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Kendrick TS, Buic D, Fuller KA, Erber WN. Abnormalities in Chromosomes 5 and 7 in Myelodysplastic Syndrome and Acute Myeloid Leukemia. Ann Lab Med 2025; 45:133-145. [PMID: 39774131 PMCID: PMC11788707 DOI: 10.3343/alm.2024.0477] [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: 09/05/2024] [Revised: 10/17/2024] [Accepted: 12/23/2024] [Indexed: 01/11/2025] Open
Abstract
Chromosomes 5 and 7 are large chromosomes that contain close to 1,000 genes each. Deletions of the long arms or loss of the entire chromosome (monosomy) are common defects in myeloid disorders, particularly MDS and AML. Loss of material from either chromosome 5 or 7 results in haploinsufficiency of multiple genes, with some implicated in leukemogenesis. Abnormalities of one or both occur in up to 15% of MDS and AML cases and co-segregate in half of these. Generally, these chromosomal abnormalities are harbingers of adverse risk in both myeloid disorders. A notable exception is del(5q) in 5q- syndrome, a subtype of MDS. In this review, we describe the pathogenesis and genetic consequences of deletions in chromosomes 5 and 7. Furthermore, we provide an overview of current testing methodologies used in the assessment of these chromosomal defects in hematological malignancies and describe the disease associations and prognostic implications of aberrations in chromosomes 5 and 7 in both MDS and AML.
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MESH Headings
- Humans
- Myelodysplastic Syndromes/genetics
- Myelodysplastic Syndromes/diagnosis
- Myelodysplastic Syndromes/pathology
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/diagnosis
- Leukemia, Myeloid, Acute/pathology
- Chromosomes, Human, Pair 5/genetics
- Chromosomes, Human, Pair 7/genetics
- Chromosome Deletion
- Chromosome Aberrations
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Affiliation(s)
- Tulene S. Kendrick
- Haematology Department, Royal Perth Hospital, Perth, Australia
- School of Biomedical Sciences, The University of Western Australia, Crawley, Australia
- PathWest Laboratory Medicine WA, Perth, Australia
| | - Daria Buic
- School of Biomedical Sciences, The University of Western Australia, Crawley, Australia
| | - Kathy A. Fuller
- School of Biomedical Sciences, The University of Western Australia, Crawley, Australia
| | - Wendy N. Erber
- School of Biomedical Sciences, The University of Western Australia, Crawley, Australia
- PathWest Laboratory Medicine WA, Perth, Australia
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Halik A, Tilgner M, Silva P, Estrada N, Altwasser R, Jahn E, Heuser M, Hou HA, Pratcorona M, Hills RK, Metzeler KH, Fenwarth L, Dolnik A, Terre C, Kopp K, Blau O, Szyska M, Christen F, Krönke J, Vasseur L, Löwenberg B, Esteve J, Valk PJM, Duchmann M, Chou WC, Linch DC, Döhner H, Gale RE, Döhner K, Bullinger L, Yoshida K, Damm F. Genomic characterization of AML with aberrations of chromosome 7: a multinational cohort of 519 patients. J Hematol Oncol 2024; 17:70. [PMID: 39160538 PMCID: PMC11331663 DOI: 10.1186/s13045-024-01590-1] [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: 05/19/2024] [Accepted: 08/05/2024] [Indexed: 08/21/2024] Open
Abstract
BACKGROUND Deletions and partial losses of chromosome 7 (chr7) are frequent in acute myeloid leukemia (AML) and are linked to dismal outcome. However, the genomic landscape and prognostic impact of concomitant genetic aberrations remain incompletely understood. METHODS To discover genetic lesions in adult AML patients with aberrations of chromosome 7 [abn(7)], 60 paired diagnostic/remission samples were investigated by whole-exome sequencing in the exploration cohort. Subsequently, a gene panel including 66 genes and a SNP backbone for copy-number variation detection was designed and applied to the remaining samples of the validation cohort. In total, 519 patients were investigated, of which 415 received intensive induction treatment, typically containing a combination of cytarabine and anthracyclines. RESULTS In the exploration cohort, the most frequently mutated gene was TP53 (33%), followed by epigenetic regulators (DNMT3A, KMT2C, IDH2) and signaling genes (NRAS, PTPN11). Thirty percent of 519 patients harbored ≥ 1 mutation in genes located in commonly deleted regions of chr7-most frequently affecting KMT2C (16%) and EZH2 (10%). KMT2C mutations were often subclonal and enriched in patients with del(7q), de novo or core-binding factor AML (45%). Cancer cell fraction analysis and reconstruction of mutation acquisition identified TP53 mutations as mainly disease-initiating events, while del(7q) or -7 appeared as subclonal events in one-third of cases. Multivariable analysis identified five genetic lesions with significant prognostic impact in intensively treated AML patients with abn(7). Mutations in TP53 and PTPN11 (11%) showed the strongest association with worse overall survival (OS, TP53: hazard ratio [HR], 2.53 [95% CI 1.66-3.86]; P < 0.001; PTPN11: HR, 2.24 [95% CI 1.56-3.22]; P < 0.001) and relapse-free survival (RFS, TP53: HR, 2.3 [95% CI 1.25-4.26]; P = 0.008; PTPN11: HR, 2.32 [95% CI 1.33-4.04]; P = 0.003). By contrast, IDH2-mutated patients (9%) displayed prolonged OS (HR, 0.51 [95% CI 0.30-0.88]; P = 0.0015) and durable responses (RFS: HR, 0.5 [95% CI 0.26-0.96]; P = 0.036). CONCLUSION This work unraveled formerly underestimated genetic lesions and provides a comprehensive overview of the spectrum of recurrent gene mutations and their clinical relevance in AML with abn(7). KMT2C mutations are among the most frequent gene mutations in this heterogeneous AML subgroup and warrant further functional investigation.
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MESH Headings
- Humans
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/mortality
- Female
- Male
- Middle Aged
- Adult
- Chromosomes, Human, Pair 7/genetics
- Aged
- Mutation
- Cohort Studies
- Young Adult
- Chromosome Aberrations
- Prognosis
- Aged, 80 and over
- Adolescent
- Exome Sequencing
- DNA Copy Number Variations
- Tumor Suppressor Protein p53/genetics
- Genomics/methods
- Protein Tyrosine Phosphatase, Non-Receptor Type 11/genetics
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Affiliation(s)
- Adriane Halik
- Department of Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Marlon Tilgner
- Department of Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Patricia Silva
- Department of Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Natalia Estrada
- Department of Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Robert Altwasser
- Department of Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Ekaterina Jahn
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, Germany
| | - Michael Heuser
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
- Department of Internal Medicine IV, University Hospital Halle (Saale), Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Hsin-An Hou
- Division of Hematology, Department of Internal Medicine, and Division of General Medicine, Department of Internal Medicine, National Taiwan University Hospital, No. 7, Chung Shan South Road, Taipei City, Taiwan
| | - Marta Pratcorona
- Hospital de la Santa Creu i Sant Pau. Institut de Recerca Sant Pau. Department of Medicine, Universitat Autonoma of Barcelona, Barcelona, Spain
| | - Robert K Hills
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Klaus H Metzeler
- Department of Hematology, Cell Therapy, Hemostaseology and Infectious Diseases, University Hospital Leipzig, Leipzig, Germany
| | - Laurene Fenwarth
- Unité Mixte de Recherche (UMR) 9020-UMR1277, Canther-Cancer Heterogeneity, Plasticity and Resistance to Therapies, University of Lille, Centre National de la Recherche Scientifique (CNRS), INSERM, Centre Hospitalo-Universitaire (CHU) Lille, Institut de Recherche sur le Cancer de Lille (IRCL), Lille, France
| | - Anna Dolnik
- Department of Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Christine Terre
- Laboratoire de Cytogénétique, Service de Biologie, CH de Versailles, Le Chesnay, France
| | - Klara Kopp
- Department of Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Olga Blau
- Department of Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Martin Szyska
- Department of Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Friederike Christen
- Department of Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Jan Krönke
- Department of Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- German Cancer Consortium (Deutsches Konsortium Für Translationale Krebsforschung, DKTK), Partner Site, Berlin, Germany
| | - Loïc Vasseur
- Hematology Department, Saint Louis Hospital, AP-HP, Paris, France
| | - Bob Löwenberg
- Department of Hematology, Erasmus MC Cancer Institute, and Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Jordi Esteve
- Hematology Department, IDIBAPS, Hospital Clínic de Barcelona, University of Barcelona, Barcelona, Spain
| | - Peter J M Valk
- Department of Hematology, Erasmus MC Cancer Institute, and Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Matthieu Duchmann
- Institut de Recherche Saint-Louis (IRSL), Institut National de la Santé et de la Recherche Médicale (INSERM) U944, Centre National de la Recherche Scientifique (CNRS) UMR 7212 GenCellDis, Université Paris Cité, Paris, France
| | - Wen-Chien Chou
- Division of Hematology, Department of Internal Medicine, and Division of General Medicine, Department of Internal Medicine, National Taiwan University Hospital, No. 7, Chung Shan South Road, Taipei City, Taiwan
| | - David C Linch
- Department of Haematology, University College London Cancer Institute, London, UK
| | - Hartmut Döhner
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, Germany
| | - Rosemary E Gale
- Department of Haematology, University College London Cancer Institute, London, UK
| | - Konstanze Döhner
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, Germany
| | - Lars Bullinger
- Department of Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- German Cancer Consortium (Deutsches Konsortium Für Translationale Krebsforschung, DKTK), Partner Site, Berlin, Germany
| | - Kenichi Yoshida
- Division of Cancer Evolution, National Cancer Center Research Institute, Tokyo, Japan
| | - Frederik Damm
- Department of Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.
- German Cancer Consortium (Deutsches Konsortium Für Translationale Krebsforschung, DKTK), Partner Site, Berlin, Germany.
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Luthra I, Jensen C, Chen XE, Salaudeen AL, Rafi AM, de Boer CG. Regulatory activity is the default DNA state in eukaryotes. Nat Struct Mol Biol 2024; 31:559-567. [PMID: 38448573 DOI: 10.1038/s41594-024-01235-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 01/29/2024] [Indexed: 03/08/2024]
Abstract
Genomes encode for genes and non-coding DNA, both capable of transcriptional activity. However, unlike canonical genes, many transcripts from non-coding DNA have limited evidence of conservation or function. Here, to determine how much biological noise is expected from non-genic sequences, we quantify the regulatory activity of evolutionarily naive DNA using RNA-seq in yeast and computational predictions in humans. In yeast, more than 99% of naive DNA bases were transcribed. Unlike the evolved transcriptome, naive transcripts frequently overlapped with opposite sense transcripts, suggesting selection favored coherent gene structures in the yeast genome. In humans, regulation-associated chromatin activity is predicted to be common in naive dinucleotide-content-matched randomized DNA. Here, naive and evolved DNA have similar co-occurrence and cell-type specificity of chromatin marks, challenging these as indicators of selection. However, in both yeast and humans, extreme high activities were rare in naive DNA, suggesting they result from selection. Overall, basal regulatory activity seems to be the default, which selection can hone to evolve a function or, if detrimental, repress.
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Affiliation(s)
- Ishika Luthra
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada
| | - Cassandra Jensen
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada
| | - Xinyi E Chen
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada
| | - Asfar Lathif Salaudeen
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada
| | - Abdul Muntakim Rafi
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada
| | - Carl G de Boer
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada.
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Chaudhary R, Steinson E. Genes and their Involvement in the Pathogenesis of Autism Spectrum Disorder: Insights from Earlier Genetic Studies. NEUROBIOLOGY OF AUTISM SPECTRUM DISORDERS 2023:375-415. [DOI: 10.1007/978-3-031-42383-3_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2025]
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Zhang Y, Hu S, Li J, Shi D, Luo B. The promoter aberrant methylation status of TMEM130 is associated with gastric cancer. Dig Liver Dis 2022; 54:819-825. [PMID: 34162508 DOI: 10.1016/j.dld.2021.05.035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 05/10/2021] [Accepted: 05/24/2021] [Indexed: 12/24/2022]
Abstract
BACKGROUND AND AIMS Gastric cancer (GC) is a malignant tumor that seriously affects human health and Epstein-Barr virus (EBV)-associated gastric cancer (EBVaGC) is a molecular subtype of GC. This study aims to determine the relationship between the methylation status of the TMEM130 gene and GC, and to explore the influence of EBV infection. METHODS qRT-PCR was conducted to investigate the transcriptional expression of TMEM130 in GC. BSP and MSP assays were used to detect the methylation level of the TMEM130 promoter. The cell migration ability was detected by Transwell and western blot after transfection of TMEM130 plasmids in GC cells. RESULTS The transcriptional expression of TMEM130 decreased in GC with hypermethylation of the promoter region. The DNA methyltransferase inhibitor could increase the mRNA expression of TMEM130. Moreover, hypermethylation of the TMEM130 promoter in GC tissues was associated with EBV infection. Overexpression of TMEM130 in GC cell lines suppresses cell migration ability. CONCLUSION This study was the first to research the expression and function of TMEM130 and found that TMEM130 gene hypermethylation might contribute to GC migration and EBV infection as a cause of hypermethylation of the TMEM130 gene. TMEM130 is a promising biomarker for the diagnosis of GC.
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Affiliation(s)
- Yan Zhang
- Department of Pathogeny Biology, Basic Medicine College, Qingdao University, Qingdao 266071, China; Department of Clinical Laboratory, Zibo Central Hospital, ZiBo 255000, China
| | - Shunxia Hu
- Department of Clinical Laboratory, Women and Children's Hospital, Qingdao University, Qingdao 266000, China
| | - Jun Li
- Department of Pathogeny Biology, Basic Medicine College, Qingdao University, Qingdao 266071, China
| | - Duo Shi
- Department of Pathogeny Biology, Basic Medicine College, Qingdao University, Qingdao 266071, China
| | - Bing Luo
- Department of Pathogeny Biology, Basic Medicine College, Qingdao University, Qingdao 266071, China.
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Liu H, Zhang Y, Chen W, Zhang Y, Zhang W. TMEM130 regulates cell migration through DNA methylation in nasopharyngeal carcinoma. Cancer Biomark 2021; 34:265-273. [PMID: 34958002 DOI: 10.3233/cbm-210338] [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] [Indexed: 12/24/2022]
Abstract
BACKGROUND Nasopharyngeal carcinoma (NPC), the common malignant head and neck cancer, is highly prevalent in southern China. The molecular mechanism underlying NPC tumorigenesis is unclear. We used 5-Aza-CdR, a DNA methyltransferase inhibitor, to treat NPC cell lines and discovered that the expression of TMEM130 changed significantly compared with the untreatment cells. This study aimed to identify the relationship between the DNA methylation status of TMEM130 and NPC, and to explore the function of TMEM130 in NPC cell migration. METHODS qRT-PCR was performed to investigate the transcriptional expression of TMEM130 in NPC. Bisulfite sequencing PCR and 5-Aza-CdR treatment were used to detect the methylation level of the TMEM130 promoter. Gene Expression Omnibus (GEO) datasets were obtained to identifiy the methylation status and mRNA expression of TMEM130 in NPC and normal control tissues. Transwell and western blot analyses were used to detect cell migration ability after transfection of TMEM130/NC plasmids in NPC cells. RESULTS The transcriptional expression of TMEM130 was decreased in NPC cell lines compared with in the NP69 cell line. TMEM130 promoter was significantly hyper methylated in three NPC cell lines (C666, CNE, and HONE) but hypo methylated in NP69 cells. The methylation level was higher in NPC than normal control tissues. Additionally, treatment of NPC cells with 5-Aza-CdR increased the TMEM130 mRNA expression level. Overexpression of TMEM130 in NPC cell lines suppressed cell migration ability and affected some epithelial-mesenchymal transition-associated gene expression. CONCLUSIONS This study is the first to investigate the expression and function of TMEM130 in NPC. It was found that TMEM130 hyper methylation might contribute to NPC migration and this gene might act as a tumor suppressor gene. TMEM130 is a promising biomarker for NPC diagnosis.
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Liu H, Xie HQ, Zhao Y, Zhang W, Zhang Y. DNA methylation-mediated down-regulation of TMEM130 promotes cell migration in breast cancer. Acta Histochem 2021; 123:151814. [PMID: 34763116 DOI: 10.1016/j.acthis.2021.151814] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 10/15/2021] [Accepted: 10/29/2021] [Indexed: 12/09/2022]
Abstract
BACKGROUND Breast cancer is the most common female cancer worldwide. DNA methylation is a common modification in epigenetics and affects the prognosis of breast cancer by changing gene expression. In the present study, we aim to investigate the role of DNA methylation in TMEM130 gene expression, and the function of TMEM130 in breast cancer cell migration. METHODS The transcriptional expression of TMEM130 was detected by qRT-PCR in breast cancer cell lines and tissues. Bisulfite sequencing PCR (BSP) was used to confirm the methylation status of TMEM130 promoter. Then, TMEM130 was transfected in breast cancer cell lines and to explore its role in cell migration by Transwell and western blot. RESULTS TMEM130 mRNA expression was decreased in breast cancer cell lines and tissues, and consistent with the data in The Cancer Genome Atlas (TCGA). The promoter of TMEM130 was hypermethylated in breast cancer and the expression of TMEM130 could be restored by the methyltransferase inhibitor. Overexpression of TMEM130 could inhibit cell migration ability in breast cancer cell lines. CONCLUSION Taken together, these results indicate TMEM130 downregulation and hypermethylation might contribute to breast cancer migration and TMEM130 might be a promising biomarker for breast cancer.
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Affiliation(s)
- Hong Liu
- Department of Clinical Laboratory, Zibo Central Hospital, Zibo 255036, China
| | - Hong-Qiang Xie
- Department of Intensive Care Unit,Zibo Central Hospital, Zibo 255036, China
| | - Yan Zhao
- Department of Clinical Laboratory, Zibo Central Hospital, Zibo 255036, China
| | - Wen Zhang
- Department of Clinical Laboratory, Zibo Central Hospital, Zibo 255036, China
| | - Yan Zhang
- Department of Clinical Laboratory, Zibo Central Hospital, Zibo 255036, China.
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Wang H, Feng Z, Han X, Xing Y, Zhang X. Downregulation of acylglycerol kinase suppresses high glucose-induced endothelial-mesenchymal transition in HRECs through regulating the LPAR1/TGF-β/Notch signaling pathway. Can J Physiol Pharmacol 2021; 100:142-150. [PMID: 34559978 DOI: 10.1139/cjpp-2021-0265] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The endothelial-mesenchymal transition (EndMT) participates in the progression of diabetic retinopathy (DR), but cell-intrinsic factors modulating this process remain elusive. In this study, we explored the role of lysophosphatidic acid (LPA)-producing enzyme, acylglycerol kinase (AGK) in the EndMT of human retinal microvascular endothelial cells (HRECs) under high glucose (HG) conditions. We found that AGK was significantly elevated in HG-treated cells. In addition, AGK knockdown reversed the HG-induced EndMT in HRECs, which was evidenced by the increased epithelial markers (CD31 and VE-cadherin) and decreased mesenchymal markers (FSP1 and α-SMA). Furthermore, downregulation of AGK inhibited the HG-induced activation of TGF-β/Notch pathways, whereas exogenous TGF-β1 (10 ng/ml) impeded the inhibitory effects of AGK knockdown on HG-induced EndMT in HRECs. Additionally, the silence of AGK abolished the HG-induced upregulation of LPA and its receptor LPAR1, and overexpression of LPAR1 further rescued the AGK knockdown-mediated inhibition of the EndMT process. In conclusion, we demonstrate that downregulation of acylglycerol kinase suppresses high glucose-induced endothelial-mesenchymal transition in HRECs through regulating the LPAR1/TGF-β/Notch signaling pathway, indicating that AGK might be a potential therapeutic target for the treatment of DR.
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Affiliation(s)
- Haijing Wang
- First Affiliated Hospital of Harbin Medical University, 74559, Harbin, Heilongjiang, China;
| | - Zhuolei Feng
- First Affiliated Hospital of Harbin Medical University, 74559, Harbin, Heilongjiang, China;
| | - Xue Han
- First Affiliated Hospital of Harbin Medical University, 74559, Harbin, Heilongjiang, China;
| | - Yue Xing
- First Affiliated Hospital of Harbin Medical University, 74559, Harbin, Heilongjiang, China;
| | - Xiaomei Zhang
- First Affiliated Hospital of Harbin Medical University, 74559, Harbin, Heilongjiang, China;
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Molecular Profiling of Docetaxel-Resistant Prostate Cancer Cells Identifies Multiple Mechanisms of Therapeutic Resistance. Cancers (Basel) 2021; 13:cancers13061290. [PMID: 33799432 PMCID: PMC7998254 DOI: 10.3390/cancers13061290] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/02/2021] [Accepted: 03/09/2021] [Indexed: 02/01/2023] Open
Abstract
Simple Summary Therapeutic options for the treatment of men with metastatic castration-resistant prostate cancer are limited. Docetaxel—a taxane-based chemotherapeutic agent—was the first treatment to demonstrate significant efficacy in the treatment of this disease. However, responses to docetaxel are frequently curtailed by development of drug resistance, and patients eventually succumb to disease progression due to acquisition of drug resistance. In this study, we established drug-resistant prostate cancer cell lines and identified several mechanisms that may be associated with the development of drug resistance in prostate cancer. Actioning these mechanisms could provide a potential approach to re-sensitize drug-resistant cancer cells to docetaxel treatment and thereby further add to the life-prolonging effects of this drug in men with metastatic castration-resistant prostate cancer. Abstract Docetaxel—a taxane-based chemotherapeutic agent—was the first treatment to demonstrate significant improvements in overall survival in men with metastatic castration-resistant prostate cancer (mCRPC). However, the response to docetaxel is generally short-lived, and relapse eventually occurs due to the development of resistance. To explore the mechanisms of acquired docetaxel resistance in prostate cancer (PCa) and set these in the context of androgen deprivation therapy, we established docetaxel-resistant PCa cell lines, derived from the androgen-dependent LNCaP cell line, and from the LNCaP lineage-derived androgen-independent C4-2B sub-line. We generated two docetaxel-resistant LNCaPR and C4-2BR sub-lines, with IC50 values 77- and 50-fold higher than those of the LNCaP and C4-2B parental cells, respectively. We performed gene expression analysis of the matched sub-lines and found several alterations that may confer docetaxel resistance. In addition to increased expression of ABCB1, an ATP-binding cassette (ABC) transporter, and a well-known gene associated with development of docetaxel resistance, we identified genes associated with androgen signaling, cell survival, and overexpression of ncRNAs. In conclusion, we identified multiple mechanisms that may be associated with the development of taxane drug resistance in PCa. Actioning these mechanisms could provide a potential approach to re-sensitization of docetaxel-resistant PCa cells to docetaxel treatment and thereby further add to the life-prolonging effects of this drug in men with mCRPC.
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C7ORF41 Regulates Inflammation by Inhibiting NF- κB Signaling Pathway. BIOMED RESEARCH INTERNATIONAL 2021; 2021:7413605. [PMID: 33506033 PMCID: PMC7806384 DOI: 10.1155/2021/7413605] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 12/02/2020] [Accepted: 12/18/2020] [Indexed: 11/18/2022]
Abstract
Inflammation is an important biological process for eliciting immune responses against physiological and pathological stimuli. Inflammation must be efficiently regulated to ensure homeostasis in the body. Nuclear factor-kappa B (NF-κB) signaling is crucial for inflammatory and immune responses. Aberrant activation of NF-κB signaling leads to development of numerous human diseases. In this study, we investigated the function of chromosome 7 open reading frame 41 (C7ORF41) in NF-κB signaling during inflammation. C7ORF41 was upregulated in cells stimulated with tumor necrosis factor-alpha or lipopolysaccharide. Moreover, overexpression of C7ORF41 inhibited the activation of NF-κB and decreased the expression of its downstream target genes. Notably, small hairpin RNA-mediated depletion of C7ORF41 increased the levels of downstream genes and enabled the activation of NF-κB. In conclusion, C7ORF41 negatively regulated inflammation via NF-κB signaling and p65 phosphorylation in vitro. These findings may help to diagnose and prognosticate inflammatory conditions and may help develop new strategies for the management of inflammation-related diseases.
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Yang T, Guo Q, Li D, Bai G, Sun H, Wang W. MicroRNA-802 Suppresses Tumorigenesis of Colorectal Cancer via Regulating UBN2. Cancer Manag Res 2020; 12:11219-11230. [PMID: 33177873 PMCID: PMC7649241 DOI: 10.2147/cmar.s267345] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 10/01/2020] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND The initiation and progression of colorectal cancer (CRC) are a multistep complex process regulated by multiple factors. Previous evidence indicated that microRNA-802 (miR-802) participated in tumorigenesis of numerous solid cancers; however, the potential roles and underlying mechanisms of miR‑802 in CRC still need further exploration. METHODS Quantitative real-time PCR (qRT-PCR) was employed to evaluate miR-802 levels in human CRC tissues and cell lines. In vitro proliferation, apoptosis, migration and invasion assays, and in vivo subcutaneous mouse xenograft model were utilized to examine the effects of miR-802 on the malignant behaviors of CRC cells. Then, bioinformatics prediction, dual-luciferase reporter, qRT-PCR, and Western blot was conducted to confirm the down-stream target of miR-802. RESULTS MiR-802 was frequently down-regulated in CRC tissues and cells. Further analyses showed that the low expression of miR-802 in CRC tissues was significantly correlated with tumor progression and poor patients' prognosis. Overexpression of miR-802 profoundly inhibited proliferation, migration and invasion but promoted apoptosis of CRC cells, by contrast, miR-802 silencing exhibited opposite effects in vitro. Further animal experiment demonstrated that miR-802 could suppress tumor growth via inhibiting the proliferation and promoting the apoptosis of CRC cells in vivo. Mechanistically, miR-802 functioned as a tumor suppressor through inhibiting the expression of Ubinuclein-2 (UBN2) on post-transcriptional level. Moreover, upregulation of UBN2 expression could reverse the biological effects of CRC cells induced by miR-802 overexpression. CONCLUSION Our study demonstrates that miR-802 inhibits the proliferation, migration and invasion while promotes the apoptosis of CRC cells via directly suppressing UBN2 expression. These findings provide a promising biomarker and potential treatment target for CRC.
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Affiliation(s)
- Tao Yang
- Department of General Surgery, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou 121001, People's Republic of China
| | - Qiuying Guo
- Operating Room, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou 121001, People's Republic of China
| | - Dongsheng Li
- Department of General Surgery, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou 121001, People's Republic of China
| | - Guang Bai
- Department of General Surgery, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou 121001, People's Republic of China
| | - Hongzhi Sun
- Department of General Surgery, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou 121001, People's Republic of China
| | - Wei Wang
- Department of General Surgery, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou 121001, People's Republic of China
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Pavone P, Corsello G, Marino SD, Ruggieri M, Falsaperla R. 7q31.32 partial duplication: First report of a child with dysmorphism, autistic spectrum disorder, moderate intellectual disability and, epilepsy. Literature review. Epilepsy Res 2019; 158:106223. [PMID: 31707317 DOI: 10.1016/j.eplepsyres.2019.106223] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 09/10/2019] [Accepted: 10/19/2019] [Indexed: 10/25/2022]
Abstract
INTRODUCTION Duplication of long arm of chromosome 7(q) is uncommon. It may occur as "pure", isolated anomaly or in association with other mutations involving the same or other chromosomes. "Pure" chromosome 7q duplication has recently been classified by segment involved: the interstitial, proximal, or distal segment of the arm. Attempts to correlate genotype with phenotype in each group has yielded questionable results even though intellective disability and minor dysmorphic features of variable types are typically seen. MATERIAL AND METHODS In a young boy showing minor facial dysmorphism, language delay, autistic spectrum disorder, epileptic seizures, behavioral disturbances and irritability an array-CGH analysis was carried out. RESULTS Array-CGH analysis found in the proband a de novo variant of partial duplication of 7q31.32 (122.254.792-122.376.908). DISCUSSION A very few cases of partial 7q duplication have been reported thus far mainly presenting with clinical signs of dysmorphic features, large head, developmental delay, epileptic seizures and skeletal anomalies. To our knowledge, this is the first report of a case of a de novo variant of 7q31.32 duplication, showing dysmorphic anomalies and neurologic impairment including ASD and seizures. In the 7q31.32 region is located the gene CADPS2, which has been associated to autistic spectrum disorder and other neurologic disorders. In the child, a genotype-phenotype correlation may be hypothesized. Further similar reports may be useful to confirm this observation.
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Affiliation(s)
- Piero Pavone
- Department of Pediatrics, University Hospital. "Vittorio Emanuele-Policlinico" Catania, Italy.
| | - Giovanni Corsello
- Department of Maternal and Child Health, University of Palermo, Italy
| | - Simona Domenica Marino
- Pediatrics and Pediatric Emergency Complex Unity, University-Hospital "Policlinico-Vittorio Emanuele", Catania, Italy
| | - Martino Ruggieri
- Unit of Rare Diseases of the Nervous System in childhood, Department of Clinical and Experimental Medicine, Section of Pediatrics and Child Neuropsychiatry, A.U.O. Vittorio Emanuele-Policlinico of Catania, Italy
| | - Raffaele Falsaperla
- Pediatrics and Pediatric Emergency Complex Unity, University-Hospital "Policlinico-Vittorio Emanuele", Catania, Italy
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Mei JW, Yang ZY, Xiang HG, Bao R, Ye YY, Ren T, Wang XF, Shu YJ. MicroRNA-1275 inhibits cell migration and invasion in gastric cancer by regulating vimentin and E-cadherin via JAZF1. BMC Cancer 2019; 19:740. [PMID: 31357957 PMCID: PMC6664777 DOI: 10.1186/s12885-019-5929-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 07/12/2019] [Indexed: 12/11/2022] Open
Abstract
Background Emerging evidence has shown that miR-1275 plays a critical role in tumour metastasis and the progression of various types of cancer. In this study, we analysed the role and mechanism of miR-1275 in the progression and prognosis of gastric cancer (GC). Methods Target genes of miR-1275 were identified and verified by luciferase assay and Western blotting. The function of miR-1275 in invasion and metastasis was analysed in vitro and in vivo in nude mice. The signal pathway regulated by miR-1275 was examined by qRT-PCR, Western blotting and chromatin immunoprecipitation analyses. The expression of miR-1275and JAZF1 were measured in specimens of GC and adjacent non cancerous tissues. Results We identified JAZF1 as a direct miR-1275 target. miR-1275 supresses migration and invasion of GC cells in vitro and in vivo, which was restored by JAZF1 overexpression. Moreover, JAZF1 was recognized as a direct regulator of Vimentin. Knocking-down miR-1275 or overexpressing JAZF1 resulted in upregulation of Vimentin but downregulation of E-cadherin. Meanwhile, we validated in 120 GC patients specimens that low miR-1275expression and high JAZF1 mRNA expression levels were closely associated with lymph node metastasis and poor prognosis. The expression of JAZF1 in protein level displayed the correlations with Vimentin but inversely with E-cadherin. Conclusions Increased miR-1275 expression inhibited GC metastasis by regulating vimentin/E-cadherin via direct suppression of JAZF1expression, suggesting that miR-1275 is a tumour-suppressor miRNA with the potential as a prognostic biomarker or therapeutic target in GC. Electronic supplementary material The online version of this article (10.1186/s12885-019-5929-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jia-Wei Mei
- Department of General Surgery and Laboratory of General Surgery, Xinhua Hospital, Affiliated with Shanghai Jiao Tong University, School of Medicine, No. 1665 Kongjiang Road, Shanghai, 200092, China.,Shanghai Key Laboratory of Biliary Tract Disease Research, No. 1665 Kongjiang Road, Shanghai, 200092, China.,Institute of Biliary Tract Disease, Shanghai Jiao Tong University School of Medicine, No. 1665 Kongjiang Road, Shanghai, 200092, China
| | - Zi-Yi Yang
- Department of General Surgery and Laboratory of General Surgery, Xinhua Hospital, Affiliated with Shanghai Jiao Tong University, School of Medicine, No. 1665 Kongjiang Road, Shanghai, 200092, China.,Shanghai Key Laboratory of Biliary Tract Disease Research, No. 1665 Kongjiang Road, Shanghai, 200092, China.,Institute of Biliary Tract Disease, Shanghai Jiao Tong University School of Medicine, No. 1665 Kongjiang Road, Shanghai, 200092, China
| | - Hong-Gang Xiang
- Department of General Surgery, Pudong New Area People's Hospital affiliated to Shanghai University of Medicine and Health Science, No. 490, South Chuanhuan Road, Pudong New Area, Shanghai, 201299, China
| | - Runfa Bao
- Department of General Surgery and Laboratory of General Surgery, Xinhua Hospital, Affiliated with Shanghai Jiao Tong University, School of Medicine, No. 1665 Kongjiang Road, Shanghai, 200092, China.,Shanghai Key Laboratory of Biliary Tract Disease Research, No. 1665 Kongjiang Road, Shanghai, 200092, China.,Institute of Biliary Tract Disease, Shanghai Jiao Tong University School of Medicine, No. 1665 Kongjiang Road, Shanghai, 200092, China
| | - Yuan-Yuan Ye
- Department of General Surgery and Laboratory of General Surgery, Xinhua Hospital, Affiliated with Shanghai Jiao Tong University, School of Medicine, No. 1665 Kongjiang Road, Shanghai, 200092, China.,Shanghai Key Laboratory of Biliary Tract Disease Research, No. 1665 Kongjiang Road, Shanghai, 200092, China.,Institute of Biliary Tract Disease, Shanghai Jiao Tong University School of Medicine, No. 1665 Kongjiang Road, Shanghai, 200092, China
| | - Tai Ren
- Department of General Surgery and Laboratory of General Surgery, Xinhua Hospital, Affiliated with Shanghai Jiao Tong University, School of Medicine, No. 1665 Kongjiang Road, Shanghai, 200092, China.,Shanghai Key Laboratory of Biliary Tract Disease Research, No. 1665 Kongjiang Road, Shanghai, 200092, China.,Institute of Biliary Tract Disease, Shanghai Jiao Tong University School of Medicine, No. 1665 Kongjiang Road, Shanghai, 200092, China
| | - Xue-Feng Wang
- Department of General Surgery and Laboratory of General Surgery, Xinhua Hospital, Affiliated with Shanghai Jiao Tong University, School of Medicine, No. 1665 Kongjiang Road, Shanghai, 200092, China. .,Shanghai Key Laboratory of Biliary Tract Disease Research, No. 1665 Kongjiang Road, Shanghai, 200092, China. .,Institute of Biliary Tract Disease, Shanghai Jiao Tong University School of Medicine, No. 1665 Kongjiang Road, Shanghai, 200092, China.
| | - Yi-Jun Shu
- Department of General Surgery and Laboratory of General Surgery, Xinhua Hospital, Affiliated with Shanghai Jiao Tong University, School of Medicine, No. 1665 Kongjiang Road, Shanghai, 200092, China. .,Shanghai Key Laboratory of Biliary Tract Disease Research, No. 1665 Kongjiang Road, Shanghai, 200092, China. .,Institute of Biliary Tract Disease, Shanghai Jiao Tong University School of Medicine, No. 1665 Kongjiang Road, Shanghai, 200092, China.
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Zhang S, Gao M, Yu L. GATAD1 gene amplification promotes glioma malignancy by directly regulating CCND1 transcription. Cancer Med 2019; 8:5242-5253. [PMID: 31286678 PMCID: PMC6718743 DOI: 10.1002/cam4.2405] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 06/08/2019] [Accepted: 06/22/2019] [Indexed: 12/31/2022] Open
Abstract
Background The GATAD1 gene overexpression induced by GATAD1 amplification upregulation is detected in different human tumors. To date, the relationship between GATAD1 amplification and glioma oncogenesis and malignancy is still unknown. Methods GATAD1 gene amplification and expression were analyzed in 187 gliomas using qPCR and immunostaining. The relation of GATAD1 to patients’ prognoses was assessed via the Kaplan–Meier method. The MTT and orthotopic tumor transplantation assays were used to identify the function of GATAD1 in glioma proliferation. cDNA microarray, ChIP qPCR, EMSA and 3C were used to screen the downstream mechanism of GATAD1 regulating glioma proliferation. Results Our results indicated that GATAD1 gene amplification and GATAD1 gene expression are novel independent diagnosis biomarkers to indicate poor outcome of glioma patients. GATAD1 knockdown can remarkably suppress GBM cell proliferation both in vitro and in vivo. GATAD1 could promote CCND1 gene transcription by inducing long range chromatin architectural interaction on the CCND1 promoter. Then GATAD1 sequentially accelerates GBM cell cycle transition and proliferation via regulating CCND1. Conclusions We identify GATAD1 as a novel potential diagnosis biomarker and promising prognosis predictor in glioma patients. Functionally, we confirm GATAD1 as an epigenetic chromatin topological regulator that promotes glioma proliferation by targeting CCND1.
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Affiliation(s)
- Shanshan Zhang
- Department of Radiology, Tianjin Medical University General Hospital, Tianjin, China
| | - Min Gao
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences of Tianjin Medical University, Tianjin, China
| | - Lin Yu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences of Tianjin Medical University, Tianjin, China
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15
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Zhao YL, Zhong SR, Zhang SH, Bi JX, Xiao ZY, Wang SY, Jiao HL, Zhang D, Qiu JF, Zhang LJ, Huang CM, Chen XL, Ding YQ, Ye YP, Liang L, Liao WT. UBN2 promotes tumor progression via the Ras/MAPK pathway and predicts poor prognosis in colorectal cancer. Cancer Cell Int 2019; 19:126. [PMID: 31110467 PMCID: PMC6511126 DOI: 10.1186/s12935-019-0848-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 05/02/2019] [Indexed: 01/09/2023] Open
Abstract
Background Ubinuclein-2 (UBN2) is a nuclear protein that interacts with many transcription factors. The molecular role and mechanism of UBN2 in the development and progression of cancers, including colorectal cancer (CRC), is not well understood. The current study explored the role of UBN2 in the development and progression CRC. Methods Oncomine network and The Cancer Genome Atlas (TCGA) database were downloaded and Gene Set Enrichment Analysis (GSEA) was performed to compare the UBN2′s expression between normal and tumor tissues, as well as the potential correlation of UBN2 expression with signaling pathways. Immunohistochemistry (IHC), qRT-PCR and Western blotting were performed to determine the expression of UBN2 in CRC tissues or cell lines. In vitro proliferation and invasion assays, and orthotopic mouse metastatic model were used to analyze the effect of UBN2 on the development and progression of CRC. Results The analysis of UBN2 expression using Oncomine network showed that UBN2 was upregulated in CRC tissues compared to matched adjacent normal intestinal epithelial tissues. IHC, qRT-PCR and Western blotting confirmed that UBN2 expression is higher in CRC tissues compared with matched adjacent normal intestinal epithelial tissues. In addition, analyses of TCGA data revealed that high UBN2 expression was associated with advanced stages of lymph node metastasis, distant metastasis, and short survival time in CRC patients. IHC showed that high UBN2 expression is correlated with advanced stages of CRC. Moreover, UBN2 is highly expressed in the liver metastatic lesions. Furthermore, knockdown of UBN2 inhibited the growth, invasiveness and metastasis of CRC cells via regulation of the Ras/MAPK signaling pathway. Conclusion The current study demonstrates that UBN2 promotes tumor progression in CRC. UBN2 may be used as a promising biomarker for predicting the prognosis of CRC patients. Electronic supplementary material The online version of this article (10.1186/s12935-019-0848-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ya-Li Zhao
- 1Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515 Guangdong China.,2Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong China.,3Guangdong Provincial Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong China
| | - Shen-Rong Zhong
- 1Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515 Guangdong China.,2Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong China.,3Guangdong Provincial Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong China
| | - Shi-Hong Zhang
- 4Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong China
| | - Jia-Xin Bi
- 1Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515 Guangdong China.,2Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong China.,3Guangdong Provincial Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong China
| | - Zhi-Yuan Xiao
- 1Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515 Guangdong China.,2Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong China.,3Guangdong Provincial Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong China
| | - Shu-Yang Wang
- 1Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515 Guangdong China.,2Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong China.,3Guangdong Provincial Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong China
| | - Hong-Li Jiao
- 1Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515 Guangdong China.,2Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong China.,3Guangdong Provincial Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong China
| | - Dan Zhang
- 1Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515 Guangdong China.,2Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong China.,3Guangdong Provincial Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong China
| | - Jun-Feng Qiu
- 1Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515 Guangdong China.,2Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong China.,3Guangdong Provincial Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong China
| | - Ling-Jie Zhang
- 1Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515 Guangdong China.,2Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong China.,3Guangdong Provincial Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong China
| | - Cheng-Mei Huang
- 1Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515 Guangdong China.,2Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong China.,3Guangdong Provincial Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong China
| | - Xiao-Ling Chen
- 1Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515 Guangdong China.,2Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong China.,3Guangdong Provincial Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong China
| | - Yan-Qing Ding
- 1Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515 Guangdong China.,2Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong China.,3Guangdong Provincial Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong China
| | - Ya-Ping Ye
- 1Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515 Guangdong China.,2Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong China.,3Guangdong Provincial Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong China
| | - Li Liang
- 1Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515 Guangdong China.,2Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong China.,3Guangdong Provincial Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong China
| | - Wen-Ting Liao
- 1Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515 Guangdong China.,2Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong China.,3Guangdong Provincial Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong China
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16
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Chen L, Wei Y, Chi W, Fang D, Jiang X, Zhang S. Potential Mutations in Chinese Pathologic Myopic Patients and Contributions to Phenotype. Curr Mol Med 2019; 18:689-697. [PMID: 30747064 PMCID: PMC6635424 DOI: 10.2174/1566524019666190211120016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Revised: 01/07/2019] [Accepted: 01/07/2019] [Indexed: 12/02/2022]
Abstract
Purpose Pathologic myopia is a leading cause of visual impairment in East Asia. The aim of this study was to investigate the potential mutations in Chinese pathologic myopic patients and to analyze the correlations between genotype and clinical phenotype. Method One hundred and three patients with pathologic myopia and one hundred and nine unrelated healthy controls were recruited from Zhongshan Ophthalmic Center. Detailed clinical data, including ultra-widefield retinal images, measurements of best-corrected visual acuity, axial length, refractive error and ophthalmic examination results, were obtained. Blood samples were collected for high-throughput DNA targeted sequencing. Based on the screening results, phenotype-genotype correlations were analyzed. Results The study included 196 eyes of 103 patients (36 men and 67 women) with an average age of 52.19 (38.92 – 65.46) years, an average refractive error of -11.80 D (-16.38 – -7.22) and a mean axial length of 28.26 mm (25.79 – 30.73). The patients were subdivided into three groups: myopic chorioretinal atrophy (190 eyes of 101 patients), myopic choroidal neovascularization (17 eyes of 15 patients), and myopic traction retinopathy (71 eyes of 61 patients). Systematic analysis of variants in the 255 genes revealed six potential pathogenic mutations: PEX7, OCA2, LRP5 (rs545382, c.1647T>C), TSPAN12 (rs41623, c.765G>T), RDH5 (rs3138142, c.423C>T) and TTC21B (rs80225158, c.2385G>C). OCA2 mutations were primarily observed in patients with myopic traction maculopathy. Conclusion Genetic alterations contribute to various clinical characteristics in Chinese pathologic myopic patients. The study may provide new insights into the etiology of pathologic myopia and potential targets for therapeutic interventions.
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Affiliation(s)
- L Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China.,Shenzhen Eye Hospital, Shenzhen Eye Institute, Jinan University, Shenzhen, China
| | - Y Wei
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - W Chi
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - D Fang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - X Jiang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - S Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
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17
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The role of Pax6 in brain development and its impact on pathogenesis of autism spectrum disorder. Brain Res 2019; 1705:95-103. [DOI: 10.1016/j.brainres.2018.02.041] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 02/23/2018] [Accepted: 02/24/2018] [Indexed: 12/14/2022]
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18
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Bikkul MU, Faragher RGA, Worthington G, Meinke P, Kerr ARW, Sammy A, Riyahi K, Horton D, Schirmer EC, Hubank M, Kill IR, Anderson RM, Slijepcevic P, Makarov E, Bridger JM. Telomere elongation through hTERT immortalization leads to chromosome repositioning in control cells and genomic instability in Hutchinson-Gilford progeria syndrome fibroblasts, expressing a novel SUN1 isoform. Genes Chromosomes Cancer 2019; 58:341-356. [PMID: 30474255 PMCID: PMC6590296 DOI: 10.1002/gcc.22711] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 11/06/2018] [Accepted: 11/22/2018] [Indexed: 02/06/2023] Open
Abstract
Immortalizing primary cells with human telomerase reverse transcriptase (hTERT) has been common practice to enable primary cells to be of extended use in the laboratory because they avoid replicative senescence. Studying exogenously expressed hTERT in cells also affords scientists models of early carcinogenesis and telomere behavior. Control and the premature ageing disease—Hutchinson‐Gilford progeria syndrome (HGPS) primary dermal fibroblasts, with and without the classical G608G mutation have been immortalized with exogenous hTERT. However, hTERT immortalization surprisingly elicits genome reorganization not only in disease cells but also in the normal control cells, such that whole chromosome territories normally located at the nuclear periphery in proliferating fibroblasts become mislocalized in the nuclear interior. This includes chromosome 18 in the control fibroblasts and both chromosomes 18 and X in HGPS cells, which physically express an isoform of the LINC complex protein SUN1 that has previously only been theoretical. Additionally, this HGPS cell line has also become genomically unstable and has a tetraploid karyotype, which could be due to the novel SUN1 isoform. Long‐term treatment with the hTERT inhibitor BIBR1532 enabled the reduction of telomere length in the immortalized cells and resulted that these mislocalized internal chromosomes to be located at the nuclear periphery, as assessed in actively proliferating cells. Taken together, these findings reveal that elongated telomeres lead to dramatic chromosome mislocalization, which can be restored with a drug treatment that results in telomere reshortening and that a novel SUN1 isoform combined with elongated telomeres leads to genomic instability. Thus, care should be taken when interpreting data from genomic studies in hTERT‐immortalized cell lines.
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Affiliation(s)
- Mehmet U. Bikkul
- Genome Engineering and Maintenance NetworkInstitute for Environment, Health and Societies, Brunel University LondonUxbridgeEngland
| | | | - Gemma Worthington
- Genome Engineering and Maintenance NetworkInstitute for Environment, Health and Societies, Brunel University LondonUxbridgeEngland
| | - Peter Meinke
- Friedrich‐Baur‐InstitutKlinikum der Universität MünchenMünchenGermany
- The Wellcome Trust Centre for Cell BiologyInstitute of Cell Biology, and Centre for Translational and Chemical Biology, University of EdinburghEdinburghEngland
| | - Alastair R. W. Kerr
- The Wellcome Trust Centre for Cell BiologyInstitute of Cell Biology, and Centre for Translational and Chemical Biology, University of EdinburghEdinburghEngland
| | - Aakila Sammy
- Genome Engineering and Maintenance NetworkInstitute for Environment, Health and Societies, Brunel University LondonUxbridgeEngland
| | - Kumars Riyahi
- Genome Engineering and Maintenance NetworkInstitute for Environment, Health and Societies, Brunel University LondonUxbridgeEngland
| | - Daniel Horton
- Genome Engineering and Maintenance NetworkInstitute for Environment, Health and Societies, Brunel University LondonUxbridgeEngland
| | - Eric C. Schirmer
- The Wellcome Trust Centre for Cell BiologyInstitute of Cell Biology, and Centre for Translational and Chemical Biology, University of EdinburghEdinburghEngland
| | - Michael Hubank
- Centre for Molecular PathologyThe Royal Marsden HospitalLondonEngland
| | - Ian R. Kill
- Genome Engineering and Maintenance NetworkInstitute for Environment, Health and Societies, Brunel University LondonUxbridgeEngland
| | - Rhona M. Anderson
- Genome Engineering and Maintenance NetworkInstitute for Environment, Health and Societies, Brunel University LondonUxbridgeEngland
| | - Predrag Slijepcevic
- Genome Engineering and Maintenance NetworkInstitute for Environment, Health and Societies, Brunel University LondonUxbridgeEngland
| | - Evgeny Makarov
- Genome Engineering and Maintenance NetworkInstitute for Environment, Health and Societies, Brunel University LondonUxbridgeEngland
| | - Joanna M. Bridger
- Genome Engineering and Maintenance NetworkInstitute for Environment, Health and Societies, Brunel University LondonUxbridgeEngland
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Wlodarski MW, Sahoo SS, Niemeyer CM. Monosomy 7 in Pediatric Myelodysplastic Syndromes. Hematol Oncol Clin North Am 2018; 32:729-743. [DOI: 10.1016/j.hoc.2018.04.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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20
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Gupta R, Harankhedkar S, Rahman K, Singh MK, Chandra D, Mittal N, Gupta A, Nityanand S. Prevalence of Chromosome 7 Abnormalities in Myelodysplastic Syndrome and Acute Myeloid Leukemia: A Single Center Study and Brief Literature Review. Indian J Hematol Blood Transfus 2018; 34:602-611. [PMID: 30369728 DOI: 10.1007/s12288-018-0941-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 02/27/2018] [Indexed: 12/20/2022] Open
Abstract
Chromosome 7 abnormalities in patients with myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML) heralds a poor prognosis. However its prevalence, morphological characteristics and clinical impact in MDS and AML in Indian subcontinent is sparsely reported. This was an observational cross-sectional study performed to evaluate the clinico-pathological profiles of MDS/AML patients with chromosome 7 abnormalities over a period of 4 years. 724 cases of MDS (n = 150) and AML (n = 574) were evaluated. Abnormal karyotype was detected in 49% (43/88) patients of MDS and 44% (127/289) cases of AML. Chromosome 7 abnormalities were detected in 18% cases of MDS (16/88) and 6.5% (19/289) cases of AML. Sole chromosome 7 abnormalities were detected in 5.7% (5/88) and 2.7% (8/289) and in adjunct to complex abnormalities in 7.9 and 3.1% cases of MDS and AML respectively. Morphologically, dyserythropoiesis, dysmyelopoiesis and eosinophilia were seen in 100, 66 and 56% cases of MDS and 38, 40 and 21% cases of AML. Majority of the patients had an aggressive natural course and outcome was dismal. Chromosome 7 abnormalities are strongly associated with the presence of morphological dysplasia and eosinophilia, irrespective of the type of aberration. It is invariably associated with very poor outcome.
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Affiliation(s)
- Ruchi Gupta
- Department of Hematology, I Block, Sanjay Gandhi Post Graduate Institute of Medical Sciences (SGPGIMS), Raibareily Road, Lucknow, Uttar Pradesh 226014 India
| | - Shivangi Harankhedkar
- Department of Hematology, I Block, Sanjay Gandhi Post Graduate Institute of Medical Sciences (SGPGIMS), Raibareily Road, Lucknow, Uttar Pradesh 226014 India
| | - Khaliqur Rahman
- Department of Hematology, I Block, Sanjay Gandhi Post Graduate Institute of Medical Sciences (SGPGIMS), Raibareily Road, Lucknow, Uttar Pradesh 226014 India
| | - Manish K Singh
- Department of Hematology, I Block, Sanjay Gandhi Post Graduate Institute of Medical Sciences (SGPGIMS), Raibareily Road, Lucknow, Uttar Pradesh 226014 India
| | - Dinesh Chandra
- Department of Hematology, I Block, Sanjay Gandhi Post Graduate Institute of Medical Sciences (SGPGIMS), Raibareily Road, Lucknow, Uttar Pradesh 226014 India
| | - Navkirti Mittal
- Department of Hematology, I Block, Sanjay Gandhi Post Graduate Institute of Medical Sciences (SGPGIMS), Raibareily Road, Lucknow, Uttar Pradesh 226014 India
| | - Anshul Gupta
- Department of Hematology, I Block, Sanjay Gandhi Post Graduate Institute of Medical Sciences (SGPGIMS), Raibareily Road, Lucknow, Uttar Pradesh 226014 India
| | - Soniya Nityanand
- Department of Hematology, I Block, Sanjay Gandhi Post Graduate Institute of Medical Sciences (SGPGIMS), Raibareily Road, Lucknow, Uttar Pradesh 226014 India
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21
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Herrero MJ, Gitton Y. The untold stories of the speech gene, the FOXP2 cancer gene. Genes Cancer 2018; 9:11-38. [PMID: 29725501 PMCID: PMC5931254 DOI: 10.18632/genesandcancer.169] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 04/02/2018] [Indexed: 12/11/2022] Open
Abstract
FOXP2 encodes a transcription factor involved in speech and language acquisition. Growing evidence now suggests that dysregulated FOXP2 activity may also be instrumental in human oncogenesis, along the lines of other cardinal developmental transcription factors such as DLX5 and DLX6 [1-4]. Several FOXP familymembers are directly involved during cancer initiation, maintenance and progression in the adult [5-8]. This may comprise either a pro-oncogenic activity or a deficient tumor-suppressor role, depending upon cell types and associated signaling pathways. While FOXP2 is expressed in numerous cell types, its expression has been found to be down-regulated in breast cancer [9], hepatocellular carcinoma [8] and gastric cancer biopsies [10]. Conversely, overexpressed FOXP2 has been reported in multiple myelomas, MGUS (Monoclonal Gammopathy of Undetermined Significance), several subtypes of lymphomas [5,11], as well as in neuroblastomas [12] and ERG fusion-negative prostate cancers [13]. According to functional evidences reported in breast cancer [9] and survey of recent transcriptomic and proteomic analyses of different tumor biopsies, we postulate that FOXP2 dysregulation may play a main role throughout cancer initiation and progression. In some cancer conditions, FOXP2 levels are now considered as a critical diagnostic marker of neoplastic cells, and in many situations, they even bear strong prognostic value [5]. Whether FOXP2 may further become a therapeutic target is an actively explored lead. Knowledge reviewed here may help improve our understanding of FOXP2 roles during oncogenesis and provide cues for diagnostic, prognostic and therapeutic analyses.
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Affiliation(s)
- Maria Jesus Herrero
- Center for Neuroscience Research, Children's National Medical Center, NW, Washington, DC, USA
| | - Yorick Gitton
- Sorbonne University, INSERM, CNRS, Vision Institute Research Center, Paris, France
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22
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Joshi PS, Modur V, Cheng J, Robinson K, Rao K. Characterization of immortalized human mammary epithelial cell line HMEC 2.6. Tumour Biol 2017; 39:1010428317724283. [PMID: 29022488 DOI: 10.1177/1010428317724283] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Primary human mammary epithelial cells have a limited life span which makes it difficult to study them in vitro for most purposes. To overcome this problem, we have developed a cell line that was immortalized using defined genetic elements, and we have characterized this immortalized non-tumorigenic human mammary epithelial cell line to establish it as a potential model system. human mammary epithelial cells were obtained from a healthy individual undergoing reduction mammoplasty at SIU School of Medicine. The cells were transduced with CDK4R24C followed by transduction with human telomerase reverse transcriptase. Post all manipulation, the cells displayed a normal cell cycle phase distribution and were near diploid in nature, which was confirmed by flow cytometry and karyotyping. In vitro studies showed that the cells were anchorage dependent and were non-invasive in nature. The cell line expressed basal epithelial markers such as cytokeratin 7, CD10, and p63 and was negative for the expression of estrogen receptor and progesterone receptor. Upon G-band karyotyping, the cell line displayed the presence of a few cytogenic abnormalities, including trisomy 20 and trisomy 7, which are also commonly present in other immortalized mammary cell lines. Furthermore, the benign nature of these cells was confirmed by multiple in vitro and in vivo experiments. Therefore, we think that this cell line could serve as a good model to understand the molecular mechanisms involved in the development and progression of breast cancer and to also assess the effect of novel therapeutics on human mammary epithelial cells.
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Affiliation(s)
- Pooja S Joshi
- 1 Department of Medical Microbiology, Immunology and Cell Biology, Southern Illinois University School of Medicine, Springfield, IL, USA
| | - Vishnu Modur
- 2 Department of Pediatrics and Cincinnati Children's Hospital, University of Cincinnati, Cincinnati, OH, USA
| | - JiMing Cheng
- 3 For You Dentistry, 477 Union Ave., Bridgewater, NJ
| | - Kathy Robinson
- 4 Division of Hematology/Oncology, Department of Internal Medicine, Southern Illinois University School of Medicine, USA.,5 Simmons Cancer Institute at Southern Illinois University, Springfield, IL, USA
| | - Krishna Rao
- 1 Department of Medical Microbiology, Immunology and Cell Biology, Southern Illinois University School of Medicine, Springfield, IL, USA.,4 Division of Hematology/Oncology, Department of Internal Medicine, Southern Illinois University School of Medicine, USA.,5 Simmons Cancer Institute at Southern Illinois University, Springfield, IL, USA
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23
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Meyer MR, Barton M. Estrogens and Coronary Artery Disease: New Clinical Perspectives. ADVANCES IN PHARMACOLOGY 2016; 77:307-60. [PMID: 27451102 DOI: 10.1016/bs.apha.2016.05.003] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In premenopausal women, endogenous estrogens are associated with reduced prevalence of arterial hypertension, coronary artery disease, myocardial infarction, and stroke. Clinical trials conducted in the 1990s such as HERS, WHI, and WISDOM have shown that postmenopausal treatment with horse hormone mixtures (so-called conjugated equine estrogens) and synthetic progestins adversely affects female cardiovascular health. Our understanding of rapid (nongenomic) and chronic (genomic) estrogen signaling has since advanced considerably, including identification of a new G protein-coupled estrogen receptor (GPER), which like the "classical" receptors ERα and ERβ is highly abundant in the cardiovascular system. Here, we discuss the role of estrogen receptors in the pathogenesis of coronary artery disease and review natural and synthetic ligands of estrogen receptors as well as their effects in physiology, on cardiovascular risk factors, and atherosclerotic vascular disease. Data from preclinical and clinical studies using nonselective compounds activating GPER, which include selective estrogen receptor modulators such as tamoxifen or raloxifene, selective estrogen receptor downregulators such as Faslodex™ (fulvestrant/ICI 182,780), vitamin B3 (niacin), green tea catechins, and soy flavonoids such as genistein or resveratrol, strongly suggest that activation of GPER may afford therapeutic benefit for primary and secondary prevention in patients with or at risk for coronary artery disease. Evidence from preclinical studies suggest similar efficacy profiles for selective small molecule GPER agonists such as G-1 which are devoid of uterotrophic activity. Further clinical research in this area is warranted to provide opportunities for future cardiovascular drug development.
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Affiliation(s)
- M R Meyer
- Triemli City Hospital, Zürich, Switzerland.
| | - M Barton
- Molecular Internal Medicine, University of Zürich, Zürich, Switzerland.
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24
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Ramos-Zaldívar HM, Martínez-Irías DG, Espinoza-Moreno NA, Napky-Rajo JS, Bueso-Aguilar TA, Reyes-Perdomo KG, Montes-Gambarelli JA, Euceda IM, Ponce-Barahona AF, Gámez-Fernández CA, Moncada-Arita WA, Palomo-Bermúdez VA, Jiménez-Faraj JE, Hernández-Padilla AG, Olivera DA, Robertson KJ, Leiva-Sanchez LA, Herrera-Paz EF. A novel description of a syndrome consisting of 7q21.3 deletion including DYNC1I1 with preserved DLX5/6 without ectrodactyly: a case report. J Med Case Rep 2016; 10:156. [PMID: 27291887 PMCID: PMC4904365 DOI: 10.1186/s13256-016-0921-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 04/29/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Chromosomal region 7q21.3 comprises approximately 5.2 mega base pairs that include genes DLX5/6, SHFM1, and DYNC1I1 associated with split hand/split foot malformation 1. So far, there are reports of eight families with deletion of DYNC1I1 and preserved DLX5/6 associated with ectrodactyly. From these families, only three patients did not present ectrodactyly and, unlike our patient, no other cases have been described as having craniofacial dysmorphology, mitral valve prolapse, kyphoscoliosis, inguinal herniae, or personality disorder. There is no designation described in the literature for patients with syndromic manifestations without ectrodactyly, which hinders diagnosis. CASE PRESENTATION We report the case of a 44-year-old mestizo (combined European and Amerindian descent) man with a 3191 kilo base pairs deletion and International System for Human Cytogenetic Nomenclature array 7q21.3 (93,389,222-96,579,845)x1. Clinical manifestations included micrognathia, retrognathia, wormian bones, auditory canal stenosis, depressed nasal bridge, epicanthal fold, fullness of upper eyelid, long philtrum, low-set ears, sensorineural hearing loss, kyphoscoliosis, bilateral inguinal herniae, mild mitral valve prolapse, and paranoid personality disorder. His isolated DNA was analyzed using a CytoScan HD Microarray system. Chromosome Analysis Suite software was utilized for the microarray analysis. All copy number changes were determined using the human genome build 19 (hg19/NCBI build 37). CONCLUSIONS Cases of deletions within chromosome 7q21.3 that include the split hand/split foot malformation 1 region represent a diagnostic challenge when not presenting ectrodactyly despite being syndromic. Due to the heterogeneity of the region, a better method to group and classify these patients is needed to facilitate their clinical diagnosis. For this purpose, we suggest that patients with 7q21.3 deletion including DYNC1I1 and preserved DLX5/6 without ectrodactyly, accompanied by craniofacial dysmorphology, personality disorder, hearing loss, musculoskeletal disorder, inguinal herniae and/or mitral valve prolapse be referred to by the eponym Ramos-Martínez syndrome.
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Affiliation(s)
- Héctor M Ramos-Zaldívar
- Campus San Pedro y San Pablo, School of Medicine, Universidad Católica de Honduras, San Pedro Sula, Honduras.
| | - Daniel G Martínez-Irías
- Campus San Pedro y San Pablo, School of Medicine, Universidad Católica de Honduras, San Pedro Sula, Honduras
| | - Nelson A Espinoza-Moreno
- Campus San Pedro y San Pablo, School of Medicine, Universidad Católica de Honduras, San Pedro Sula, Honduras
| | - José S Napky-Rajo
- Campus San Pedro y San Pablo, School of Medicine, Universidad Católica de Honduras, San Pedro Sula, Honduras
| | - Tulio A Bueso-Aguilar
- Campus San Pedro y San Pablo, School of Medicine, Universidad Católica de Honduras, San Pedro Sula, Honduras
| | - Karla G Reyes-Perdomo
- Campus San Pedro y San Pablo, School of Medicine, Universidad Católica de Honduras, San Pedro Sula, Honduras
| | - Jimena A Montes-Gambarelli
- Campus San Pedro y San Pablo, School of Medicine, Universidad Católica de Honduras, San Pedro Sula, Honduras
| | - Isis M Euceda
- Campus San Pedro y San Pablo, School of Medicine, Universidad Católica de Honduras, San Pedro Sula, Honduras
| | - Aldo F Ponce-Barahona
- Campus San Pedro y San Pablo, School of Medicine, Universidad Católica de Honduras, San Pedro Sula, Honduras
| | - Carlos A Gámez-Fernández
- Campus San Pedro y San Pablo, School of Medicine, Universidad Católica de Honduras, San Pedro Sula, Honduras
| | - Wilberg A Moncada-Arita
- Campus San Pedro y San Pablo, School of Medicine, Universidad Católica de Honduras, San Pedro Sula, Honduras
| | - Victoria A Palomo-Bermúdez
- Campus San Pedro y San Pablo, School of Medicine, Universidad Católica de Honduras, San Pedro Sula, Honduras
| | - Julia E Jiménez-Faraj
- Campus San Pedro y San Pablo, School of Medicine, Universidad Católica de Honduras, San Pedro Sula, Honduras
| | - Amanda G Hernández-Padilla
- Campus San Pedro y San Pablo, School of Medicine, Universidad Católica de Honduras, San Pedro Sula, Honduras
| | - Denys A Olivera
- Campus San Pedro y San Pablo, School of Medicine, Universidad Católica de Honduras, San Pedro Sula, Honduras
| | - Kevin J Robertson
- Campus San Pedro y San Pablo, School of Medicine, Universidad Católica de Honduras, San Pedro Sula, Honduras
| | - Luis A Leiva-Sanchez
- Campus San Pedro y San Pablo, School of Medicine, Universidad Católica de Honduras, San Pedro Sula, Honduras
| | - Edwin Francisco Herrera-Paz
- Campus San Pedro y San Pablo, School of Medicine, Universidad Católica de Honduras, San Pedro Sula, Honduras
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25
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Ayub S, Gadji M, Krabchi K, Côté S, Gekas J, Maranda B, Drouin R. Three new cases of terminal deletion of the long arm of chromosome 7 and literature review to correlate genotype and phenotype manifestations. Am J Med Genet A 2016; 170A:896-907. [PMID: 26822682 DOI: 10.1002/ajmg.a.37428] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 09/18/2015] [Indexed: 11/10/2022]
Abstract
Partial monosomy of the long arm of chromosome 7 has been characterized by wide phenotypic manifestations, but holoprosencephaly (HPE) and sacral agenesis have frequently been associated with this chromosomal deletion. A clear relationship between genotype and phenotype remains to be defined in the 7q deletion syndrome. Three patients (1, 2, and 3) were investigated with 7q terminal deletion and compared with similar deletion cases in the literature in order to stratify the phenotypes associated with 7q35 and 7q36 terminal deletion patients. Patients 1, 2, and 3 were carrying a de novo terminal deletion at bands 7q36.2, 7q35, and 7q36.1, respectively. In patient 3, a small Xq28 duplication was also identified by array-CGH. Our patients presented with heterogeneous phenotypic manifestations, which could imply the possible role of environmental factors (multifactorial inheritance), structural variations in the non-coding regions, penetrance, and/or polymorphism. The varying length of deletion was also taken into account. Growth retardation was the most frequent symptom found in both 7q35 and 7q36 patients we reviewed. The occurrence of HPE and sacral malformation together was seen in less than 10% of the reviewed cases in both kinds of deletion. HPE was associated mainly in cases with an unbalanced translocation.
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Affiliation(s)
- Seemi Ayub
- Division of Genetics, Department of Pediatrics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Macoura Gadji
- Division of Genetics, Department of Pediatrics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada
- Manitoba Institute of Cell Biology (MICB), CancerCare Manitoba (CCMB), The Genomic Centre for Cancer Research and Diagnosis (GCCRD), The University of Manitoba, Winnipeg, Manitoba, Canada
- Laboratory of Hematology and Immunology, National Centre of Blood Transfusion of Dakar (CNTS), The Cheikh Anta Diop University of Dakar (UCAD), Dakar Fann, Senegal
| | - Kada Krabchi
- Division of Genetics, Department of Pediatrics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Sylvie Côté
- Department of Pediatrics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Jean Gekas
- Centre de Recherche du Centre Hospitalier Universitaire de Québec (CHUQ), Division of Medical Genetics, Unité de Diagnostic Prénatal, Faculty of Medicine, Laval University, Quebec City, Québec, Canada
| | - Bruno Maranda
- Division of Genetics, Department of Pediatrics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada
- Division of Medical Genetics, CHUQ, Faculty of Medicine, Laval University, Quebec City, Québec, Canada
| | - Régen Drouin
- Division of Genetics, Department of Pediatrics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada
- Division of Medical Genetics, CHUQ, Faculty of Medicine, Laval University, Quebec City, Québec, Canada
- Department of Biological Sciences, Faculty of Sciences, Université du Québec à Montréal, Montreal, Québec, Canada
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Zhou J, Lai PBS, Tsui SKW. Identification of a non-coding KLF4 transcript generated from intron retention and downregulated in human hepatocellular carcinoma. Int J Oncol 2015; 47:1554-62. [PMID: 26238073 DOI: 10.3892/ijo.2015.3104] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 06/29/2015] [Indexed: 11/06/2022] Open
Abstract
The Krüppel-like factor 4 (KLF4) gene is related to various biological processes including stem cell reprogramming and tumorigenesis. In this study, we identified and characterized a non-coding transcript of KLF4, which was designated KLF4‑003, in human liver tissue samples. KLF4‑003 was identified in a number of cell lines by reverse transcription PCR and DNA sequencing. Its expression levels were determined in 54 pairs of human hepatocellular carcinoma (HCC) tissues and a number of HCC cell lines by real-time PCR (RT-PCR). Methylation status of KLF4‑003 CpG islands was determined by bisulfite sequencing. The regulatory effect of KLF4‑003 CpG islands hypermethylation in Hep3B cells was then validated by the 5-aza-dC demethylation treatment, followed by RT-PCR analysis. Receiver operating characteristic (ROC) curve was created to evaluate the diagnostic value for differentiating between HCC cancer and benign diseases. The association study between KLF4‑003 expression level and clinical traits of HCC patients was performed with SPSS. We found that KLF4‑003 was downregulated in 46 out of 54 HCC samples compared with their adjunct normal tissues. The reduced KLF4‑003 expression was significantly associated with HCC recurrence (P=0.045) in the follow-up of 31 HCC patients. Significant differences were detected between the methylation status of HCC specimens and their adjacent normal controls. Demethylation treatment significantly rescued the expression of KLF4‑003 in Hep3B cells. Such observation indicated that the CpG island hypermethylation was at least partially responsible for the downregulation of KLF4‑003 in HCC. The area under ROC curve for the prediction of HCC reached 0.803 (95% CI=0.719-0.886, P<0.001). Our results suggested that the expression of KLF4‑003 was epigenetically regulated by methylation status of a KLF4‑003 CpG island in HCC. The differential expression of KLF4‑003 might play an important role in HCC development and might serve as a potential biomarker for the diagnosis of HCC.
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Affiliation(s)
- Junwei Zhou
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, P.R. China
| | - Paul Bo-San Lai
- Department of Surgery, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, P.R. China
| | - Stephen Kwok-Wing Tsui
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, P.R. China
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Abstract
To facilitate the integration and querying of genomics data, a number of generic data warehousing frameworks have been developed. They differ in their design and capabilities, as well as their intended audience. We provide a comprehensive and quantitative review of those genomic data warehousing frameworks in the context of large-scale systems biology. We reviewed in detail four genomic data warehouses (BioMart, BioXRT, InterMine and PathwayTools) freely available to the academic community. We quantified 20 aspects of the warehouses, covering the accuracy of their responses, their computational requirements and development efforts. Performance of the warehouses was evaluated under various hardware configurations to help laboratories optimize hardware expenses. Each aspect of the benchmark may be dynamically weighted by scientists using our online tool BenchDW (http://warehousebenchmark.fungalgenomics.ca/benchmark/) to build custom warehouse profiles and tailor our results to their specific needs.
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28
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Guglielmi L, Servettini I, Caramia M, Catacuzzeno L, Franciolini F, D'Adamo MC, Pessia M. Update on the implication of potassium channels in autism: K(+) channelautism spectrum disorder. Front Cell Neurosci 2015; 9:34. [PMID: 25784856 PMCID: PMC4345917 DOI: 10.3389/fncel.2015.00034] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Accepted: 01/20/2015] [Indexed: 11/16/2022] Open
Abstract
Autism spectrum disorders (ASDs) are characterized by impaired ability to properly implement environmental stimuli that are essential to achieve a state of social and cultural exchange. Indeed, the main features of ASD are impairments of interpersonal relationships, verbal and non-verbal communication and restricted and repetitive behaviors. These aspects are often accompanied by several comorbidities such as motor delay, praxis impairment, gait abnormalities, insomnia, and above all epilepsy. Genetic analyses of autistic individuals uncovered deleterious mutations in several K+ channel types strengthening the notion that their intrinsic dysfunction may play a central etiologic role in ASD. However, indirect implication of K+ channels in ASD has been also reported. For instance, loss of fragile X mental retardation protein (FMRP) results in K+ channels deregulation, network dysfunction and ASD-like cognitive and behavioral symptoms. This review provides an update on direct and indirect implications of K+ channels in ASDs. Owing to a mounting body of evidence associating a channelopathy pathogenesis to autism and showing that nearly 500 ion channel proteins are encoded by the human genome, we propose to classify ASDs - whose susceptibility is significantly enhanced by ion channels defects, either in a monogenic or multigenic condition - in a new category named “channelAutismSpectrumDisorder” (channelASD; cASD) and introduce a new taxonomy (e.g., Kvx.y-channelASD and likewise Navx.y-channelASD, Cavx.y-channelASD; etc.). This review also highlights some degree of clinical and genetic overlap between K+ channelASDs and K+ channelepsies, whereby such correlation suggests that a subcategory characterized by a channelASD-channelepsy phenotype may be distinguished. Ultimately, this overview aims to further understand the different clinical subgroups and help parse out the distinct biological basis of autism that are essential to establish patient-tailored treatments.
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Affiliation(s)
- Luca Guglielmi
- Section of Physiology and Biochemistry, Department of Experimental Medicine, University of Perugia School of Medicine, Perugia Italy
| | - Ilenio Servettini
- Section of Physiology and Biochemistry, Department of Experimental Medicine, University of Perugia School of Medicine, Perugia Italy
| | - Martino Caramia
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia Italy
| | - Luigi Catacuzzeno
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia Italy
| | - Fabio Franciolini
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia Italy
| | - Maria Cristina D'Adamo
- Section of Physiology and Biochemistry, Department of Experimental Medicine, University of Perugia School of Medicine, Perugia Italy
| | - Mauro Pessia
- Section of Physiology and Biochemistry, Department of Experimental Medicine, University of Perugia School of Medicine, Perugia Italy
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29
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ICRmax: an optimized approach to detect tumor-specific interchromosomal rearrangements for clinical application. Genomics 2015; 105:265-72. [PMID: 25666663 DOI: 10.1016/j.ygeno.2015.01.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 01/23/2015] [Accepted: 01/26/2015] [Indexed: 01/26/2023]
Abstract
Somatically acquired chromosomal rearrangements occur at early stages during tumorigenesis and can be used to indirectly detect tumor cells, serving as highly sensitive and tumor-specific biomarkers. Advances in high-throughput sequencing have allowed the genome-wide identification of patient-specific chromosomal rearrangements to be used as personalized biomarkers to efficiently assess response to treatment, detect residual disease and monitor disease recurrence. However, sequencing and data processing costs still represent major obstacles for the widespread application of personalized biomarkers in oncology. We developed a computational pipeline (ICRmax) for the cost-effective identification of a minimal set of tumor-specific interchromosomal rearrangements (ICRs). We examined ICRmax performance on sequencing data from rectal tumors and simulated data achieving an average accuracy of 68% for ICR identification. ICRmax identifies ICRs from low-coverage sequenced tumors, eliminates the need to sequence a matched normal tissue and significantly reduces the costs that limit the utilization of personalized biomarkers in the clinical setting.
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30
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Hyohyeon C, Lee CG. A 13-year-old boy with a 7q36.1q36.3 deletion with additional findings. Am J Med Genet A 2014; 167A:198-203. [DOI: 10.1002/ajmg.a.36792] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2014] [Accepted: 08/29/2014] [Indexed: 02/06/2023]
Affiliation(s)
- Cha Hyohyeon
- Department of Pediatrics; Eulji General Hospital; College of Medicine; Eulji University; Seoul Korea
| | - Cha Gon Lee
- Department of Pediatrics; Eulji General Hospital; College of Medicine; Eulji University; Seoul Korea
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31
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Sp6 and Sp8 transcription factors control AER formation and dorsal-ventral patterning in limb development. PLoS Genet 2014; 10:e1004468. [PMID: 25166858 PMCID: PMC4148220 DOI: 10.1371/journal.pgen.1004468] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 05/14/2014] [Indexed: 12/27/2022] Open
Abstract
The formation and maintenance of the apical ectodermal ridge (AER) is critical for the outgrowth and patterning of the vertebrate limb. The induction of the AER is a complex process that relies on integrated interactions among the Fgf, Wnt, and Bmp signaling pathways that operate within the ectoderm and between the ectoderm and the mesoderm of the early limb bud. The transcription factors Sp6 and Sp8 are expressed in the limb ectoderm and AER during limb development. Sp6 mutant mice display a mild syndactyly phenotype while Sp8 mutants exhibit severe limb truncations. Both mutants show defects in AER maturation and in dorsal-ventral patterning. To gain further insights into the role Sp6 and Sp8 play in limb development, we have produced mice lacking both Sp6 and Sp8 activity in the limb ectoderm. Remarkably, the elimination or significant reduction in Sp6;Sp8 gene dosage leads to tetra-amelia; initial budding occurs, but neither Fgf8 nor En1 are activated. Mutants bearing a single functional allele of Sp8 (Sp6−/−;Sp8+/−) exhibit a split-hand/foot malformation phenotype with double dorsal digit tips probably due to an irregular and immature AER that is not maintained in the center of the bud and on the abnormal expansion of Wnt7a expression to the ventral ectoderm. Our data are compatible with Sp6 and Sp8 working together and in a dose-dependent manner as indispensable mediators of Wnt/βcatenin and Bmp signaling in the limb ectoderm. We suggest that the function of these factors links proximal-distal and dorsal-ventral patterning. In this report we examined the functional roles of Sp6 and Sp8 during limb development using compound loss-of-function mutants. Sp6 and Sp8, two members of the Sp gene family, are expressed in the limb bud ectoderm and function downstream of WNT/βcatenin signaling for Fgf8 induction. The analysis of the allelic series shows that the progressive reduction in the dose of Sp6 and Sp8 gene products leads to predictable morphology, from syndactyly, to split hand/foot malformation, oligodactyly, truncation and finally amelia, indicating that these two factors act in a complementary manner. The molecular characterization of the mutant limbs reveal that Sp6/Sp8 are required in a dose-dependent manner for Fgf8 and En1 induction, thereby placing them as an important link between the induction of the AER and the establishment of dorsal-ventral patterning during limb development.
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Guan Y, Guo L, Yang E, Liao Y, Liu L, Che Y, Zhang Y, Wang L, Wang J, Li Q. HSV-1 nucleocapsid egress mediated by UL31 in association with UL34 is impeded by cellular transmembrane protein 140. Virology 2014; 464-465:1-10. [PMID: 25036476 DOI: 10.1016/j.virol.2014.06.034] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2014] [Revised: 04/07/2014] [Accepted: 06/24/2014] [Indexed: 10/25/2022]
Abstract
During HSV-1 infection, the viral UL31 protein forms a complex with the UL34 protein at the cellular nuclear membrane, where both proteins play important roles in the envelopment of viral nucleocapsids and their egress into the cytoplasm. To characterize the mechanism of HSV-1 nucleocapsid egress, we screened host proteins to identify proteins that interacted with UL31 via yeast two-hybrid analysis. Transmembrane protein 140 (TMEM140), was identified and confirmed to bind to and co-localize with UL31 during viral infection. Further studies indicated that TMEM140 inhibits HSV-1 proliferation through selectively blocking viral nucleocapsid egress during the viral assembly process. The blockage function of TMEM140 is mediated by impeding the formation of the UL31-UL34 complex due to competitive binding to UL31. Collectively, these data suggest the essentiality of the UL31-UL34 interaction in the viral nucleocapsid egress process and provide a new anti-HSV-1 strategy in viral assembly process of nucleocapsid egress.
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Affiliation(s)
- Ying Guan
- Department of Viral Immunology, Institute of Medical Biology, Chinese Academy of Medicine Science, Peking Union Medical College, Kunming 650118, PR China; Yunnan Academy of Tobacco Science, Kunming, Yunnan 650106, PR China
| | - Lei Guo
- Department of Viral Immunology, Institute of Medical Biology, Chinese Academy of Medicine Science, Peking Union Medical College, Kunming 650118, PR China
| | - Erxia Yang
- Department of Viral Immunology, Institute of Medical Biology, Chinese Academy of Medicine Science, Peking Union Medical College, Kunming 650118, PR China
| | - Yun Liao
- Department of Viral Immunology, Institute of Medical Biology, Chinese Academy of Medicine Science, Peking Union Medical College, Kunming 650118, PR China
| | - Longding Liu
- Department of Viral Immunology, Institute of Medical Biology, Chinese Academy of Medicine Science, Peking Union Medical College, Kunming 650118, PR China
| | - Yanchun Che
- Department of Viral Immunology, Institute of Medical Biology, Chinese Academy of Medicine Science, Peking Union Medical College, Kunming 650118, PR China
| | - Ying Zhang
- Department of Viral Immunology, Institute of Medical Biology, Chinese Academy of Medicine Science, Peking Union Medical College, Kunming 650118, PR China
| | - Lichun Wang
- Department of Viral Immunology, Institute of Medical Biology, Chinese Academy of Medicine Science, Peking Union Medical College, Kunming 650118, PR China
| | - Jingjing Wang
- Department of Viral Immunology, Institute of Medical Biology, Chinese Academy of Medicine Science, Peking Union Medical College, Kunming 650118, PR China
| | - Qihan Li
- Department of Viral Immunology, Institute of Medical Biology, Chinese Academy of Medicine Science, Peking Union Medical College, Kunming 650118, PR China.
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Ebert G, Steininger A, Weißmann R, Boldt V, Lind-Thomsen A, Grune J, Badelt S, Heßler M, Peiser M, Hitzler M, Jensen LR, Müller I, Hu H, Arndt PF, Kuss AW, Tebel K, Ullmann R. Distribution of segmental duplications in the context of higher order chromatin organisation of human chromosome 7. BMC Genomics 2014; 15:537. [PMID: 24973960 PMCID: PMC4092221 DOI: 10.1186/1471-2164-15-537] [Citation(s) in RCA: 4] [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: 12/09/2013] [Accepted: 06/17/2014] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Segmental duplications (SDs) are not evenly distributed along chromosomes. The reasons for this biased susceptibility to SD insertion are poorly understood. Accumulation of SDs is associated with increased genomic instability, which can lead to structural variants and genomic disorders such as the Williams-Beuren syndrome. Despite these adverse effects, SDs have become fixed in the human genome. Focusing on chromosome 7, which is particularly rich in interstitial SDs, we have investigated the distribution of SDs in the context of evolution and the three dimensional organisation of the chromosome in order to gain insights into the mutual relationship of SDs and chromatin topology. RESULTS Intrachromosomal SDs preferentially accumulate in those segments of chromosome 7 that are homologous to marmoset chromosome 2. Although this formerly compact segment has been re-distributed to three different sites during primate evolution, we can show by means of public data on long distance chromatin interactions that these three intervals, and consequently the paralogous SDs mapping to them, have retained their spatial proximity in the nucleus. Focusing on SD clusters implicated in the aetiology of the Williams-Beuren syndrome locus we demonstrate by cross-species comparison that these SDs have inserted at the borders of a topological domain and that they flank regions with distinct DNA conformation. CONCLUSIONS Our study suggests a link of nuclear architecture and the propagation of SDs across chromosome 7, either by promoting regional SD insertion or by contributing to the establishment of higher order chromatin organisation themselves. The latter could compensate for the high risk of structural rearrangements and thus may have contributed to their evolutionary fixation in the human genome.
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Affiliation(s)
- Grit Ebert
- />Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
- />Department of Biology, Chemistry and Pharmacy, Free University Berlin, 14195 Berlin, Germany
| | - Anne Steininger
- />Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
- />Department of Biology, Chemistry and Pharmacy, Free University Berlin, 14195 Berlin, Germany
| | - Robert Weißmann
- />Department of Human Genetics, University Medicine Greifswald, and Interfaculty Institute of Genetics and Functional Genomics, University of Greifswald, Fleischmannstraße 42-44, 17475 Greifswald, Germany
| | - Vivien Boldt
- />Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
- />Department of Biology, Chemistry and Pharmacy, Free University Berlin, 14195 Berlin, Germany
| | - Allan Lind-Thomsen
- />Wilhelm Johannsen Centre for Functional Genome Research, Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen, Denmark
| | - Jana Grune
- />Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
| | - Stefan Badelt
- />Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
- />Institute for Theoretical Chemistry, University of Vienna, Waehringer Straße 17, A-1090 Vienna, Austria
| | - Melanie Heßler
- />Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
| | - Matthias Peiser
- />Unit Experimental Research, Department of Product Safety, Federal Institute for Bundeswehr Institute of Radiobiology affiliated, the University of Ulm, Neuherbergstraße 11, 80937 Munich, Germany
| | - Manuel Hitzler
- />Unit Experimental Research, Department of Product Safety, Federal Institute for Bundeswehr Institute of Radiobiology affiliated, the University of Ulm, Neuherbergstraße 11, 80937 Munich, Germany
| | - Lars R Jensen
- />Department of Human Genetics, University Medicine Greifswald, and Interfaculty Institute of Genetics and Functional Genomics, University of Greifswald, Fleischmannstraße 42-44, 17475 Greifswald, Germany
| | - Ines Müller
- />Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
| | - Hao Hu
- />Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
| | - Peter F Arndt
- />Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
| | - Andreas W Kuss
- />Department of Human Genetics, University Medicine Greifswald, and Interfaculty Institute of Genetics and Functional Genomics, University of Greifswald, Fleischmannstraße 42-44, 17475 Greifswald, Germany
| | - Katrin Tebel
- />Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
| | - Reinhard Ullmann
- />Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
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Li L, Chen H, Yin C, Yang C, Wang B, Zheng S, Zhang J, Fan W. Mapping breakpoints of a familial chromosome insertion (18,7) (q22.1; q36.2q21.11) to DPP6 and CACNA2D1 genes in an azoospermic male. Gene 2014; 547:43-9. [PMID: 24937803 DOI: 10.1016/j.gene.2014.06.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Revised: 06/03/2014] [Accepted: 06/05/2014] [Indexed: 11/16/2022]
Abstract
It is widely accepted that the incidence of chromosomal aberration is 10-15.2% in the azoospermic male; however, the exact genetic damages are currently unknown for more than 40% of azoospermia. To elucidate the causative gene defects, we used the next generation sequencing (NGS) to map the breakpoints of a chromosome insertion from an azoospermic male who carries a balanced, maternally inherited karyotype 46, XY, inv ins (18,7) (q22.1; q36.2q21.11). The analysis revealed that the breakage in chromosome 7 disrupts two genes, dipeptidyl aminopeptidase-like protein 6 (DPP6) and contactin-associated protein-like 2 (CACNA2D1), the former participates in regulation of voltage-gated potassium channels, and the latter is one of the components in voltage-gated calcium channels. The deletion and duplication were not identified equal or beyond 100 kb, but 4 homologous DNA elements were verified proximal to the breakpoints. One of the proband's sisters inherited the same aberrant karyotype and experienced recurrent miscarriages and consecutive fetus death, while in contrast, another sister with a normal karyotype experienced normal labor and gave birth to healthy babies. The insertional translocation is confirmed with FISH and the Y-chromosome microdeletions were excluded by genetic testing. This is the first report describing chromosome insertion inv ins (18,7) and attributes DPP6 and CACNA2D1 to azoospermia.
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Affiliation(s)
- Lin Li
- Institute of Medical Genetics, Linyi People's Hospital, Shandong 276003, China
| | - Haixiao Chen
- BGI, 11-2 Building, Northern Industry District, Shenzhen 518083, China
| | - Chenxing Yin
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Hebei University School of Life Sciences, Baoding, Hebei 071002, China
| | - Chuanchun Yang
- BGI, 11-2 Building, Northern Industry District, Shenzhen 518083, China
| | - Bei Wang
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Hebei University School of Life Sciences, Baoding, Hebei 071002, China
| | - Shuqi Zheng
- Institute of Medical Genetics, Linyi People's Hospital, Shandong 276003, China
| | - Jixia Zhang
- Institute of Medical Genetics, Linyi People's Hospital, Shandong 276003, China
| | - Wufang Fan
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Hebei University School of Life Sciences, Baoding, Hebei 071002, China
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35
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Varvagiannis K, Papoulidis I, Koromila T, Kefalas K, Ziegler M, Liehr T, Petersen MB, Gyftodimou Y, Manolakos E. De novo 393 kb microdeletion of 7p11.2 characterized by aCGH in a boy with psychomotor retardation and dysmorphic features. Meta Gene 2014; 2:274-82. [PMID: 25606410 PMCID: PMC4287824 DOI: 10.1016/j.mgene.2014.03.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Revised: 03/08/2014] [Accepted: 03/17/2014] [Indexed: 01/03/2023] Open
Abstract
We report on a 27 month old boy presenting with psychomotor delay and dysmorphic features, mainly mild facial asymmetry, prominent cup-shaped ears, long eyelashes, open mouth appearance and slight abnormalities of the hands and feet. Array comparative genomic hybridization revealed a 393 kb microdeletion in 7p11.2. We discuss the possible involvement of CHCHD2, GBAS, MRPS17, SEPT14 and PSPH on our patient's phenotype. Additionally, we studied the expression of two other genes deleted in the patient, CCT6A and SUMF2, for which there is scarce data in the literature. Based on current knowledge and the de novo occurrence of this finding in our proband we presume that the aberration is likely to be pathogenic in our case. However, a single gene disorder, elsewhere in the genome or in this very region cannot be ruled out. Further elucidation of the properties of this chromosomal region, as well as of the role of the genes involved will be needed in order to draw safe conclusions regarding the association of the chromosomal deletion with the patient's features. We report in detail the clinical and cytogenetic findings of a 27-month old male. We compare our findings with current literature and online databases. We discuss the possible involvement of certain genes in our patient’s phenotype.
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Affiliation(s)
| | | | - Theodora Koromila
- Laboratory of Human Genetics, Department of Biology, University of Athens, Athens, Greece
| | | | - Monika Ziegler
- Institute of Human Genetics Anthropology, Jena University Hospital, Jena, Germany
| | - Thomas Liehr
- Institute of Human Genetics Anthropology, Jena University Hospital, Jena, Germany
| | | | | | - Emmanouil Manolakos
- Eurogenetica S.A., Laboratory of Genetics, Athens-Thessaloniki, Greece ; Cattedra di Genetica Medica, Ospedale Binaghi, Cagliari, Italy
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36
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Lee H, Lin MCA, Kornblum HI, Papazian DM, Nelson SF. Exome sequencing identifies de novo gain of function missense mutation in KCND2 in identical twins with autism and seizures that slows potassium channel inactivation. Hum Mol Genet 2014; 23:3481-9. [PMID: 24501278 DOI: 10.1093/hmg/ddu056] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Numerous studies and case reports show comorbidity of autism and epilepsy, suggesting some common molecular underpinnings of the two phenotypes. However, the relationship between the two, on the molecular level, remains unclear. Here, whole exome sequencing was performed on a family with identical twins affected with autism and severe, intractable seizures. A de novo variant was identified in the KCND2 gene, which encodes the Kv4.2 potassium channel. Kv4.2 is a major pore-forming subunit in somatodendritic subthreshold A-type potassium current (ISA) channels. The de novo mutation p.Val404Met is novel and occurs at a highly conserved residue within the C-terminal end of the transmembrane helix S6 region of the ion permeation pathway. Functional analysis revealed the likely pathogenicity of the variant in that the p.Val404Met mutant construct showed significantly slowed inactivation, either by itself or after equimolar coexpression with the wild-type Kv4.2 channel construct consistent with a dominant effect. Further, the effect of the mutation on closed-state inactivation was evident in the presence of auxiliary subunits that associate with Kv4 subunits to form ISA channels in vivo. Discovery of a functionally relevant novel de novo variant, coupled with physiological evidence that the mutant protein disrupts potassium current inactivation, strongly supports KCND2 as the causal gene for epilepsy in this family. Interaction of KCND2 with other genes implicated in autism and the role of KCND2 in synaptic plasticity provide suggestive evidence of an etiological role in autism.
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Affiliation(s)
- Hane Lee
- Department of Pathology and Laboratory Medicine
| | | | - Harley I Kornblum
- Department of Psychiatry, Department of Molecular and Medical Pharmacology, Department of Pediatrics
| | | | - Stanley F Nelson
- Department of Pathology and Laboratory Medicine, Department of Human Genetics, University of California, Los Angeles, CA 90095, USA
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37
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Winther M, Walmod PS. Neural cell adhesion molecules belonging to the family of leucine-rich repeat proteins. ADVANCES IN NEUROBIOLOGY 2014; 8:315-95. [PMID: 25300143 DOI: 10.1007/978-1-4614-8090-7_14] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Leucine-rich repeats (LRRs) are motifs that form protein-ligand interaction domains. There are approximately 140 human genes encoding proteins with extracellular LRRs. These encode cell adhesion molecules (CAMs), proteoglycans, G-protein-coupled receptors, and other types of receptors. Here we give a brief description of 36 proteins with extracellular LRRs that all can be characterized as CAMs or putative CAMs expressed in the nervous system. The proteins are involved in multiple biological processes in the nervous system including the proliferation and survival of cells, neuritogenesis, axon guidance, fasciculation, myelination, and the formation and maintenance of synapses. Moreover, the proteins are functionally implicated in multiple diseases including cancer, hearing impairment, glaucoma, Alzheimer's disease, multiple sclerosis, Parkinson's disease, autism spectrum disorders, schizophrenia, and obsessive-compulsive disorders. Thus, LRR-containing CAMs constitute a large group of proteins of pivotal importance for the development, maintenance, and regeneration of the nervous system.
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38
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Noriega DB, Savelkoul HFJ. Immune dysregulation in autism spectrum disorder. Eur J Pediatr 2014; 173:33-43. [PMID: 24297668 DOI: 10.1007/s00431-013-2183-4] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 10/09/2013] [Indexed: 12/25/2022]
Abstract
UNLABELLED Autism spectrum disorder (ASD) is a common and severe neuro-developmental disorder in early childhood which is defined by social and communication deficits and repetitive and stereotypic behaviours. The aetiology of ASD remains poorly understood. Susceptibility to development of ASD has significant environmental components, in addition to the profound genetic heritability. Few genes have been associated to the risk for ASD development. There is substantial evidence implicating chronic neurological inflammation and immune dysregulation leading to upregulation of inflammatory cytokines in the ASD brain, probably due to altered blood-brain barrier function. The immune system is characterized by excessive and skewed cytokine responses, modulated T cell reactivity, decreased regulation and production of immunosuppressive cytokines, modified NK function and increased autoantibody production. CONCLUSION The perinatal environment generates vulnerability to chronic neuro-inflammation in the brain associated with profound modulation and dysregulation in the immune system leading to the rapid development of ASD in genetically susceptible children.
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Affiliation(s)
- Daniela Briceno Noriega
- Cell Biology and Immunology Group, Wageningen University, P.O. Box 338, 6700 AH, Wageningen, The Netherlands
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39
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Hassan MI, Waheed A, Grubb JH, Klei HE, Korolev S, Sly WS. High resolution crystal structure of human β-glucuronidase reveals structural basis of lysosome targeting. PLoS One 2013; 8:e79687. [PMID: 24260279 PMCID: PMC3834196 DOI: 10.1371/journal.pone.0079687] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Accepted: 09/24/2013] [Indexed: 11/19/2022] Open
Abstract
Human β-glucuronidase (GUS) cleaves β-D-glucuronic acid residues from the non-reducing termini of glycosaminoglycan and its deficiency leads to mucopolysaccharidosis type VII (MPSVII). Here we report a high resolution crystal structure of human GUS at 1.7 Å resolution and present an extensive analysis of the structural features, unifying recent findings in the field of lysosome targeting and glycosyl hydrolases. The structure revealed several new details including a new glycan chain at Asn272, in addition to that previously observed at Asn173, and coordination of the glycan chain at Asn173 with Lys197 of the lysosomal targeting motif which is essential for phosphotransferase recognition. Analysis of the high resolution structure not only provided new insights into the structural basis for lysosomal targeting but showed significant differences between human GUS, which is medically important in its own right, and E. coli GUS, which can be selectively inhibited in the human gut to prevent prodrug activation and is also widely used as a reporter gene by plant biologists. Despite these differences, both human and E. coli GUS share a high structure homology in all three domains with most of the glycosyl hydrolases, suggesting that they all evolved from a common ancestral gene.
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Affiliation(s)
- Md. Imtaiyaz Hassan
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, India
| | - Abdul Waheed
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - Jeffery H. Grubb
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - Herbert E. Klei
- Research and Development, Bristol-Myers Squibb Company, Princeton, New Jersey, United States of America
| | - Sergey Korolev
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - William S. Sly
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
- * E-mail:
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40
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Hu VW. The expanding genomic landscape of autism: discovering the 'forest' beyond the 'trees'. FUTURE NEUROLOGY 2013; 8:29-42. [PMID: 23637569 DOI: 10.2217/fnl.12.83] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Autism spectrum disorders are neurodevelopmental disorders characterized by significant deficits in reciprocal social interactions, impaired communication and restricted, repetitive behaviors. As autism spectrum disorders are among the most heritable of neuropsychiatric disorders, much of autism research has focused on the search for genetic variants in protein-coding genes (i.e., the 'trees'). However, no single gene can account for more than 1% of the cases of autism spectrum disorders. Yet, genome-wide association studies have often identified statistically significant associations of genetic variations in regions of DNA that do not code for proteins (i.e., intergenic regions). There is increasing evidence that such noncoding regions are actively transcribed and may participate in the regulation of genes, including genes on different chromosomes. This article summarizes evidence that suggests that the research spotlight needs to be expanded to encompass far-reaching gene-regulatory mechanisms that include a variety of epigenetic modifications, as well as noncoding RNA (i.e., the 'forest'). Given that noncoding RNA represents over 90% of the transcripts in most cells, we may be observing just the 'tip of the iceberg' or the 'edge of the forest' in the genomic landscape of autism.
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Affiliation(s)
- Valerie W Hu
- Department of Biochemistry & Molecular Medicine, The George Washington University, School of Medicine & Health Sciences, 2300 Eye St., N.W., Washington, DC 20037, USA Tel.: +1 202 994 8431
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41
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Fanayan S, Smith JT, Sethi MK, Cantor D, Goode R, Simpson RJ, Baker MS, Hancock WS, Nice E. Chromosome 7-Centric Analysis of Proteomics Data from a Panel of Human Colon Carcinoma Cell Lines. J Proteome Res 2012; 12:89-96. [DOI: 10.1021/pr300906y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Susan Fanayan
- Department of Chemistry and
Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Joshua T. Smith
- Barnett Institute and Department
of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Manveen K. Sethi
- Department of Chemistry and
Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - David Cantor
- Department of Chemistry and
Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Robert Goode
- Department of Biochemistry & Molecular Biology, Monash University, Clayton, VIC 3800, Australia
| | - Richard J. Simpson
- La
Trobe Institute for Molecular
Science, La Trobe University, Bundoora,
Victoria 3086, Australia
| | - Mark S. Baker
- Department of Chemistry and
Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - William S. Hancock
- Department of Chemistry and
Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
- Barnett Institute and Department
of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Edouard Nice
- Department of Biochemistry & Molecular Biology, Monash University, Clayton, VIC 3800, Australia
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42
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Pang AWC, Migita O, Macdonald JR, Feuk L, Scherer SW. Mechanisms of formation of structural variation in a fully sequenced human genome. Hum Mutat 2012; 34:345-54. [PMID: 23086744 DOI: 10.1002/humu.22240] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Accepted: 10/02/2012] [Indexed: 12/12/2022]
Abstract
Even with significant advances in technology, few studies of structural variation have yet resolved to the level of the precise nucleotide junction. We examined the sequence of 408,532 gains, 383,804 losses, and 166 inversions from the first sequenced personal genome, to quantify the relative proportion of mutational mechanisms. Among small variants (<1 kb), we observed that 72.6% of them were associated with nonhomologous processes and 24.9% with microsatellites events. Medium-size variants (<10 kb) were commonly related to minisatellites (25.8%) and retrotransposons (24%), whereas 46.2% of large variants (>10 kb) were associated with nonallelic homologous recombination. We genotyped eight new breakpoint-resolved inversions at (3q26.1, Xp11.22, 7q11.22, 16q23.1, 4q22.1, 1q31.3, 6q27, and 16q24.1) in human populations to elucidate the structure of these presumed benign variants. Three of these inversions (3q26.1, 7q11.22, and 16q23.1) were accompanied by unexpected complex rearrangements. In particular, the 16q23.1 inversion and an accompanying deletion would create conjoined chymotrypsinogen genes (CTRB1 and CTRB2), disrupt their gene structure, and exhibit differentiated allelic frequencies among populations. Also, two loci (Xp11.3 and 6q27) of potential reference assembly orientation errors were found. This study provides a thorough account of formation mechanisms for structural variants, and reveals a glimpse of the dynamic structure of inversions.
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Affiliation(s)
- Andy Wing Chun Pang
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
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Li X, Zou H, Brown WT. Genes associated with autism spectrum disorder. Brain Res Bull 2012; 88:543-52. [PMID: 22688012 DOI: 10.1016/j.brainresbull.2012.05.017] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Accepted: 05/31/2012] [Indexed: 01/06/2023]
Abstract
Autism spectrum disorder (ASD) is a heterogeneous grouping of neurodevelopmental disorders characterized by impairment in social interaction, verbal communication and repetitive/stereotypic behaviors. Much evidence suggests that ASD is multifactorial with a strong genetic basis, but the underlying mechanisms are far from clear. Recent advances in genetic technologies are beginning to shed light on possible etiologies of ASD. This review discusses current evidence for several widely studied candidate ASD genes, as well as various rare genes that supports their relationship to the etiology of ASD. The majority of the data are based on molecular, cytogenetic, linkage and association studies of autistic subjects, but newer methods, including whole-exome sequencing, are also beginning to make significant contributions to our understanding of autism.
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Affiliation(s)
- Xiaohong Li
- Department of Neurochemistry, New York State Institute for Basic Research in Developmental Disabilities, New York, NY 10314, United States.
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Vertebrate patatin-like phospholipase domain-containing protein 4 (PNPLA4) genes and proteins: a gene with a role in retinol metabolism. 3 Biotech 2012. [PMCID: PMC3482448 DOI: 10.1007/s13205-012-0063-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
At least eight families of mammalian patatin-like phospholipase domain-containing proteins (PNPLA) (E.C. 3.1.1.3) catalyse the hydrolysis of triglycerides, including PNPLA4 (alternatively PLPL4 or GS2), which also acts as a retinol transacylase and participates in retinol-ester metabolism in the body. Bioinformatic methods were used to predict the amino acid sequences, secondary and tertiary structures and gene locations for PNPLA4 genes and encoded proteins using data from several vertebrate genome projects. PNPLA4 genes were located on the X-chromosome for the eutherian mammalian genomes examined. Opossum (marsupial), chicken, anole lizard, clawed toad, zebrafish and lancelet PNPLA4 genes were also identified. Most vertebrate PNPLA4 genes typically contained six coding exons whereas the lancelet PNPLA4 gene contained five coding exons. PNPLA4 subunits were the smallest among the PNPLA-like proteins examined containing 252–255 residues, shared >64 % sequence identities and key amino acid residues and predicted motifs, including ‘patatin’ (residues 6–176); putative catalytic dyad active site residues, Ser43 and Asp163; oxy-anion ‘hole’ residues (10–15); and conserved serine residues, which may perform structural roles for this enzyme. Predicted tertiary structures for PNPLA4 ‘patatin’ were similar to those reported for potato ‘patatin’, suggesting that it is strongly conserved during evolution. Human PNPLA4 contained a CpG49 island within the gene promoter, a miRNA-186 binding site within the mRNA 3′-noncoding region for the PNPLA4b isoform and exhibited wide tissue expression at a higher than average level. These and previous studies of vertebrate PNPLA-like gene families have suggested that PNPLA4 is an ancient gene in evolution which has resulted from a duplication of an ancestral invertebrate ATGL-like gene (encoding adipose triglyceride lipase).
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Lee HY, Ge WP, Huang W, He Y, Wang GX, Rowson-Baldwin A, Smith SJ, Jan YN, Jan LY. Bidirectional regulation of dendritic voltage-gated potassium channels by the fragile X mental retardation protein. Neuron 2012; 72:630-42. [PMID: 22099464 DOI: 10.1016/j.neuron.2011.09.033] [Citation(s) in RCA: 124] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/02/2011] [Indexed: 02/01/2023]
Abstract
How transmitter receptors modulate neuronal signaling by regulating voltage-gated ion channel expression remains an open question. Here we report dendritic localization of mRNA of Kv4.2 voltage-gated potassium channel, which regulates synaptic plasticity, and its local translational regulation by fragile X mental retardation protein (FMRP) linked to fragile X syndrome (FXS), the most common heritable mental retardation. FMRP suppression of Kv4.2 is revealed by elevation of Kv4.2 in neurons from fmr1 knockout (KO) mice and in neurons expressing Kv4.2-3'UTR that binds FMRP. Moreover, treating hippocampal slices from fmr1 KO mice with Kv4 channel blocker restores long-term potentiation induced by moderate stimuli. Surprisingly, recovery of Kv4.2 after N-methyl-D-aspartate receptor (NMDAR)-induced degradation also requires FMRP, likely due to NMDAR-induced FMRP dephosphorylation, which turns off FMRP suppression of Kv4.2. Our study of FMRP regulation of Kv4.2 deepens our knowledge of NMDAR signaling and reveals a FMRP target of potential relevance to FXS.
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Affiliation(s)
- Hye Young Lee
- Howard Hughes Medical Institute Departments of Physiology, Biochemistry, and Biophysics, University of California, San Francisco, CA 94158, USA
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Sbacchi S, Acquadro F, Calò I, Calì F, Romano V. Functional annotation of genes overlapping copy number variants in autistic patients: focus on axon pathfinding. Curr Genomics 2011; 11:136-45. [PMID: 20885821 PMCID: PMC2874223 DOI: 10.2174/138920210790886880] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2009] [Revised: 12/12/2009] [Accepted: 12/15/2009] [Indexed: 12/30/2022] Open
Abstract
We have used Gene Ontology (GO) and pathway analyses to uncover the common functions associated to the genes overlapping Copy Number Variants (CNVs) in autistic patients. Our source of data were four published studies [1-4]. We first applied a two-step enrichment strategy for autism-specific genes. We fished out from the four mentioned studies a list of 2928 genes overall overlapping 328 CNVs in patients and we first selected a sub-group of 2044 genes after excluding those ones that are also involved in CNVs reported in the Database of Genomic Variants (enrichment step 1). We then selected from the step 1-enriched list a sub-group of 514 genes each of which was found to be deleted or duplicated in at least two patients (enrichment step 2). The number of statistically significant processes and pathways identified by the Database for Annotation, Visualization and Integrated Discovery and Ingenuity Pathways Analysis softwares with the step 2-enriched list was significantly higher compared to the step 1-enriched list. In addition, statistically significant GO terms, biofunctions and pathways related to nervous system development and function were exclusively identified by the step 2-enriched list of genes. Interestingly, 21 genes were associated to axon growth and pathfinding. The latter genes and other ones associated to nervous system in this study represent a new set of autism candidate genes deserving further investigation. In summary, our results suggest that the autism’s “connectivity genes” in some patients affect very early phases of neurodevelopment, i.e., earlier than synaptogenesis.
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Affiliation(s)
- Silvia Sbacchi
- Dipartimento di Oncologia Sperimentale e Applicazioni Cliniche, Università degli Studi di Palermo, Palermo
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A de novo balanced translocation t(7;12)(p21.2;p12.3) in a patient with Saethre-Chotzen-like phenotype downregulates TWIST and an osteoclastic protein-tyrosine phosphatase, PTP-oc. Eur J Med Genet 2011; 54:e478-83. [PMID: 21708297 DOI: 10.1016/j.ejmg.2011.05.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2011] [Accepted: 05/23/2011] [Indexed: 11/21/2022]
Abstract
Saethre-Chotzen syndrome (SCS) is an autosomal dominant craniosynostosis syndrome with variable expression. Here we report on a female infant with a de novo balanced translocation 46, XX, t(7;12)(p21.2;p12.3) and presenting at birth brachycephaly, antimongolic palpebral fissures, ocular hypertelorism, broad nose with low nasal bridge and low-set ears. This phenotype is suggestive of a subtle form of SCS, given the absence of limbs anomalies. Cloning of both breakpoints revealed that the translocation does not interrupt the TWIST1 coding region, on 7p21, known to be causative for SCS, but downregulates TWIST1 expression due to a position effect. On chromosome 12, the breakpoint translocates a shorter transcript of PTPRO gene, the osteoclastic protein-tyrosine phosphatase, PTP-oc, near to regulatory region of 7p leading to down-regulation of PTP-oc in the proband's fibroblasts. This is a confirmatory case report providing further evidence for TWIST1 haploinsufficiency in SCS, although a possible role of PTP-oc as genetic factor underlying or at least influencing the development of craniosynostosis could not be a priori excluded.
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Salabei JK, Li XP, Petrash JM, Bhatnagar A, Barski OA. Functional expression of novel human and murine AKR1B genes. Chem Biol Interact 2011; 191:177-84. [PMID: 21276782 PMCID: PMC3103657 DOI: 10.1016/j.cbi.2011.01.020] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2010] [Revised: 01/12/2011] [Accepted: 01/19/2011] [Indexed: 02/05/2023]
Abstract
The Aldo Keto Reductases (AKRs) are a superfamily of enzymes that catalyze the reduction of biogenic and xenobiotic aldehydes and ketones. AKR1B family has 2 known members in humans and 3 in rodents. Two novel gene loci, hereafter referred to as AKR1B15 in human and Akr1b16 in mouse have been predicted to exist within the AKR1B clusters. AKR1B15 displays 91% and 67% sequence identity with human genes AKR1B10 and AKR1B1, respectively while Akr1b16 shares 82-84% identity with murine Akr1b8 and Akr1b7. We tested the hypothesis that AKR1B15 and Akr1b16 genes are expressed as functional proteins in human and murine tissues, respectively. Using whole tissue mRNA, we were able to clone the full-length open reading frames for AKR1B15 from human eye and testes, and Akr1b16 from murine spleen, demonstrating that these genes are transcriptionally active. The corresponding cDNAs were cloned into pET28a and pIRES-hrGFP-1α vectors for bacterial and mammalian expression, respectively. Both genes were expressed as 36kDa proteins found in the insoluble fraction of bacterial cell lysate. These proteins, expressed in bacteria showed no enzymatic activity. However, lysates from COS-7 cells transfected with AKR1B15 showed a 4.8-fold (with p-nitrobenzaldehyde) and 3.3-fold (with dl-glyceraldehyde) increase in enzyme activity compared with untransfected COS-7 cells. The Akr1b16 transcript was shown to be ubiquitously expressed in murine tissues. Highest levels of transcript were found in heart, spleen, and lung. From these observations we conclude that the predicted AKR1B15 and 1b16 genes are expressed in several murine and human tissues. Further studies are required to elucidate their physiological roles.
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Affiliation(s)
- Joshua K. Salabei
- Diabetes and Obesity Center, School of Medicine, University of Louisville, Louisville, KY 40202
| | - Xiao-Ping Li
- Diabetes and Obesity Center, School of Medicine, University of Louisville, Louisville, KY 40202
| | - J. Mark Petrash
- Department of Ophthalmology, University of Colorado School of Medicine, Denver, CO 80045
| | - Aruni Bhatnagar
- Diabetes and Obesity Center, School of Medicine, University of Louisville, Louisville, KY 40202
| | - Oleg A. Barski
- Diabetes and Obesity Center, School of Medicine, University of Louisville, Louisville, KY 40202
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Guerrini L, Costanzo A, Merlo GR. A symphony of regulations centered on p63 to control development of ectoderm-derived structures. J Biomed Biotechnol 2011; 2011:864904. [PMID: 21716671 PMCID: PMC3118300 DOI: 10.1155/2011/864904] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2010] [Revised: 01/25/2011] [Accepted: 03/16/2011] [Indexed: 12/27/2022] Open
Abstract
The p53-related transcription factor p63 is critically important for basic cellular functions during development of the ectoderm and derived structure and tissues, including skin, limb, palate, and hair. On the one side, p63 is required to sustain the proliferation of keratinocyte progenitors, while on the other side it is required for cell stratification, commitment to differentiate, cell adhesion, and epithelial-mesenchymal signaling. Molecules that are components or regulators of the p63 pathway(s) are rapidly being identified, and it comes with no surprise that alterations in the p63 pathway lead to congenital conditions in which the skin and other ectoderm-derived structures are affected. In this paper, we summarize the current knowledge of the molecular and cellular regulations centered on p63, derived from the comprehension of p63-linked human diseases and the corresponding animal models, as well as from cellular models and high-throughput molecular approaches. We point out common themes and features, that allow to speculate on the possible role of p63 downstream events and their potential exploitation in future attempts to correct the congenital defect in preclinical studies.
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Affiliation(s)
- Luisa Guerrini
- Department of Biomolecular Science and Biotechnology, University of Milan, 20133 Milano, Italy
| | - Antonio Costanzo
- Department of Dermatology, University of Rome “Tor Vergata”, 00133 Rome, Italy
- Rome Oncogenomic Centre, Via Elio Chianesi 53, 00144 Rome, Italy
| | - Giorgio R. Merlo
- Molecular Biotechnology Center, Dulbecco Telethon Institute, University of Torino, 10126 Torino, Italy
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Obenauf AC, Schwarzbraun T, Auer M, Hoffmann EM, Waldispuehl-Geigl J, Ulz P, Günther B, Duba HC, Speicher MR, Geigl JB. Mapping of balanced chromosome translocation breakpoints to the basepair level from microdissected chromosomes. J Cell Mol Med 2011; 14:2078-84. [PMID: 20597996 PMCID: PMC3822999 DOI: 10.1111/j.1582-4934.2010.01116.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
The analysis of structural variants associated with specific phenotypic features is promising for the elucidation of the function of involved genes. There is, however, at present no approach allowing the rapid mapping of chromosomal translocation breakpoints to the basepair level from a single chromosome. Here we demonstrate that we have advanced both the microdissection and the subsequent unbiased amplification to an extent that breakpoint mapping to the basepair level has become possible. As a case in point we analysed the two breakpoints of a t(7;13) translocation observed in a patient with split hand/foot malformation (SHFM1). The amplification products of the der(7) and of the der(13) were hybridized to custom-made arrays, enabling us to define primers at flanking breakpoint regions and thus to fine-map the breakpoints to the basepair level. Consequently, our results will also contribute to a further delineation of causative mechanisms underlying SHFM1 which are currently unknown.
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Affiliation(s)
- Anna C Obenauf
- Institute of Human Genetics, Medical University of Graz, Graz, Austria
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