Cai N, Chen HZ, Ye SL, Hu F. A tumor-specific conditionally replicative adenovirus vector expressing TRAIL for gene therapy of hepatocellular carcinoma. Cancer Gene Ther 2006; 13:159-68. [PMID: 16082383 DOI: 10.1038/sj.cgt.7700868] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
We constructed a novel hepatocellular carcinoma-specific conditionally replicative adenovirus (CRAd). This adenovirus, designated Ad.HS4.AFP.E1A/TRAIL, expresses E1A to mediate viral replication and TRAIL to enhance HCC-killing efficacy under the control of a modified AFP promoter. An insulator HS-4 was placed in front of the AFP promoter to enhance the fidelity of the heterologous promoter. This virus was shown to have specific cytolytic activity in AFP-expressing HCC cells in vitro. Furthermore, the replication efficiency of Ad.HS4.AFP.E1A/TRAIL correlated well with AFP expression of the host cells, showing a 100-fold and 1 000 000-fold decrease in the low-and non-AFP-expressing HCC cells, respectively, compared to the high AFP-expressing HCC cells. An increase in mRNA of TRAIL and the elevated Caspase-3 activity were also observed in Ad.HS4.AFP.E1A/TRAIL-infected HCC cells. These results indicated that TRAIL expression from the viral vector activated the Caspase-3 enzymatic capacity and the HCC cells were sensitive to TRAIL. In vivo, Ad.HS4.AFP.E1A/TRAIL effectively prevented the growth of low AFP-expressing BEL-7404 xenografts. These results indicate that Ad.HS4.AFP.E1A/TRAIL could provide a new strategy of gene therapy for HCC.
Collapse
Affiliation(s)
- X-W Ren
- Shanghai Sunway Biotech Co., Ltd, Pudong, Shanghai, China
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Deng T, Shan S, Li PP, Shen ZF, Lu XP, Cheng J, Ning ZQ. Peroxisome proliferator-activated receptor-gamma transcriptionally up-regulates hormone-sensitive lipase via the involvement of specificity protein-1. Endocrinology 2006; 147:875-84. [PMID: 16269451 DOI: 10.1210/en.2005-0623] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Both peroxisome proliferator-activated receptor (PPAR)-gamma and hormone-sensitive lipase (HSL) play important roles in lipid metabolism and insulin sensitivity. We demonstrate that expression of the HSL gene is up-regulated by PPARgamma and PPARgamma agonists (rosiglitazone and pioglitazone) in the cultured hepatic cells and differentiating preadipocytes. Rosiglitazone treatment also results in up-regulation of the HSL gene in liver and skeleton muscle from an experimental obese rat model, accompanied by the decreased triglyceride content in these tissues. The proximal promoter (-87 bp of the human HSL gene) was found to be essential for PPARgamma-mediated transactivating activity. This important promoter region contains two GC-boxes and binds the transcription factor specificity protein-1 (Sp1) but not PPARgamma. The Sp1-promoter binding activity can be endogenously enhanced by PPARgamma and rosiglitazone, as demonstrated by analysis of EMSA and chromatin immunoprecipitation assay. Mutations in the GC-box sequences reduce the promoter binding activity of Sp1 and the transactivating activity of PPARgamma. In addition, mithramycin A, the specific inhibitor for Sp1-DNA binding activity, abolishes the PPARgamma-mediated up-regulation of HSL. These results indicate that PPARgamma positively regulates the HSL gene expression, and up-regulation of HSL by PPARgamma requires the involvement of Sp1. Taken together, this study suggests that HSL may be a newly identified PPARgamma target gene, and up-regulation of HSL may be an important mechanism involved in action of PPARgamma agonists in type 2 diabetes.
Collapse
Affiliation(s)
- Tuo Deng
- Department of Biological Science and Biotechnology, Tsinghua University, Beijing, China
| | | | | | | | | | | | | |
Collapse
|
25
|
Abstract
Many eukaryotic proteins share a sequence designated as the zona pellucida (ZP) domain. This structural element, present in extracellular proteins from a wide variety of organisms, from nematodes to mammals, consists of approximately 260 amino acids with eight conserved cysteine (Cys) residues and is located close to the C terminus of the polypeptide. ZP domain proteins are often glycosylated, modular structures consisting of multiple types of domains. Predictions can be made about some of the structural features of the ZP domain and ZP domain proteins. The functions of ZP domain proteins vary tremendously, from serving as structural components of egg coats, appendicularian mucous houses, and nematode dauer larvae, to serving as mechanotransducers in flies and receptors in mammals and nonmammals. Generally, ZP domain proteins are present in filaments and/or matrices, which is consistent with the role of the domain in protein polymerization. A general mechanism for assembly of ZP domain proteins has been presented. It is likely that the ZP domain plays a common role despite its presence in proteins of widely diverse functions.
Collapse
Affiliation(s)
- Luca Jovine
- Brookdale Department of Molecular, Cell, and Developmental Biology, Mount Sinai School of Medicine, New York, New York 10029-6574, USA.
| | | | | | | |
Collapse
|
26
|
Yang H, Wu C, Zhao S, Guo J. Identification and characterization of D8C, a novel domain present in liver-specific LZP, uromodulin and glycoprotein 2, mutated in familial juvenile hyperuricaemic nephropathy. FEBS Lett 2004; 578:236-8. [PMID: 15589826 DOI: 10.1016/j.febslet.2004.10.092] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2004] [Revised: 10/28/2004] [Accepted: 10/29/2004] [Indexed: 11/19/2022]
Abstract
Present work reported a novel domain--D8C (domain with conserved eight cysteines in liver-specific ZP domain-containing protein, glycoprotein 2 (GP-2) and uromodulin (UMOD)), present in liver-specific LZP, UMOD, GP-2 and some uncharacterized proteins, most of which are membrane proteins, extracellular proteins or nuclear membrane proteins. D8C contains eight well-conserved cysteine residues, which were predicted to form four pairs of disulfide bridges. D8C is composed mainly of beta-strands. Mutation in the D8C at Cys217 in human UMOD is associated with familial juvenile hyperuricaemic nephropathy, which might be due to the disruption of the disulfide bridge. Identification of D8C would further the understandings of related proteins.
Collapse
Affiliation(s)
- Huirong Yang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Handan Rd 220, Shanghai 200433, PR China
| | | | | | | |
Collapse
|
27
|
Jovine L, Qi H, Williams Z, Litscher ES, Wassarman PM. A duplicated motif controls assembly of zona pellucida domain proteins. Proc Natl Acad Sci U S A 2004; 101:5922-7. [PMID: 15079052 PMCID: PMC395899 DOI: 10.1073/pnas.0401600101] [Citation(s) in RCA: 111] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Many secreted eukaryotic glycoproteins that play fundamental roles in development, hearing, immunity, and cancer polymerize into filaments and extracellular matrices through zona pellucida (ZP) domains. ZP domain proteins are synthesized as precursors containing C-terminal propeptides that are cleaved at conserved sites. However, the consequences of this processing and the mechanism by which nascent proteins assemble are unclear. By microinjection of mutated DNA constructs into growing oocytes and mammalian cell transfection, we have identified a conserved duplicated motif [EHP (external hydrophobic patch)/IHP (internal hydrophobic patch)] regulating the assembly of mouse ZP proteins. Whereas the transmembrane domain (TMD) of ZP3 can be functionally replaced by an unrelated TMD, mutations in either EHP or IHP do not hinder secretion of full-length ZP3 but completely abolish its assembly. Because mutants truncated before the TMD are not processed, we conclude that the conserved TMD of mammalian ZP proteins does not engage them in specific interactions but is essential for C-terminal processing. Cleavage of ZP precursors results in loss of the EHP, thereby activating secreted polypeptides to assemble by using the IHP within the ZP domain. Taken together, these findings suggest a general mechanism for assembly of ZP domain proteins.
Collapse
Affiliation(s)
- Luca Jovine
- Brookdale Department of Molecular, Cell, and Developmental Biology, Mount Sinai School of Medicine, One Gustave L. Levy Place, New York, NY 10029-6574, USA
| | | | | | | | | |
Collapse
|