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Pommerenke C, Nagel S, Haake J, Koelz AL, Christgen M, Steenpass L, Eberth S. Molecular Characterization and Subtyping of Breast Cancer Cell Lines Provide Novel Insights into Cancer Relevant Genes. Cells 2024; 13:301. [PMID: 38391914 PMCID: PMC10886524 DOI: 10.3390/cells13040301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/26/2024] [Accepted: 02/02/2024] [Indexed: 02/24/2024] Open
Abstract
Continuous cell lines are important and commonly used in vitro models in breast cancer (BC) research. Selection of the appropriate model cell line is crucial and requires consideration of their molecular characteristics. To characterize BC cell line models in depth, we profiled a panel of 29 authenticated and publicly available BC cell lines by mRNA-sequencing, mutation analysis, and immunoblotting. Gene expression profiles separated BC cell lines in two major clusters that represent basal-like (mainly triple-negative BC) and luminal BC subtypes, respectively. HER2-positive cell lines were located within the luminal cluster. Mutation calling highlighted the frequent aberration of TP53 and BRCA2 in BC cell lines, which, therefore, share relevant characteristics with primary BC. Furthermore, we showed that the data can be used to find novel, potential oncogenic fusion transcripts, e.g., FGFR2::CRYBG1 and RTN4IP1::CRYBG1 in cell line MFM-223, and to elucidate the regulatory circuit of IRX genes and KLF15 as novel candidate tumor suppressor genes in BC. Our data indicated that KLF15 was activated by IRX1 and inhibited by IRX3. Moreover, KLF15 inhibited IRX1 in cell line HCC-1599. Each BC cell line carries unique molecular features. Therefore, the molecular characteristics of BC cell lines described here might serve as a valuable resource to improve the selection of appropriate models for BC research.
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Affiliation(s)
- Claudia Pommerenke
- Department of Bioinformatics, IT and Databases, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany;
| | - Stefan Nagel
- Department of Human and Animal Cell Lines, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany; (S.N.)
| | - Josephine Haake
- Department of Human and Animal Cell Lines, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany; (S.N.)
| | - Anne Leena Koelz
- Department of Human and Animal Cell Lines, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany; (S.N.)
| | - Matthias Christgen
- Institute of Pathology, Hannover Medical School, 30625 Hannover, Germany
| | - Laura Steenpass
- Department of Human and Animal Cell Lines, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany; (S.N.)
- Zoological Institute, Technische Universität Braunschweig, 38106 Braunschweig, Germany
| | - Sonja Eberth
- Department of Human and Animal Cell Lines, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany; (S.N.)
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Del Corvo M, Bongiorni S, Stefanon B, Sgorlon S, Valentini A, Ajmone Marsan P, Chillemi G. Genome-Wide DNA Methylation and Gene Expression Profiles in Cows Subjected to Different Stress Level as Assessed by Cortisol in Milk. Genes (Basel) 2020; 11:genes11080850. [PMID: 32722461 PMCID: PMC7464205 DOI: 10.3390/genes11080850] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/10/2020] [Accepted: 07/22/2020] [Indexed: 12/20/2022] Open
Abstract
Dairy cattle health, wellbeing and productivity are deeply affected by stress. Its influence on metabolism and immune response is well known, but the underlying epigenetic mechanisms require further investigation. In this study, we compared DNA methylation and gene expression signatures between two dairy cattle populations falling in the high- and low-variant tails of the distribution of milk cortisol concentration (MC), a neuroendocrine marker of stress in dairy cows. Reduced Representation Bisulfite Sequencing was used to obtain a methylation map from blood samples of these animals. The high and low groups exhibited similar amounts of methylated CpGs, while we found differences among non-CpG sites. Significant methylation changes were detected in 248 genes. We also identified significant fold differences in the expression of 324 genes. KEGG and Gene Ontology (GO) analysis showed that genes of both groups act together in several pathways, such as nervous system activity, immune regulatory functions and glucocorticoid metabolism. These preliminary results suggest that, in livestock, cortisol secretion could act as a trigger for epigenetic regulation and that peripheral changes in methylation can provide an insight into central nervous system functions.
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Affiliation(s)
- Marcello Del Corvo
- Department of Animal Science Food and Nutrition—DIANA, Nutrigenomics and Proteomics Research Centre—PRONUTRIGEN, and Biodiversity and Ancient DNA Research Centre, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy;
- Istituto di Biologia e BiotecnologiaAgraria, Consiglio Nazionale delle Ricerche, 20133 Milan, Italy
- Correspondence:
| | - Silvia Bongiorni
- Department of Ecological and Biological sciences DEB, University of Tuscia, 01100 Viterbo, Italy;
| | - Bruno Stefanon
- Department of Agrifood, Environmental and Animal Science–University of Udine, 33100 Udine, Italy; (B.S.); (S.S.)
| | - Sandy Sgorlon
- Department of Agrifood, Environmental and Animal Science–University of Udine, 33100 Udine, Italy; (B.S.); (S.S.)
| | - Alessio Valentini
- Department for Innovation in Biological, Agro-food and Forest systems DIBAF, University of Tuscia, 01100 Viterbo, Italy; (A.V.); (G.C.)
| | - Paolo Ajmone Marsan
- Department of Animal Science Food and Nutrition—DIANA, Nutrigenomics and Proteomics Research Centre—PRONUTRIGEN, and Biodiversity and Ancient DNA Research Centre, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy;
| | - Giovanni Chillemi
- Department for Innovation in Biological, Agro-food and Forest systems DIBAF, University of Tuscia, 01100 Viterbo, Italy; (A.V.); (G.C.)
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, IBIOM, CNR, 70126 Bari, Italy
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Peng Y, Shui L, Xie J, Liu S. Development and validation of a novel 15-CpG-based signature for predicting prognosis in triple-negative breast cancer. J Cell Mol Med 2020; 24:9378-9387. [PMID: 32649035 PMCID: PMC7417707 DOI: 10.1111/jcmm.15588] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 06/05/2020] [Accepted: 06/07/2020] [Indexed: 02/05/2023] Open
Abstract
DNA methylation is an important biological regulatory mechanism that changes gene expression without altering the DNA sequence. Increasing studies have revealed that DNA methylation data play a vital role in the field of oncology. However, the methylation site signature in triple‐negative breast cancer (TNBC) remains unknown. In our research, we analysed 158 TNBC samples and 98 noncancerous samples from The Cancer Genome Atlas (TCGA) in three phases. In the discovery phase, 86 CpGs were identified by univariate Cox proportional hazards regression (CPHR) analyses to be significantly correlated with overall survival (P < 0.01). In the training phase, these candidate CpGs were further narrowed down to a 15‐CpG‐based signature by conducting least absolute shrinkage and selector operator (LASSO) Cox regression in the training set. In the validation phase, the 15‐CpG‐based signature was verified using two different internal sets and one external validation set. Furthermore, a nomogram comprising the CpG‐based signature and TNM stage was generated to predict the 1‐, 3‐ and 5‐year overall survival in the primary set, and it showed excellent performance in the three validation sets (concordance indexes: 0.924, 0.974 and 0.637). This study showed that our nomogram has a precise predictive effect on the prognosis of TNBC and can potentially be implemented for clinical treatment and diagnosis.
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Affiliation(s)
- Yang Peng
- Department of Endocrine and Breast Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Lin Shui
- Department of Medical Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Jian Xie
- Department of General Surgery, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - Shengchun Liu
- Department of Endocrine and Breast Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
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Doaei S, Mosavi Jarrahi SA, Sanjari Moghadam A, Akbari ME, Javadi Kooshesh S, Badeli M, Azizi Tabesh G, Abbas Torki S, Gholamalizadeh M, Zhu ZH, Montazeri F, Mirzaei Dahka S. The effect of rs9930506 FTO gene polymorphism on obesity risk: a meta-analysis. Biomol Concepts 2020; 10:237-242. [PMID: 31855561 DOI: 10.1515/bmc-2019-0025] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 10/28/2019] [Indexed: 12/28/2022] Open
Abstract
Obesity is associated with polymorphisms of the fat mass and obesity associated gene (FTO). This meta-analysis aimed to investigate the association of the rs9930506 FTO gene polymorphism and obesity. To the best of our knowledge, this study is the first meta-analysis to evaluate the relation between FTO rs9930506 polymorphism and obesity. We searched PubMed, Web of Science, and Embase to identify studies investigating the relations between the rs9930506 FTO gene polymorphism and obesity risk. We pooled adjusted odds ratios (OR) as overall and in continent subgroups. A Fixed-effects model was used to analyze the results of these studies in dominant and recessive models. By examining 3337 obesity cases and 3159 healthy controls, we identified 8 eligible case-control studies. Considering the dominant model of inheritance, there was a relationship between the rs9939506 polymorphism and obesity (OR=1.34 [1.03- 1.74]). The association remained significant in the European subgroup (OR=1.68 [1.2-2.36]), but not in the Asian subgroup. Using the recessive model, we also found a significant relationship when the overall association was investigated (OR=2.47; 95% CI 1.56-3.91). In conclusion, this study identified that the carriers of the risk allele of FTO rs9930506 polymorphism are at higher risk for obesity.
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Affiliation(s)
- S Doaei
- Research Center of Health and Environment, Guilan University of Medical Sciences, Rasht, Iran.,Department of Public Health, School of Health, Guilan University of Medical Sciences, Rasht, Iran
| | - S A Mosavi Jarrahi
- School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - A Sanjari Moghadam
- School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - M E Akbari
- Cancer Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - S Javadi Kooshesh
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - M Badeli
- Department of Nutrition, Urmia University of Medical Science, Urmia, Iran
| | - Gh Azizi Tabesh
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - S Abbas Torki
- Department of Nutrition, Faculty of Nutrition Sciences, Shiraz University of MedicalSciences, Shiraz, Iran
| | - M Gholamalizadeh
- Student Research Committee, Cancer Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Z H Zhu
- School of Public Health, Peking Union Medical College Beijing, Beijing China
| | - F Montazeri
- School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - S Mirzaei Dahka
- Student Research Committee, Guilan University of Medical Sciences, Rasht, Iran
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Doaei S, Kalantari N, Izadi P, Salonurmi T, Jarrahi AM, Rafieifar S, Azizi Tabesh G, Rahimzadeh G, Gholamalizadeh M, Goodarzi MO. Interactions between macro-nutrients' intake, FTO and IRX3 gene expression, and FTO genotype in obese and overweight male adolescents. Adipocyte 2019; 8:386-391. [PMID: 31771407 PMCID: PMC6948981 DOI: 10.1080/21623945.2019.1693745] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 10/10/2019] [Accepted: 11/08/2019] [Indexed: 10/25/2022] Open
Abstract
This study is the first to identify the effects of FTO genotype on the interactions between the level of macro-nutrients intake and the expression level of fat mass and obesity associated (FTO) and homeobox transcription factor iriquois-3 (IRX3) genes This longitudinal study was carried out on 84 overweight and obese adolescent boys in Tehran, Iran. The rs9930506 SNP in FTO was genotyped at baseline and the level of FTO and IRX3 expression in PBMCs and macro-nutrients' intake were assessed at baseline and after 18 weeks of the intervention. The results identified that the higher carbohydrates intake significantly up-regulated the FTO gene (P = 0.001) and down-regulated the IRX3 gene (P = 0.01). Protein intake up-regulated the FTO gene (P = 0.001). In carriers of GG genotype of FTO gene, the amount of dietary carbohydrate had a positive association with FTO gene expression (p = 0.001, and p = 0.04, respectively). In AA/AG carriers, dietary protein was positively associated with FTO gene expression (p = 0.001) and dietary carbohydrate was negatively associated with IRX3 gene expression (P = 0.04). Therefore, dietary carbohydrateseems to be associated with FTO and IRX3 genes expression. These associations are influenced by FTO genotype.
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Affiliation(s)
- Saeid Doaei
- Research Center of Health and Environment, Guilan University of Medical Sciences, Rasht, Iran
- Student Research Committee, Cancer Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Naser Kalantari
- Department of Community Nutrition, School of Nutrition and Food Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Pantea Izadi
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Tuire Salonurmi
- Department of Internal Medicine, Oulu University Hospital and University of Oulu, Oulu, Finland
| | | | - Shahram Rafieifar
- Health Promotion and Education Department, Ministry of Health, Tehran, Iran
| | - Ghasem Azizi Tabesh
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ghazaleh Rahimzadeh
- Institute for Intelligent Systems Research and Innovation (IISRI), Deakin University, Geelong Waurn Ponds, Australia
| | - Maryam Gholamalizadeh
- Student Research Committee, Cancer Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mark O. Goodarzi
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
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The possible mechanisms of the effects of IRX3 gene on body weight: an overview. ACTA ACUST UNITED AC 2019; 4:e225-e230. [PMID: 31538128 PMCID: PMC6749179 DOI: 10.5114/amsad.2019.87545] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Accepted: 04/29/2019] [Indexed: 12/19/2022]
Abstract
Introduction Recent studies reported that FTO exert its effects on body weight through change the expression IRX3. The aim of this study was investigation of the possible mechanisms of the effects of IRX3 gene on obesity. Material and methods The present review was carried out using keywords such as polymorphism and/or obesity and/or BMI and/or IRX3 gene and/or Iroquois homeobox protein 3. Databases including PubMed, Science Direct, web of sciences, Scopus, and Cochran databases were used to collect all related articles published from 2000 to 2019. Results Based on this review, there are some evidences on the association between the IRX3 polymorphisms and the IRX3 expression level with body weight. In some studies, the up-regulation of IRX3 expression was related to increased body weight, while in some other studies down-regulation of IRX3 expression was related to obesity. Conclusions This review investigated the probable mechanisms of the effects of the IRX3 gene on obesity. Studies in this are limited and reported contradictory results. Further studies are required to evaluate the role of IRX3 gene in the associations between genes, diet, and obesity.
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Jung IH, Jung DE, Chung YY, Kim KS, Park SW. Iroquois Homeobox 1 Acts as a True Tumor Suppressor in Multiple Organs by Regulating Cell Cycle Progression. Neoplasia 2019; 21:1003-1014. [PMID: 31450023 PMCID: PMC6715957 DOI: 10.1016/j.neo.2019.08.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 07/16/2019] [Accepted: 08/05/2019] [Indexed: 02/07/2023] Open
Abstract
Iroquois homeobox 1 (IRX1) belongs to the Iroquois homeobox family known to play an important role during embryonic development. Interestingly, however, recent studies have suggested that IRX1 also acts as a tumor suppressor. Here, we use homozygous knockout mutants of zebrafish to demonstrate that the IRX1 gene is a true tumor suppressor gene and mechanism of the tumor suppression is mediated by repressing cell cycle progression. In this study, we found that knockout of zebrafish Irx1 gene induced hyperplasia and tumorigenesis in the multiple organs where the gene was expressed. On the other hands, overexpression of the IRX1 gene in human tumor cell lines showed delayed cell proliferation of the tumor cells. These results suggest that the IRX1 gene is truly involved in tumor suppression. In an attempt to identify the genes regulated by the transcription factor IRX1, we performed microarray assay using the cRNA obtained from the knockout mutants. Our result indicated that the highest fold change of the differential genes fell into the gene category of cell cycle regulation, suggesting that the significant canonical pathway of IRX1 in antitumorigenesis is done by regulating cell cycle. Experiment with cell cycle blockers treated to IRX1 overexpressing tumor cells showed that the IRX1 overexpression actually delayed the cell cycle. Furthermore, Western blot analysis with cyclin antibodies showed that IRX1 overexpression induced decrease of cyclin production in the cancer cells. In conclusion, our in vivo and in vitro studies revealed that IRX1 gene functionally acts as a true tumor suppressor, inhibiting tumor cell growth by regulating cell cycle.
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Affiliation(s)
- In Hye Jung
- Department of Internal Medicine, Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, Republic of Korea.
| | - Dawoon E Jung
- Department of Internal Medicine, Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, Republic of Korea.
| | - Yong-Yoon Chung
- Research Institute of SMT Bio, SMT Bio Co., Ltd., Seoul, Republic of Korea.
| | - Kyung-Sik Kim
- Department of Surgery, Yonsei University College of Medicine, Seoul, Republic of Korea.
| | - Seung Woo Park
- Department of Internal Medicine, Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, Republic of Korea.
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Taira M, Imamura M, Takahashi A, Kamatani Y, Yamauchi T, Araki SI, Tanaka N, van Zuydam NR, Ahlqvist E, Toyoda M, Umezono T, Kawai K, Imanishi M, Watada H, Suzuki D, Maegawa H, Babazono T, Kaku K, Kawamori R, Groop LC, McCarthy MI, Kadowaki T, Maeda S. A variant within the FTO confers susceptibility to diabetic nephropathy in Japanese patients with type 2 diabetes. PLoS One 2018; 13:e0208654. [PMID: 30566433 PMCID: PMC6300288 DOI: 10.1371/journal.pone.0208654] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 11/20/2018] [Indexed: 11/18/2022] Open
Abstract
To explore novel genetic loci for diabetic nephropathy, we performed genome-wide association studies (GWAS) for diabetic nephropathy in Japanese patients with type 2 diabetes. We analyzed the association of 5,768,242 single nucleotide polymorphisms (SNPs) in Japanese patients with type 2 diabetes, 2,380 nephropathy cases and 5,234 controls. We further performed GWAS for diabetic nephropathy using independent Japanese patients with type 2 diabetes, 429 cases and 358 controls and the results of these two GWAS were combined with an inverse variance meta-analysis (stage-1), followed by a de novo genotyping for the candidate SNP loci (p < 1.0 × 10−4) in an independent case-control study (Stage-2; 1,213 cases and 1,298 controls). After integrating stage-1 and stage-2 data, we identified one SNP locus, significantly associated with diabetic nephropathy; rs56094641 in FTO, P = 7.74 × 10−10. We further examined the association of rs56094641 with diabetic nephropathy in independent Japanese patients with type 2 diabetes (902 cases and 1,221 controls), and found that the association of this locus with diabetic nephropathy remained significant after integrating all association data (P = 7.62 × 10−10). We have identified FTO locus as a novel locus for conferring susceptibility to diabetic nephropathy in Japanese patients with type 2 diabetes.
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Affiliation(s)
- Makiko Taira
- Laboratory for Endocrinology, Metabolism and Kidney Diseases, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | - Minako Imamura
- Laboratory for Endocrinology, Metabolism and Kidney Diseases, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
- Department of Advanced Genomic and Laboratory Medicine, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
- Division of Clinical Laboratory and Blood Transfusion, University of the Ryukyus Hospital, Okinawa, Japan
| | - Atsushi Takahashi
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
- Department of Genomic Medicine, Research Institute, National Cerebral and Cardiovascular Center, Osaka, Japan
| | - Yoichiro Kamatani
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
- Kyoto-McGill International Collaborative School in Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Toshimasa Yamauchi
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Shin-ichi Araki
- Department of Medicine, Shiga University of Medical Science, Shiga, Japan
| | - Nobue Tanaka
- Diabetes Center, Tokyo Women’s Medical University School of Medicine, Tokyo, Japan
| | - Natalie R. van Zuydam
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Oxford Center for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Emma Ahlqvist
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden
| | - Masao Toyoda
- Division of Nephrology, Endocrinology and Metabolism, Department of Internal Medicine, Tokai University School of Medicine, Kanagawa, Japan
| | - Tomoya Umezono
- Division of Nephrology, Endocrinology and Metabolism, Department of Internal Medicine, Tokai University School of Medicine, Kanagawa, Japan
| | | | - Masahito Imanishi
- Division of Nephrology and Hypertension, Department of Internal Medicine, Osaka City General Hospital, Osaka, Japan
- Department of Nephrology, and Hemodialysis Unit, Ishikiriseiki Hospital, Higashi-Osaka, Japan
| | - Hirotaka Watada
- Department of Metabolism and Endocrinology, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Sportology Center, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | | | - Hiroshi Maegawa
- Department of Medicine, Shiga University of Medical Science, Shiga, Japan
| | - Tetsuya Babazono
- Diabetes Center, Tokyo Women’s Medical University School of Medicine, Tokyo, Japan
| | - Kohei Kaku
- Department of Internal Medicine, Kawasaki Medical School, Okayama, Japan
| | - Ryuzo Kawamori
- Sportology Center, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | | | - Leif C. Groop
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Mark I. McCarthy
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Oxford Center for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
- Oxford NIHR BIOMEDICAL Research Centre, Oxford University Hospitals Trust, Oxford, United Kingdom
| | - Takashi Kadowaki
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Prevention of Diabetes and Lifestyle-Related Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Metabolism and Nutrition, Mizonokuchi Hospital, Faculty of Medicine, Teikyo University, Kanagawa, Japan
| | - Shiro Maeda
- Laboratory for Endocrinology, Metabolism and Kidney Diseases, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
- Department of Advanced Genomic and Laboratory Medicine, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
- Division of Clinical Laboratory and Blood Transfusion, University of the Ryukyus Hospital, Okinawa, Japan
- * E-mail:
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Kernel machine SNP set analysis provides new insight into the association between obesity and polymorphisms located on the chromosomal 16q.12.2 region: Tehran Lipid and Glucose Study. Gene 2018. [PMID: 29524577 DOI: 10.1016/j.gene.2018.03.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
INTRODUCTION Obesity is a serious health problem that leads to low quality of life and early mortality. To the purpose of prevention and gene therapy for such a worldwide disease, genome wide association study is a powerful tool for finding SNPs associated with increased risk of obesity. To conduct an association analysis, kernel machine regression is a generalized regression method, has an advantage of considering the epistasis effects as well as the correlation between individuals due to unknown factors. MATERIALS AND METHODS In this study, information of the people who participated in Tehran cardio-metabolic genetic study was used. They were genotyped for the chromosomal region, evaluation 986 variations located at 16q12.2; build 38hg. Kernel machine regression and single SNP analysis were used to assess the association between obesity and SNPs genotyped data. RESULTS We found that associated SNP sets with obesity, were almost in the FTO (P = 0.01), AIKTIP (P = 0.02) and MMP2 (P = 0.02) genes. Moreover, two SNPs, i.e., rs10521296 and rs11647470, showed significant association with obesity using kernel regression (P = 0.02). CONCLUSION In conclusion, significant sets were randomly distributed throughout the region with more density around the FTO, AIKTIP and MMP2 genes. Furthermore, two intergenic SNPs showed significant association after using kernel machine regression. Therefore, more studies have to be conducted to assess their functionality or precise mechanism.
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Iroquois homeobox 2 suppresses cellular motility and chemokine expression in breast cancer cells. BMC Cancer 2015; 15:896. [PMID: 26560478 PMCID: PMC4642646 DOI: 10.1186/s12885-015-1907-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 11/03/2015] [Indexed: 12/11/2022] Open
Abstract
Background Disseminated tumor cells (DTCs) can be detected using ultrasensitive immunocytochemical assays and their presence in the bone marrow can predict the subsequent occurrence of overt metastasis formation and metastatic relapse. Using expression profiling on early stage primary breast tumors, low IRX2 expression was previously shown to be associated with the presence of DTCs in the bone marrow, suggesting a possible role of IRX2 in the early steps of metastasis formation. The purpose of this study is to gain insights into the significance of IRX2 protein function in the progression of breast cancer. Methods To assess the physiological relevance of IRX2 in breast cancer, we evaluated IRX2 expression in a large breast cancer cohort (n = 1992). Additionally, constitutive IRX2 over expression was established in BT-549 and Hs578T breast cancer cell lines. Subsequently we analyzed whether IRX2 overexpression effects chemokine secretion and cellular motility of these cells. Results Low IRX2 mRNA expression was found to correlate with high tumor grade, positive lymph node status, negative hormone receptor status, and basal type of primary breast tumors. Also in cell lines low IRX2 expression was associated with mainly basal breast cancer cell lines. The functional studies show that overexpression of the IRX2 transcription factor in basal cell lines suppressed secretion of the pro-metastatic chemokines and inhibited cellular motility but did not influence cell proliferation. Conclusion Our results imply that the IRX2 transcription factor might represent a novel metastasis associated protein that acts as a negative regulator of cellular motility and as a repressor of chemokine expression. Loss of IRX2 expression could therefore contribute to early hematogenous dissemination of breast cancer by sustaining chemokine secretion and enabling mobilization of tumor cells. Electronic supplementary material The online version of this article (doi:10.1186/s12885-015-1907-4) contains supplementary material, which is available to authorized users.
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Rotondo JC, Bosi S, Bassi C, Ferracin M, Lanza G, Gafà R, Magri E, Selvatici R, Torresani S, Marci R, Garutti P, Negrini M, Tognon M, Martini F. Gene expression changes in progression of cervical neoplasia revealed by microarray analysis of cervical neoplastic keratinocytes. J Cell Physiol 2015; 230:806-12. [PMID: 25205602 DOI: 10.1002/jcp.24808] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 09/05/2014] [Indexed: 12/28/2022]
Abstract
To evaluate the gene expression changes involved in neoplastic progression of cervical intraepithelial neoplasia. Using microarray analysis, large-scale gene expression profile was carried out on HPV16-CIN2, HPV16-CIN3, and normal cervical keratinocytes derived from two HPV16-CIN2, two HPV-CIN3 lesions, and two corresponding normal cervical tissues, respectively. Differentially expressed genes were analyzed in normal cervical keratinocytes compared with HPV16-CIN2 keratinocytes and in HPV16-CIN2 keratinocytes compared with HPV16-CIN3 keratinocytes; 37 candidate genes with continuously increasing or decreasing expression during CIN progression were identified. One of these genes, phosphoglycerate dehydrogenase, was chosen for further characterization. Quantitative reverse transcription-polymerase chain reaction and immunohistochemical analysis confirmed that expression of phosphoglycerate dehydrogenase consistently increases during progression of CIN toward cancer. Gene expression changes occurring during CIN progression were investigated using microarray analysis, for the first time, in CIN2 and CIN3 keratinocytes naturally infected with HPV16. Phosphoglycerate dehydrogenase is likely to be associated with tumorigenesis and may be a potential prognostic marker for CIN progression.
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Affiliation(s)
- John Charles Rotondo
- Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, via Fossato di Mortara 64/B, Ferrara, Italy
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12
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Cao Q, Zhou M, Wang X, Meyer CA, Zhang Y, Chen Z, Li C, Liu XS. CaSNP: a database for interrogating copy number alterations of cancer genome from SNP array data. Nucleic Acids Res 2010; 39:D968-74. [PMID: 20972221 PMCID: PMC3013814 DOI: 10.1093/nar/gkq997] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Cancer is known to have abundant copy number alterations (CNAs) that greatly contribute to its pathogenesis and progression. Investigation of CNA regions could potentially help identify oncogenes and tumor suppressor genes and infer cancer mechanisms. Although single-nucleotide polymorphism (SNP) arrays have strengthened our ability to identify CNAs with unprecedented resolution, a comprehensive collection of CNA information from SNP array data is still lacking. We developed a web-based CaSNP (http://cistrome.dfci.harvard.edu/CaSNP/) database for storing and interrogating quantitative CNA data, which curated ∼11,500 SNP arrays on 34 different cancer types in 104 studies. With a user input of region or gene of interest, CaSNP will return the CNA information summarizing the frequencies of gain/loss and averaged copy number for each study, and provide links to download the data or visualize it in UCSC Genome Browser. CaSNP also displays the heatmap showing copy numbers estimated at each SNP marker around the query region across all studies for a more comprehensive visualization. Finally, we used CaSNP to study the CNA of protein-coding genes as well as LincRNA genes across all cancer SNP arrays, and found putative regions harboring novel oncogenes and tumor suppressors. In summary, CaSNP is a useful tool for cancer CNA association studies, with the potential to facilitate both basic science and translational research on cancer.
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Affiliation(s)
- Qingyi Cao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310012, China
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13
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Guo X, Liu W, Pan Y, Ni P, Ji J, Guo L, Zhang J, Wu J, Jiang J, Chen X, Cai Q, Li J, Zhang J, Gu Q, Liu B, Zhu Z, Yu Y. Homeobox gene IRX1 is a tumor suppressor gene in gastric carcinoma. Oncogene 2010; 29:3908-20. [PMID: 20440264 DOI: 10.1038/onc.2010.143] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The IRX1 tumor suppressor gene is located on 5p15.33, a cancer susceptibility locus. Loss of heterozygosity of 5p15.33 in gastric cancer was identified in our previous work. In this study, we analyzed the molecular features and function of IRX1. We found that IRX1 expression was lost or reduced in gastric cancer. However, no mutations were identified in IRX1-encoding regions. IRX1 transcription was suppressed by hypermethylation, and the expression of IRX1 mRNA was partially restored in gastric cancer cells after 5-Aza-dC treatment. Restoring IRX1 expression in SGC-7901 and NCI-N87 gastric cancer cells inhibited growth, invasion and tumorigenesis in vitro and in vivo. We identified a number of target genes by global microarray analysis after IRX1 transfection combined with real-time PCR and chromatin immunoprecipitation assay. BDKRB2, an angiogenesis-related gene, HIST2H2BE and FGF7, cell proliferation and invasion-related genes, were identified as direct IRX1 target genes. The hypermethylation of IRX1 was not only detected in primary gastric cancer tissues but also in the peripheral blood of gastric cancer patients, suggesting IRX1 could potentially serve as a biomarker for gastric cancer.
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Affiliation(s)
- X Guo
- Department of Surgery of Shanghai Ruijin Hospital and Shanghai Institute of Digestive Surgery, Shanghai, PR China
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14
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Kadota M, Sato M, Duncan B, Ooshima A, Yang HH, Diaz-Meyer N, Gere S, Kageyama SI, Fukuoka J, Nagata T, Tsukada K, Dunn BK, Wakefield LM, Lee MP. Identification of novel gene amplifications in breast cancer and coexistence of gene amplification with an activating mutation of PIK3CA. Cancer Res 2009; 69:7357-65. [PMID: 19706770 DOI: 10.1158/0008-5472.can-09-0064] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
To identify genetic events that characterize cancer progression, we conducted a comprehensive genetic evaluation of 161 primary breast tumors. Similar to the "mountain-and-hill" view of mutations, gene amplification also shows high- and low-frequency alterations in breast cancers. The frequently amplified genes include the well-known oncogenes ERBB2, FGFR1, MYC, CCND1, and PIK3CA, whereas other known oncogenes that are amplified, although less frequently, include CCND2, EGFR, FGFR2, and NOTCH3. More importantly, by honing in on minimally amplified regions containing three or fewer genes, we identified six new amplified genes: POLD3, IRAK4, IRX2, TBL1XR1, ASPH, and BRD4. We found that both the IRX2 and TBL1XR1 proteins showed higher expression in the malignant cell lines MCF10CA1h and MCF10CA1a than in their precursor, MCF10A, a normal immortalized mammary epithelial cell line. To study oncogenic roles of TBL1XR1, we performed knockdown experiments using a short hairpin RNA approach and found that depletion of TBL1XR1 in MCF10CA1h cells resulted in reduction of cell migration and invasion as well as suppression of tumorigenesis in mouse xenografts. Intriguingly, our mutation analysis showed the presence of activation mutations in the PIK3CA gene in a subset of tumors that also had DNA copy number increases in the PIK3CA locus, suggesting an additive effect of coexisting activating amino acid substitution and dosage increase from amplification. Our gene amplification and somatic mutation analysis of breast primary tumors provides a coherent picture of genetic events, both corroborating and novel, offering insight into the genetic underpinnings of breast cancer progression.
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Affiliation(s)
- Mitsutaka Kadota
- Laboratory of Population Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
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15
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Sotgia F, Casimiro MC, Bonuccelli G, Liu M, Whitaker-Menezes D, Er O, Daumer KM, Mercier I, Witkiewicz AK, Minetti C, Capozza F, Gormley M, Quong AA, Rui H, Frank PG, Milliman JN, Knudsen ES, Zhou J, Wang C, Pestell RG, Lisanti MP. Loss of caveolin-3 induces a lactogenic microenvironment that is protective against mammary tumor formation. THE AMERICAN JOURNAL OF PATHOLOGY 2009; 174:613-29. [PMID: 19164602 DOI: 10.2353/ajpath.2009.080653] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Here, we show that functional loss of a single gene is sufficient to confer constitutive milk protein production and protection against mammary tumor formation. Caveolin-3 (Cav-3), a muscle-specific caveolin-related gene, is highly expressed in muscle cells. We demonstrate that Cav-3 is also expressed in myoepithelial cells within the mammary gland. To determine whether genetic ablation of Cav-3 expression affects adult mammary gland development, we studied the phenotype(s) of Cav-3(-/-)-null mice. Interestingly, Cav-3(-/-) virgin mammary glands developed lobulo-alveolar hyperplasia, akin to the changes normally observed during pregnancy and lactation. Genome-wide expression profiling revealed up-regulation of gene transcripts associated with pregnancy/lactation, mammary stem cells, and human breast cancers, consistent with a constitutive lactogenic phenotype. Expression levels of three key transcriptional regulators of lactation, namely Elf5, Stat5a, and c-Myc, were also significantly elevated. Experiments with pregnant mice directly showed that Cav-3(-/-) mice underwent precocious lactation. Finally, using orthotopic tumor cell implantation, we demonstrated that virgin Cav-3(-/-) mice were dramatically protected against mammary tumor formation. Thus, Cav-3(-/-) mice are a novel preclinical model to study the protective effects of a lactogenic microenvironment on mammary tumor onset and progression. Our current studies have broad implications for using the lactogenic microenvironment as a paradigm to discover new therapies for the prevention and/or treatment of human breast cancers.
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Affiliation(s)
- Federica Sotgia
- Department of Cancer Biology, Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, 19107, USA.
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16
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Raouf A, Zhao Y, To K, Stingl J, Delaney A, Barbara M, Iscove N, Jones S, McKinney S, Emerman J, Aparicio S, Marra M, Eaves C. Transcriptome analysis of the normal human mammary cell commitment and differentiation process. Cell Stem Cell 2008; 3:109-18. [PMID: 18593563 DOI: 10.1016/j.stem.2008.05.018] [Citation(s) in RCA: 264] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2007] [Revised: 04/09/2008] [Accepted: 05/15/2008] [Indexed: 01/16/2023]
Abstract
Mature mammary epithelial cells are generated from undifferentiated precursors through a hierarchical process, but the molecular mechanisms involved, particularly in the human mammary gland, are poorly understood. To address this issue, we isolated highly purified subpopulations of primitive bipotent and committed luminal progenitor cells as well as mature luminal and myoepithelial cells from normal human mammary tissue and compared their transcriptomes obtained using three different methods. Elements unique to each subset of mammary cells were identified, and changes that accompany their differentiation in vivo were shown to be recapitulated in vitro. These include a stage-specific change in NOTCH pathway gene expression during the commitment of bipotent progenitors to the luminal lineage. Functional studies further showed NOTCH3 signaling to be critical for this differentiation event to occur in vitro. Taken together, these findings provide an initial foundation for future delineation of mechanisms that perturb primitive human mammary cell growth and differentiation.
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Affiliation(s)
- Afshin Raouf
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada
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17
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Duverger O, Morasso MI. Role of homeobox genes in the patterning, specification, and differentiation of ectodermal appendages in mammals. J Cell Physiol 2008; 216:337-46. [PMID: 18459147 DOI: 10.1002/jcp.21491] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Homeobox genes are an evolutionarily conserved class of transcription factors that are key regulators during developmental processes such as regional specification, patterning, and differentiation. In this review, we summarize the expression pattern, loss- and/or gain-of-function mouse models, and naturally occurring mouse and human mutations of known homeobox genes required for the development of ectodermal appendages.
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Affiliation(s)
- Olivier Duverger
- Developmental Skin Biology Unit, National Institute of Arthritis Musculoskeletal and Skin Diseases, NIH, Bethesda, Maryland, USA
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18
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Abstract
The development of adaptive immunity and responses to foreign molecules and organisms relies on the highly regulated production of hundreds of proteins. B-cell maturation, from committed progenitors to terminally differentiated plasma cells, is a multistep process that requires the ordered expression of a large number of genes. We studied anti-IgM-stimulated Ramos cells to explore genome-wide expression patterns in differentiating human B-cells. cDNA microarrays were used to measure changes in transcript levels over several days. A large set of genes ( approximately 1,500) showed significantly altered expression at one or more time points. The expression profiles were used to construct gene clusters that were then characterized further with respect to the functions of the encoded proteins. Several groups of genes relevant to B-cells were analyzed in detail including early response genes and genes related to transcription, apoptosis and cell cycle regulation. Extensive bioinformatics analyses were conducted to identify the genes/proteins and to study functions and pathways involving B-cells. The results pave the way for understanding the development of humoral immunity, and provide new candidate genes and targets for research and drug development.
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Affiliation(s)
- J Ollila
- Department of Biosciences, Division of Biochemistry, PO Box 56, University of Helsinki, Finland
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19
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Chen H, Sukumar S. Role of homeobox genes in normal mammary gland development and breast tumorigenesis. J Mammary Gland Biol Neoplasia 2003; 8:159-75. [PMID: 14635792 DOI: 10.1023/a:1025996707117] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
The role of homeobox-containing genes in embryogenesis and organogenesis is well documented. Also, a sizeable body of evidence has accumulated and supports the fact that homeobox genes, when dysregulated, are involved in tumorigenesis. However, the precise mechanisms of homeobox gene functions are largely unknown. The mammary gland, in which most maturation occurs postnatally, provides an ideal model for studying the functions of homeobox genes in both development and tumorigenesis. The expression of many homeobox genes has been detected in both normal mammary gland and neoplastic breast tissues. In the normal mammary gland, the expression of homeobox genes is coordinately regulated by hormone and extracellular matrix (ECM) and other unknown factors in a spatial and temporal manner in both stromal and epithelial cells. Animals with misexpressed homeobox genes displayed different extents of defects in ductal proliferation, side branching, and alveoli formation, implying that homeobox genes are important for normal mammary gland development. Recent studies of homeobox genes in breast cancer cells and primary tumors indicate that they may also play a contributory or causal role in tumorigenesis by regulating the cell cycle, apoptosis, angiogenesis, and/or metastasis.
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Affiliation(s)
- Hexin Chen
- Breast Cancer Program, the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland, USA
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20
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Wang X, Emelyanov A, Sleptsova-Friedrich I, Korzh V, Gong Z. Expression of two novel zebrafish iroquois homologues (ziro1 and ziro5) during early development of axial structures and central nervous system. Mech Dev 2001; 105:191-5. [PMID: 11429297 DOI: 10.1016/s0925-4773(01)00400-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Previously, we reported a zebrafish iroquois gene, ziro3, and its expression during early embryogenesis (Mech. Dev. 87 (1999) 165). In the present study, we have isolated two novel zebrafish iroquois genes, ziro1 and ziro5, homologs of mouse Irx1 and mouse Irx5, respectively. The expression of both genes is initiated in dorsal neuroectoderm and mesoderm during gastrulation. Later, their expression appears in the central nervous system (CNS), excluding the telencephalon and most of the diencephalon. ziro1 expression is complementary to that of ziro3 in the notochord and later in the gut. In contrast, ziro5 expression mostly overlaps with that of ziro3. Interestingly, all three iroquois zebrafish genes are expressed in the notochord while only Irx3 is active in the mouse notochord. Their expression in later stages of embryogenesis was also compared.
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Affiliation(s)
- X Wang
- Department of Biological Sciences, National University of Singapore, 119260, Singapore, Singapore
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21
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Abstract
Genetic analyses of two hedgehog signal transduction network genes, Patched-1 and Gli2, has demonstrated a critical role for hedgehog signaling in mediating epithelial-stromal tissue interactions during ductal development. Disruption of either gene leads to similar, yet distinct, defects in ductal morphogenesis. Defects are mainly ductal dysplasias that closely resemble some hyperplasias of the human breast. Phenotypic analyses have been coupled with in situ hybridization, transplantation and tissue recombination analyses to formulate a model for tissue compartment-specific control of mouse mammary gland development by hedgehog signaling. In addition, the similarities among hedgehog mutation-induced ductal dysplasias and human breast pathologies suggest a role for altered hedgehog signaling in the development of mammary cancer.
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Affiliation(s)
- M T Lewis
- University of Colorado Health Sciences Center, Department of Physiology, Denver 80262, USA.
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22
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Peters T, Dildrop R, Ausmeier K, Rüther U. Organization of mouse Iroquois homeobox genes in two clusters suggests a conserved regulation and function in vertebrate development. Genome Res 2000; 10:1453-62. [PMID: 11042145 PMCID: PMC310936 DOI: 10.1101/gr.144100] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Iroquois proteins comprise a conserved family of homeodomain-containing transcription factors involved in patterning and regionalization of embryonic tissues in both vertebrates and invertebrates. Earlier studies identified four murine Iroquois (Irx) genes. Here we report the isolation of two additional members of the murine gene family, Irx5 and Irx6. Phylogenetic analysis of the Irx gene family revealed distinct clades for fly and vertebrate genes, and vertebrate members themselves were classified into three pairs of cognate genes. Mapping of the murine Irx genes identified two gene clusters located on mouse chromosomes 8 and 13, respectively. Each gene cluster is represented by three Irx genes whose relative positions within both clusters are strictly conserved. Combined results from phylogenetic, linkage, and physical mapping studies provide evidence for the evolution of two Irx gene clusters by duplication of a larger chromosomal region and dispersion to two chromosomal locations. The maintenance of two cognate Irx gene clusters during vertebrate evolution suggests that their genomic organization is important for the regulation, expression, and function of Irx genes during embryonic development.
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Affiliation(s)
- T Peters
- Entwicklungs- und Molekularbiologie der Tiere, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
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23
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Lewis MT. Homeobox genes in mammary gland development and neoplasia. Breast Cancer Res 2000; 2:158-69. [PMID: 11250705 PMCID: PMC138770 DOI: 10.1186/bcr49] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/1999] [Revised: 01/25/2000] [Accepted: 02/04/2000] [Indexed: 02/03/2023] Open
Abstract
Both normal development and neoplastic progression involve cellular transitions from one physiological state to another. Whereas much is being discovered about signal transduction networks involved in regulating these transitions, little progress has been made in identifying the higher order genetic determinants that establish and maintain mammary cell identity and dictate cell type-specific responses to mammotropic signals. Homeobox genes are a large superfamily of genes whose members function in establishing and maintaining cell fate and cell identity throughout embryonic development. Recent genetic and expression analyses strongly suggest that homeobox genes may perform similar functions at specific developmental transition points in the mammary gland. These analyses also suggest that homeobox genes may play a contributory or causal role in breast cancer.
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Affiliation(s)
- M T Lewis
- Department of Physiology and Biophysics, University of Colorado Health Sciences Center, Denver, Colorado 80262, USA.
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