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Liu Y, Chen X, Ma Y, Song C, Ma J, Chen C, Su J, Ma L, Saiyin H. Endogenous mutant Huntingtin alters the corticogenesis via lowering Golgi recruiting ARF1 in cortical organoid. Mol Psychiatry 2024:10.1038/s41380-024-02562-0. [PMID: 38654124 DOI: 10.1038/s41380-024-02562-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 04/10/2024] [Accepted: 04/12/2024] [Indexed: 04/25/2024]
Abstract
Pathogenic mutant huntingtin (mHTT) infiltrates the adult Huntington's disease (HD) brain and impairs fetal corticogenesis. However, most HD animal models rarely recapitulate neuroanatomical alterations in adult HD and developing brains. Thus, the human cortical organoid (hCO) is an alternative approach to decode mHTT pathogenesis precisely during human corticogenesis. Here, we replicated the altered corticogenesis in the HD fetal brain using HD patient-derived hCOs. Our HD-hCOs had pathological phenotypes, including deficient junctional complexes in the neural tubes, delayed postmitotic neuronal maturation, dysregulated fate specification of cortical neuron subtypes, and abnormalities in early HD subcortical projections during corticogenesis, revealing a causal link between impaired progenitor cells and chaotic cortical neuronal layering in the HD brain. We identified novel long, oriented, and enriched polyQ assemblies of HTTs that hold large flat Golgi stacks and scaffold clathrin+ vesicles in the neural tubes of hCOs. Flat Golgi stacks conjugated polyQ assemblies by ADP-ribosylation factor 1 (ARF1). Inhibiting ARF1 activation with Brefeldin A (BFA) disassociated polyQ assemblies from Golgi. PolyQ assembles with mHTT scaffolded fewer ARF1 and formed shorter polyQ assembles with fewer and shorter Golgi and clathrin vesicles in neural tubes of HD-hCOs compared with those in hCOs. Inhibiting the activation of ARF1 by BFA in healthy hCOs replicated impaired junctional complexes in the neural tubes. Together, endogenous polyQ assemblies with mHTT reduced the Golgi recruiting ARF1 in the neuroepithelium, impaired the Golgi structure and activities, and altered the corticogenesis in HD-hCO.
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Affiliation(s)
- Yang Liu
- Department of Anatomy and Histology & Embryology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Xinyu Chen
- Department of Anatomy and Histology & Embryology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Yunlong Ma
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
| | - Chenyun Song
- Department of Anatomy and Histology & Embryology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Jixin Ma
- Department of Anatomy and Histology & Embryology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Cheng Chen
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
| | - Jianzhong Su
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
| | - Lixiang Ma
- Department of Anatomy and Histology & Embryology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China.
| | - Hexige Saiyin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200433, China.
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Boesze-Battaglia K, Cohen GH, Bates PF, Walker LM, Zekavat A, Shenker BJ. Cellugyrin (synaptogyrin-2) dependent pathways are used by bacterial cytolethal distending toxin and SARS-CoV-2 virus to gain cell entry. Front Cell Infect Microbiol 2024; 14:1334224. [PMID: 38698905 PMCID: PMC11063343 DOI: 10.3389/fcimb.2024.1334224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 03/19/2024] [Indexed: 05/05/2024] Open
Abstract
Aggregatibacter actinomycetemcomitans cytolethal distending toxin (Cdt) is capable of intoxicating lymphocytes macrophages, mast cells and epithelial cells. Following Cdt binding to cholesterol, in the region of membrane lipid rafts, the CdtB and CdtC subunits are internalized and traffic to intracellular compartments. These events are dependent upon, cellugyrin, a critical component of synaptic like microvesicles (SLMVCg+). Target cells, such as Jurkat cells, rendered unable to express cellugyrin are resistant to Cdt-induced toxicity. Similar to Cdt, SARS-CoV-2 entry into host cells is initiated by binding to cell surface receptors, ACE-2, also associated with cholesterol-rich lipid rafts; this association leads to fusion and/or endocytosis of viral and host cell membranes and intracellular trafficking. The similarity in internalization pathways for both Cdt and SARS-CoV-2 led us to consider the possibility that cellugyrin was a critical component in both processes. Cellugyrin deficient Calu-3 cells (Calu-3Cg-) were prepared using Lentiviral particles containing shRNA; these cells were resistant to infection by VSV/SARS-CoV-2-spike pseudotype virus and partially resistant to VSV/VSV-G pseudotype virus. Synthetic peptides representing various regions of the cellugyrin protein were prepared and assessed for their ability to bind to Cdt subunits using surface plasmon resonance. Cdt was capable of binding to a region designated the middle outer loop (MOL) which corresponds to a region extending into the cytoplasmic surface of the SLMVCg+. SARS-CoV-2 spike proteins were assessed for their ability to bind to cellugyrin peptides; SARS-CoV-2 full length spike protein preferentially binds to a region within the SLMVCg+ lumen, designated intraluminal loop 1A. SARS-CoV-2-spike protein domain S1, which contains the receptor binding domains, binds to cellugyrin N-terminus which extends out from the cytoplasmic surface of SLMV. Binding specificity was further analyzed using cellugyrin scrambled peptide mutants. We propose that SLMVCg+ represent a component of a common pathway that facilitates pathogen and/or pathogen-derived toxins to gain host cell entry.
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Affiliation(s)
- Kathleen Boesze-Battaglia
- Department of Basic and Translational Sciences, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Gary H. Cohen
- Department of Basic and Translational Sciences, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Paul F. Bates
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Lisa M. Walker
- Department of Basic and Translational Sciences, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Ali Zekavat
- Department of Basic and Translational Sciences, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Bruce J. Shenker
- Department of Basic and Translational Sciences, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, United States
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Liu C, Qu Z, Zhao H, Wang P, Zhan C, Zhang Y. Pan-cancer analysis of SYNGR2 with a focus on clinical implications and immune landscape in liver hepatocellular carcinoma. BMC Bioinformatics 2023; 24:192. [PMID: 37170221 PMCID: PMC10173524 DOI: 10.1186/s12859-023-05323-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 05/05/2023] [Indexed: 05/13/2023] Open
Abstract
BACKGROUND Synaptogyrin-2 (SYNGR2), as a member of synaptogyrin gene family, is overexpressed in several types of cancer. However, the role of SYNGR2 in pan-cancer is largely unexplored. METHODS From the TCGA and GEO databases, we obtained bulk transcriptomes, and clinical information. We examined the expression patterns, prognostic values, and diagnostic value of SYNGR2 in pan-cancer, and investigated the relationship of SYNGR2 expression with tumor mutation burden (TMB), microsatellite instability (MSI), immune infiltration, and immune checkpoint (ICP) genes. The gene set enrichment analysis (GSEA) software was used to perform pathway analysis. Besides, we built a nomogram of liver hepatocellular carcinoma patients (LIHC) and validated its prediction accuracy. RESULTS SYNGR2 was highly expressed in most cancers. The high expression of SYNGR2 significantly reduced the overall survival (OS), disease-specific survival (DSS), disease-free interval (DFI), and progression-free interval (PFI) in multiple types of cancer. Also, receiver operating characteristic (ROC) curve analysis demonstrated that SYNGR2 showed high accuracy in distinguishing cancerous tissues from normal ones. Moreover, SYNGR2 expression was correlated with TMB, MSI, immune scores, and immune cell infiltrations. We also analyzed the association of SYNGR2 with immunotherapy response in LIHC. Finally, a nomogram including SYNGR2 and pathologic T, N, M stage was built and exhibited good predictive power for the OS, DSS, and PFI of LIHC patients. CONCLUSION Overall, SYNGR2 is a critical oncogene in various tumors. SYNGR2 participates in the carcinogenic progression, and may contribute to the immune infiltration in tumor microenvironment. Our study suggests that SYNGR2 can serve as a predictor related to prognosis in pan-cancer, especially LIHC.
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Affiliation(s)
- Chunxun Liu
- Department of Hepatopancreatobiliary Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Zhaowei Qu
- Department of Hepatopancreatobiliary Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Haoran Zhao
- Department of Hepatopancreatobiliary Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Peng Wang
- Department of Hepatopancreatobiliary Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Chao Zhan
- Department of Hepatopancreatobiliary Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yubao Zhang
- Department of Hepatopancreatobiliary Surgery, Harbin Medical University Cancer Hospital, Harbin, China.
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Molecular-evaluated and explainable drug repurposing for COVID-19 using ensemble knowledge graph embedding. Sci Rep 2023; 13:3643. [PMID: 36871056 PMCID: PMC9985643 DOI: 10.1038/s41598-023-30095-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 02/15/2023] [Indexed: 03/06/2023] Open
Abstract
The search for an effective drug is still urgent for COVID-19 as no drug with proven clinical efficacy is available. Finding the new purpose of an approved or investigational drug, known as drug repurposing, has become increasingly popular in recent years. We propose here a new drug repurposing approach for COVID-19, based on knowledge graph (KG) embeddings. Our approach learns "ensemble embeddings" of entities and relations in a COVID-19 centric KG, in order to get a better latent representation of the graph elements. Ensemble KG-embeddings are subsequently used in a deep neural network trained for discovering potential drugs for COVID-19. Compared to related works, we retrieve more in-trial drugs among our top-ranked predictions, thus giving greater confidence in our prediction for out-of-trial drugs. For the first time to our knowledge, molecular docking is then used to evaluate the predictions obtained from drug repurposing using KG embedding. We show that Fosinopril is a potential ligand for the SARS-CoV-2 nsp13 target. We also provide explanations of our predictions thanks to rules extracted from the KG and instanciated by KG-derived explanatory paths. Molecular evaluation and explanatory paths bring reliability to our results and constitute new complementary and reusable methods for assessing KG-based drug repurposing.
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Ho PWL, Li L, Liu HF, Choi ZYK, Chang EES, Pang SYY, Malki Y, Leung CT, Kung MHW, Ramsden DB, Ho SL. In vivo overexpression of synaptogyrin-3 promotes striatal synaptic dopamine uptake in LRRK2 R1441G mutant mouse model of Parkinson's disease. Brain Behav 2023; 13:e2886. [PMID: 36624932 PMCID: PMC9927849 DOI: 10.1002/brb3.2886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 11/17/2022] [Accepted: 12/24/2022] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Leucine-rich repeat kinase 2 (LRRK2) mutation is a common genetic risk factor of Parkinson's disease (PD). Presynaptic dysfunction is an early pathogenic event associated with dopamine (DA) dysregulation in striatum of the brain. DA uptake activity of DA uptake transporter (DAT) affects synaptic plasticity and motor and non-motor behavior. Synaptogyrin-3 (SYNGR3) is part of the synaptogyrin family, especially abundant in brain. Previous in vitro studies demonstrated interaction between SYNGR3 and DAT. Reduced SYNGR3 expression was observed in human PD brains with unclear reasons. METHODS Here, we further explored whether inducing SYNGR3 expression can influence (i) cellular DA uptake using differentiated human SH-SY5Y neuronal cells, (ii) striatal synaptosomal DA uptake in a mutant LRRK2R1441G knockin mouse model of PD, and (iii) innate rodent behavior using the marble burying test. RESULTS Young LRRK2 mutant mice exhibited significantly lower SYNGR3 levels in striatum compared to age-matched wild-type (WT) controls, resembling level in aged WT mice. SYNGR3 is spatially co-localized with DAT at striatal presynaptic terminals, visualized by immuno-gold transmission electron microscopy and immunohistochemistry. Their protein-protein interaction was confirmed by co-immunoprecipitation. Transient overexpression of SYNGR3 in differentiated SH-SY5Y cells increased cellular DA uptake activity without affecting total DAT levels. Inducing SYNGR3 overexpression by adeno-associated virus-7 (AAV7) injection in vivo into striatum increased ex vivo synaptosomal DA uptake in LRRK2 mutant mice and improved their innate marble burying behavior. CONCLUSION Brain SYNGR3 expression may be an important determinant to striatal DA homeostasis and synaptic function. Our preliminary behavioral test showed improved innate behavior after SYNGR3 overexpression in LRRK2 mutant mice, advocating further studies to determine the influence of SYNGR3 in the pathophysiology of DA neurons in PD.
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Affiliation(s)
- Philip Wing-Lok Ho
- Division of Neurology, Department of Medicine, School of Clinical Medicine, University of Hong Kong, Hong Kong, China
| | - Lingfei Li
- Division of Neurology, Department of Medicine, School of Clinical Medicine, University of Hong Kong, Hong Kong, China
| | - Hui-Fang Liu
- Division of Neurology, Department of Medicine, School of Clinical Medicine, University of Hong Kong, Hong Kong, China
| | - Zoe Yuen-Kiu Choi
- Division of Neurology, Department of Medicine, School of Clinical Medicine, University of Hong Kong, Hong Kong, China
| | - Eunice Eun Seo Chang
- Division of Neurology, Department of Medicine, School of Clinical Medicine, University of Hong Kong, Hong Kong, China
| | - Shirley Yin-Yu Pang
- Division of Neurology, Department of Medicine, School of Clinical Medicine, University of Hong Kong, Hong Kong, China
| | - Yasine Malki
- Division of Neurology, Department of Medicine, School of Clinical Medicine, University of Hong Kong, Hong Kong, China
| | - Chi-Ting Leung
- Division of Neurology, Department of Medicine, School of Clinical Medicine, University of Hong Kong, Hong Kong, China
| | - Michelle Hiu-Wai Kung
- Division of Neurology, Department of Medicine, School of Clinical Medicine, University of Hong Kong, Hong Kong, China
| | - David Boyer Ramsden
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, UK
| | - Shu-Leong Ho
- Division of Neurology, Department of Medicine, School of Clinical Medicine, University of Hong Kong, Hong Kong, China
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Murphy RM, Tasoulas J, Porrello A, Carper MB, Tsai YH, Coffey AR, Kumar S, Zeng PYF, Schrank TP, Midkiff BR, Cohen S, Salazar AH, Hayward MC, Hayes DN, Olshan A, Gupta GP, Nichols AC, Yarbrough WG, Pecot CV, Amelio AL. Tumor Cell Extrinsic Synaptogyrin 3 Expression as a Diagnostic and Prognostic Biomarker in Head and Neck Cancer. CANCER RESEARCH COMMUNICATIONS 2022; 2:987-1004. [PMID: 36148399 PMCID: PMC9491693 DOI: 10.1158/2767-9764.crc-21-0135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 04/15/2022] [Accepted: 08/11/2022] [Indexed: 12/24/2022]
Abstract
Over 70% of oropharyngeal head and neck squamous cell carcinoma (HNSC) cases in the United States are positive for human papillomavirus (HPV) yet biomarkers for stratifying oropharyngeal head and neck squamous cell carcinoma (HNSC) patient risk are limited. We used immunogenomics to identify differentially expressed genes in immune cells of HPV(+) and HPV(-) squamous carcinomas. Candidate genes were tested in clinical specimens using both quantitative RT-PCR and IHC and validated by IHC using the Carolina Head and Neck Cancer Study (CHANCE) tissue microarray of HNSC cases. We performed multiplex immunofluorescent staining to confirm expression within the immune cells of HPV(+) tumors, receiver operating characteristic (ROC) curve analyses, and assessed survival outcomes. The neuronal gene Synaptogyrin-3 (SYNGR3) is robustly expressed in immune cells of HPV(+) squamous cancers. Multiplex immunostaining and single cell RNA-seq analyses confirmed SYNGR3 expression in T cells, but also unexpectedly in B cells of HPV(+) tumors. ROC curve analyses revealed that combining SYNGR3 and p16 provides more sensitivity and specificity for HPV detection compared to p16 IHC alone. SYNGR3-high HNSC patients have significantly better prognosis with five-year OS and DSS rates of 60% and 71%, respectively. Moreover, combining p16 localization and SYNGR3 expression can further risk stratify HPV(+) patients such that high cytoplasmic, low nuclear p16 do significantly worse (Hazard Ratio, 8.6; P = 0.032) compared to patients with high cytoplasmic, high nuclear p16. SYNGR3 expression in T and B cells is associated with HPV status and enhanced survival outcomes of HNSC patients.
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Affiliation(s)
- Ryan M. Murphy
- Graduate Curriculum in Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Division of Oral and Craniofacial Health Sciences, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Jason Tasoulas
- Division of Oral and Craniofacial Health Sciences, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Alessandro Porrello
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Miranda B. Carper
- Division of Oral and Craniofacial Health Sciences, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Yi-Hsuan Tsai
- Bioinformatics Core, Lineberger Comprehensive Cancer Center, UNC School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Alisha R. Coffey
- Bioinformatics Core, Lineberger Comprehensive Cancer Center, UNC School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Sunil Kumar
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Technology Development, Naveris Inc., Natick, Massachusetts
| | - Peter YF. Zeng
- Department of Otolaryngology - Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada
- Department of Pathology and Laboratory Medicine, University of Western Ontario, London, Ontario, Canada
| | - Travis P. Schrank
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Department of Otolaryngology/Head and Neck Surgery, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Bentley R. Midkiff
- Pathology Services Core, Lineberger Comprehensive Cancer Center, UNC School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Stephanie Cohen
- Pathology Services Core, Lineberger Comprehensive Cancer Center, UNC School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Ashley H. Salazar
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Michele C. Hayward
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - D. Neil Hayes
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Center for Cancer Research, University of Tennessee Health Sciences, Memphis, Tennessee
| | - Andrew Olshan
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Gaorav P. Gupta
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Department of Radiation Oncology, UNC School of Medicine, Chapel Hill, North Carolina
| | - Anthony C. Nichols
- Department of Otolaryngology - Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada
- Department of Oncology, University of Western Ontario, London, Ontario, Canada
| | - Wendell G. Yarbrough
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Department of Otolaryngology/Head and Neck Surgery, University of North Carolina School of Medicine, Chapel Hill, North Carolina
- Department of Pathology and Lab Medicine, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Chad V. Pecot
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Antonio L. Amelio
- Division of Oral and Craniofacial Health Sciences, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Department of Cell Biology and Physiology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Cancer Cell Biology Program, Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
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Li B, Ren MY, Chen YZ, Meng YQ, Song TN, Su ZP, Yang B. SYNGR2 serves as a prognostic biomarker and correlates with immune infiltrates in esophageal squamous cell carcinoma. J Gene Med 2022; 24:e3441. [PMID: 35840542 DOI: 10.1002/jgm.3441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/05/2022] [Accepted: 06/28/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Synaptogyrin-2 (SYNGR2) plays an important role in regulating membrane traffic in nonneuronal cells. However, the role of SYNGR2 in esophageal squamous cell carcinoma (ESCC) remains unclear. METHODS All original data were downloaded from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases and integrated via R 3.5.3. SYNGR2 expression was explored in the TCGA and GEO databases. The correlations between SYNGR2 and cancer immune characteristics were analyzed via the TIMER and TISIDB databases. RESULTS In general, SYNGR2 was predominantly overexpressed and had reference value in the diagnosis and prognostic estimation of ESCC. Upregulated SYNGR2 was associated with poorer overall survival, poorer disease-specific survival and T stage in ESCC. Mechanistically, we identified hub genes that included a total of 38 SYNGR2-related genes, which were tightly associated with the protein polyubiquitination pathway in ESCC patients. SYNGR2 expression was negatively related to the infiltrating levels of T helper cells. SYNGR2 methylation was positively correlated with the expression of chemokines (CCL2 and CXCL12), chemokine receptors (CCR1 and CCR2), immunoinhibitors (CXCL12 and TNFRSF4) and immunostimulators (CSF1R and PDCD1LG2) in ESCC. CONCLUSION SYNGR2 may be used as a biomarker for determining prognosis and immune infiltration in ESCC.
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Affiliation(s)
- Bin Li
- Department of Thoracic Surgery, Lanzhou University Second Hospital, Lanzhou University Second Clinical Medical College, Lanzhou, China
| | - Mei-Yu Ren
- Department of Thoracic Surgery, Lanzhou University Second Hospital, Lanzhou University Second Clinical Medical College, Lanzhou, China
| | - Yu-Zhen Chen
- Department of Thoracic Surgery, Lanzhou University Second Hospital, Lanzhou University Second Clinical Medical College, Lanzhou, China
| | - Yu-Qi Meng
- Department of Thoracic Surgery, Lanzhou University Second Hospital, Lanzhou University Second Clinical Medical College, Lanzhou, China
| | - Tie-Niu Song
- Department of Thoracic Surgery, Lanzhou University Second Hospital, Lanzhou University Second Clinical Medical College, Lanzhou, China
| | - Zhi-Peng Su
- Department of Thoracic Surgery, Lanzhou University Second Hospital, Lanzhou University Second Clinical Medical College, Lanzhou, China
| | - Bo Yang
- Department of Thoracic Surgery, Lanzhou University Second Hospital, Lanzhou University Second Clinical Medical College, Lanzhou, China
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Transcriptomics of angiotensin II-induced long noncoding and coding RNAs in endothelial cells. J Hypertens 2022; 40:1303-1313. [PMID: 35762471 DOI: 10.1097/hjh.0000000000003140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE Angiotensin II (Ang II)-induced endothelial dysfunction plays an important role in the pathogenesis of cardiovascular diseases such as systemic hypertension, cardiac hypertrophy and atherosclerosis. Recently, long noncoding RNAs (lncRNAs) have been shown to play an essential role in the pathobiology of cardiovascular diseases; however, the effect of Ang II on lncRNAs and coding RNAs expression in endothelial cells has not been evaluated. Accordingly, we sought to evaluate the expression profiles of lncRNAs and coding RNAs in endothelial cells following treatment with Ang II. METHODS Human umbilical vein endothelial cells (HUVECs) were cultured and treated with Ang II (10-6 mol/l) for 24 h. The cells were then profiled for the expression of lncRNAs and mRNAs using the Arraystar Human lncRNA Expression Microarray V3.0. RESULTS In HUVECs following Ang II treatment, from a total of 30 584 lncRNA targets screened, 25 targets were significantly upregulated, while 69 were downregulated. In the same HUVECs samples, from 26 106 mRNA targets screened, 28 targets were significantly upregulated and 67 were downregulated. Of the differentially expressed lncRNAs, RP11-354P11.2 and RP11-360F5.1 were the most upregulated (11-fold) and downregulated (three-fold) lncRNAs, respectively. Assigning the differentially regulated genes into functional groups using bioinformatics reveals numerous genes involved in the nucleotide excision repair and ECM-receptor interaction. CONCLUSION This is the first study to profile the Ang II-induced differentially expressed lncRNAs and mRNAs in human endothelial cells. Our results reveal novel targets and substantially extend the list of potential candidate genes involved in Ang II-induced endothelial dysfunction and cardiovascular diseases.
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Li L, Ho PWL, Liu H, Pang SYY, Chang EES, Choi ZYK, Malki Y, Kung MHW, Ramsden DB, Ho SL. Transcriptional Regulation of the Synaptic Vesicle Protein Synaptogyrin-3 (SYNGR3) Gene: The Effects of NURR1 on Its Expression. Int J Mol Sci 2022; 23:ijms23073646. [PMID: 35409005 PMCID: PMC8998927 DOI: 10.3390/ijms23073646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 03/24/2022] [Accepted: 03/24/2022] [Indexed: 11/24/2022] Open
Abstract
Synaptogyrin-3 (SYNGR3) is a synaptic vesicular membrane protein. Amongst four homologues (SYNGR1 to 4), SYNGR1 and 3 are especially abundant in the brain. SYNGR3 interacts with the dopamine transporter (DAT) to facilitate dopamine (DA) uptake and synaptic DA turnover in dopaminergic transmission. Perturbed SYNGR3 expression is observed in Parkinson’s disease (PD). The regulatory elements which affect SYNGR3 expression are unknown. Nuclear-receptor-related-1 protein (NURR1) can regulate dopaminergic neuronal differentiation and maintenance via binding to NGFI-B response elements (NBRE). We explored whether NURR1 can regulate SYNGR3 expression using an in silico analysis of the 5′-flanking region of the human SYNGR3 gene, reporter gene activity and an electrophoretic mobility shift assay (EMSA) of potential cis-acting sites. In silico analysis of two genomic DNA segments (1870 bp 5′-flanking region and 1870 + 159 bp of first exon) revealed one X Core Promoter Element 1 (XCPE1), two SP1, and three potential non-canonical NBRE response elements (ncNBRE) but no CAAT or TATA box. The longer segment exhibited gene promoter activity in luciferase reporter assays. Site-directed mutagenesis of XCPE1 decreased promoter activity in human neuroblastoma SH-SY5Y (↓43.2%) and human embryonic kidney HEK293 cells (↓39.7%). EMSA demonstrated NURR1 binding to these three ncNBRE. Site-directed mutagenesis of these ncNBRE reduced promoter activity by 11–17% in SH-SY5Y (neuronal) but not in HEK293 (non-neuronal) cells. C-DIM12 (Nurr1 activator) increased SYNGR3 protein expression in SH-SY5Y cells and its promoter activity using a real-time luciferase assay. As perturbed vesicular function is a feature of major neurodegenerative diseases, inducing SYNGR3 expression by NURR1 activators may be a potential therapeutic target to attenuate synaptic dysfunction in PD.
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Affiliation(s)
- Lingfei Li
- Division of Neurology, Department of Medicine, University of Hong Kong, Hong Kong SAR, China; (L.L.); (P.W.-L.H.); (H.L.); (S.Y.-Y.P.); (E.E.-S.C.); (Z.Y.-K.C.); (Y.M.); (M.H.-W.K.)
| | - Philip Wing-Lok Ho
- Division of Neurology, Department of Medicine, University of Hong Kong, Hong Kong SAR, China; (L.L.); (P.W.-L.H.); (H.L.); (S.Y.-Y.P.); (E.E.-S.C.); (Z.Y.-K.C.); (Y.M.); (M.H.-W.K.)
| | - Huifang Liu
- Division of Neurology, Department of Medicine, University of Hong Kong, Hong Kong SAR, China; (L.L.); (P.W.-L.H.); (H.L.); (S.Y.-Y.P.); (E.E.-S.C.); (Z.Y.-K.C.); (Y.M.); (M.H.-W.K.)
| | - Shirley Yin-Yu Pang
- Division of Neurology, Department of Medicine, University of Hong Kong, Hong Kong SAR, China; (L.L.); (P.W.-L.H.); (H.L.); (S.Y.-Y.P.); (E.E.-S.C.); (Z.Y.-K.C.); (Y.M.); (M.H.-W.K.)
| | - Eunice Eun-Seo Chang
- Division of Neurology, Department of Medicine, University of Hong Kong, Hong Kong SAR, China; (L.L.); (P.W.-L.H.); (H.L.); (S.Y.-Y.P.); (E.E.-S.C.); (Z.Y.-K.C.); (Y.M.); (M.H.-W.K.)
| | - Zoe Yuen-Kiu Choi
- Division of Neurology, Department of Medicine, University of Hong Kong, Hong Kong SAR, China; (L.L.); (P.W.-L.H.); (H.L.); (S.Y.-Y.P.); (E.E.-S.C.); (Z.Y.-K.C.); (Y.M.); (M.H.-W.K.)
| | - Yasine Malki
- Division of Neurology, Department of Medicine, University of Hong Kong, Hong Kong SAR, China; (L.L.); (P.W.-L.H.); (H.L.); (S.Y.-Y.P.); (E.E.-S.C.); (Z.Y.-K.C.); (Y.M.); (M.H.-W.K.)
| | - Michelle Hiu-Wai Kung
- Division of Neurology, Department of Medicine, University of Hong Kong, Hong Kong SAR, China; (L.L.); (P.W.-L.H.); (H.L.); (S.Y.-Y.P.); (E.E.-S.C.); (Z.Y.-K.C.); (Y.M.); (M.H.-W.K.)
| | - David Boyer Ramsden
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham B15 2TT, UK
- Correspondence: (D.B.R.); (S.-L.H.)
| | - Shu-Leong Ho
- Division of Neurology, Department of Medicine, University of Hong Kong, Hong Kong SAR, China; (L.L.); (P.W.-L.H.); (H.L.); (S.Y.-Y.P.); (E.E.-S.C.); (Z.Y.-K.C.); (Y.M.); (M.H.-W.K.)
- Correspondence: (D.B.R.); (S.-L.H.)
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10
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Johnsson M, Jungnickel MK. Evidence for and localization of proposed causative variants in cattle and pig genomes. Genet Sel Evol 2021; 53:67. [PMID: 34461824 PMCID: PMC8404348 DOI: 10.1186/s12711-021-00662-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 08/20/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND This paper reviews the localization of published potential causative variants in contemporary pig and cattle reference genomes, and the evidence for their causality. In spite of the difficulties inherent to the identification of causative variants from genetic mapping and genome-wide association studies, researchers in animal genetics have proposed putative causative variants for several traits relevant to livestock breeding. RESULTS For this review, we read the literature that supports potential causative variants in 13 genes (ABCG2, DGAT1, GHR, IGF2, MC4R, MSTN, NR6A1, PHGK1, PRKAG3, PLRL, RYR1, SYNGR2 and VRTN) in cattle and pigs, and localized them in contemporary reference genomes. We review the evidence for their causality, by aiming to separate the evidence for the locus, the proposed causative gene and the proposed causative variant, and report the bioinformatic searches and tactics needed to localize the sequence variants in the cattle or pig genome. CONCLUSIONS Taken together, there is usually good evidence for the association at the locus level, some evidence for a specific causative gene at eight of the loci, and some experimental evidence for a specific causative variant at six of the loci. We recommend that researchers who report new potential causative variants use referenced coordinate systems, show local sequence context, and submit variants to repositories.
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Affiliation(s)
- Martin Johnsson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, 750 07 Uppsala, Sweden
| | - Melissa K. Jungnickel
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, EH25 9RG Scotland, UK
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11
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Boesze-Battaglia K, Dhingra A, Walker LM, Zekavat A, Shenker BJ. Internalization and Intoxication of Human Macrophages by the Active Subunit of the Aggregatibacter actinomycetemcomitans Cytolethal Distending Toxin Is Dependent Upon Cellugyrin (Synaptogyrin-2). Front Immunol 2020; 11:1262. [PMID: 32655562 PMCID: PMC7325893 DOI: 10.3389/fimmu.2020.01262] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 05/18/2020] [Indexed: 12/20/2022] Open
Abstract
The Aggregatibacter actinomycetemcomitans cytolethal distending toxin (Cdt) is a heterotrimeric AB2 toxin capable of inducing cell cycle arrest and apoptosis in lymphocytes and other cell types. Recently, we have demonstrated that human macrophages are resistant to Cdt-induced apoptosis but are susceptible to toxin-induced pro-inflammatory cytokine response involving activation of the NLRP3 inflammasome. Exposure to Cdt results in binding to the cell surface followed by internalization and translocation of the active subunit, CdtB, to intracellular compartments. Internalization involves hijacking of retrograde pathways; treatment of cells with Retro-2 leads to a decrease in CdtB-Golgi association. These events are dependent upon toxin binding to cholesterol in the context of lipid rich membrane microdomains often referred to as lipid rafts. We now demonstrate that within 1 h of exposure of macrophages to Cdt, CdtB is internalized and found primarily within lipid rafts; concurrently, cellugyrin (synaptogyrin-2) also translocates into lipid rafts. Further analysis by immunoprecipitation indicates that CdtB associates with complexes containing both cellugyrin and Derlin-2. Moreover, a human macrophage cell line deficient in cellugyrin expression (THP-1Cg-) challenged with Cdt failed to internalize CdtB and was resistant to the Cdt-induced pro-inflammatory response. We propose that lipid rafts along with cellugyrin play a critical role in the internalization and translocation of CdtB to critical intracellular target sites in human macrophages. These studies provide the first evidence that cellugyrin is expressed in human macrophages and plays a critical role in Cdt toxicity of these cells.
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Affiliation(s)
- Kathleen Boesze-Battaglia
- Department of Biochemistry, University of Pennsylvania School of Dental Medicine, Philadelphia, PA, United States
| | - Anuradha Dhingra
- Department of Biochemistry, University of Pennsylvania School of Dental Medicine, Philadelphia, PA, United States
| | - Lisa M Walker
- Department of Pathology, University of Pennsylvania School of Dental Medicine, Philadelphia, PA, United States
| | - Ali Zekavat
- Department of Pathology, University of Pennsylvania School of Dental Medicine, Philadelphia, PA, United States
| | - Bruce J Shenker
- Department of Pathology, University of Pennsylvania School of Dental Medicine, Philadelphia, PA, United States
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12
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McInnes J, Wierda K, Snellinx A, Bounti L, Wang YC, Stancu IC, Apóstolo N, Gevaert K, Dewachter I, Spires-Jones TL, De Strooper B, De Wit J, Zhou L, Verstreken P. Synaptogyrin-3 Mediates Presynaptic Dysfunction Induced by Tau. Neuron 2018; 97:823-835.e8. [DOI: 10.1016/j.neuron.2018.01.022] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 12/07/2017] [Accepted: 01/09/2018] [Indexed: 11/25/2022]
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13
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Boesze-Battaglia K, Walker LP, Dhingra A, Kandror K, Tang HY, Shenker BJ. Internalization of the Active Subunit of the Aggregatibacter actinomycetemcomitans Cytolethal Distending Toxin Is Dependent upon Cellugyrin (Synaptogyrin 2), a Host Cell Non-Neuronal Paralog of the Synaptic Vesicle Protein, Synaptogyrin 1. Front Cell Infect Microbiol 2017; 7:469. [PMID: 29184850 PMCID: PMC5694546 DOI: 10.3389/fcimb.2017.00469] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 10/25/2017] [Indexed: 12/17/2022] Open
Abstract
The Aggregatibacter actinomycetemcomitans cytolethal distending toxin (Cdt) is a heterotrimeric AB2 toxin capable of inducing lymphocytes, and other cell types, to undergo cell cycle arrest and apoptosis. Exposure to Cdt results in binding to the cell surface followed by internalization and translocation of the active subunit, CdtB, to intracellular compartments. These events are dependent upon toxin binding to cholesterol in the context of lipid rich membrane microdomains often referred to as lipid rafts. We now demonstrate that, in addition to binding to the plasma membrane of lymphocytes, another early and critical event initiated by Cdt is the translocation of the host cell protein, cellugyrin (synaptogyrin-2) to the same cholesterol-rich microdomains. Furthermore, we demonstrate that cellugyrin is an intracellular binding partner for CdtB as demonstrated by immunoprecipitation. Using CRISPR/cas9 gene editing we established a Jurkat cell line deficient in cellugyrin expression (JurkatCg−); these cells were capable of binding Cdt, but unable to internalize CdtB. Furthermore, JurkatCg− cells were not susceptible to Cdt-induced toxicity; these cells failed to exhibit blockade of the PI-3K signaling pathway, cell cycle arrest or cell death. We propose that cellugyrin plays a critical role in the internalization and translocation of CdtB to critical intracellular target sites. These studies provide critical new insight into the mechanism by which Cdt, and in particular, CdtB is able to induce toxicity.
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Affiliation(s)
- Kathleen Boesze-Battaglia
- Department of Biochemistry, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Lisa P Walker
- Department of Pathology, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Anuradha Dhingra
- Department of Biochemistry, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Konstantin Kandror
- Department of Biochemistry, School of Medicine, Boston University, Boston, MA, United States
| | - Hsin-Yao Tang
- Wistar Proteomics and Metabolomics Core Facility, Wistar Institute, Philadelphia, PA, United States
| | - Bruce J Shenker
- Department of Pathology, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, United States
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14
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Schmölders J, Manske C, Otto A, Hoffmann C, Steiner B, Welin A, Becher D, Hilbi H. Comparative Proteomics of Purified Pathogen Vacuoles Correlates Intracellular Replication of Legionella pneumophila with the Small GTPase Ras-related protein 1 (Rap1). Mol Cell Proteomics 2017; 16:622-641. [PMID: 28183814 DOI: 10.1074/mcp.m116.063453] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 01/24/2017] [Indexed: 12/19/2022] Open
Abstract
Legionella pneumophila is an opportunistic bacterial pathogen that causes a severe lung infection termed "Legionnaires' disease." The pathogen replicates in environmental protozoa as well as in macrophages within a unique membrane-bound compartment, the Legionella-containing-vacuole (LCV). LCV formation requires the bacterial Icm/Dot type IV secretion system, which translocates ca. 300 "effector proteins" into host cells, where they target distinct host factors. The L. pneumophila "pentuple" mutant (Δpentuple) lacks 5 gene clusters (31% of the effector proteins) and replicates in macrophages but not in Dictyostelium discoideum amoeba. To elucidate the host factors defining a replication-permissive compartment, we compare here the proteomes of intact LCVs isolated from D. discoideum or macrophages infected with Δpentuple or the parental strain Lp02. This analysis revealed that the majority of host proteins are shared in D. discoideum or macrophage LCVs containing the mutant or the parental strain, respectively, whereas some proteins preferentially localize to distinct LCVs. The small GTPase Rap1 was identified on D. discoideum LCVs containing strain Lp02 but not the Δpentuple mutant and on macrophage LCVs containing either strain. The localization pattern of active Rap1 on D. discoideum or macrophage LCVs was confirmed by fluorescence microscopy and imaging flow cytometry, and the depletion of Rap1 by RNA interference significantly reduced the intracellular growth of L. pneumophila Thus, comparative proteomics identified Rap1 as a novel LCV host component implicated in intracellular replication of L. pneumophila.
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Affiliation(s)
- Johanna Schmölders
- From the ‡Max von Pettenkofer Institute, Ludwig-Maximilians University, Munich, Germany
| | - Christian Manske
- From the ‡Max von Pettenkofer Institute, Ludwig-Maximilians University, Munich, Germany
| | - Andreas Otto
- §Institute for Microbiology, Ernst Moritz Arndt University, Greifswald, Germany
| | - Christine Hoffmann
- From the ‡Max von Pettenkofer Institute, Ludwig-Maximilians University, Munich, Germany
| | - Bernhard Steiner
- ¶Institute of Medical Microbiology, University of Zürich, Switzerland
| | - Amanda Welin
- ¶Institute of Medical Microbiology, University of Zürich, Switzerland
| | - Dörte Becher
- §Institute for Microbiology, Ernst Moritz Arndt University, Greifswald, Germany;
| | - Hubert Hilbi
- From the ‡Max von Pettenkofer Institute, Ludwig-Maximilians University, Munich, Germany; .,¶Institute of Medical Microbiology, University of Zürich, Switzerland
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15
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Sun Q, Qi X, Zhang Y, Wu X, Liang M, Li C, Li D, Cardona CJ, Xing Z. Synaptogyrin-2 Promotes Replication of a Novel Tick-borne Bunyavirus through Interacting with Viral Nonstructural Protein NSs. J Biol Chem 2016; 291:16138-49. [PMID: 27226560 DOI: 10.1074/jbc.m116.715599] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Indexed: 01/24/2023] Open
Abstract
Synaptogyrin-2 is a non-neuronal member of the synaptogyrin family involved in synaptic vesicle biogenesis and trafficking. Little is known about the function of synaptogyrin-2. Severe fever with thrombocytopenia syndrome (SFTS) is an emerging infectious disease characterized by high fever, thrombocytopenia, and leukocytopenia with high mortality, caused by a novel tick-borne phlebovirus in the family Bunyaviridae. Our previous studies have shown that the viral nonstructural protein NSs forms inclusion bodies (IBs) that are involved in viral immune evasion, as well as viral RNA replication. In this study, we sought to elucidate the mechanism by which NSs formed the IBs, a lipid droplet-based structure confirmed by NSs co-localization with perilipin A and adipose differentiation-related protein (ADRP). Through a high throughput screening, we identified synaptogyrin-2 to be highly up-regulated in response to SFTS bunyavirus (SFTSV) infection and to be a promoter of viral replication. We demonstrated that synaptogyrin-2 interacted with NSs and was translocated into the IBs, which were reconstructed from lipid droplets into large structures in infection. Viral RNA replication decreased, and infectious virus titers were lowered significantly when synaptogyrin-2 was silenced in specific shRNA-expressing cells, which correlated with the reduced number of the large IBs restructured from regular lipid droplets. We hypothesize that synaptogyrin-2 is essential to promoting the formation of the IBs to become virus factories for viral RNA replication through its interaction with NSs. These findings unveil the function of synaptogyrin-2 as an enhancer in viral infection.
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Affiliation(s)
- Qiyu Sun
- From the State Key Laboratory of Pharmaceutical Biotechnology and Medical School, Nanjing University, Nanjing 210093, China
| | - Xian Qi
- the Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China
| | - Yan Zhang
- From the State Key Laboratory of Pharmaceutical Biotechnology and Medical School, Nanjing University, Nanjing 210093, China
| | - Xiaodong Wu
- From the State Key Laboratory of Pharmaceutical Biotechnology and Medical School, Nanjing University, Nanjing 210093, China
| | - Mifang Liang
- the National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China, and
| | - Chuan Li
- the National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China, and
| | - Dexin Li
- the National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China, and
| | - Carol J Cardona
- the Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Twin Cities, St. Paul, Minnesota 55108
| | - Zheng Xing
- From the State Key Laboratory of Pharmaceutical Biotechnology and Medical School, Nanjing University, Nanjing 210093, China, the Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Twin Cities, St. Paul, Minnesota 55108
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16
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Wang Z, Seow WJ, Shiraishi K, Hsiung CA, Matsuo K, Liu J, Chen K, Yamji T, Yang Y, Chang IS, Wu C, Hong YC, Burdett L, Wyatt K, Chung CC, Li SA, Yeager M, Hutchinson A, Hu W, Caporaso N, Landi MT, Chatterjee N, Song M, Fraumeni JF, Kohno T, Yokota J, Kunitoh H, Ashikawa K, Momozawa Y, Daigo Y, Mitsudomi T, Yatabe Y, Hida T, Hu Z, Dai J, Ma H, Jin G, Song B, Wang Z, Cheng S, Yin Z, Li X, Ren Y, Guan P, Chang J, Tan W, Chen CJ, Chang GC, Tsai YH, Su WC, Chen KY, Huang MS, Chen YM, Zheng H, Li H, Cui P, Guo H, Xu P, Liu L, Iwasaki M, Shimazu T, Tsugane S, Zhu J, Jiang G, Fei K, Park JY, Kim YH, Sung JS, Park KH, Kim YT, Jung YJ, Kang CH, Park IK, Kim HN, Jeon HS, Choi JE, Choi YY, Kim JH, Oh IJ, Kim YC, Sung SW, Kim JS, Yoon HI, Kweon SS, Shin MH, Seow A, Chen Y, Lim WY, Liu J, Wong MP, Lee VHF, Bassig BA, Tucker M, Berndt SI, Chow WH, Ji BT, Wang J, Xu J, Sihoe ADL, Ho JCM, Chan JKC, Wang JC, Lu D, Zhao X, Zhao Z, Wu J, Chen H, Jin L, Wei F, Wu G, An SJ, Zhang XC, Su J, Wu YL, Gao YT, Xiang YB, He X, Li J, Zheng W, Shu XO, Cai Q, Klein R, Pao W, Lawrence C, Hosgood HD, Hsiao CF, Chien LH, Chen YH, Chen CH, Wang WC, Chen CY, Wang CL, Yu CJ, Chen HL, Su YC, Tsai FY, Chen YS, Li YJ, Yang TY, Lin CC, Yang PC, Wu T, Lin D, Zhou B, Yu J, Shen H, Kubo M, Chanock SJ, Rothman N, Lan Q. Meta-analysis of genome-wide association studies identifies multiple lung cancer susceptibility loci in never-smoking Asian women. Hum Mol Genet 2016; 25:620-9. [PMID: 26732429 PMCID: PMC4731021 DOI: 10.1093/hmg/ddv494] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Revised: 10/30/2015] [Accepted: 11/26/2015] [Indexed: 12/20/2022] Open
Abstract
Genome-wide association studies (GWAS) of lung cancer in Asian never-smoking women have previously identified six susceptibility loci associated with lung cancer risk. To further discover new susceptibility loci, we imputed data from four GWAS of Asian non-smoking female lung cancer (6877 cases and 6277 controls) using the 1000 Genomes Project (Phase 1 Release 3) data as the reference and genotyped additional samples (5878 cases and 7046 controls) for possible replication. In our meta-analysis, three new loci achieved genome-wide significance, marked by single nucleotide polymorphism (SNP) rs7741164 at 6p21.1 (per-allele odds ratio (OR) = 1.17; P = 5.8 × 10(-13)), rs72658409 at 9p21.3 (per-allele OR = 0.77; P = 1.41 × 10(-10)) and rs11610143 at 12q13.13 (per-allele OR = 0.89; P = 4.96 × 10(-9)). These findings identified new genetic susceptibility alleles for lung cancer in never-smoking women in Asia and merit follow-up to understand their biological underpinnings.
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Affiliation(s)
- Zhaoming Wang
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Gaithersburg, MD, USA, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA,
| | - Wei Jie Seow
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Kouya Shiraishi
- Division of Genome Biology, National Cancer Center Hospital, Tokyo, Japan
| | | | - Keitaro Matsuo
- Division of Molecular Medicine, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Jie Liu
- Department of Oncology, Shandong Cancer Hospital and Institute, Shandong Academy of Medical Sciences, Jinan, China
| | - Kexin Chen
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Taiki Yamji
- Epidemiology and Prevention Group, Research Center for Cancer Prevention and Screening, National Cancer Center, Tokyo, Japan
| | - Yang Yang
- Shanghai Pulmonary Hospital, Shanghai, China
| | - I-Shou Chang
- National Institute of Cancer Research, National Health Research Institutes, Zhunan, Taiwan
| | - Chen Wu
- Department of Etiology & Carcinogenesis and State Key Laboratory of Molecular Oncology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | | | - Laurie Burdett
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Gaithersburg, MD, USA, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Kathleen Wyatt
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Gaithersburg, MD, USA, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Charles C Chung
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Gaithersburg, MD, USA, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Shengchao A Li
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Gaithersburg, MD, USA, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Meredith Yeager
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Gaithersburg, MD, USA, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Amy Hutchinson
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Gaithersburg, MD, USA, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Wei Hu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Neil Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Maria T Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Nilanjan Chatterjee
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Minsun Song
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Joseph F Fraumeni
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Takashi Kohno
- Division of Genome Biology, National Cancer Center Hospital, Tokyo, Japan
| | - Jun Yokota
- Cancer Genome Biology Group, Institute of Predictive and Personalized Medicine of Cancer, Barcelona, Spain
| | - Hideo Kunitoh
- Department of Medical Oncology, Japanese Red Cross Medical Center, Tokyo, Japan
| | - Kyota Ashikawa
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yataro Daigo
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Tetsuya Mitsudomi
- Division of Thoracic Surgery, Kinki University School of Medicine, Sayama, Japan
| | | | - Toyoaki Hida
- Department of Thoracic Oncology, Aichi Cancer Center Central Hospital, Nagoya, Japan
| | - Zhibin Hu
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Juncheng Dai
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Hongxia Ma
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Guangfu Jin
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Bao Song
- Department of Oncology, Shandong Cancer Hospital and Institute, Shandong Academy of Medical Sciences, Jinan, China
| | - Zhehai Wang
- Department of Oncology, Shandong Cancer Hospital and Institute, Shandong Academy of Medical Sciences, Jinan, China
| | - Sensen Cheng
- Department of Oncology, Shandong Cancer Hospital and Institute, Shandong Academy of Medical Sciences, Jinan, China
| | - Zhihua Yin
- Department of Epidemiology, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, China, Key Laboratory of Cancer Etiology and Intervention, University of Liaoning Province, Shenyang, China
| | - Xuelian Li
- Department of Epidemiology, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, China, Key Laboratory of Cancer Etiology and Intervention, University of Liaoning Province, Shenyang, China
| | - Yangwu Ren
- Department of Epidemiology, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, China, Key Laboratory of Cancer Etiology and Intervention, University of Liaoning Province, Shenyang, China
| | - Peng Guan
- Department of Epidemiology, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, China, Key Laboratory of Cancer Etiology and Intervention, University of Liaoning Province, Shenyang, China
| | - Jiang Chang
- Department of Etiology & Carcinogenesis and State Key Laboratory of Molecular Oncology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wen Tan
- Department of Etiology & Carcinogenesis and State Key Laboratory of Molecular Oncology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chien-Jen Chen
- Genomic Research Center, Academia Sinica, Taipei, Taiwan
| | - Gee-Chen Chang
- Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan, Division of Chest Medicine, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Ying-Huang Tsai
- Division of Pulmonary and Critical Care Medicine, Chiayi Chang Gung Memorial Hospital, Chiayi, Taiwan
| | - Wu-Chou Su
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Kuan-Yu Chen
- Division of Pulmonary Medicine, Department of Internal Medicine, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Ming-Shyan Huang
- Department of Internal Medicine, Kaohsiung Medical University Hospital, School of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yuh-Min Chen
- Department of Chest Medicine, Taipei Veterans General Hospital, Taipei, Taiwan, College of Medical Science and Technology
| | - Hong Zheng
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Haixin Li
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Ping Cui
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Huan Guo
- Department of Occupational and Environmental Health and Ministry of Education Key Lab for Environment and Health, School of Public Health, Tongji Medical College
| | - Ping Xu
- Department of Oncology, Wuhan Iron and Steel (Group) Corporation Staff-Worker Hospital, Wuhan, China
| | - Li Liu
- Department of Oncology, Cancer Center, Union Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Motoki Iwasaki
- Epidemiology and Prevention Group, Research Center for Cancer Prevention and Screening, National Cancer Center, Tokyo, Japan
| | - Taichi Shimazu
- Epidemiology and Prevention Group, Research Center for Cancer Prevention and Screening, National Cancer Center, Tokyo, Japan
| | - Shoichiro Tsugane
- Epidemiology and Prevention Group, Research Center for Cancer Prevention and Screening, National Cancer Center, Tokyo, Japan
| | - Junjie Zhu
- Shanghai Pulmonary Hospital, Shanghai, China
| | | | - Ke Fei
- Shanghai Pulmonary Hospital, Shanghai, China
| | | | - Yeul Hong Kim
- Department of Internal Medicine, Division of Oncology/Hematology, College of Medicine, Korea University Anam Hospital, Seoul, Republic of Korea
| | - Jae Sook Sung
- Department of Internal Medicine, Division of Oncology/Hematology, College of Medicine, Korea University Anam Hospital, Seoul, Republic of Korea
| | - Kyong Hwa Park
- Department of Internal Medicine, Division of Oncology/Hematology, College of Medicine, Korea University Anam Hospital, Seoul, Republic of Korea
| | - Young Tae Kim
- Department of Thoracic and Cardiovascular Surgery, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Yoo Jin Jung
- Department of Thoracic and Cardiovascular Surgery, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Chang Hyun Kang
- Department of Thoracic and Cardiovascular Surgery, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - In Kyu Park
- Department of Thoracic and Cardiovascular Surgery, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Hee Nam Kim
- Center for Creative Biomedical Scientists, Chonnam National University, Gwangju, Republic of Korea
| | - Hyo-Sung Jeon
- Cancer Research Center, Kyungpook National University Medical Center, Daegu, Republic of Korea
| | - Jin Eun Choi
- Cancer Research Center, Kyungpook National University Medical Center, Daegu, Republic of Korea
| | - Yi Young Choi
- Cancer Research Center, Kyungpook National University Medical Center, Daegu, Republic of Korea
| | - Jin Hee Kim
- Department of Environmental Health, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea
| | - In-Jae Oh
- Lung and Esophageal Cancer Clinic, Department of Internal Medicine
| | - Young-Chul Kim
- Lung and Esophageal Cancer Clinic, Department of Internal Medicine
| | | | - Jun Suk Kim
- Department of Internal Medicine, Division of Medical Oncology, College of Medicine, Korea University Guro Hospital, Seoul, Republic of Korea
| | - Ho-Il Yoon
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Sun-Seog Kweon
- Jeonnam Regional Cancer Center, Chonnam National University Hwasun Hospital, Hwasun-eup, Republic of Korea, Department of Preventive Medicine, Chonnam National University Medical School, Gwangju, Republic of Korea
| | - Min-Ho Shin
- Department of Preventive Medicine, Chonnam National University Medical School, Gwangju, Republic of Korea
| | - Adeline Seow
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Ying Chen
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Wei-Yen Lim
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Jianjun Liu
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore, Department of Human Genetics, Genome Institute of Singapore, Singapore, Singapore, School of Life Sciences, Anhui Medical University, Hefei, China
| | - Maria Pik Wong
- Department of Pathology, Li Ka Shing (LKS) Faculty of Medicine
| | | | - Bryan A Bassig
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Margaret Tucker
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Wong-Ho Chow
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Bu-Tian Ji
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Junwen Wang
- Department of Biochemistry, LKS Faculty of Medicine, Centre for Genomic Sciences, LKS Faculty of Medicine
| | - Jun Xu
- School of Public Health, Li Ka Shing (LKS) Faculty of Medicine
| | | | - James C M Ho
- Department of Medicine, Li Ka Shing (LKS) Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - John K C Chan
- Department of Pathology, Queen Elizabeth Hospital, Hong Kong, China
| | - Jiu-Cun Wang
- Ministry of Education Key Laboratory of Contemporary Anthropology, State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Daru Lu
- Ministry of Education Key Laboratory of Contemporary Anthropology, State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Xueying Zhao
- Ministry of Education Key Laboratory of Contemporary Anthropology, State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Zhenhong Zhao
- Ministry of Education Key Laboratory of Contemporary Anthropology, State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Junjie Wu
- Ministry of Education Key Laboratory of Contemporary Anthropology, State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Hongyan Chen
- Ministry of Education Key Laboratory of Contemporary Anthropology, State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Li Jin
- Ministry of Education Key Laboratory of Contemporary Anthropology, State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Fusheng Wei
- China National Environmental Monitoring Center, Beijing, China
| | - Guoping Wu
- China National Environmental Monitoring Center, Beijing, China
| | - She-Juan An
- Guangdong Lung Cancer Institute, Medical Research Center and Cancer Center of Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Xu-Chao Zhang
- Guangdong Lung Cancer Institute, Medical Research Center and Cancer Center of Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Jian Su
- Guangdong Lung Cancer Institute, Medical Research Center and Cancer Center of Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Yi-Long Wu
- Guangdong Lung Cancer Institute, Medical Research Center and Cancer Center of Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Yu-Tang Gao
- Department of Epidemiology, Shanghai Cancer Institute, Shanghai, China
| | - Yong-Bing Xiang
- Department of Epidemiology, Shanghai Cancer Institute, Shanghai, China
| | - Xingzhou He
- Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jihua Li
- Qujing Center for Diseases Control and Prevention, Sanjiangdadao, Qujing, China
| | - Wei Zheng
- Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN, USA
| | - Xiao-Ou Shu
- Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN, USA
| | - Qiuyin Cai
- Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN, USA
| | - Robert Klein
- Program in Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - William Pao
- Division of Hematology and Oncology, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - H Dean Hosgood
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | | | | | | | - Chung-Hsing Chen
- National Institute of Cancer Research, National Health Research Institutes, Zhunan, Taiwan
| | - Wen-Chang Wang
- The PhD Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Chih-Yi Chen
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan, Division of Thoracic Surgery, Department of Surgery, Chung Shan Medical University Hospital, Taichung, Taiwan and
| | - Chih-Liang Wang
- Department of Pulmonary and Critical Care, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Chong-Jen Yu
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | | | | | - Fang-Yu Tsai
- National Institute of Cancer Research, National Health Research Institutes, Zhunan, Taiwan
| | | | - Yao-Jen Li
- Genomic Research Center, Academia Sinica, Taipei, Taiwan
| | - Tsung-Ying Yang
- Division of Chest Medicine, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Chien-Chung Lin
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Pan-Chyr Yang
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Tangchun Wu
- Department of Occupational and Environmental Health and Ministry of Education Key Lab for Environment and Health, School of Public Health, Tongji Medical College
| | - Dongxin Lin
- Department of Etiology & Carcinogenesis and State Key Laboratory of Molecular Oncology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Baosen Zhou
- Department of Epidemiology, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, China, Key Laboratory of Cancer Etiology and Intervention, University of Liaoning Province, Shenyang, China
| | - Jinming Yu
- Department of Oncology, Shandong Cancer Hospital and Institute, Shandong Academy of Medical Sciences, Jinan, China
| | - Hongbing Shen
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Michiaki Kubo
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Qing Lan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
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17
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Abstract
Synaptic vesicles release their vesicular contents to the extracellular space by Ca(2+)-triggered exocytosis. The Ca(2+)-triggered exocytotic process is regulated by synaptotagmin (Syt), a vesicular Ca(2+)-binding C2 domain protein. Synaptotagmin 1 (Syt1), the most studied major isoform among 16 Syt isoforms, mediates Ca(2+)-triggered synaptic vesicle exocytosis by interacting with the target membranes and SNARE/complexin complex. In synapses of the central nervous system, synaptobrevin 2, a major vesicular SNARE protein, forms a ternary SNARE complex with the plasma membrane SNARE proteins, syntaxin 1 and SNAP25. The affinities of Ca(2+)-dependent interactions between Syt1 and its targets (i.e., SNARE complexes and membranes) are well correlated with the efficacies of the corresponding exocytotic processes. Therefore, different SNARE protein isoforms and membrane lipids, which interact with Syt1 with various affinities, are capable of regulating the efficacy of Syt1-mediated exocytosis. Otoferlin, another type of vesicular C2 domain protein that binds to the membrane in a Ca(2+)-dependent manner, is also involved in the Ca(2+)-triggered synaptic vesicle exocytosis in auditory hair cells. However, the functions of otoferlin in the exocytotic process are not well understood. In addition, at least five different types of synaptic vesicle proteins such as synaptic vesicle protein 2, cysteine string protein α, rab3, synapsin, and a group of proteins containing four transmembrane regions, which includes synaptophysin, synaptogyrin, and secretory carrier membrane protein, are involved in modulating the exocytotic process by regulating the formation and trafficking of synaptic vesicles.
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Affiliation(s)
- Ok-Ho Shin
- Department of Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas
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Report of interstitial 22q13.1q13.2 microduplication in two siblings with distinctive dysmorphic features, heart defect and mental retardation. Eur J Med Genet 2013; 56:389-96. [PMID: 23707653 DOI: 10.1016/j.ejmg.2013.05.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Accepted: 05/07/2013] [Indexed: 11/22/2022]
Abstract
We present two siblings (a boy and a girl) with a submicroscopic 4 Mb duplication at 22q13.1q13.2. Both children manifested infantile hypotonia and delayed motor milestones, congenital heart defect, growth deficiency, and strikingly similar and distinctive craniofacial dysmorphism including brachycephaly, blepharophimosis, short broad-based nose and wide mouth with thin upper lip. The boy had also a submucous cleft palate. Both had fair skin and hair compared with their parents. Both had moderate mental retardation associated with a short attention span. A 4-Mb interstitial duplication at 22q13.1q13.2 was detected by whole genome microarray comparative genomic hybridisation (array CGH) in both children. The duplication was confirmed by fluorescence in situ hybridisation (FISH) analysis. Their parents had normal array CGH results. FISH analysis revealed that the father was a carrier of a balanced interchromosomal submicroscopic insertion of 22q13 into chromosome 11q23, explaining the unbalanced aberration detected in both children. This report narrows down the critical region at 22q13.1q13.2, which is associated with mental retardation, pre- and post-natal growth retardation, hippocampal malformation, psychiatric symptoms such as short attention span and facial dysmorphism including hypertelorism, epicanthal folds and low set/abnormal ears.
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19
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Cortical beta amyloid protein triggers an immune response, but no synaptic changes in the APPswe/PS1dE9 Alzheimer's disease mouse model. Neurobiol Aging 2012; 34:1328-42. [PMID: 23245294 DOI: 10.1016/j.neurobiolaging.2012.11.008] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Revised: 11/14/2012] [Accepted: 11/16/2012] [Indexed: 01/06/2023]
Abstract
Using microarray technology we studied the genome-wide gene expression profiles in the frontal cortex of APPswe/PS1dE9 mice and age and sex-matched littermates at the age of 2, 3, 6, 9, 12, and 15-18 months to investigate transcriptional changes that are associated with beta amyloid protein (Aβ) plaque formation and buildup. We observed the occurrence of an immune response with glial activation, but no changes in genes involved in synaptic transmission or plasticity. Comparison of the mouse gene expression data set with a human data set representing the course of Alzheimer's disease revealed a strikingly limited overlap between gene expression in the APPswe/PS1dE9 and human Alzheimer's disease prefrontal cortex. Only plexin domain containing 2, complement component 4b, and solute carrier family 14 (urea transporter) member 1 were significantly upregulated in the mouse and human brain which might suggest a function in Aβ pathology for these 3 genes. In both data sets we detected clusters of upregulated genes involved in immune-related processes. We conclude that the APPswe/PS1dE9 mouse can be a good model to study the immune response associated with cortical Aβ plaques.
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20
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Blesson CS, Sahlin L. Expression pattern and signalling pathways in neutrophil like HL-60 cells after treatment with estrogen receptor selective ligands. Mol Cell Endocrinol 2012; 361:179-90. [PMID: 22554835 DOI: 10.1016/j.mce.2012.04.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2012] [Revised: 04/18/2012] [Accepted: 04/18/2012] [Indexed: 02/04/2023]
Abstract
Estrogens play a role in the regulation of genes associated with inflammation and immunity in neutrophils. Estrogen signalling is mediated by estrogen receptor (ER)α, ERβ, and G-protein-coupled estrogen receptor-1 (GPER). The mechanisms by which estrogen regulate genes in neutrophils are poorly understood. Our aim was to identify the presence of ERs and to characterize estrogen responsive genes in terminally differentiated neutrophil like HL-60 (nHL-60) cells using estradiol and selective ER agonists. ERs were identified by Western blotting and immunocytochemistry. Microarray technique was used to screen for differentially expressed genes and the selected genes were verified by quantitative PCR. We show the presence of functional ERα, ERβ and GPER. Microarray analysis showed the presence of genes that are uniquely regulated by a single ligand and also genes that are regulated by multiple ligands. We conclude that ERs are functionally active in nHL-60 cells regulating genes involved in key physiological functions.
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Affiliation(s)
- Chellakkan Selvanesan Blesson
- Division for Reproductive Endocrinology and The Pediatric Endocrinology Unit, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden.
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21
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A molecular computational model improves the preoperative diagnosis of thyroid nodules. BMC Cancer 2012; 12:396. [PMID: 22958914 PMCID: PMC3503705 DOI: 10.1186/1471-2407-12-396] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2012] [Accepted: 07/31/2012] [Indexed: 11/25/2022] Open
Abstract
Background Thyroid nodules with indeterminate cytological features on fine needle aspiration (FNA) cytology have a 20% risk of thyroid cancer. The aim of the current study was to determine the diagnostic utility of an 8-gene assay to distinguish benign from malignant thyroid neoplasm. Methods The mRNA expression level of 9 genes (KIT, SYNGR2, C21orf4, Hs.296031, DDI2, CDH1, LSM7, TC1, NATH) was analysed by quantitative PCR (q-PCR) in 93 FNA cytological samples. To evaluate the diagnostic utility of all the genes analysed, we assessed the area under the curve (AUC) for each gene individually and in combination. BRAF exon 15 status was determined by pyrosequencing. An 8-gene computational model (Neural Network Bayesian Classifier) was built and a multiple-variable analysis was then performed to assess the correlation between the markers. Results The AUC for each significant marker ranged between 0.625 and 0.900, thus all the significant markers, alone and in combination, can be used to distinguish between malignant and benign FNA samples. The classifier made up of KIT, CDH1, LSM7, C21orf4, DDI2, TC1, Hs.296031 and BRAF had a predictive power of 88.8%. It proved to be useful for risk stratification of the most critical cytological group of the indeterminate lesions for which there is the greatest need of accurate diagnostic markers. Conclusion The genetic classification obtained with this model is highly accurate at differentiating malignant from benign thyroid lesions and might be a useful adjunct in the preoperative management of patients with thyroid nodules.
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22
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Löw C, Jegerschöld C, Kovermann M, Moberg P, Nordlund P. Optimisation of over-expression in E. coli and biophysical characterisation of human membrane protein synaptogyrin 1. PLoS One 2012; 7:e38244. [PMID: 22675529 PMCID: PMC3365889 DOI: 10.1371/journal.pone.0038244] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Accepted: 05/02/2012] [Indexed: 11/25/2022] Open
Abstract
Progress in functional and structural studies of integral membrane proteins (IMPs) is lacking behind their soluble counterparts due to the great challenge in producing stable and homogeneous IMPs. Low natural abundance, toxicity when over-expressed and potential lipid requirements of IMPs are only a few reasons for the limited progress. Here, we describe an optimised workflow for the recombinant over-expression of the human tetraspan vesicle protein (TVP) synaptogyrin in Escherichia coli and its biophysical characterisation. TVPs are ubiquitous and abundant components of vesicles. They are believed to be involved in various aspects of the synaptic vesicle cycle, including vesicle biogenesis, exocytosis and endocytotic recycling. Even though TVPs are found in most cell types, high-resolution structural information for this class of membrane proteins is still missing. The optimisation of the N-terminal sequence of the gene together with the usage of the recently developed Lemo21(DE3) strain which allows the balancing of the translation with the membrane insertion rate led to a 50-fold increased expression rate compared to the classical BL21(DE3) strain. The protein was soluble and stable in a variety of mild detergents and multiple biophysical methods confirmed the folded state of the protein. Crosslinking experiments suggest an oligomeric architecture of at least four subunits. The protein stability is significantly improved in the presence of cholesteryl hemisuccinate as judged by differential light scattering. The approach described here can easily be adapted to other eukaryotic IMPs.
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Affiliation(s)
- Christian Löw
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- * E-mail: (CL); (PN)
| | - Caroline Jegerschöld
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Michael Kovermann
- Institut für Physik, Biophysik, Martin-Luther-Universität Halle-Wittenberg, Saale, Germany
| | - Per Moberg
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Pär Nordlund
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- * E-mail: (CL); (PN)
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Association study and mutational screening of SYNGR1 as a candidate susceptibility gene for schizophrenia. Psychiatr Genet 2009; 19:237-43. [DOI: 10.1097/ypg.0b013e32832cebf7] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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24
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Cheng MC, Chen CH. Identification of rare mutations of synaptogyrin 1 gene in patients with schizophrenia. J Psychiatr Res 2007; 41:1027-31. [PMID: 17049558 DOI: 10.1016/j.jpsychires.2006.08.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2006] [Revised: 07/25/2006] [Accepted: 08/30/2006] [Indexed: 10/24/2022]
Abstract
Synaptogyrin 1 gene (SYNGR1) is considered as a positional candidate gene for schizophrenia because of its location at chromosome 22q13, a region linked to schizophrenia, and its reduced expression in postmortem brain of patients with schizophrenia. Additionally, genetic studies also reported association of SYNGR1 is with schizophrenia and bipolar disorder in southern India. Prompted by these findings, we were interested to know if SYNGR1 is also associated with schizophrenia in our population. Therefore, we systematically searched for SYNGR1 mutations in a cohort of Han Chinese patients from Taiwan. Four single nucleotide polymorphisms (SNPs) were identified, including three at the putative core promoter region (g.-673A>C, g.-377G>A and g.-318G>T) that are in strong linkage disequilibrium and one in intron 2 (IVS2-64C>G). Computer program predicts that g.-637A>C and g.318G>T may change transcription binding sites of AP-1 and TGT3, respectively. We further carried out SNP- and haplotype-based case-control association studies of these tress SNPs with schizophrenia. However, no association was detected between these SNPs and schizophrenia in our sample. Nevertheless, we identified several rare mutations in exon 6 of SYNGR1 gene in our patient cohort (n=497), including a 3-bp (AAC) in-frame insertion between codon 202 and 203 (P202_T203insN) in two patients, an A-to-G missense mutation (c.665A>G) at codon 222 (D222G) in one patient, a synonymous mutation (c.669C>T) at codon 223 (T223T) in one patient, and a C-to-T at 3' UTR of SYNGR1 (c.772C>T) in one patient. These are mutations were not found in 507 control subjects, suggesting further functional assays are warranted to verify their relevance to the pathogenesis of schizophrenia.
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Affiliation(s)
- Min-Chih Cheng
- Institute of Medical Sciences, Tzu-Chi University, Hualien City 970, Taiwan
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25
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Olesen C, Nyeng P, Kalisz M, Jensen TH, Møller M, Tommerup N, Byskov AG. Global gene expression analysis in fetal mouse ovaries with and without meiosis and comparison of selected genes with meiosis in the testis. Cell Tissue Res 2006; 328:207-21. [PMID: 17431699 DOI: 10.1007/s00441-006-0205-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2006] [Accepted: 03/22/2006] [Indexed: 10/23/2022]
Abstract
In order to identify novel genes involved in early meiosis and early ovarian development in the mouse, we used microarray technology to compare transcriptional activity in ovaries without meiotic germ cells at embryonic age 11.5 (E11.5) and E13.5 ovaries with meiosis. Overall, 182 genes were differentially expressed; 134 were known genes and 48 were functionally uncharacterized. A comparison of our data with the literature associated, for the first time, at least eight of the known genes with female meiosis/germ cell differentiation (Aldh1a1, C2pa, Tex12, Stk31, Lig3, Id4, Recql, Piwil2). These genes had previously only been described in spermatogenesis. The microarray also detected an abundance of vesicle-related genes of which four were upregulated (Syngr2, Stxbp1, Ric-8, SytIX) and one (Myo1c) was downregulated in E13.5 ovaries. Detailed analysis showed that the temporal expression of SytIX also coincided with the first meiotic wave in the pubertal testis. This is the first time that SytIX has been reported in non-neuronal tissue. Finally, we examined the expression of one of the uncharacterized genes and found it to be gonad-specific in adulthood. We named this novel transcript "Gonad-expressed transcript 1" (Get-1). In situ hybridization showed that Get-1 was expressed in meiotic germ cells in both fetal ovaries and mature testis. Get-1 is therefore a novel gene in both male and female meiosis.
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Affiliation(s)
- C Olesen
- Laboratory of Reproductive Biology, Center for Children, Women and Reproduction, Copenhagen University Hospital, Copenhagen, Denmark.
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26
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Xu Z, Huang G, Kandror KV. Phosphatidylinositol 4-kinase type IIalpha is targeted specifically to cellugyrin-positive glucose transporter 4 vesicles. Mol Endocrinol 2006; 20:2890-7. [PMID: 16772528 DOI: 10.1210/me.2006-0193] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Phosphoinositides now emerge as important regulators of membrane traffic. In particular, phosphatidylinositol 4-phosphate may serve as a precursor for polyphosphorylated derivatives of phosphatidylinositol and, also, may regulate vesicular traffic by recruiting specific proteins to the membrane. Early results have demonstrated the presence of phosphatidylinositol 4-kinase (PI4K) activity in glucose transporter 4 (Glut4) vesicles from fat and skeletal muscle cells. However, the molecular identity of phosphatidylinositol 4-kinase(s) associated with Glut4 vesicles has not been characterized. It has also been determined that Glut4 vesicles are not homogeneous and represent a mixture of at least two vesicular populations: ubiquitous cellugyrin-positive transport vesicles and specialized cellugyrin-negative insulin-responsive Glut4 storage vesicles, which are different in size, protein composition, and functional properties. Using sequential immunoadsorption, subcellular fractionation, and immunofluorescence staining, we show that virtually all PI4K activity in Glut4 vesicles is represented by PI4K type IIalpha, which is associated with cellugyrin-positive vesicles and is not detectable in the Glut4 storage vesicles. The unique N terminus of PI4K type IIalpha is required for the targeting of the enzyme to cellugyrin-positive vesicles. Knockdown of PI4K type IIalpha with the help of short hairpin RNA does not decrease the amount of cellugyrin-positive vesicles in human embryonic kidney 293 cells.
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Affiliation(s)
- Zhao Xu
- Boston University School of Medicine, Department of Biochemistry, K124D, 715 Albany Street, Boston, Massachusetts 02118, USA
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Rosen J, He M, Umbricht C, Alexander HR, Dackiw APB, Zeiger MA, Libutti SK. A six-gene model for differentiating benign from malignant thyroid tumors on the basis of gene expression. Surgery 2006; 138:1050-6; discussion 1056-7. [PMID: 16360390 DOI: 10.1016/j.surg.2005.09.010] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2005] [Revised: 09/08/2005] [Accepted: 09/10/2005] [Indexed: 10/25/2022]
Abstract
BACKGROUND Thyroid nodules are common; fine-needle aspirations commonly are read as indeterminate, necessitating surgery to exclude carcinoma. We developed a 6-gene array-based predictor model to diagnose benign versus malignant thyroid lesions. In this study, we verified whether quantitative reverse transcription-polymerase chain reaction (qRT-PCR) using this model reliably can differentiate benign from malignant thyroid nodules. METHODS Molecular profiles of benign (follicular adenomas, hyperplastic nodules) and malignant tumors (papillary thyroid carcinomas, follicular variants of papillary thyroid carcinomas) were analyzed using qRT-PCR from our 6-gene model (kit, Hs.296031, Hs.24183, LSM7, SYNGR2, C21orf4). The gold standard was standard pathologic criteria. A diagnosis-predictor model was built by using the training samples and was then used to predict the class of 10 additional samples analyzed as unknowns. RESULTS Our predictor model using 47 training samples correctly predicted 9/10 unknowns. One sample diagnosed as benign by standard histologic criteria was diagnosed as malignant by our model (sensitivity 75%; specificity, 100%; positive predictive value, 100%; negative predictive value, 85.7%). CONCLUSIONS Molecular diagnosis with our 6-gene model can differentiate between benign and malignant thyroid tumors with high sensitivity and specificity. In combination, these genetic markers may be a reliable test to preoperatively diagnose the malignant potential of thyroid nodules.
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MESH Headings
- Adenoma/classification
- Adenoma/diagnosis
- Adenoma/genetics
- Carcinoma, Papillary/classification
- Carcinoma, Papillary/diagnosis
- Carcinoma, Papillary/genetics
- Carcinoma, Papillary, Follicular/classification
- Carcinoma, Papillary, Follicular/diagnosis
- Carcinoma, Papillary, Follicular/genetics
- Diagnosis, Differential
- Humans
- Hyperplasia/classification
- Hyperplasia/diagnosis
- Hyperplasia/genetics
- Models, Genetic
- Predictive Value of Tests
- Reproducibility of Results
- Reverse Transcriptase Polymerase Chain Reaction
- Thyroid Gland/pathology
- Thyroid Neoplasms/classification
- Thyroid Neoplasms/diagnosis
- Thyroid Neoplasms/genetics
- Thyroid Nodule/classification
- Thyroid Nodule/diagnosis
- Thyroid Nodule/genetics
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Affiliation(s)
- Jennifer Rosen
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institute of Health, Bethesda, MD 20892, USA
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28
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Verma R, Kubendran S, Das SK, Jain S, Brahmachari SK. SYNGR1 is associated with schizophrenia and bipolar disorder in southern India. J Hum Genet 2005; 50:635-40. [PMID: 16215643 DOI: 10.1007/s10038-005-0307-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2005] [Accepted: 08/23/2005] [Indexed: 11/26/2022]
Abstract
Chromosome 22q11-13 is one of the most consistent linkage regions for schizophrenia (SCZ) and bipolar disorder (BPAD). The SYNGR1 gene, which is associated with presynaptic vesicles in neuronal cells, is located on 22q13.1. We have previously identified a novel nonsense mutation in the SYNGR1 gene in a SCZ pedigree. In the present study, a detailed analysis of this gene was performed in a case-control cohort (198 BPAD, 193 SCZ and 107 controls from southern India) to test for association with SCZ and BPAD. Sequence analysis of all exonic and flanking intronic regions of the SYNGR1 gene in 198 BPAD and 193 SCZ cases revealed a novel mutation Lsy99Glu (in one BPAD patient) and two other novel common polymorphisms [synonymous single nucleotide polymorphism (SNP--Ser97Ser) and an Asn ins/del] in the SYNGR1 gene. We also validated 9 out of 14 dbSNPs in our population. Case-control analysis revealed allelic (P = 0.028-0.00007) association of five polymorphisms with SCZ and/or BPAD cases. Further, 3-SNP (with LD block 1 SNPs) and 2-SNP (with LD block 2 SNPs) haplotype analyses did not show any association with either SCZ or BPAD. Our results support SYNGR1 as a probable susceptibility gene for SCZ and BPAD. Also, the observed association of SYNGR1 with both SCZ and BPAD suggests the likely involvement of a common pathway in the etiology of these disorders.
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Affiliation(s)
- Ranjana Verma
- Functional Genomics Unit, Institute of Genomics and Integrative Biology (CSIR), Delhi University Campus, Mall Road, Delhi, 110007, India
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29
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Ferguson DA, Chiang JTA, Richardson JA, Graff J. eXPRESSION: an in silico tool to predict patterns of gene expression. Gene Expr Patterns 2005; 5:619-28. [PMID: 15939374 DOI: 10.1016/j.modgep.2005.03.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2004] [Revised: 01/17/2005] [Accepted: 03/09/2005] [Indexed: 11/22/2022]
Abstract
In embryological studies, expression pattern analyses are of special importance since genes that have temporally and spatially restricted expression are not only essential as lineage markers but are often causative in formation of specific fates. Further, where a molecule is expressed can be quite revealing in regard to its endogenous function. We present a gene discovery tool, termed eXPRESSION, that utilizes the public EST databases to identify genes matching desired transcriptional profiles. We first tested and validated the ability of eXPRESSION to discover tissue-specific genes in the adult mouse; empirically as well as with DNA microarrays and RT-PCRs. These studies showed that eXPRESSION predictions could identify genes that are specifically expressed in adult mouse tissues. Next, we developed a novel search strategy to find genes that are expressed in specific regions or tissues of the developing mouse embryo. With these tools, we identified several novel genes that exhibited a neural-specific or neural-enriched expression pattern during murine development. The data show that eXPRESSION is widely applicable and may be used to identify both adult and embryonic tissue- or organ-specific genes with minimal cost and effort.
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Affiliation(s)
- Deborah A Ferguson
- Center for Developmental Biology, UT Southwestern Medical Center, Dallas, TX 75390-9133, USA
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30
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Pinto D, Westland B, de Haan GJ, Rudolf G, da Silva BM, Hirsch E, Lindhout D, Trenité DGAKN, Koeleman BPC. Genome-wide linkage scan of epilepsy-related photoparoxysmal electroencephalographic response: evidence for linkage on chromosomes 7q32 and 16p13. Hum Mol Genet 2004; 14:171-8. [PMID: 15548544 DOI: 10.1093/hmg/ddi018] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Photoparoxysmal response (PPR) is an abnormal visual sensitivity of the brain in reaction to intermittent photic stimulation. It is an epilepsy-related electroencephalographic trait with high prevalence in idiopathic epilepsies, especially in common idiopathic generalized epilepsies (IGEs), such as childhood absence epilepsy and juvenile myoclonic epilepsy. This degree of co-morbidity suggests that PPR may be involved in the predisposition to IGE. The identification of genes for PPR would, therefore, aid the dissection of the genetic basis of IGE. Sixteen PPR-multiplex families were collected to conduct a genome-wide linkage scan using broad (all PPR types) and narrow (exclusion of PPR types I and II and the occipital epilepsy cases) models of affectedness for PPR. We found an empirical genome-wide significance for parametric (HLOD) and non-parametric (NPL) linkage (Pgw(HLOD)=0.004 and Pgw(NPL)=0.01) for two respective chromosomal regions, 7q32 at D7S1804 (HLOD=3.47 with alpha=1, P(NPL)=3.39x10(-5)) and 16p13 at D16S3395 (HLOD=2.44 with alpha=1, P(NPL)=7.91x10(-5)). These two genomic regions contain genes that are important for the neuromodulation of cortical dynamics and may represent good targets for candidate-gene studies. Our study identified two susceptibility loci for PPR, which may be related to the underlying myoclonic epilepsy phenotype present in the families studied.
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Affiliation(s)
- Dalila Pinto
- Complex Genetics Section, DBG-Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
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31
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Zhang J, Moseley A, Jegga AG, Gupta A, Witte DP, Sartor M, Medvedovic M, Williams SS, Ley-Ebert C, Coolen LM, Egnaczyk G, Genter MB, Lehman M, Lingrel J, Maggio J, Parysek L, Walsh R, Xu M, Aronow BJ. Neural system-enriched gene expression: relationship to biological pathways and neurological diseases. Physiol Genomics 2004; 18:167-83. [PMID: 15126645 DOI: 10.1152/physiolgenomics.00220.2003] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
To understand the commitment of the genome to nervous system differentiation and function, we sought to compare nervous system gene expression to that of a wide variety of other tissues by gene expression database construction and mining. Gene expression profiles of 10 different adult nervous tissues were compared with that of 72 other tissues. Using ANOVA, we identified 1,361 genes whose expression was higher in the nervous system than other organs and, separately, 600 genes whose expression was at least threefold higher in one or more regions of the nervous system compared with their median expression across all organs. Of the 600 genes, 381 overlapped with the 1,361-gene list. Limited in situ gene expression analysis confirmed that identified genes did represent nervous system-enriched gene expression, and we therefore sought to evaluate the validity and significance of these top-ranked nervous system genes using known gene literature and gene ontology categorization criteria. Diverse functional categories were present in the 381 genes, including genes involved in intracellular signaling, cytoskeleton structure and function, enzymes, RNA metabolism and transcription, membrane proteins, as well as cell differentiation, death, proliferation, and division. We searched existing public sites and identified 110 known genes related to mental retardation, neurological disease, and neurodegeneration. Twenty-one of the 381 genes were within the 110-gene list, compared with a random expectation of 5. This suggests that the 381 genes provide a candidate set for further analyses in neurological and psychiatric disease studies and that as a field, we are as yet, far from a large-scale understanding of the genes that are critical for nervous system structure and function. Together, our data indicate the power of profiling an individual biologic system in a multisystem context to gain insight into the genomic basis of its structure and function.
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Affiliation(s)
- Jianhua Zhang
- Department of Cell Biology, University of Cincinnati College of Medicine, Cincinnati 45267, USA.
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32
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Valtorta F, Pennuto M, Bonanomi D, Benfenati F. Synaptophysin: leading actor or walk-on role in synaptic vesicle exocytosis? Bioessays 2004; 26:445-53. [PMID: 15057942 DOI: 10.1002/bies.20012] [Citation(s) in RCA: 252] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Synaptophysin (Syp) was the first synaptic vesicle (SV) protein to be cloned. Since its discovery in 1985, it has been used by us and by many laboratories around the world as an invaluable marker to study the distribution of synapses in the brain and to uncover the basic features of the life cycle of SVs. Although single gene ablation of Syp does not lead to an overt phenotype, a large body of experimental data both in vitro and in vivo indicate that Syp (alone or in association with homologous proteins) is involved in multiple, important aspects of SV exo-endocytosis, including regulation of SNARE assembly into the fusion core complex, formation of the fusion pore initiating neurotransmitter release, activation of SV endocytosis and SV biogenesis. In this article, we summarise the main results of the studies on Syp carried out by our and other laboratories, and explain why we believe that Syp plays a major role in SV trafficking.
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Affiliation(s)
- Flavia Valtorta
- Department of Neuroscience, S. Raffaele Scientific Institute and Vita-Salute University, Milan, Italy.
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Belizaire R, Komanduri C, Wooten K, Chen M, Thaller C, Janz R. Characterization of synaptogyrin 3 as a new synaptic vesicle protein. J Comp Neurol 2004; 470:266-81. [PMID: 14755516 DOI: 10.1002/cne.20008] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Synaptogyrins comprise a family of tyrosine-phosphorylated proteins with two neuronal (synaptogyrins 1 and 3) and one ubiquitous (cellugyrin) isoform. Previous studies have indicated that synaptogyrins are involved in the regulation of neurotransmitter release. Synaptogyrin 1 is a synaptic vesicle protein; cellugyrin, by contrast, is absent from synaptic vesicles. In an effort to further characterize the synaptogyrin family, we studied the distribution of the synaptogyrin 3 protein in the nervous system. Subcellular fractionation and immunoprecipitation of synaptic vesicles from mouse brain showed that synaptogyrin 3 is associated with synaptic vesicles and that synaptogyrins 1 and 3 can reside on the same synaptic vesicle. Immunofluorescent staining of cultured hippocampal neurons confirmed the synaptic localization of synaptogyrin 3. Analysis of the relative distributions of synaptogyrins 1 and 3 in mouse brain revealed a more restricted expression pattern for synaptogyrin 3 compared to the ubiquitous distribution of synaptogyrin 1. Strong synaptogyrin 3 labeling was observed in the mossy fiber region of the hippocampus, substantia nigra pars reticulata, pallidum, and deep cerebellar nuclei. By comparison, the striatum and reticular and ventral posterolateral thalamic nuclei, which all showed synaptogyrin 1 labeling, contained significantly less synaptogyrin 3. Finally, we used in situ hybridization experiments to correlate synaptogyrin 3 mRNA in cell bodies with synaptogyrin 3 protein at synapses. Altogether, our data indicate that neuronal synaptogyrins are differentially expressed protein isoforms that may represent functionally distinct populations of synapses and/or synaptic vesicles.
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Affiliation(s)
- Roger Belizaire
- W.M. Keck Center for Learning and Memory, Department of Neurobiology and Anatomy, University of Texas-Houston Medical School, Houston, Texas, 77030, USA.
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Verma R, Chauhan C, Saleem Q, Gandhi C, Jain S, Brahmachari SK. A nonsense mutation in the synaptogyrin 1 gene in a family with schizophrenia. Biol Psychiatry 2004; 55:196-9. [PMID: 14732601 DOI: 10.1016/j.biopsych.2003.10.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
BACKGROUND Chromosome 22q is one of the important regions repeatedly being implicated in schizophrenia. In this region, our group previously reported an association of a CAG repeat marker (22CH3) with schizophrenia in the Indian population. Because Synaptogyrin 1 (SYNGR1), associated with presynaptic vesicles in neuronal cells, lies within 1 million base pairs of this marker, it is a potential candidate gene for schizophrenia. METHODS We sequenced all six exons and flanking splice junctions of the SYNGR1 gene. We also carried out reverse transcriptase polymerase chain reaction and Northern blot analysis for exon 2 containing transcript of the SYNGR1 gene. RESULTS We found a novel nonsense mutation (Trp27Ter) in exon 2 of the SYNGR1 gene in a family multiply affected with schizophrenia. Reverse transcriptase polymerase chain reaction and Northern blot analyses revealed that exon 2 containing transcript of this gene is expressed in the brain. CONCLUSIONS Because the SYNGR1 gene is involved in presynaptic pathways, reduced levels of this protein might play some role in the pathogenesis of schizophrenia.
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Affiliation(s)
- Ranjana Verma
- Functional Genomics Unit, Institute of Genomics and Integrative Biology, Council of Scientific and Industrial Research, Delhi University Campus, Delhi, India
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35
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Belfort GM, Kandror KV. Cellugyrin and synaptogyrin facilitate targeting of synaptophysin to a ubiquitous synaptic vesicle-sized compartment in PC12 cells. J Biol Chem 2003; 278:47971-8. [PMID: 12928441 DOI: 10.1074/jbc.m304174200] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cellugyrin represents a ubiquitously expressed four-transmembrane domain protein that is closely related to synaptic vesicle protein synaptogyrin and, more remotely, to synaptophysin. We report here that, in PC12 cells, cellugyrin is localized in synaptic-like microvesicles (SLMVs), along with synaptogyrin and synaptophysin. Upon overexpression of synaptophysin in PC12 cells, it is localized in rapidly sedimenting membranes and practically is not delivered to the SLMVs. On the contrary, the efficiency of the SLMV targeting of exogenously expressed cellugyrin and synaptogyrin is high. Moreover, expression of cellugyrin (or synaptogyrin) in PC12 cells dramatically and specifically increases SLMV targeting of endogenous synaptophysin. Finally, we utilized the SLMV purification scheme on a series of non-neuroendocrine cell types including the mouse fibroblast cell line 3T3-L1, the Chinese hamster ovary cell line CHO-K1, and the monkey kidney epithelial cell line COS7 and found that a cellugyrin-positive microvesicular compartment was present in all cell types tested. We suggest that synaptic vesicles have evolved from cellugyrin-positive ubiquitous microvesicles and that neuroendocrine SLMVs represent a step along that pathway of evolution.
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Affiliation(s)
- Gabriel M Belfort
- Boston University School of Medicine, Boston, Massachusetts 02118, USA
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36
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Huminiecki L, Lloyd AT, Wolfe KH. Congruence of tissue expression profiles from Gene Expression Atlas, SAGEmap and TissueInfo databases. BMC Genomics 2003; 4:31. [PMID: 12885301 PMCID: PMC183867 DOI: 10.1186/1471-2164-4-31] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2003] [Accepted: 07/29/2003] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Extracting biological knowledge from large amounts of gene expression information deposited in public databases is a major challenge of the postgenomic era. Additional insights may be derived by data integration and cross-platform comparisons of expression profiles. However, database meta-analysis is complicated by differences in experimental technologies, data post-processing, database formats, and inconsistent gene and sample annotation. RESULTS We have analysed expression profiles from three public databases: Gene Expression Atlas, SAGEmap and TissueInfo. These are repositories of oligonucleotide microarray, Serial Analysis of Gene Expression and Expressed Sequence Tag human gene expression data respectively. We devised a method, Preferential Expression Measure, to identify genes that are significantly over- or under-expressed in any given tissue. We examined intra- and inter-database consistency of Preferential Expression Measures. There was good correlation between replicate experiments of oligonucleotide microarray data, but there was less coherence in expression profiles as measured by Serial Analysis of Gene Expression and Expressed Sequence Tag counts. We investigated inter-database correlations for six tissue categories, for which data were present in the three databases. Significant positive correlations were found for brain, prostate and vascular endothelium but not for ovary, kidney, and pancreas. CONCLUSION We show that data from Gene Expression Atlas, SAGEmap and TissueInfo can be integrated using the UniGene gene index, and that expression profiles correlate relatively well when large numbers of tags are available or when tissue cellular composition is simple. Finally, in the case of brain, we demonstrate that when PEM values show good correlation, predictions of tissue-specific expression based on integrated data are very accurate.
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Affiliation(s)
- Lukasz Huminiecki
- Department of Genetics, Smurfit Institute, University of Dublin Trinity College, Dublin 2, Ireland
| | - Andrew T Lloyd
- Department of Genetics, Smurfit Institute, University of Dublin Trinity College, Dublin 2, Ireland
| | - Kenneth H Wolfe
- Department of Genetics, Smurfit Institute, University of Dublin Trinity College, Dublin 2, Ireland
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Hübner K, Windoffer R, Hutter H, Leube RE. Tetraspan vesicle membrane proteins: synthesis, subcellular localization, and functional properties. INTERNATIONAL REVIEW OF CYTOLOGY 2002; 214:103-59. [PMID: 11893164 DOI: 10.1016/s0074-7696(02)14004-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Tetraspan vesicle membrane proteins (TVPs) are characterized by four transmembrane regions and cytoplasmically located end domains. They are ubiquitous and abundant components of vesicles in most, if not all, cells of multicellular organisms. TVP-containing vesicles shuttle between various membranous compartments and are localized in biosynthetic and endocytotic pathways. Based on gene organization and amino acid sequence similarities TVPs can be grouped into three distinct families that are referred to as physins, gyrins, and secretory carrier-associated membrane proteins (SCAMPs). In mammals synaptophysin, synaptoporin, pantophysin, and mitsugumin29 constitute the physins, synaptogyrin 1-4 the gyrins, and SCAMP1-5 the SCAMPs. Members of each family are cell-type-specifically synthesized resulting in unique patterns of TVP coexpression and subcellular colocalization. TVP orthologs have been identified in most multicellular organisms, including diverse animal and plant species, but have not been detected in unicellular organisms. They are subject to protein modification, most notably to phosphorylation, and are part of multimeric complexes. Experimental evidence is reviewed showing that TVPs contribute to vesicle trafficking and membrane morphogenesis.
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Affiliation(s)
- Kirsten Hübner
- Department of Anatomy, Johannes Gutenberg University, Mainz, Germany
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38
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Mellick AS, Day CJ, Weinstein SR, Griffiths LR, Morrison NA. Differential gene expression in breast cancer cell lines and stroma-tumor differences in microdissected breast cancer biopsies revealed by display array analysis. Int J Cancer 2002; 100:172-80. [PMID: 12115566 DOI: 10.1002/ijc.10451] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
To examine gene-expression patterning in late-stage breast cancer biopsies, we used a microdissection technique to separate tumor from the surrounding breast tissue or stroma. A DD-PCR protocol was then used to amplify expressed products, which were resolved using PAGE and used as probe to hybridize with representative human arrays and cDNA libraries. The probe derived from the tumor-stroma comparison was hybridized with a gene array and an arrayed cDNA library derived from a GCT of bone; 21 known genes or expressed sequence tags were detected, of which 17 showed differential expression. These included factors associated with epithelial to mesenchymal transition (vimentin), the cargo selection protein (TIP47) and the signal transducer and activator of transcription (STAT3). Northern blot analysis was used to confirm those genes also expressed by representative breast cancer cell lines. Notably, 6 genes of unknown function were restricted to tumor while the majority of stroma-associated genes were known. When applied to transformed breast cancer cell lines (MDA-MB-435 and T47D) that are known to have different metastatic potential, DD array analysis revealed a further 20 genes; 17 of these genes showed differential expression. Use of microdissection and the DD-PCR array protocol allowed us to identify factors whose localized expression within the breast may play a role in abnormal breast development or breast carcinogenesis.
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Affiliation(s)
- Albert S Mellick
- Genomics Research Centre, School of Health Science, Gold Coast Campus of Griffith University, Gold Coast, Queensland, Australia
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Kiss H, Yang Y, Kiss C, Andersson K, Klein G, Imreh S, Dumanski JP. The transcriptional map of the common eliminated region 1 (C3CER1) in 3p21.3. Eur J Hum Genet 2002; 10:52-61. [PMID: 11896456 DOI: 10.1038/sj.ejhg.5200758] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2001] [Revised: 11/13/2001] [Accepted: 11/19/2001] [Indexed: 11/09/2022] Open
Abstract
Occurrence of chromosome 3p deletions in a large number of human tumours suggests the existence of uncharted tumour suppressor gene(s). We previously applied a functional assay, named the Elimination test (Et), for the identification of regions containing tumour growth antagonising genes. This resulted in the definition of chromosome 3 common eliminated region 1 (C3CER1) on 3p21.3, which is regularly eliminated from SCID-derived tumours. Systematic genomic sequencing of 11 PAC clones, combined with comparisons of genomic sequence against EST databases and PCR-based cloning of cDNA sequences allowed us to assemble a comprehensive transcriptional map of 1.4 Mb that includes 19 active genes and three processed pseudogenes. We report four novel genes: FYVE and coiled-coil domain containing 1 (FYCO1), transmembrane protein 7 (TMEM7), leucine-rich repeat-containing 2 (LRRC2) and leucine zipper protein 3 (LUZP3). A striking feature of C3CER1 is a presence of a cluster of eight chemokine receptor genes. Based on a new analysis of the microcell hybrid-derived panel of SCID tumours we also redefined the centromeric border of the C3CER1. It is now located within LRRC2 gene, which is a relative of RSP-1 (Ras Suppressor Protein 1). The detailed knowledge of gene content in C3CER1 is a prerequisite for functional analysis of these genes and understanding of their possible role in tumorigenesis.
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Affiliation(s)
- Hajnalka Kiss
- Microbiology and Tumor Biology Center (MTC), Karolinska Institutet, S-17177, Stockholm, Sweden.
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Saleem Q, Dash D, Gandhi C, Kishore A, Benegal V, Sherrin T, Mukherjee O, Jain S, Brahmachari SK. Association of CAG repeat loci on chromosome 22 with schizophrenia and bipolar disorder. Mol Psychiatry 2001; 6:694-700. [PMID: 11673798 DOI: 10.1038/sj.mp.4000924] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2000] [Revised: 03/08/2001] [Accepted: 03/12/2001] [Indexed: 11/09/2022]
Abstract
Chromosome 22 has been implicated in schizophrenia and bipolar disorder in a number of linkage, association and cytogenetic studies. Recent evidence has also implicated CAG repeat tract expansion in these diseases. In order to explore the involvement of CAG repeats on chromosome 22 in these diseases, we have created an integrated map of all CAG repeats > or =5 on this chromosome together with microsatellite markers associated with these diseases using the recently completed nucleotide sequence of chromosome 22. Of the 52 CAG repeat loci identified in this manner, four of the longest repeat stretches in regions previously implicated by linkage analyses were chosen for further study. Three of the four repeat containing loci, were found in the coding region with the CAG repeats coding for glutamine and were expressed in the brain. All the loci studied showed varying degrees of polymorphism with one of the loci exhibiting two alleles of 7 and 8 CAG repeats. The 8-repeat allele at this locus was significantly overrepresented in both schizophrenia and bipolar patient groups when compared to ethnically matched controls, while alleles at the other three loci did not show any such difference. The repeat lies within a gene which shows homology to an androgen receptor related apoptosis protein in rat. We have also identified other candidate genes in the vicinity of this locus. Our results suggest that the repeats within this gene or other genes in the vicinity of this locus are likely to be implicated in bipolar disorder and schizophrenia.
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Affiliation(s)
- Q Saleem
- Functional Genomics Unit, Centre for Biochemical Technology (CSIR), Mall Rd, Delhi University Campus, Delhi 110 007, India
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Seroussi E, Shani N, Ben-Meir D, Chajut A, Divinski I, Faier S, Gery S, Karby S, Kariv-Inbal Z, Sella O, Smorodinsky NI, Lavi S. Uniquely conserved non-translated regions are involved in generation of the two major transcripts of protein phosphatase 2Cbeta. J Mol Biol 2001; 312:439-51. [PMID: 11563908 DOI: 10.1006/jmbi.2001.4967] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Partial cDNAs of different isoforms of protein phosphatase 2Cbeta (PP2Cbeta or PPM1B) have been characterized in mammals. We disclose here the full cDNAs of two major PP2Cbeta isoforms from human, rat and mouse. These cDNAs (2.6 and 3.3 kb) are able to encode 53 kDa (PP2Cbetal) and 43 kDa (PP2Cbetas) polypeptides, respectively. The isoforms are co-expressed ubiquitously with the highest level in skeletal muscle, as assessed by Northern-blot analysis. Western and in situ analyses using monoclonal antibodies against PP2Cbeta confirmed the existence of two isoforms in the cytoplasm. Comparative sequence analysis revealed that both cDNAs consist of six exons with an alternate usage of the 3' exons that underlies the differences between them. The genomic structure of PP2Cbeta is similar to that of other PP2C paralogs and includes a non-coding first exon followed by a large intron and a large second exon that encoded most of the catalytic domain. Both variants of the ending exon include large non-coding regions. All non-translated regions (NTRs) are highly conserved between the orthologous genes, indicating their regulatory function. The 5'-NTR is long (379 bp), includes upstream start codons and is predicted to contain stable secondary structures. Such features inhibit translation initiation by the scanning mechanism. Introduction of this NTR element into a bi-luciferase expression-cassette enabled expression of the second cistron, suggesting that it might serve as an internal ribosome entry site, or it contains a cryptic promoter. Overexpression of PP2Cbeta under CMV-promoter in 293 cells led to cell-growth arrest or cell death.
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Affiliation(s)
- E Seroussi
- Institute of Animal Science, Volcani Center, Bet-Dagan, 50250, Israel
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Kiss H, Kedra D, Kiss C, Kost-Alimova M, Yang Y, Klein G, Imreh S, Dumanski JP. The LZTFL1 gene is a part of a transcriptional map covering 250 kb within the common eliminated region 1 (C3CER1) in 3p21.3. Genomics 2001; 73:10-9. [PMID: 11352561 DOI: 10.1006/geno.2000.6498] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Deletions on 3p have been described in a large number of human tumors, suggesting the presence of a tumor suppressor gene(s). Using the elimination test, we previously defined a 1-Mb segment from human 3p21.3 (C3CER1). Genomic sequencing allowed us to construct a transcription map covering 250 kb containing five genes. We have characterized a human leucine zipper containing gene, leucine zipper transcription factor-like 1 (LZTFL1), and its mouse orthologue (Lztfl1), which was also mapped to mouse chromosome 9F. The LZTFL1 gene has two transcript isoforms displaying alternative polyadenylation. We have localized the human orthologue of the yeast SAC1 (suppressor of actin) gene as well as characterized and mapped the mouse Sac1 gene. Furthermore, the XT3 gene was characterized, encoding a member of the Na(+)/Cl(-) neurotransmitter superfamily. It has been shown that the XT3 gene had an alternatively spliced brain-specific isoform, predicted to remove 1 of 12 putative transmembrane domains. The transcription map also includes the CC chemokine receptor 9 gene (CCR9) and the LIM domain containing gene 1 (LIMD1). This work partially defines the gene content of C3CER1 that is a prerequisite for delineation of its role in tumorigenesis.
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Affiliation(s)
- H Kiss
- Microbiology and Tumor Biology Center (MTC), Karolinska Institute, Stockholm, S-17177, Sweden.
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Abstract
We have studied the localization of synaptogyrin family members in vivo. Both native and green fluorescent protein (GFP)-tagged Caenorhabditis elegans synaptogyrin (SNG-1) are expressed in neurons and synaptically localized. Deletion and mutational analysis with the use of GFP-tagged SNG-1 has defined a 38 amino acid sequence within the C terminus of SNG-1 and a single arginine in the cytoplasmic loop between transmembrane domain 2 and 3 that are required for SNG-1 localization. These domains may represent components of signals that target synaptogyrin for endocytosis from the plasma membrane and direct synaptogyrin to synaptic vesicles, respectively. In chimeric studies, these regions were sufficient to relocalize cellugyrin, a nonneuronal form of synaptogyrin, from nonsynaptic regions such as the sensory dendrites and the cell body to synaptic vesicles. Furthermore, GFP-tagged rat synaptogyrin is synaptically localized in neurons of C. elegans and in cultured hippocampal neurons. Similarly, the C-terminal domain of rat synaptogyrin is necessary for localization in hippocampal neurons. Our study suggests that the mechanisms for synaptogyrin localization are likely to be conserved from C. elegans to vertebrates.
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Affiliation(s)
- H Zhao
- Department of Anatomy and Neurobiology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
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44
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Kupriyanova TA, Kandror KV. Cellugyrin is a marker for a distinct population of intracellular Glut4-containing vesicles. J Biol Chem 2000; 275:36263-8. [PMID: 10967091 DOI: 10.1074/jbc.m002797200] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Although Glut4 traffic is routinely described as translocation from an "intracellular storage pool" to the plasma membrane, it has been long realized that Glut4 travels through at least two functionally distinct intracellular membrane compartments on the way to and from the cell surface. Biochemical separation and systematic studies of the individual Glut4-containing compartments have been limited by the lack of appropriate reagents. We have prepared a monoclonal antibody against a novel component protein of Glut4 vesicles and have identified this protein as cellugyrin, a ubiquitously expressed homologue of a major synaptic vesicle protein, synaptogyrin. By means of sucrose gradient centrifugation, immunoadsorption, and confocal microscopy, we have shown that virtually all cellugyrin is co-localized with Glut4 in the same vesicles. However, unlike Glut4, cellugyrin is not re-distributed to the plasma membrane in response to insulin stimulation, and at least 40-50% of the total population of Glut4 vesicles do not contain this protein. We suggest that cellugyrin represents a specific marker of a functionally distinct population of Glut4 vesicles that permanently maintains its intracellular localization and is not recruited to the plasma membrane by insulin.
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Affiliation(s)
- T A Kupriyanova
- Boston University School of Medicine, Boston, Massachusetts 02118, USA
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45
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Zara F, Gennaro E, Stabile M, Carbone I, Malacarne M, Majello L, Santangelo R, de Falco FA, Bricarelli FD. Mapping of a locus for a familial autosomal recessive idiopathic myoclonic epilepsy of infancy to chromosome 16p13. Am J Hum Genet 2000; 66:1552-7. [PMID: 10741954 PMCID: PMC1378007 DOI: 10.1086/302876] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2000] [Accepted: 02/28/2000] [Indexed: 11/03/2022] Open
Abstract
Myoclonic epilepsies with onset in infancy and childhood are clinically and etiologically heterogeneous. Although genetic factors are thought to play an important role, to date very little is known about the etiology of these disorders. We ascertained a large Italian pedigree segregating a recessive idiopathic myoclonic epilepsy that starts in early infancy as myoclonic seizures, febrile convulsions, and tonic-clonic seizures. We typed 304 microsatellite markers spanning the 22 autosomes and mapped the locus on chromosome 16p13 by linkage analysis. A maximum LOD score of 4.48 was obtained for marker D16S3027 at recombination fraction 0. Haplotype analysis placed the critical region within a 3.4-cM interval between D16S3024 and D16S423. The present report constitutes the first example of an idiopathic epilepsy that is inherited as an autosomal recessive trait.
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Affiliation(s)
- F Zara
- Laboratorio di Genetica Umana, E.O. Ospedali Galliera, 16128 Genoa, Italy.
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46
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Janz R, Südhof TC, Hammer RE, Unni V, Siegelbaum SA, Bolshakov VY. Essential roles in synaptic plasticity for synaptogyrin I and synaptophysin I. Neuron 1999; 24:687-700. [PMID: 10595519 DOI: 10.1016/s0896-6273(00)81122-8] [Citation(s) in RCA: 250] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
We have generated mice lacking synaptogyrin I and synaptophysin I to explore the functions of these abundant tyrosine-phosphorylated proteins of synaptic vesicles. Single and double knockout mice were alive and fertile without significant morphological or biochemical changes. Electrophysiological recordings in the hippocampal CA1 region revealed that short-term and long-term synaptic plasticity were severely reduced in the synaptophysin/synaptogyrin double knockout mice. LTP was decreased independent of the induction protocol, suggesting that the defect in LTP was not caused by insufficient induction. Our data show that synaptogyrin I and synaptophysin I perform redundant and essential functions in synaptic plasticity without being required for neurotransmitter release itself.
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Affiliation(s)
- R Janz
- Howard Hughes Medical Institute, The University of Texas Southwestern Medical School, Dallas 75235, USA
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47
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Zimmer Y, Milo-Landesman D, Svetlanov A, Efrat S. Genes induced by growth arrest in a pancreatic beta cell line: identification by analysis of cDNA arrays. FEBS Lett 1999; 457:65-70. [PMID: 10486565 DOI: 10.1016/s0014-5793(99)01008-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Pancreatic beta cell lines are a potentially attractive source of material for cell therapy of insulin-dependent diabetes mellitus. However, induction of proliferation in post-mitotic, differentiated beta cells is likely to affect the expression of multiple genes associated with cell function, resulting in dedifferentiation. We have developed a murine beta cell line by conditional transformation with the SV40 T antigen oncoprotein. These cells can undergo reversible induction of proliferation and growth arrest. Here we utilized this model to identify differences in gene expression between proliferating and quiescent beta cells, by analyzing known beta cell genes and differentially secreted proteins, as well as by a systematic survey of a mouse cDNA array. Our findings demonstrate that growth arrest stimulates expression of the insulin gene and genes encoding components of the insulin secretory vesicles. Screening of the cDNA array revealed the activation of multiple genes following growth arrest, many of them novel genes which may be related to beta cell function. Characterization of these genes is likely to contribute to our understanding of beta cell function and the ability to employ beta cell lines in cell therapy of diabetes.
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Affiliation(s)
- Y Zimmer
- Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Ramat Aviv, Israel
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48
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Sugita S, Janz R, Südhof TC. Synaptogyrins regulate Ca2+-dependent exocytosis in PC12 cells. J Biol Chem 1999; 274:18893-901. [PMID: 10383386 DOI: 10.1074/jbc.274.27.18893] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Synaptogyrins constitute a family of synaptic vesicle proteins of unknown function. With the full-length structure of a new brain synaptogyrin isoform, we now show that the synaptogyrin family in vertebrates includes two neuronal and one ubiquitous isoform. All of these synaptogyrins are composed of a short conserved N-terminal cytoplasmic sequence, four homologous transmembrane regions, and a variable cytoplasmic C-terminal tail that is tyrosine-phosphorylated. The localization, abundance, and conservation of synaptogyrins suggest a function in exocytosis. To test this, we employed a secretion assay in PC12 cells expressing transfected human growth hormone (hGH) as a reporter protein. When Ca2+-dependent hGH secretion from PC12 cells was triggered by high K+ or alpha-latrotoxin, co-transfection of all synaptogyrins with hGH inhibited hGH exocytosis as strongly as co-transfection of tetanus toxin light chain. Synaptophysin I, which is distantly related to synaptogyrins, was also inhibitory but less active. Inhibition was independent of the amount of hGH expressed but correlated with the amount of synaptogyrin transfected. Inhibition of exocytosis was not observed with several other synaptic proteins, suggesting specificity. Analysis of the regions of synaptogyrin required for inhibition revealed that the conserved N-terminal domain of synaptogyrin is essential for inhibition, whereas the long C-terminal cytoplasmic tail is largely dispensable. Our results suggest that synaptogyrins are conserved components of the exocytotic apparatus, which function as regulators of Ca2+-dependent exocytosis.
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Affiliation(s)
- S Sugita
- Center for Basic Neuroscience, Department of Molecular Genetics and Howard Hughes Medical Institute, The University of Texas Southwestern Medical Center, Dallas, Texas 75235-9050, USA
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49
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Peyrard M, Seroussi E, Sandberg-Nordqvist AC, Xie YG, Han FY, Fransson I, Collins J, Dunham I, Kost-Alimova M, Imreh S, Dumanski JP. The human LARGE gene from 22q12.3-q13.1 is a new, distinct member of the glycosyltransferase gene family. Proc Natl Acad Sci U S A 1999; 96:598-603. [PMID: 9892679 PMCID: PMC15182 DOI: 10.1073/pnas.96.2.598] [Citation(s) in RCA: 103] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/1998] [Accepted: 11/20/1998] [Indexed: 11/18/2022] Open
Abstract
Meningioma, a tumor of the meninges covering the central nervous system, shows frequent loss of material from human chromosome 22. Homozygous and heterozygous deletions in meningiomas defined a candidate region of >1 Mbp in 22q12.3-q13.1 and directed us to gene cloning in this segment. We characterized a new member of the N-acetylglucosaminyltransferase gene family, the LARGE gene. It occupies >664 kilobases and is one of the largest human genes. The predicted 756-aa N-acetylglucosaminyltransferase encoded by LARGE displays features that are absent in other glycosyltransferases. The human like-acetylglucosaminyltransferase polypeptide is much longer and contains putative coiled-coil domains. We characterized the mouse LARGE ortholog, which encodes a protein 97.75% identical with the human counterpart. Both genes reveal ubiquitous expression as assessed by Northern blot analysis and in situ histochemistry. Chromosomal mapping of the mouse gene reveals that mouse chromosome 8C1 corresponds to human 22q12.3-q13.1. Abnormal glycosylation of proteins and glycosphingolipids has been shown as a mechanism behind an increased potential of tumor formation and/or progression. Human tumors overexpress ganglioside GD3 (NeuAcalpha2,8NeuAcalpha2, 3Galbeta1,4Glc-Cer), which in meningiomas correlates with deletions on chromosome 22. It is the first time that a glycosyltransferase gene is involved in tumor-specific genomic rearrangements. An abnormal function of the human like-acetylglucosaminyltransferase protein may be linked to the development/progression of meningioma by altering the composition of gangliosides and/or by effect(s) on other glycosylated molecules in tumor cells.
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Affiliation(s)
- M Peyrard
- Department of Molecular Medicine, Karolinska Hospital, S-171 76 Stockholm, Sweden
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