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Gabbert C, Klein C, Trinh J. How Do I Report Genes in a Paper? Mov Disord Clin Pract 2024; 11:594-597. [PMID: 38469948 PMCID: PMC11078486 DOI: 10.1002/mdc3.13984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 01/15/2024] [Indexed: 03/13/2024] Open
Abstract
Genetic testing, including whole genome, whole exome, and other next-generation sequencing technologies, has evolved vastly in the past decade. With this, the number of identified genes and genetic variants is constantly increasing. Although a variety of databases and online tools exist that summarize, categorize, and classify genes, a clear guideline of which information is needed when reporting a gene and what to do when identifying a new gene is lacking. This includes the correct nomenclature, descriptive information about genetic loci and genetic variation, aliases, and correlated phenotypes. This tutorial is meant to serve as an introduction to reporting genes in a paper and provides an overview of available databases and tools to obtain all necessary information on the genes of interest.
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Affiliation(s)
- Carolin Gabbert
- Institute of Neurogenetics, University of LübeckLübeckGermany
| | - Christine Klein
- Institute of Neurogenetics, University of LübeckLübeckGermany
| | - Joanne Trinh
- Institute of Neurogenetics, University of LübeckLübeckGermany
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Cancers in Agreement? Exploring the Cross-Talk of Cancer Metabolomic and Transcriptomic Landscapes Using Publicly Available Data. Cancers (Basel) 2021; 13:cancers13030393. [PMID: 33494351 PMCID: PMC7865504 DOI: 10.3390/cancers13030393] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 01/12/2021] [Accepted: 01/19/2021] [Indexed: 12/13/2022] Open
Abstract
Simple Summary Changes in metabolism are a well-known characteristic of cancer cells. Different cancer types are unique in their genetic aspects, but also in their metabolism, which is in turn, governed by genetics. The aim of our study was to find these differences in metabolic behavior across different cancer types and uncovering intersections between gene expression and metabolic deregulations. We scoured the public domain for metabolomics and transcriptomics data from clinical profiling studies to perform a comprehensive comparison study. By combining evidence from both the genetic and the metabolic aspects, we described the most prominently aberrated pathways across eight different cancer types together with their metabolomic and transcriptomics similarities. Abstract One of the major hallmarks of cancer is the derailment of a cell’s metabolism. The multifaceted nature of cancer and different cancer types is transduced by both its transcriptomic and metabolomic landscapes. In this study, we re-purposed the publicly available transcriptomic and metabolomics data of eight cancer types (breast, lung, gastric, renal, liver, colorectal, prostate, and multiple myeloma) to find and investigate differences and commonalities on a pathway level among different cancer types. Topological analysis of inferred graphical Gaussian association networks showed that cancer was strongly defined in genetic networks, but not in metabolic networks. Using different statistical approaches to find significant differences between cancer and control cases, we highlighted the difficulties of high-level data-merging and in using statistical association networks. Cancer transcriptomics and metabolomics and landscapes were characterized by changed macro-molecule production, however, only major metabolic deregulations with highly impacted pathways were found in liver cancer. Cell cycle was enriched in breast, liver, and colorectal cancer, while breast and lung cancer were distinguished by highly enriched oncogene signaling pathways. A strong inflammatory response was observed in lung cancer and, to some extent, renal cancer. This study highlights the necessity of combining different omics levels to obtain a better description of cancer characteristics.
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Ren W, Li Z, Han F, Zhang B, Li X, Fang Z, Yang L, Zhuang M, Lv H, Liu Y, Wang Y, Yu H, Zhang Y. Utilization of Ogura CMS germplasm with the clubroot resistance gene by fertility restoration and cytoplasm replacement in Brassica oleracea L. HORTICULTURE RESEARCH 2020; 7:61. [PMID: 32377352 PMCID: PMC7193625 DOI: 10.1038/s41438-020-0282-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 01/25/2020] [Accepted: 02/24/2020] [Indexed: 06/11/2023]
Abstract
Clubroot disease, a major plant root disease caused by Plasmodiophora brassicae, has become one of the most destructive diseases among cultivated cruciferous vegetables. However, clubroot-resistant Brassica oleracea materials are rare. A few clubroot-resistant cabbage varieties are available on the market, but all are Ogura cytoplasmic male sterile (CMS) types. Therefore, in this study, to reutilize the clubroot-resistant Ogura CMS germplasm of cabbage, a new fertility-restored Ogura CMS material, 16Q2-11, was used as a bridge to transfer the clubroot resistance (CR) gene from the Ogura CMS cytoplasm to the normal cytoplasm by a two-step method (a fertility restoration and cytoplasm replacement method). In the first cross for fertility restoration of Ogura CMS clubroot-resistant cabbage (FRCRC), 16Q2-11 was used as a restorer to cross with Ogura CMS materials containing the CR gene CRb2. Eleven Rfo-positive progenies were generated, of which four contained CRb2: F8-514, F8-620, F8-732 and F8-839. After inoculation with race 4 of P. brassicae, these four CRb2-positive individuals showed resistance. Furthermore, F8-514 and F8-839 were then used as male parents in the second cross of FRCRC to cross with cabbage inbred lines, resulting in the successful introgression of the CRb2 gene into the inbred lines. All offspring produced from this step of cross, which had a normal cytoplasm, showed a high resistance to race 4 of P. brassicae and could be utilized for the breeding of clubroot-resistant cabbage varieties in the future. This is the first time that the Ogura CMS restorer has been used to restore the fertility of Ogura CMS clubroot-resistant cabbages, which could improve germplasm diversity in cabbage and provide a reference method for using CMS germplasm in Brassica crops.
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Affiliation(s)
- Wenjing Ren
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, #12 Zhong Guan Cun Nandajie Street, Beijing, 100081 China
| | - Zhiyuan Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, #12 Zhong Guan Cun Nandajie Street, Beijing, 100081 China
| | - Fengqing Han
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, #12 Zhong Guan Cun Nandajie Street, Beijing, 100081 China
| | - Bin Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, #12 Zhong Guan Cun Nandajie Street, Beijing, 100081 China
| | - Xing Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, #12 Zhong Guan Cun Nandajie Street, Beijing, 100081 China
| | - Zhiyuan Fang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, #12 Zhong Guan Cun Nandajie Street, Beijing, 100081 China
| | - Limei Yang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, #12 Zhong Guan Cun Nandajie Street, Beijing, 100081 China
| | - Mu Zhuang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, #12 Zhong Guan Cun Nandajie Street, Beijing, 100081 China
| | - Honghao Lv
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, #12 Zhong Guan Cun Nandajie Street, Beijing, 100081 China
| | - Yumei Liu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, #12 Zhong Guan Cun Nandajie Street, Beijing, 100081 China
| | - Yong Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, #12 Zhong Guan Cun Nandajie Street, Beijing, 100081 China
| | - Hailong Yu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, #12 Zhong Guan Cun Nandajie Street, Beijing, 100081 China
| | - Yangyong Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, #12 Zhong Guan Cun Nandajie Street, Beijing, 100081 China
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Park S, Moon S, Lee K, Park IB, Lee DH, Nam S. miR2Diabetes: A Literature-Curated Database of microRNA Expression Patterns, in Diabetic Microvascular Complications. Genes (Basel) 2019; 10:genes10100784. [PMID: 31601051 PMCID: PMC6826485 DOI: 10.3390/genes10100784] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 10/02/2019] [Accepted: 10/03/2019] [Indexed: 12/27/2022] Open
Abstract
microRNAs (miRNAs) have been established as critical regulators of the pathogenesis of diabetes mellitus (DM), and diabetes microvascular complications (DMCs). However, manually curated databases for miRNAs, and DM (including DMCs) association studies, have yet to be established. Here, we constructed a user-friendly database, “miR2Diabetes,” equipped with a graphical web interface for simple browsing or searching manually curated annotations. The annotations in our database cover 14 DM and DMC phenotypes, involving 156 miRNAs, by browsing diverse sample origins (e.g., blood, kidney, liver, and other tissues). Additionally, we provide miRNA annotations for disease-model organisms (including rats and mice), of DM and DMCs, for the purpose of improving knowledge of the biological complexity of these pathologies. We assert that our database will be a comprehensive resource for miRNA biomarker studies, as well as for prioritizing miRNAs for functional validation, in DM and DMCs, with likely extension to other diseases.
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Affiliation(s)
- Sungjin Park
- College of Medicine, Gachon University, Incheon 21565, Korea.
- Gachon Institute of Genome Medicine and Science, Gachon University Gil Medical Center, Incheon 21565, Korea.
| | - SeongRyeol Moon
- Department of Health Sciences and Technology, Gachon Advanced Institute for Health Sciences and Technology, Gachon University, Incheon 21565, Korea.
| | - Kiyoung Lee
- Department of Internal Medicine, Gachon University Gil Medical Center, Incheon 21565, Korea.
- Department of Internal Medicine, Gachon University School of Medicine, Incheon 21565, Korea.
| | - Ie Byung Park
- Department of Internal Medicine, Gachon University Gil Medical Center, Incheon 21565, Korea.
- Department of Internal Medicine, Gachon University School of Medicine, Incheon 21565, Korea.
| | - Dae Ho Lee
- Department of Internal Medicine, Gachon University Gil Medical Center, Incheon 21565, Korea.
- Department of Internal Medicine, Gachon University School of Medicine, Incheon 21565, Korea.
| | - Seungyoon Nam
- College of Medicine, Gachon University, Incheon 21565, Korea.
- Gachon Institute of Genome Medicine and Science, Gachon University Gil Medical Center, Incheon 21565, Korea.
- Department of Health Sciences and Technology, Gachon Advanced Institute for Health Sciences and Technology, Gachon University, Incheon 21565, Korea.
- Department of Life Sciences, Gachon University, Seongnam 13120, Korea.
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Brodehl A, Ebbinghaus H, Deutsch MA, Gummert J, Gärtner A, Ratnavadivel S, Milting H. Human Induced Pluripotent Stem-Cell-Derived Cardiomyocytes as Models for Genetic Cardiomyopathies. Int J Mol Sci 2019; 20:ijms20184381. [PMID: 31489928 PMCID: PMC6770343 DOI: 10.3390/ijms20184381] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 08/29/2019] [Accepted: 09/03/2019] [Indexed: 12/17/2022] Open
Abstract
In the last few decades, many pathogenic or likely pathogenic genetic mutations in over hundred different genes have been described for non-ischemic, genetic cardiomyopathies. However, the functional knowledge about most of these mutations is still limited because the generation of adequate animal models is time-consuming and challenging. Therefore, human induced pluripotent stem cells (iPSCs) carrying specific cardiomyopathy-associated mutations are a promising alternative. Since the original discovery that pluripotency can be artificially induced by the expression of different transcription factors, various patient-specific-induced pluripotent stem cell lines have been generated to model non-ischemic, genetic cardiomyopathies in vitro. In this review, we describe the genetic landscape of non-ischemic, genetic cardiomyopathies and give an overview about different human iPSC lines, which have been developed for the disease modeling of inherited cardiomyopathies. We summarize different methods and protocols for the general differentiation of human iPSCs into cardiomyocytes. In addition, we describe methods and technologies to investigate functionally human iPSC-derived cardiomyocytes. Furthermore, we summarize novel genome editing approaches for the genetic manipulation of human iPSCs. This review provides an overview about the genetic landscape of inherited cardiomyopathies with a focus on iPSC technology, which might be of interest for clinicians and basic scientists interested in genetic cardiomyopathies.
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Affiliation(s)
- Andreas Brodehl
- Erich and Hanna Klessmann Institute, Heart and Diabetes Center NRW, University Hospital of the Ruhr-University Bochum, Georgstrasse 11, D-32545 Bad Oeynhausen, Germany.
| | - Hans Ebbinghaus
- Erich and Hanna Klessmann Institute, Heart and Diabetes Center NRW, University Hospital of the Ruhr-University Bochum, Georgstrasse 11, D-32545 Bad Oeynhausen, Germany.
| | - Marcus-André Deutsch
- Department of Thoracic and Cardiovascular Surgery, Heart and Diabetes Center NRW, University Hospital Ruhr-University Bochum, Georgstrasse 11, D-32545 Bad Oeynhausen, Germany.
| | - Jan Gummert
- Erich and Hanna Klessmann Institute, Heart and Diabetes Center NRW, University Hospital of the Ruhr-University Bochum, Georgstrasse 11, D-32545 Bad Oeynhausen, Germany.
- Department of Thoracic and Cardiovascular Surgery, Heart and Diabetes Center NRW, University Hospital Ruhr-University Bochum, Georgstrasse 11, D-32545 Bad Oeynhausen, Germany.
| | - Anna Gärtner
- Erich and Hanna Klessmann Institute, Heart and Diabetes Center NRW, University Hospital of the Ruhr-University Bochum, Georgstrasse 11, D-32545 Bad Oeynhausen, Germany.
| | - Sandra Ratnavadivel
- Erich and Hanna Klessmann Institute, Heart and Diabetes Center NRW, University Hospital of the Ruhr-University Bochum, Georgstrasse 11, D-32545 Bad Oeynhausen, Germany.
| | - Hendrik Milting
- Erich and Hanna Klessmann Institute, Heart and Diabetes Center NRW, University Hospital of the Ruhr-University Bochum, Georgstrasse 11, D-32545 Bad Oeynhausen, Germany.
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Campbell WS, Carter AB, Cushman-Vokoun AM, Greiner TC, Dash RC, Routbort M, de Baca ME, Campbell JR. A Model Information Management Plan for Molecular Pathology Sequence Data Using Standards: From Sequencer to Electronic Health Record. J Mol Diagn 2019; 21:408-417. [PMID: 30797065 DOI: 10.1016/j.jmoldx.2018.12.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 11/10/2018] [Accepted: 12/04/2018] [Indexed: 10/27/2022] Open
Abstract
Incorporating genetic variant data into the electronic health record (EHR) in discrete computable fashion has vexed the informatics community for years. Genetic sequence test results are typically communicated by the molecular laboratory and stored in the EHR as textual documents. Although text documents are useful for human readability and initial use, they are not conducive for data retrieval and reuse. As a result, clinicians often struggle to find historical gene sequence results on a series of oncology patients within the EHR that might influence the care of the current patient. Second, identification of patients with specific mutation results in the EHR who are now eligible for new and/or changing therapy is not easily accomplished. Third, the molecular laboratory is challenged to monitor its sequencing processes for nonrandom process variation and other quality metrics. A novel approach to address each of these issues is presented and demonstrated. The authors use standard Health Level 7 laboratory result message formats in conjunction with international standards, Systematized Nomenclature of Medicine Clinical Terms and Human Genome Variant Society nomenclature, to represent, communicate, and store discrete gene sequence data within the EHR in a scalable fashion. This information management plan enables the support of the clinician at the point of care, enhances population management, and facilitates audits for maintaining laboratory quality.
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Affiliation(s)
- Walter S Campbell
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska.
| | - Alexis B Carter
- Department of Pathology, Children's Healthcare of Atlanta, Atlanta, Georgia
| | - Allison M Cushman-Vokoun
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska
| | - Timothy C Greiner
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska
| | - Rajesh C Dash
- Department of Pathology, Duke University Health System, Durham, North Carolina
| | - Mark Routbort
- Department of Hematopathology, University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - James R Campbell
- Department of Internal Medicine, University of Nebraska Medical Center, Omaha, Nebraska
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Memon A, Lee WK. KLF10 as a Tumor Suppressor Gene and Its TGF-β Signaling. Cancers (Basel) 2018; 10:E161. [PMID: 29799499 PMCID: PMC6025274 DOI: 10.3390/cancers10060161] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 05/15/2018] [Accepted: 05/23/2018] [Indexed: 12/17/2022] Open
Abstract
Krüppel-like factor 10 (KLF10), originally named TGF-β (Transforming growth factor beta) inducible early gene 1 (TIEG1), is a DNA-binding transcriptional regulator containing a triple C2H2 zinc finger domain. By binding to Sp1 (specificity protein 1) sites on the DNA and interactions with other regulatory transcription factors, KLF10 encourages and suppresses the expression of multiple genes in many cell types. Many studies have investigated its signaling cascade, but other than the TGF-β/Smad signaling pathway, these are still not clear. KLF10 plays a role in proliferation, differentiation as well as apoptosis, just like other members of the SP (specificity proteins)/KLF (Krüppel-like Factors). Recently, several studies reported that KLF10 KO (Knock out) is associated with defects in cell and organs such as osteopenia, abnormal tendon or cardiac hypertrophy. Since KLF10 was first discovered, several studies have defined its role in cancer as a tumor suppressor. KLF10 demonstrate anti-proliferative effects and induce apoptosis in various carcinoma cells including pancreatic cancer, leukemia, and osteoporosis. Collectively, these data indicate that KLF10 plays a significant role in various biological processes and diseases, but its role in cancer is still unclear. Therefore, this review was conducted to describe and discuss the role and function of KLF10 in diseases, including cancer, with a special emphasis on its signaling with TGF-β.
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Affiliation(s)
- Azra Memon
- Laboratory of Developmental Genetics, Department of Biomedical Sciences, School of Medicine, Inha University, Incheon 22212, Korea.
| | - Woon Kyu Lee
- Laboratory of Developmental Genetics, Department of Biomedical Sciences, School of Medicine, Inha University, Incheon 22212, Korea.
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Catucci I, Casadei S, Ding YC, Volorio S, Ficarazzi F, Falanga A, Marchetti M, Tondini C, Franchi M, Adamson A, Mandell J, Walsh T, Olopade OI, Manoukian S, Radice P, Ricker C, Weitzel J, King MC, Peterlongo P, Neuhausen SL. Haplotype analyses of the c.1027C>T and c.2167_2168delAT recurrent truncating mutations in the breast cancer-predisposing gene PALB2. Breast Cancer Res Treat 2016; 160:121-129. [PMID: 27624329 DOI: 10.1007/s10549-016-3981-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 09/07/2016] [Indexed: 12/19/2022]
Abstract
PURPOSE Breast cancer-predisposing mutations PALB2 c.1027C>T (p.Gln343*) and PALB2 c.2167_2168delAT have each been observed multiple times in breast cancer families of Italian ancestry. More recently, the c2167_2168delAT mutation was identified in unrelated breast cancer cases of various ancestries. For each mutation, we investigated whether the origin was multiple mutational events (a "hot-spot") or a single event (a founder allele). METHODS We genotyped and reconstructed haplotypes for 36 participants of Italian, Italian-American, Hispanic, and Nigerian ancestries, using seven short tandem repeat (STR) markers that covered 3 Megabases within and flanking PALB2 on chromosome 16. RESULTS For PALB2 c.1027C>T, a shared haplotype with a minimum size of 150 kb was shared by all 19 carriers investigated, all of Italian ancestry. This result suggests that this allele arose as a single event in a shared ancestor. For PALB2 c.2167_2168delAT, all 12 carriers from American-Italian and Italian families shared a 1-Mb haplotype, the 3 Hispanic carriers shared a different haplotype of size 2 Mb, and the Nigerian carrier had different alleles at all 7 STR markers. These results suggest that PALB2 c.2167_2168delAT arose multiple times, but that within each population, PALB2 c.2167_2168delAT likely represents a single mutational event. CONCLUSION We identified two PALB2 mutations that are founder alleles in Italian families, one of which is, independently, also a founder mutation in American-Hispanic breast cancers.
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Affiliation(s)
- Irene Catucci
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy
| | - Silvia Casadei
- Departments of Medicine and Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Yuan Chun Ding
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Sara Volorio
- Cogentech, Cancer Genetic Test Laboratory, Milan, Italy
| | | | - Anna Falanga
- Department of Immunohematology and Transfusion Medicine, Ospedale Papa Giovanni XXIII, Bergamo, Italy
| | - Marina Marchetti
- Department of Immunohematology and Transfusion Medicine, Ospedale Papa Giovanni XXIII, Bergamo, Italy
| | - Carlo Tondini
- Unit of Oncology, Ospedale Papa Giovanni XXIII, Bergamo, Italy
| | - Michela Franchi
- Unit of Oncology, Ospedale Papa Giovanni XXIII, Bergamo, Italy
| | - Aaron Adamson
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Jessica Mandell
- Departments of Medicine and Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Tom Walsh
- Departments of Medicine and Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Olufunmilayo I Olopade
- Department of Medicine, Center for Clinical Cancer Genetics and Global Health, University of Chicago, Chicago, IL, USA
| | - Siranoush Manoukian
- Unit of Medical Genetics, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Charite Ricker
- Department Medicine, Keck School of Medicine at University of Southern California, Los Angeles, CA, USA
| | - Jeffrey Weitzel
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Mary-Claire King
- Departments of Medicine and Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | | | - Susan L Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA.
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Verleyen W, Ballouz S, Gillis J. Positive and negative forms of replicability in gene network analysis. Bioinformatics 2015; 32:1065-73. [PMID: 26668004 DOI: 10.1093/bioinformatics/btv734] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 12/09/2015] [Indexed: 02/07/2023] Open
Abstract
MOTIVATION Gene networks have become a central tool in the analysis of genomic data but are widely regarded as hard to interpret. This has motivated a great deal of comparative evaluation and research into best practices. We explore the possibility that this may lead to overfitting in the field as a whole. RESULTS We construct a model of 'research communities' sampling from real gene network data and machine learning methods to characterize performance trends. Our analysis reveals an important principle limiting the value of replication, namely that targeting it directly causes 'easy' or uninformative replication to dominate analyses. We find that when sampling across network data and algorithms with similar variability, the relationship between replicability and accuracy is positive (Spearman's correlation, rs ∼0.33) but where no such constraint is imposed, the relationship becomes negative for a given gene function (rs ∼ -0.13). We predict factors driving replicability in some prior analyses of gene networks and show that they are unconnected with the correctness of the original result, instead reflecting replicable biases. Without these biases, the original results also vanish replicably. We show these effects can occur quite far upstream in network data and that there is a strong tendency within protein-protein interaction data for highly replicable interactions to be associated with poor quality control. AVAILABILITY AND IMPLEMENTATION Algorithms, network data and a guide to the code available at: https://github.com/wimverleyen/AggregateGeneFunctionPrediction CONTACT jgillis@cshl.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- W Verleyen
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, 500 Sunnyside Boulevard Woodbury, NY 11797, USA
| | - S Ballouz
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, 500 Sunnyside Boulevard Woodbury, NY 11797, USA
| | - J Gillis
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, 500 Sunnyside Boulevard Woodbury, NY 11797, USA
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Pei J, Grishin NV. C2H2 zinc finger proteins of the SP/KLF, Wilms tumor, EGR, Huckebein, and Klumpfuss families in metazoans and beyond. Gene 2015; 573:91-9. [PMID: 26187067 DOI: 10.1016/j.gene.2015.07.031] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 07/08/2015] [Accepted: 07/10/2015] [Indexed: 10/23/2022]
Abstract
Specificity proteins (SPs) and Krüppel-Like Factors (KLFs) are C2H2-type zinc finger transcription factors that play essential roles in differentiation, development, proliferation and cell death. SP/KLF proteins, similarly to Wilms tumor protein 1 (WT1), Early Growth Response (EGR), Huckebein, and Klumpfuss, prefer to bind GC-rich sequences such as GC-box and CACCC-box (GT-box). We searched various genomes and transcriptomes of metazoans and single-cell holozoans for members of these families. Seven groups of KLFs (KLFA-G) and three groups of SPs (SPA-C) were identified in the three lineages of Bilateria (Deuterostomia, Ecdysozoa, and Lophotrochozoa). The last ancestor of jawed vertebrates was inferred to have at least 18 KLFs (group A: KLF1/2/4/17, group B: KLF3/8/12; group C: KLF5/5l; group D: KLF6/7; group E: KLF9/13/16; group F: KLF10/KLF11; group G: KLF15/15l) and 10 SPs (group A: SP1/2/3/4; group B: SP5/5l; group C: SP6/7/8/9), since they were found in both cartilaginous and boned fishes. Placental mammals have added KLF14 (group E) and KLF18 (group A), and lost KLF5l (KLF5-like) and KLF15l (KLF15-like). Multiple KLF members were found in basal metazoans (Ctenophora, Porifera, Placozoa, and Cnidaria). Ctenophora has the least number of KLFs and no SPs, which could be attributed to its proposed sister group relationship to other metazoans or gene loss. While SP, EGR and Klumpfuss were only detected in metazoans, KLF, WT1, and Huckebein are present in nonmetazoan holozoans. Of the seven metazoan KLF groups, only KLFG, represented by KLF15 in human, was found in nonmetazoans. In addition, two nonmetazoan groups of KLFs are present in Choanoflagellatea and Filasterea. WT1 could be evolutionarily the earliest among these GC/GT-box-binding families due to its sole presence in Ichthyosporea.
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Affiliation(s)
- Jimin Pei
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Nick V Grishin
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Biophysics and Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
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12
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Abstract
The drug-metabolizing enzyme thiopurine methyltransferase (TPMT) has become one of the best examples of pharmacogenomics to be translated into routine clinical practice. TPMT metabolizes the thiopurines 6-mercaptopurine, 6-thioguanine, and azathioprine, drugs that are widely used for treatment of acute leukemias, inflammatory bowel diseases, and other disorders of immune regulation. Since the discovery of genetic polymorphisms in the TPMT gene, many sequence variants that cause a decreased enzyme activity have been identified and characterized. Increasingly, to optimize dose, pretreatment determination of TPMT status before commencing thiopurine therapy is now routine in many countries. Novel TPMT sequence variants are currently numbered sequentially using PubMed as a source of information; however, this has caused some problems as exemplified by two instances in which authors' articles appeared on PubMed at the same time, resulting in the same allele numbers given to different polymorphisms. Hence, there is an urgent need to establish an order and consensus to the numbering of known and novel TPMT sequence variants. To address this problem, a TPMT nomenclature committee was formed in 2010, to define the nomenclature and numbering of novel variants for the TPMT gene. A website (http://www.imh.liu.se/tpmtalleles) serves as a platform for this work. Researchers are encouraged to submit novel TPMT alleles to the committee for designation and reservation of unique allele numbers. The committee has decided to renumber two alleles: nucleotide position 106 (G>A) from TPMT*24 to TPMT*30 and position 611 (T>C, rs79901429) from TPMT*28 to TPMT*31. Nomenclature for all other known alleles remains unchanged.
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Carter CJ. Susceptibility genes are enriched in those of the herpes simplex virus 1/host interactome in psychiatric and neurological disorders. Pathog Dis 2013; 69:240-61. [PMID: 23913659 DOI: 10.1111/2049-632x.12077] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2013] [Revised: 07/11/2013] [Accepted: 07/24/2013] [Indexed: 12/22/2022] Open
Abstract
Herpes simplex virus 1 (HSV-1) can promote beta-amyloid deposition and tau phosphorylation, demyelination or cognitive deficits relevant to Alzheimer's disease or multiple sclerosis and to many neuropsychiatric disorders with which it has been implicated. A seroprevalence much higher than disease incidence has called into question any primary causal role. However, as also the case with risk-promoting polymorphisms (also present in control populations), any causal effects are likely to be conditional. During its life cycle, the virus binds to many proteins and modifies the expression of multiple genes creating a host/pathogen interactome involving 1347 host genes. This data set is heavily enriched in the susceptibility genes for multiple sclerosis (P = 1.3E-99) > Alzheimer's disease > schizophrenia > Parkinsonism > depression > bipolar disorder > childhood obesity > chronic fatigue > autism > and anorexia (P = 0.047) but not attention deficit hyperactivity disorder, a relationship maintained for genome-wide association study data sets in multiple sclerosis and Alzheimer's disease. Overlapping susceptibility gene/interactome data sets disrupt signalling networks relevant to each disease, suggesting that disease susceptibility genes may filter the attentions of the pathogen towards particular pathways and pathologies. In this way, the same pathogen could contribute to multiple diseases in a gene-dependent manner and condition the risk-promoting effects of the genes whose function it disrupts.
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14
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Abel O, Powell JF, Andersen PM, Al-Chalabi A. ALSoD: A user-friendly online bioinformatics tool for amyotrophic lateral sclerosis genetics. Hum Mutat 2012; 33:1345-51. [PMID: 22753137 DOI: 10.1002/humu.22157] [Citation(s) in RCA: 216] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Accepted: 06/19/2012] [Indexed: 12/11/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is the commonest adult onset motor neuron disease, with a peak age of onset in the seventh decade. With advances in genetic technology, there is an enormous increase in the volume of genetic data produced, and a corresponding need for storage, analysis, and interpretation, particularly as our understanding of the relationships between genotype and phenotype mature. Here, we present a system to enable this in the form of the ALS Online Database (ALSoD at http://alsod.iop.kcl.ac.uk), a freely available database that has been transformed from a single gene storage facility recording mutations in the SOD1 gene to a multigene ALS bioinformatics repository and analytical instrument combining genotype, phenotype, and geographical information with associated analysis tools. These include a comparison tool to evaluate genes side by side or jointly with user configurable features, a pathogenicity prediction tool using a combination of computational approaches to distinguish variants with nonfunctional characteristics from disease-associated mutations with more dangerous consequences, and a credibility tool to enable ALS researchers to objectively assess the evidence for gene causation in ALS. Furthermore, integration of external tools, systems for feedback, annotation by users, and two-way links to collaborators hosting complementary databases further enhance the functionality of ALSoD.
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Affiliation(s)
- Olubunmi Abel
- Department of Clinical Neuroscience, King's College London, Institute of Psychiatry, London, UK
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15
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Mittal RA, Hammel M, Schwarz J, Heschl KM, Bretschneider N, Flemmer AW, Herber-Jonat S, Königshoff M, Eickelberg O, Holzinger A. SFTA2--a novel secretory peptide highly expressed in the lung--is modulated by lipopolysaccharide but not hyperoxia. PLoS One 2012; 7:e40011. [PMID: 22768197 PMCID: PMC3386909 DOI: 10.1371/journal.pone.0040011] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Accepted: 06/05/2012] [Indexed: 11/19/2022] Open
Abstract
Tissue-specific transcripts are likely to be of importance for the corresponding organ. While attempting to define the specific transcriptome of the human lung, we identified the transcript of a yet uncharacterized protein, SFTA2. In silico analyses, biochemical methods, fluorescence imaging and animal challenge experiments were employed to characterize SFTA2. Human SFTA2 is located on Chr. 6p21.33, a disease-susceptibility locus for diffuse panbronchiolitis. RT-PCR verified the abundance of SFTA2-specific transcripts in human and mouse lung. SFTA2 is synthesized as a hydrophilic precursor releasing a 59 amino acid mature peptide after cleavage of an N-terminal secretory signal. SFTA2 has no recognizable homology to other proteins while orthologues are present in all mammals. SFTA2 is a glycosylated protein and specifically expressed in nonciliated bronchiolar epithelium and type II pneumocytes. In accordance with other hydrophilic surfactant proteins, SFTA2 did not colocalize with lamellar bodies but colocalized with golgin97 and clathrin-labelled vesicles, suggesting a classical secretory pathway for its expression and secretion. In the mouse lung, Sfta2 was significantly downregulated after induction of an inflammatory reaction by intratracheal lipopolysaccharides paralleling surfactant proteins B and C but not D. Hyperoxia, however, did not alter SFTA2 mRNA levels. We have characterized SFTA2 and present it as a novel unique secretory peptide highly expressed in the lung.
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Affiliation(s)
- Rashmi A. Mittal
- Neonatology, Dr. von Haunersches Kinderspital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Markus Hammel
- Neonatology, Dr. von Haunersches Kinderspital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Johannes Schwarz
- Comprehensive Pneumology Center, Institute of Experimental Pneumology, University Hospital, Ludwig-Maximilians-Universität München and Helmholtz Zentrum München, Munich, Germany
| | - Katharina M. Heschl
- Neonatology, Dr. von Haunersches Kinderspital, Ludwig-Maximilians-Universität München, Munich, Germany
| | | | - Andreas W. Flemmer
- Neonatology, Dr. von Haunersches Kinderspital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Susanne Herber-Jonat
- Neonatology, Dr. von Haunersches Kinderspital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Melanie Königshoff
- Comprehensive Pneumology Center, Institute of Experimental Pneumology, University Hospital, Ludwig-Maximilians-Universität München and Helmholtz Zentrum München, Munich, Germany
| | - Oliver Eickelberg
- Comprehensive Pneumology Center, Institute of Experimental Pneumology, University Hospital, Ludwig-Maximilians-Universität München and Helmholtz Zentrum München, Munich, Germany
| | - Andreas Holzinger
- Neonatology, Dr. von Haunersches Kinderspital, Ludwig-Maximilians-Universität München, Munich, Germany
- * E-mail:
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16
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Galvez C, de Moya‐Anegón F. A dictionary‐based approach to normalizing gene names in one domain of knowledge from the biomedical literature. JOURNAL OF DOCUMENTATION 2012. [DOI: 10.1108/00220411211200301] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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17
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Lacroix Z, Raschid L, Eckman BA. TECHNIQUES FOR OPTIMIZATION OF QUERIES ON INTEGRATED BIOLOGICAL RESOURCES. J Bioinform Comput Biol 2011; 2:375-411. [PMID: 15297988 DOI: 10.1142/s0219720004000648] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Today, scientific data are inevitably digitized, stored in a wide variety of formats, and are accessible over the Internet. Scientific discovery increasingly involves accessing multiple heterogeneous data sources, integrating the results of complex queries, and applying further analysis and visualization applications in order to collect datasets of interest. Building a scientific integration platform to support these critical tasks requires accessing and manipulating data extracted from flat files or databases, documents retrieved from the Web, as well as data that are locally materialized in warehouses or generated by software. The lack of efficiency of existing approaches can significantly affect the process with lengthy delays while accessing critical resources or with the failure of the system to report any results. Some queries take so much time to be answered that their results are returned via email, making their integration with other results a tedious task. This paper presents several issues that need to be addressed to provide seamless and efficient integration of biomolecular data. Identified challenges include: capturing and representing various domain specific computational capabilities supported by a source including sequence or text search engines and traditional query processing; developing a methodology to acquire and represent semantic knowledge and metadata about source contents, overlap in source contents, and access costs; developing cost and semantics based decision support tools to select sources and capabilities, and to generate efficient query evaluation plans.
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Affiliation(s)
- Zoé Lacroix
- Arizona State University, PO Box 876106, Tempe, Arizona 85287-6106, USA.
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18
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Berwouts S, Morris MA, Girodon E, Schwarz M, Stuhrmann M, Dequeker E. Mutation nomenclature in practice: Findings and recommendations from the cystic fibrosis external quality assessment scheme. Hum Mutat 2011; 32:1197-203. [DOI: 10.1002/humu.21569] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2010] [Accepted: 06/27/2011] [Indexed: 11/08/2022]
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19
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Wain H, Povey S, Maltais L. Human and mouse gene nomenclature. CURRENT PROTOCOLS IN HUMAN GENETICS 2008; Appendix 1:Appendix 1C. [PMID: 18428336 DOI: 10.1002/0471142905.hga01cs35] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Standard genetic nomenclature is necessary to help researchers, clinicians, and the public to access data on their genes of interest, and to communicate in a globally understood language of approved gene symbols. In both human and mouse, one unique symbol (acronym/abbreviation) and one name are assigned for each gene. Co-ordination between human and mouse gene nomenclature is a successful endeavor, due in part to the historical interaction between the two nomenclature committee groups. This interaction grew out of the Human Gene Mapping (HGM) Workshops. This appendix discusses development and organization of gene nomenclature, how to find a gene and how to name a new gene.
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Affiliation(s)
- Hester Wain
- University College London, London, United Kingdom
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20
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Linkage disequilibrium maps and location databases. Methods Mol Biol 2007. [PMID: 17984536 DOI: 10.1007/978-1-59745-389-9_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Effective application of association mapping for complex traits requires characterization of linkage disequilibrium (LD) patterns that reflect the dominant process of recombination and its duration in addition to the more subtle influences of mutation, selection, and genetic drift. Maps expressed in linkage disequilibrium units (LDUs) reflect the influences of these factors with the use of a modified version of Malecot's isolation-by-distance model. As a result, LDU maps are analogous to linkage maps in so far as their provision of an additive metric that is related to recombination and facilitates association-mapping studies. However, unlike linkage maps, LDUs also reflect the partly cumulative effects of multiple historical bottlenecks that account for substantial variations in LD patterns between populations. This chapter provides an overview of the data requirements and methodology used to construct LDU maps, their applications outside association mapping, and their integration into location databases.
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21
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Alm T, Steen J, Ottosson J, Hober S. High-throughput protein purification under denaturating conditions by the use of cation exchange chromatography. Biotechnol J 2007; 2:709-16. [PMID: 17492715 DOI: 10.1002/biot.200700060] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
A high-throughput protein purification strategy using the polycationic Z(basic) tag has been developed. In order for the strategy to be useful both for soluble and less soluble proteins, a denaturating agent, urea, was used in all purification steps. First, four target proteins were genetically fused to the purification tag, Z(basic). These protein constructs were purified by cation exchange chromatography and eluted using a salt gradient. From the data achieved, a purification strategy was planned including stepwise elution to enable parallel protein purification using a laboratory robot. A protocol that includes all steps, equilibration of the chromatography resin, load of sample, wash, and elution, all without any manual handling steps, was handled by the laboratory robot. The program allows automated purification giving milligram amounts of pure recombinant protein of up to 60 cell lysates. In this study 22 different protein constructs, with different characteristics regarding pI and solubility, were successfully purified by the laboratory robot. The data show that Z(basic) can be used as a general purification tag also under denaturating conditions. Moreover, the strategy enables purification of proteins with different pI and solubility using ion exchange chromatography (IEXC). The procedure is highly reproducible and allows for high protein yield and purity and is therefore a good complement to the commonly used His(6)-tag.
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Affiliation(s)
- Tove Alm
- School of Biotechnology, Department of Proteomics, Royal Institute of Technology, AlbaNova University Center, Stockholm, Sweden
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22
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Buttar NS, Fernandez-Zapico ME, Urrutia R. Key role of Krüppel-like factor proteins in pancreatic cancer and other gastrointestinal neoplasias. Curr Opin Gastroenterol 2006; 22:505-11. [PMID: 16891881 DOI: 10.1097/01.mog.0000239864.73962.db] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
PURPOSE OF REVIEW To describe recent studies on Krüppel-like factor transcription factors and their relationship with gastrointestinal neoplasias, in particular pancreatic cancer. RECENT FINDINGS Krüppel-like factor proteins are a subfamily of transcription factors characterized by the presence of a conserved DNA-binding domain comprising three Krüppel-like zinc fingers. Each distinct family member differs in its ability to regulate transcription, and, as a consequence, to influence cellular processes including cell growth and differentiation. Recently, a number of publications have provided evidence of the implication of Krüppel-like factor proteins in gastrointestinal carcinogenesis. SUMMARY This article will focus on the results of studies in the field published in the last year.
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Affiliation(s)
- Navtej S Buttar
- Gastroenterology Research Unit, Saint Mary's Hospital, Mayo Clinic College of Medicine, Rochester, Minnesota, USA
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23
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Judge SIV, Bever CT. Potassium channel blockers in multiple sclerosis: Neuronal Kv channels and effects of symptomatic treatment. Pharmacol Ther 2006; 111:224-59. [PMID: 16472864 DOI: 10.1016/j.pharmthera.2005.10.006] [Citation(s) in RCA: 200] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2005] [Accepted: 10/12/2005] [Indexed: 02/07/2023]
Abstract
Multiple sclerosis (MS) is an inflammatory disease of the central nervous system (CNS) characterized by demyelination, with a relative sparing of axons. In MS patients, many neurologic signs and symptoms have been attributed to the underlying conduction deficits. The idea that neurologic function might be improved if conduction could be restored in CNS demyelinated axons led to the testing of potassium (K(+)) channel blockers as a symptomatic treatment. To date, only 2 broad-spectrum K(+) channel blockers, 4-aminopyridine (4-AP) and 3,4-diaminopyridine (3,4-DAP), have been tested in MS patients. Although both 4-AP and 3,4-DAP produce clear neurologic benefits, their use has been limited by toxicity. Here we review the current status of basic science and clinical research related to the therapeutic targeting of voltage-gated K(+) channels (K(v)) in MS. By bringing together 3 distinct but interrelated disciplines, we aim to provide perspective on a vast body of work highlighting the lengthy and ongoing process entailed in translating fundamental K(v) channel knowledge into new clinical treatments for patients with MS and other demyelinating diseases. Covered are (1) K(v) channel nomenclature, structure, function, and pharmacology; (2) classic and current experimental morphology and neurophysiology studies of demyelination and conduction deficits; and (3) a comprehensive overview of clinical trials utilizing 4-AP and 3,4-DAP in MS patients.
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Affiliation(s)
- Susan I V Judge
- MS Center of Excellence-East, Research and Neurology Services, VA Maryland Health Care System, USA.
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24
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Chen B, Zhong D, Monteiro A. Comparative genomics and evolution of the HSP90 family of genes across all kingdoms of organisms. BMC Genomics 2006; 7:156. [PMID: 16780600 PMCID: PMC1525184 DOI: 10.1186/1471-2164-7-156] [Citation(s) in RCA: 212] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2006] [Accepted: 06/17/2006] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND HSP90 proteins are essential molecular chaperones involved in signal transduction, cell cycle control, stress management, and folding, degradation, and transport of proteins. HSP90 proteins have been found in a variety of organisms suggesting that they are ancient and conserved. In this study we investigate the nuclear genomes of 32 species across all kingdoms of organisms, and all sequences available in GenBank, and address the diversity, evolution, gene structure, conservation and nomenclature of the HSP90 family of genes across all organisms. RESULTS Twelve new genes and a new type HSP90C2 were identified. The chromosomal location, exon splicing, and prediction of whether they are functional copies were documented, as well as the amino acid length and molecular mass of their polypeptides. The conserved regions across all protein sequences, and signature sequences in each subfamily were determined, and a standardized nomenclature system for this gene family is presented. The proeukaryote HSP90 homologue, HTPG, exists in most Bacteria species but not in Archaea, and it evolved into three lineages (Groups A, B and C) via two gene duplication events. None of the organellar-localized HSP90s were derived from endosymbionts of early eukaryotes. Mitochondrial TRAP and endoplasmic reticulum HSP90B separately originated from the ancestors of HTPG Group A in Firmicutes-like organisms very early in the formation of the eukaryotic cell. TRAP is monophyletic and present in all Animalia and some Protista species, while HSP90B is paraphyletic and present in all eukaryotes with the exception of some Fungi species, which appear to have lost it. Both HSP90C (chloroplast HSP90C1 and location-undetermined SP90C2) and cytosolic HSP90A are monophyletic, and originated from HSP90B by independent gene duplications. HSP90C exists only in Plantae, and was duplicated into HSP90C1 and HSP90C2 isoforms in higher plants. HSP90A occurs across all eukaryotes, and duplicated into HSP90AA and HSP90AB in vertebrates. Diplomonadida was identified as the most basal organism in the eukaryote lineage. CONCLUSION The present study presents the first comparative genomic study and evolutionary analysis of the HSP90 family of genes across all kingdoms of organisms. HSP90 family members underwent multiple duplications and also subsequent losses during their evolution. This study established an overall framework of information for the family of genes, which may facilitate and stimulate the study of this gene family across all organisms.
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Affiliation(s)
- Bin Chen
- School of Life Sciences, Southwest University, Chongqing 400715, P.R. China
- Department of Biological Sciences, The State University of New York at Buffalo, NY 14260, USA
| | - Daibin Zhong
- Department of Biological Sciences, The State University of New York at Buffalo, NY 14260, USA
| | - Antónia Monteiro
- Department of Biological Sciences, The State University of New York at Buffalo, NY 14260, USA
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25
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Mitchell DA, Vasudevan A, Linder ME, Deschenes RJ. Protein palmitoylation by a family of DHHC protein S-acyltransferases. J Lipid Res 2006; 47:1118-27. [PMID: 16582420 DOI: 10.1194/jlr.r600007-jlr200] [Citation(s) in RCA: 325] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Protein palmitoylation refers to the posttranslational addition of a 16 carbon fatty acid to the side chain of cysteine, forming a thioester linkage. This acyl modification is readily reversible, providing a potential regulatory mechanism to mediate protein-membrane interactions and subcellular trafficking of proteins. The mechanism that underlies the transfer of palmitate or other long-chain fatty acids to protein was uncovered through genetic screens in yeast. Two related S-palmitoyltransferases were discovered. Erf2 palmitoylates yeast Ras proteins, whereas Akr1 modifies the yeast casein kinase, Yck2. Erf2 and Akr1 share a common sequence referred to as a DHHC (aspartate-histidine-histidine-cysteine) domain. Numerous genes encoding DHHC domain proteins are found in all eukaryotic genome databases. Mounting evidence is consistent with this signature motif playing a direct role in protein acyltransferase (PAT) reactions, although many questions remain. This review presents the genetic and biochemical evidence for the PAT activity of DHHC proteins and discusses the mechanism of protein-mediated palmitoylation.
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Affiliation(s)
- David A Mitchell
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
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26
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Abstract
Sp1 is one of the best characterized transcriptional activators. The biological importance of Sp1 is underscored by the fact that several hundreds of genes are thought to be regulated by this protein. However, during the last 5 years, a more extended family of Sp1-like transcription factors has been identified and characterized by the presence of a conserved DNA-binding domain comprising three Krüppel-like zinc fingers. Each distinct family member differs in its ability to regulate transcription, and, as a consequence, to influence cellular processes. Specific activation and repression domains located within the N-terminal regions of these proteins are responsible for these differences by facilitating interactions with various co-activators and co-repressors. The present review primarily focuses on discussing the structural, biochemical and biological functions of the repressor members of this family of transcription factors. The existence of these transcriptional repressors provides a tightly regulated mechanism for silencing a large number of genes that are already known to be activated by Sp1.
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Affiliation(s)
- Gwen Lomberk
- *Gastroenterology Research Unit, Mayo Clinic, Rochester, MN 55901, U.S.A
| | - Raul Urrutia
- *Gastroenterology Research Unit, Mayo Clinic, Rochester, MN 55901, U.S.A
- †Tumor Biology Program, Mayo Clinic, Rochester, MN 55901, U.S.A
- ‡Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55901, U.S.A
- To whom correspondence should be addressed (email )
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Hahn ME, Karchner SI, Franks DG, Merson RR. Aryl hydrocarbon receptor polymorphisms and dioxin resistance in Atlantic killifish (Fundulus heteroclitus). ACTA ACUST UNITED AC 2004; 14:131-43. [PMID: 15077014 DOI: 10.1097/00008571-200402000-00007] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The aryl hydrocarbon receptor (AHR) gene encodes a ligand-activated transcription factor through which planar halogenated aromatic hydrocarbons (HAHs) such as 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) as well as polynuclear aromatic hydrocarbons (PAHs) cause altered gene expression and toxicity. To understand the role of AHR genetic variability in differential sensitivity to HAHs and PAHs, we are currently studying a population of the teleost Fundulus heteroclitus (Atlantic killifish) that has evolved genetic resistance to the toxic and biochemical effects of these compounds. Here, we report that the killifish AHR1 locus is highly polymorphic and that the frequencies of the major allele types differ between dioxin-sensitive and dioxin-resistant populations. Twenty-five single nucleotide polymorphisms (SNPs), nine of which are non-synonymous, were identified in the AHR1 coding sequence. Seven identified alleles were assigned to three groups, designated AHR1*1, AHR1*2 and AHR1*3. AHR1*1 alleles were under-represented in a population of dioxin- and polychlorinated biphenyl (PCB)-resistant fish from a PCB-contaminated Superfund site (New Bedford Harbor, Massachusetts, USA) compared to dioxin-sensitive fish from a less contaminated reference site (Scorton Creek, Massachusetts, USA). To determine the possible role of these AHR1 variants in differential HAH sensitivity, we expressed representative variant proteins from the two most divergent allelic groups (AHR1*1 and AHR1*3) by in-vitro transcription and translation and assessed their functional properties. AHR1*1A and AHR1*3A proteins displayed similar binding capacities and affinities for [H]TCDD. In transient transfection assays using mammalian cells, AHR1*1A and AHR1*3A exhibited similar abilities to support TCDD-dependent transactivation of a luciferase reporter gene under control of AHR-responsive enhancer elements. We discuss the possibility of other functional differences in AHR1 variants or their interaction with other killifish loci (AHR2, AHRR) that may contribute to differences in dioxin sensitivity.
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Affiliation(s)
- Mark E Hahn
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543-1049, USA.
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Gutman GA, Chandy KG, Adelman JP, Aiyar J, Bayliss DA, Clapham DE, Covarriubias M, Desir GV, Furuichi K, Ganetzky B, Garcia ML, Grissmer S, Jan LY, Karschin A, Kim D, Kuperschmidt S, Kurachi Y, Lazdunski M, Lesage F, Lester HA, McKinnon D, Nichols CG, O'Kelly I, Robbins J, Robertson GA, Rudy B, Sanguinetti M, Seino S, Stuehmer W, Tamkun MM, Vandenberg CA, Wei A, Wulff H, Wymore RS. International Union of Pharmacology. XLI. Compendium of voltage-gated ion channels: potassium channels. Pharmacol Rev 2004; 55:583-6. [PMID: 14657415 DOI: 10.1124/pr.55.4.9] [Citation(s) in RCA: 216] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
This summary article presents an overview of the molecular relationships among the voltage-gated potassium channels and a standard nomenclature for them, which is derived from the IUPHAR Compendium of Voltage-Gated Ion Channels. The complete Compendium, including data tables for each member of the potassium channel family can be found at http://www.iuphar-db.org/iuphar-ic/.
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Affiliation(s)
- George A Gutman
- Department of Microbiology and Molecular Genetics, University of California-Irvine, Irvine, CA 92697, USA.
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29
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Wright JM, Zeitlin PL, Cebotaru L, Guggino SE, Guggino WB. Gene expression profile analysis of 4-phenylbutyrate treatment of IB3-1 bronchial epithelial cell line demonstrates a major influence on heat-shock proteins. Physiol Genomics 2004; 16:204-11. [PMID: 14583596 DOI: 10.1152/physiolgenomics.00160.2003] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Most individuals with cystic fibrosis (CF) carry one or two mutations that result in a maturation defect of the full-length CFTR protein. The ΔF508 mutation results in a mutant protein that is degraded by the proteosome instead of progressing to the apical membrane where it functions as a cAMP-regulated chloride channel. 4-Phenylbutyrate (PBA) modulates heat-shock protein expression and promotes trafficking of ΔF508, thus permitting maturation and membrane insertion. The goal of this study was to gain insight into the genetic mechanism of PBA action through a large-scale analysis of gene expression. The Affymetrix genome-spanning U133 microarray set was used to compare mRNA expression levels in untreated IB3-1 cell line cultures with cultures treated with 1 mM PBA for 12 and 24 h. The most notable changes in mRNA levels were transient elevations in heat-shock proteins. The majority of genes downregulated throughout the application period were functionally associated with control of gene expression. Another set of genes increased in expression starting at 24 h, suggesting these are downstream effects of altered gene expression initiated by PBA. More than one-third of the genes in this late expressing set were identified as having potential significance in understanding the pathology of CF. Our results demonstrate the usefulness of gene expression profile analysis in understanding the consequences of PBA treatment and provide insights in how this drug exerts its effect on the trafficking of CFTR.
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Affiliation(s)
- Jerry M Wright
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA.
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30
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Rebholz-Schuhmann D, Marcel S, Albert S, Tolle R, Casari G, Kirsch H. Automatic extraction of mutations from Medline and cross-validation with OMIM. Nucleic Acids Res 2004; 32:135-42. [PMID: 14704350 PMCID: PMC373272 DOI: 10.1093/nar/gkh162] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Mutations help us to understand the molecular origins of diseases. Researchers, therefore, both publish and seek disease-relevant mutations in public databases and in scientific literature, e.g. Medline. The retrieval tends to be time-consuming and incomplete. Automated screening of the literature is more efficient. We developed extraction methods (called MEMA) that scan Medline abstracts for mutations. MEMA identified 24,351 singleton mutations in conjunction with a HUGO gene name out of 16,728 abstracts. From a sample of 100 abstracts we estimated the recall for the identification of mutation-gene pairs to 35% at a precision of 93%. Recall for the mutation detection alone was >67% with a precision rate of >96%. This shows that our system produces reliable data. The subset consisting of protein sequence mutations (PSMs) from MEMA was compared to the entries in OMIM (20,503 entries versus 6699, respectively). We found 1826 PSM-gene pairs to be in common to both datasets (cross-validated). This is 27% of all PSM-gene pairs in OMIM and 91% of those pairs from OMIM which co-occur in at least one Medline abstract. We conclude that Medline covers a large portion of the mutations known to OMIM. Another large portion could be artificially produced mutations from mutagenesis experiments. Access to the database of extracted mutation-gene pairs is available through the web pages of the EBI (refer to http://www.ebi. ac.uk/rebholz/index.html).
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31
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Nebert DW, Wain HM. Update on human genome completion and annotations: gene nomenclature. Hum Genomics 2003; 1:66-71. [PMID: 15601535 PMCID: PMC3525003 DOI: 10.1186/1479-7364-1-1-66] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2003] [Accepted: 07/31/2003] [Indexed: 11/10/2022] Open
Abstract
Why is agreeing on one particular name for each gene important? As one genome after another becomes sequenced, it is imperative to consider the complexity of genes, genetic architecture, gene expression, gene-gene and gene-product interactions and evolutionary relatedness across species. To agree on a particular gene name not only makes one's own research easier, but will also be helpful to the present generation, as well as future generations, of graduate students and postdoctoral fellows who are about to enter genomics research.
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Affiliation(s)
- Daniel W Nebert
- Department of Environmental Health and Center for Environmental Genetics, University of Cincinnati Medical Center, Cincinnati, OH 45267-0056, USA.
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Zhang WJ, Koltun WA, Tilberg AF, Thompson JL, Chorney MJ. Genetic control of interleukin-4-induced activation of the human signal transducer and activator of transcription 6 signaling pathway. Hum Immunol 2003; 64:402-15. [PMID: 12651067 DOI: 10.1016/s0198-8859(03)00002-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The interleukin (IL)-4-induced Stat6 signaling pathway is active in a variety of cell types, including immune cells and cancer cells, and plays an important role in the regulation of gene expression, such as CD23 and major histocompatibility complex class II. Using a semiquantitative gel shift assay in which nuclear Stat6 activities were scored, three Stat6 activation phenotypes were defined as Stat6(high) (intense banding), Stat6(low) (medium intensity banding), and Stat6(null) (very low to no discernible banding). These Stat6 phenotypes correlated well with levels of CD23 expression, but not with those of human leukocyte antigen-DR cell-surface display. Pedigree analyses revealed a Mendelian inheritance pattern that can be explained by two STAT6 Pathway (STAT6P) activation genotypes, which we term A and a, where STAT6P*A determines an active Stat6 signaling and STAT6P*a determines an inactive Stat6 signaling, with incomplete dominance. Total Stat6 protein levels failed to correlate with the above Stat6 phenotypes allowing us to propose that IL-4-induced Stat6 signaling is a polygenic quantitative trait regulated by a collection of several contributing genetic loci that functionally interact. The Stat6(null) phenotype may result from a defect in Stat6 signaling, which has important implications with respect to the pathogenesis of cancer and Th1/Th2 cytokine imbalance in autoimmune diseases in general.
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Affiliation(s)
- Wen Jie Zhang
- Department of Surgery, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA.
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33
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Pruitt KD, Tatusova T, Maglott DR. NCBI Reference Sequence project: update and current status. Nucleic Acids Res 2003; 31:34-7. [PMID: 12519942 PMCID: PMC165558 DOI: 10.1093/nar/gkg111] [Citation(s) in RCA: 130] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The goal of the NCBI Reference Sequence (RefSeq) project is to provide the single best non-redundant and comprehensive collection of naturally occurring biological molecules, representing the central dogma. Nucleotide and protein sequences are explicitly linked on a residue-by-residue basis in this collection. Ideally all molecule types will be available for each well-studied organism, but the initial database collection pragmatically includes only those molecules and organisms that are most readily identified. Thus different amounts of information are available for different organisms at any given time. Furthermore, for some organisms additional intermediate records are provided when the genome sequence is not yet finished. The collection is supplied by NCBI through three distinct pipelines in addition to collaborations with community groups. The collection is curated on an ongoing basis. Additional information about the NCBI RefSeq project is available at http://www.ncbi.nih.gov/RefSeq/.
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Affiliation(s)
- Kim D Pruitt
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A Room 6N605, 8600 Rockville Pike, Bethesda, MD 20894, USA.
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34
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Dang DT, Zhao W, Mahatan CS, Geiman DE, Yang VW. Opposing effects of Krüppel-like factor 4 (gut-enriched Krüppel-like factor) and Krüppel-like factor 5 (intestinal-enriched Krüppel-like factor) on the promoter of the Krüppel-like factor 4 gene. Nucleic Acids Res 2002; 30:2736-41. [PMID: 12087155 PMCID: PMC117055 DOI: 10.1093/nar/gkf400] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
KLF4 (Krüppel-like factor 4 or gut-enriched Krüppel-like factor, GKLF) and KLF5 (Krüppel-like factor 5 or intestinal-enriched Krüppel-like factor, IKLF) are two closely related members of the zinc finger-containing Krüppel-like factor family of transcription factors. Although both genes are expressed in the intestinal epithelium, their distributions are different: Klf4 is primarily expressed in the terminally differentiated villus cells while Klf5 is primarily in the proliferating crypt cells. Previous studies show that Klf4 is a negative regulator of cell proliferation and Klf5 is a positive regulator of cell proliferation. In this study, we demonstrate that Klf5 binds to a number of cis-DNA elements that have previously been shown to bind to Klf4. However, while Klf4 activates the promoter of its own gene, Klf5 suppresses the Klf4 promoter. Moreover, Klf5 abrogates the activating effect of Klf4 on the Klf4 promoter and Klf4 abrogates the inhibitory effect of Klf5 on the same promoter. An explanation of this competing effect is due to physical competition of the two proteins for binding to cognate DNA sequence. The complementary tissue localization of expression of Klf4 and Klf5 and the opposing effect of the two Klfs on the Klf4 promoter activity may provide a basis for the coordinated regulation of expression of the Klf4 gene in the intestinal epithelium.
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Affiliation(s)
- Duyen T Dang
- Division of Gastroenterology, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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35
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Wain HM, Bruford EA, Lovering RC, Lush MJ, Wright MW, Povey S. Guidelines for human gene nomenclature. Genomics 2002; 79:464-70. [PMID: 11944974 DOI: 10.1006/geno.2002.6748] [Citation(s) in RCA: 289] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Hester M Wain
- HUGO Gene Nomenclature Committee, The Galton Laboratory, Department of Biology, University College London, Wolfson House, 4, Stephenson Way, London, NW1 2HE, UK
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36
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Karchner SI, Franks DG, Powell WH, Hahn ME. Regulatory interactions among three members of the vertebrate aryl hydrocarbon receptor family: AHR repressor, AHR1, and AHR2. J Biol Chem 2002; 277:6949-59. [PMID: 11742002 DOI: 10.1074/jbc.m110779200] [Citation(s) in RCA: 110] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The effects of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and related compounds occur via the aryl hydrocarbon receptor (AHR), a member of the basic helix-loop-helix-Per-ARNT-Sim homology (bHLH-PAS) protein superfamily. A single AHR gene has been identified in mammals, whereas many fish species, including the Atlantic killifish (Fundulus heteroclitus) possess two distinct AHR genes (AHR1 and a novel form, AHR2). A mouse bHLH-PAS protein closely related to AHR and designated AHR repressor (AHRR) is induced by 3-methylcholanthrene and represses the transcriptional activity of the AHR. To determine whether AHRR is the mammalian ortholog of fish AHR2 and to investigate the mechanisms by which AHRR regulates AHR function, we cloned an AHRR ortholog in F. heteroclitus with high sequence identity to the mouse and human AHRRs. Killifish AHRR encodes a 680-residue protein with a predicted molecular mass of 75.2 kDa. We show that in vitro expressed AHRR proteins from human, mouse, and killifish all fail to bind [(3)H]TCDD or [(3)H]beta-naphthoflavone. In transient transfection experiments using a luciferase reporter gene under control of AHR response elements, killifish AHRR inhibited the TCDD-dependent transactivation function of both AHR1 and AHR2. AHRR mRNA is widely expressed in killifish tissues and is inducible by TCDD or polychlorinated biphenyls, but its expression is not altered in a population of fish exhibiting genetic resistance to these compounds. The F. heteroclitus AHRR promoter contains three putative AHR response elements. Both AHR1 and AHR2 activated transcription of luciferase driven by the AHRR promoter, and AHRR could repress its own promoter. Thus, AHRR is an evolutionarily conserved, TCDD-inducible repressor of AHR1 and AHR2 function. Phylogenetic analysis shows that AHRR, AHR1, and AHR2 are distinct genes, members of an AHR gene family; these three vertebrate AHR-like genes descended from a single invertebrate AHR.
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Affiliation(s)
- Sibel I Karchner
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
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37
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Simonds WF, James-Newton LA, Agarwal SK, Yang B, Skarulis MC, Hendy GN, Marx SJ. Familial isolated hyperparathyroidism: clinical and genetic characteristics of 36 kindreds. Medicine (Baltimore) 2002; 81:1-26. [PMID: 11807402 DOI: 10.1097/00005792-200201000-00001] [Citation(s) in RCA: 202] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Affiliation(s)
- William F Simonds
- Metabolic Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-1752, USA.
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38
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Affiliation(s)
- Thomas E. Broad
- AgResearch Molecular Biology Unit, University of Otago, Dunedin, New Zealand
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39
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Jenssen TK, Laegreid A, Komorowski J, Hovig E. A literature network of human genes for high-throughput analysis of gene expression. Nat Genet 2001; 28:21-8. [PMID: 11326270 DOI: 10.1038/ng0501-21] [Citation(s) in RCA: 382] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We have carried out automated extraction of explicit and implicit biomedical knowledge from publicly available gene and text databases to create a gene-to-gene co-citation network for 13,712 named human genes by automated analysis of titles and abstracts in over 10 million MEDLINE records. The associations between genes have been annotated by linking genes to terms from the medical subject heading (MeSH) index and terms from the gene ontology (GO) database. The extracted database and accompanying web tools for gene-expression analysis have collectively been named 'PubGene'. We validated the extracted networks by three large-scale experiments showing that co-occurrence reflects biologically meaningful relationships, thus providing an approach to extract and structure known biology. We validated the applicability of the tools by analyzing two publicly available microarray data sets.
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Affiliation(s)
- T K Jenssen
- Department of Computer and Information Science, Norwegian University of Science and Technology, Trondheim, Norway
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40
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Smith CI, Islam TC, Mattsson PT, Mohamed AJ, Nore BF, Vihinen M. The Tec family of cytoplasmic tyrosine kinases: mammalian Btk, Bmx, Itk, Tec, Txk and homologs in other species. Bioessays 2001; 23:436-46. [PMID: 11340625 DOI: 10.1002/bies.1062] [Citation(s) in RCA: 201] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Cytoplasmic protein-tyrosine kinases (PTKs) are enzymes involved in transducing a vast number of signals in metazoans. The importance of the Tec family of kinases was immediately recognized when, in 1993, mutations in the gene encoding Bruton's tyrosine kinase (Btk) were reported to cause the human disease X-linked agammaglobulinemia (XLA). Since then, additional kinases belonging to this family have been isolated, and the availability of full genome sequences allows identification of all members in selected species enabling phylogenetic considerations. Tec kinases are endowed with Pleckstrin homology (PH) and Tec homology (TH) domains and are involved in diverse biological processes related to the control of survival and differentiation fate. Membrane translocation resulting in the activation of Tec kinases with subsequent Ca2+ release seems to be a general feature. However, nuclear translocation may also be of importance. The purpose of this essay is to characterize members of the Tec family and discuss their involvement in signaling. The three-dimensional structure, expression pattern and evolutionary aspects will also be considered.
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Affiliation(s)
- C I Smith
- Clinical Research Centre, Karolinska Institutet, Stockholm, Sweden.
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41
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Sun R, Chen X, Yang VW. Intestinal-enriched Krüppel-like factor (Krüppel-like factor 5) is a positive regulator of cellular proliferation. J Biol Chem 2001; 276:6897-900. [PMID: 11152667 PMCID: PMC2268089 DOI: 10.1074/jbc.c000870200] [Citation(s) in RCA: 127] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Intestinal-enriched Krüppel-like factor (IKLF or KLF5) belongs to the family of mammalian Krüppel-like transcription factors. Previous studies indicate that expression of IKLF is enriched in the proliferating crypt epithelial cells of the intestinal tract. However, the biological function of IKLF is unknown. In the current study, we have shown that the level of IKLF mRNA was nearly undetectable in serum-deprived NIH3T3 fibroblasts but became acutely and significantly increased upon the addition of fetal bovine serum or the phorbol ester, PMA. This induction required protein synthesis because it was prevented by cycloheximide. Transfection of IKLF into NIH3T3 cells resulted in the formation of foci in a manner similar to that caused by the activated Ha-ras oncogene. Constitutive expression of IKLF in transfected NIH3T3 cells significantly increased the rate of proliferation when compared with cells transfected with an empty vector. The growth of IKLF-transfected cells was no longer inhibited by cell-cell contact or by low serum content. Moreover, these cells proliferated in an anchorage-independent fashion. We conclude that IKLF encodes a delayed early response gene product that positively regulates cellular proliferation and may give rise to a transformed phenotype when overexpressed.
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Affiliation(s)
- Ronggai Sun
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Xinming Chen
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Vincent W. Yang
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
- ¶ To whom correspondence should be addressed: Dept. of Medicine, Ross 918, The Johns Hopkins University School of Medicine, 720 Rutland Ave., Baltimore, MD 21205. Tel.: 410-955-9691; Fax: 410-955-9677; E-mail:
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42
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Abstract
Thousands of genes have been painstakingly identified and characterized a few genes at a time. Many thousands more are being predicted by large scale cDNA and genomic sequencing projects, with levels of evidence ranging from supporting mRNA sequence and comparative genomics to computing ab initio models. This, coupled with the burgeoning scientific literature, makes it critical to have a comprehensive directory for genes and reference sequences for key genomes. The NCBI provides two resources, LocusLink and RefSeq, to meet these needs. LocusLink organizes information around genes to generate a central hub for accessing gene-specific information for fruit fly, human, mouse, rat and zebrafish. RefSeq provides reference sequence standards for genomes, transcripts and proteins; human, mouse and rat mRNA RefSeqs, and their corresponding proteins, are discussed here. Together, RefSeq and LocusLink provide a non-redundant view of genes and other loci to support research on genes and gene families, variation, gene expression and genome annotation. Additional information about LocusLink and RefSeq is available at http://www.ncbi.nlm.nih.gov/LocusLink/.
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Affiliation(s)
- K D Pruitt
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A Room 6N605, 8600 Rockville Pike, Bethesda, MD 20894 USA.
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43
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Hicar MD, Liu Y, Allen CE, Wu LC. Structure of the human zinc finger protein HIVEP3: molecular cloning, expression, exon-intron structure, and comparison with paralogous genes HIVEP1 and HIVEP2. Genomics 2001; 71:89-100. [PMID: 11161801 DOI: 10.1006/geno.2000.6425] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Here we report the cloning and characterization of HIVEP3, the newest member in the human immunodeficiency virus type 1 enhancer-binding protein family that encodes large zinc finger proteins and regulates transcription via the kappaB enhancer motif. The largest open reading frame of HIVEP3 contains 2406 aa. and is approximately 80% identical to the mouse counterpart. The HIVEP3 gene is located in the chromosomal region 1p34 and is at least 300 kb with 10 exons. RNA studies show that multiple HIVEP3 transcripts are differentially expressed and regulated. Additionally, transcription termination occurs in the ultimate exon, exon 10, or in exon 6. Therefore, HIVEP3 may produce protein isoforms that contain or exclude the carboxyl DNA binding domain and the leucine zipper by alternative RNA splicing and differential polyadenylation. Sequence homologous to HIVEP3 exon 6 is not found in mouse nor are the paralogous genes HIVEP1 and HIVEP2. Zoo-blot analysis suggests that sequences homologous to the human exon 6 are present only in primates and cow. Therefore, a foreign DNA harboring a termination exon likely was inserted into the HIVEP3 locus relatively recently in evolution, resulting in the acquisition of novel gene regulatory mechanisms as well as the generation of structural and functional diversity.
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MESH Headings
- Amino Acid Sequence
- Animals
- Blotting, Northern
- Blotting, Southern
- Brain/metabolism
- Carrier Proteins/chemistry
- Carrier Proteins/genetics
- Chromosomes, Human, Pair 1
- Cloning, Molecular
- Cosmids
- DNA, Complementary/metabolism
- DNA-Binding Proteins/biosynthesis
- DNA-Binding Proteins/chemistry
- DNA-Binding Proteins/genetics
- Exons
- Expressed Sequence Tags
- Gene Library
- Humans
- Introns
- Mice
- Models, Genetic
- Molecular Sequence Data
- Oligonucleotide Probes/metabolism
- Open Reading Frames
- Phylogeny
- Poly A/metabolism
- Protein Isoforms
- Protein Structure, Tertiary
- Reverse Transcriptase Polymerase Chain Reaction
- Sequence Homology, Amino Acid
- Tissue Distribution
- Transcription Factors
- Transcription, Genetic
- Zinc Fingers
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Affiliation(s)
- M D Hicar
- Department of Molecular Virology, Immunology, and Medical Genetics, College of Medicine and Public Health, The Ohio State University, Columbus, Ohio 43210, USA
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Abstract
As the sequencing of the human genome is completed by the Human Genome Project, the analysis of this rich source of information will illuminate many areas in medicine and biology. The protein tyrosine kinases are a large multigene family with particular relevance to many human diseases, including cancer. A search of the human genome for tyrosine kinase coding elements identified several novel genes and enabled the creation of a nonredundant catalog of tyrosine kinase genes. Ninety unique kinase genes can be identified in the human genome, along with five pseudogenes. Of the 90 tyrosine kinases, 58 are receptor type, distributed into 20 subfamilies. The 32 nonreceptor tyrosine kinases can be placed in 10 subfamilies. Additionally, mouse orthologs can be identified for nearly all the human tyrosine kinases. The completion of the human tyrosine kinase family tree provides a framework for further advances in biomedical science.
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Affiliation(s)
- D R Robinson
- Department of Biological Chemistry, UC Davis School of Medicine, UC Davis Cancer Center, Sacramento, California, CA 95817, USA
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45
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Trama J, Lu Q, Hawley RG, Ho SN. The NFAT-related protein NFATL1 (TonEBP/NFAT5) is induced upon T cell activation in a calcineurin-dependent manner. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2000; 165:4884-94. [PMID: 11046013 DOI: 10.4049/jimmunol.165.9.4884] [Citation(s) in RCA: 132] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
NFAT DNA binding complexes regulate programs of cellular activation and differentiation by translating receptor-dependent signaling events into specific transcriptional responses. NFAT proteins, originally defined as calcium/calcineurin-dependent regulators of cytokine gene transcription in T lymphocytes, are expressed in many different cell types and represent critical signaling intermediates that mediate an increasingly wide spectrum of biologic responses. Recent studies have identified a novel protein containing a region of similarity to the NFAT DNA binding domain. Here we demonstrate that this protein, designated NFATL1 (also known as tonicity enhancer binding protein and NFAT5) is expressed at high levels in the thymus but is undetectable in mature lymphocytes. However, NFATL1 can be induced in both primary quiescent T lymphocytes and differentiated Th1 and Th2 cell populations upon mitogen- or Ag receptor-dependent activation. The induction of NFATL1 protein, as well as NFATL1-dependent transcription, is inhibited by cyclosporin A and FK506, and expression of constitutively active calcineurin induces NFATL1-dependent transcription. Overexpression of NFATc1 and inhibition of NFATc activity through the use of a dominant negative NFATc1 protein have no affect on NFATL1-dependent transcription, indicating that NFATc proteins do not play a role in the calcineurin-dependent induction of NFATL1. Interestingly, induction of NFATL1 by a hyperosmotic stimulus is not blocked by the inhibition of calcineurin. Moreover, osmotic stress response genes such as aldose reductase are not induced upon T cell activation. Thus inducible expression of NFATL1 represents a mechanism by which receptor-dependent signals as well as osmotic stress signals are translated into transcriptional responses that regulate cell function.
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Affiliation(s)
- J Trama
- Department of Pathology, University of California at San Diego, La Jolla, CA 92093, USA
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46
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Hirose S, Okada M, Kaneko S, Mitsudome A. Are some idiopathic epilepsies disorders of ion channels?: A working hypothesis. Epilepsy Res 2000; 41:191-204. [PMID: 10962210 DOI: 10.1016/s0920-1211(00)00141-8] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Epilepsy is a common neurological disease and encompasses a variety of disorders with paroxysms. Although there is a genetic component in the pathogenesis of epilepsy, the molecular mechanisms of this syndrome remains poorly understood. Linkage analysis and positional cloning have not been sufficient tools for determining the pathogenic mechanisms of common idiopathic epilepsies, and hence, novel approaches, based on the etiology of epilepsy, are necessary. Recently, many paroxysmal disorders, including, epilepsy, have been considered to be due to ion channel abnormalities or channelopathies. Results of recent studies employing gene analysis in animal models of epilepsy and human familial epilepsies support the hypothesis that at least some of the so called idiopathic epilepsies, i.e. epilepsies currently, classified as idiopathic could be considered as a channelopathy. This hypothesis is consistent with the putative prerequisites for genes responsible for the majority of idiopathic epilepsies that can adequately explain the following characteristics of epilepsy. Neuronal hyperexcitability, dominant inheritance with various penetrance, pharmacological role of some conventional antiepileptic drugs, age dependency in the onset of epilepsy, and the involvement of genetic factors in the pathogenesis of post-traumatic epilepsy. Search for mutations in ion channels expressed in the central nervous system may help in finding defects underlying some of idiopathic epilepsies, thereby enhancing, our understanding of the molecular pathogenesis of epilepsy. A working hypothesis to view certain idiopathic epilepsies as disorders of ion channels should provide a new insight to our understanding of epilepsy and allow the design of novel therapies.
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Affiliation(s)
- S Hirose
- Department of Pediatrics, School of Medicine, Fukuoka University, 45-1, 7-chome Nanakuma, Jonan-ku, 814-0180, Fukuoka, Japan.
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47
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Good PJ, Chen Q, Warner SJ, Herring DC. A family of human RNA-binding proteins related to the Drosophila Bruno translational regulator. J Biol Chem 2000; 275:28583-92. [PMID: 10893231 DOI: 10.1074/jbc.m003083200] [Citation(s) in RCA: 108] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The post-transcriptional regulation of gene expression by RNA-binding proteins is an important element in controlling both normal cell functions and animal development. The diverse roles are demonstrated by the Elav family of RNA-binding proteins, where various members have been shown to regulate several processes involving mRNA. We have identified another family of RNA-binding proteins distantly related to the Elav family but closely related to Bruno, a translational regulator in Drosophila melanogaster. In humans, six Bruno-like genes have been identified, whereas other species such as Drosophila, Xenopus laevis, and Caenorhabditis elegans have at least two members of this family, and related genes have also been detected in plants and ascidians. The human BRUNOL2 and BRUNOL3 are 92% identical in the RNA-binding domains, although the BRUNOL2 gene is expressed ubiquitously whereas BRUNOL3 is expressed predominantly in the heart, muscle, and nervous system. Both of these proteins bind the same target RNA, the Bruno response element. The RNA-binding domain that recognizes the Bruno response element is composed of two consecutive RNA recognition motifs at the amino terminus of vertebrate Bruno protein. The possible involvement of the Bruno family of proteins in the CUG repeat expansion disease myotonic dystrophy is discussed.
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Affiliation(s)
- P J Good
- Department of Biochemistry and Molecular Biology and Feist-Weiller Cancer Center, Louisiana State University, Health Sciences Center, Shreveport, Lousiana 71130, USA.
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Saitoh Y, Miyamoto N, Okada T, Gondo Y, Showguchi-Miyata J, Hadano S, Ikeda JE. The RS447 human megasatellite tandem repetitive sequence encodes a novel deubiquitinating enzyme with a functional promoter. Genomics 2000; 67:291-300. [PMID: 10936051 DOI: 10.1006/geno.2000.6261] [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
We have recently identified a tandem repetitive DNA sequence that we designated the RS447 megasatellite. In this study, we describe a functional novel deubiquitinating enzyme (USP17, 60 kDa) gene that is intronless and encoded by the RS447 repeating unit. Northern blot analysis in conjunction with 5' and 3' rapid amplification of cDNA ends confirmed the presence of poly(A)(+) containing RS447 RNA in normal cells. We also identified a functional promoter sequence as well as an open reading frame within every RS447 repeat. When USP17 was expressed in Escherichia coli, it exhibited deubiquitinating activity in vivo. An antibody against USP17 detected USP17 protein in human cells. Our results indicate that the RS447 repeating unit on this megasatellite repeat codes for and actively expresses a functional deubiquitinating enzyme. Although it is expressed ubiquitously in human tissues, USP17 exhibited a unique expression pattern in that its complementary strand is transcribed as an antisense transcript that may modulate the level of USP17 expression in the human brain.
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Affiliation(s)
- Y Saitoh
- Department of Molecular Neuroscience, The Institute of Medical Sciences, Isehara, Japan
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Wain H, Bruford E, Duncanson A, Lovering R, Povey S. Nomenclature: Genes, Weights and Measures, Animals, Elements, and Planets. Radiat Res 2000. [DOI: 10.1667/0033-7587(2000)154[0001:ngwama]2.0.co;2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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