1
|
Alsharairi NA. Exploring the Diet-Gut Microbiota-Epigenetics Crosstalk Relevant to Neonatal Diabetes. Genes (Basel) 2023; 14:genes14051017. [PMID: 37239377 DOI: 10.3390/genes14051017] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/24/2023] [Accepted: 04/28/2023] [Indexed: 05/28/2023] Open
Abstract
Neonatal diabetes (NDM) is a rare monogenic disorder that presents as hyperglycemia during the first six months of life. The link between early-life gut microbiota dysbiosis and susceptibility to NDM remains uncertain. Experimental studies have demonstrated that gestational diabetes mellitus (GDM) could develop into meconium/gut microbiota dysbiosis in newborns, and thus, it is thought to be a mediator in the pathogenesis of NDM. Epigenetic modifications have been considered as potential mechanisms by which the gut microbiota and susceptibility genes interact with the neonatal immune system. Several epigenome-wide association studies have revealed that GDM is associated with neonatal cord blood and/or placental DNA methylation alterations. However, the mechanisms linking diet in GDM with gut microbiota alterations, which may in turn induce the expression of genes linked to NDM, are yet to be unraveled. Therefore, the focus of this review is to highlight the impacts of diet, gut microbiota, and epigenetic crosstalk on altered gene expression in NDM.
Collapse
Affiliation(s)
- Naser A Alsharairi
- Heart, Mind & Body Research Group, Griffith University, Gold Coast, QLD P.O. Box 4222, Australia
| |
Collapse
|
2
|
Royer-Pokora B, Wruck W, Adjaye J, Beier M. Gene expression studies of WT1 mutant Wilms tumor cell lines in the frame work of published kidney development data reveals their early kidney stem cell origin. PLoS One 2023; 18:e0270380. [PMID: 36689432 PMCID: PMC9870146 DOI: 10.1371/journal.pone.0270380] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 11/21/2022] [Indexed: 01/24/2023] Open
Abstract
In order to get a better insight into the timing of WT1 mutant Wilms tumor development, we compared the gene expression profiles of nine established WT1 mutant Wilms tumor cell lines with published data from different kidney cell types during development. Publications describing genes expressed in nephrogenic precursor cells, ureteric bud cells, more mature nephrogenic epithelial cells and interstitial cell types were used. These studies uncovered that the WT1 mutant Wilms tumor cells lines express genes from the earliest nephrogenic progenitor cells, as well as from more differentiated nephron cells with the highest expression from the stromal/interstitial compartment. The expression of genes from all cell compartments points to an early developmental origin of the tumor in a common stem cell. Although variability of the expression of specific genes was evident between the cell lines the overall expression pattern was very similar. This is likely dependent on their different genetic backgrounds with distinct WT1 mutations and the absence/presence of mutant CTNNB1.
Collapse
Affiliation(s)
- Brigitte Royer-Pokora
- Institute of Human Genetics, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Wasco Wruck
- Institute for Stem Cell Research and Regenerative Medicine, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - James Adjaye
- Institute for Stem Cell Research and Regenerative Medicine, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Manfred Beier
- Institute of Human Genetics, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| |
Collapse
|
3
|
Hofmeister RJ, Rubinacci S, Ribeiro DM, Buil A, Kutalik Z, Delaneau O. Parent-of-Origin inference for biobanks. Nat Commun 2022; 13:6668. [PMID: 36335127 PMCID: PMC9637181 DOI: 10.1038/s41467-022-34383-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022] Open
Abstract
Identical genetic variations can have different phenotypic effects depending on their parent of origin. Yet, studies focusing on parent-of-origin effects have been limited in terms of sample size due to the lack of parental genomes or known genealogies. We propose a probabilistic approach to infer the parent-of-origin of individual alleles that does not require parental genomes nor prior knowledge of genealogy. Our model uses Identity-By-Descent sharing with second- and third-degree relatives to assign alleles to parental groups and leverages chromosome X data in males to distinguish maternal from paternal groups. We combine this with robust haplotype inference and haploid imputation to infer the parent-of-origin for 26,393 UK Biobank individuals. We screen 99 phenotypes for parent-of-origin effects and replicate the discoveries of 6 GWAS studies, confirming signals on body mass index, type 2 diabetes, standing height and multiple blood biomarkers, including the known maternal effect at the MEG3/DLK1 locus on platelet phenotypes. We also report a novel maternal effect at the TERT gene on telomere length, thereby providing new insights on the heritability of this phenotype. All our summary statistics are publicly available to help the community to better characterize the molecular mechanisms leading to parent-of-origin effects and their implications for human health.
Collapse
Affiliation(s)
- Robin J Hofmeister
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Simone Rubinacci
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Diogo M Ribeiro
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Alfonso Buil
- Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, Copenhagen, Denmark.,Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Zoltán Kutalik
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.,University Center for Primary Care and Public Health, University of Lausanne, Lausanne, Switzerland
| | - Olivier Delaneau
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland. .,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.
| |
Collapse
|
4
|
Vincent KM, Stavropoulos DJ, Beaulieu-Bergeron M, Yang C, Jiang M, Zuijdwijk C, Dyment DA, Graham GE. A 79-kb paternally inherited 7q32.2 microdeletion involving MEST in a patient with a Silver-Russell syndrome-like phenotype. Am J Med Genet A 2022; 188:2421-2428. [PMID: 35593535 DOI: 10.1002/ajmg.a.62782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 04/05/2022] [Accepted: 04/14/2022] [Indexed: 11/07/2022]
Abstract
Maternal uniparental disomy of human chromosome 7 [upd(7)mat] is well-characterized as a cause of the growth disorder Silver-Russell syndrome (SRS). However, the causative gene is not currently known. There is growing evidence that molecular changes at the imprinted MEST region in 7q32.2 are associated with a phenotype evocative of SRS. This report details a patient with a SRS-like phenotype and a paternally inherited microdeletion of 79 kilobases (35-fold smaller than the previously reported smallest deletion) in the 7q32.2 region. This microdeletion encompasses only five genes, including MEST, which corroborates the hypothesis that MEST plays a central role in the 7q32.2 microdeletion growth disorder, as well as further implicating MEST in upd(7)mat SRS itself.
Collapse
Affiliation(s)
- Krista Marie Vincent
- Department of Medical Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada.,Department of Pediatrics, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Dimitri J Stavropoulos
- Genome Diagnostics, Department of Pediatric Laboratory Medicine, The Hospital for Sick Children and University of Toronto, Toronto, Ontario, Canada
| | - Melanie Beaulieu-Bergeron
- Department of Medical Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada.,Department of Pediatrics, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Chen Yang
- Department of Pediatrics, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, USA.,Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Mary Jiang
- Department of Pediatrics, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada.,Division of Endocrinology and Metabolism, Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Caroline Zuijdwijk
- Department of Pediatrics, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada.,Division of Endocrinology and Metabolism, Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - David A Dyment
- Department of Medical Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada.,Department of Pediatrics, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Gail E Graham
- Department of Medical Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada.,Department of Pediatrics, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| |
Collapse
|
5
|
Lundin-Ström KB, Biloglav A, Lazarevic V, Behrendtz M, Castor A, Johansson B. Parental origin of monosomy 7 in acute leukaemia. Br J Haematol 2021; 192:e132-e135. [PMID: 33548143 DOI: 10.1111/bjh.17356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 01/12/2021] [Indexed: 12/01/2022]
Affiliation(s)
- Kristina B Lundin-Ström
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Andrea Biloglav
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Vladimir Lazarevic
- Department of Haematology, Oncology and Radiation Physics, Skåne University Hospital, Lund, Sweden.,Stem Cell Centre, Lund University, Lund, Sweden
| | - Mikael Behrendtz
- Department of Paediatrics, Linköping University Hospital, Linköping, Sweden
| | - Anders Castor
- Department of Paediatrics, Skåne University Hospital, Lund, Sweden
| | - Bertil Johansson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden.,Department of Clinical Genetics and Pathology, Division of Laboratory Medicine, Lund, Sweden
| |
Collapse
|
6
|
Fu Y, Su L, Cai M, Yao B, Xiao S, He Q, Xu L, Yang L, Zhao C, Wan T, Shao L, Wang L, Huang X. Downregulation of CPA4 inhibits non small-cell lung cancer growth by suppressing the AKT/c-MYC pathway. Mol Carcinog 2019; 58:2026-2039. [PMID: 31397502 PMCID: PMC6851884 DOI: 10.1002/mc.23095] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 07/23/2019] [Accepted: 07/25/2019] [Indexed: 12/28/2022]
Abstract
Carboxypeptidase A4 (CPA4) is a member of the metallocarboxypeptidase family. A previous study indicated that CPA4 may participate in the modulation of peptide hormone activity and hormone-regulated tissue growth and differentiation. However, the role of CPA4 in lung tumorigenesis remains unclear. Our study revealed that CPA4 expression was higher in both lung cancer cells and tumor tissues. We performed 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide assays, colony-formation assays, and Cellomics ArrayScan Infinity analysis to demonstrate that CPA4 knockdown inhibited non small-cell lung cancer (NSCLC) cell proliferation. Conversely, ectopic expression of CPA4 enhanced lung cancer cell proliferation. Consistent with these observations, we generated xenograft tumor models to confirm that CPA4 downregulation suppressed NSCLC cell growth. Mechanistically, we revealed that CPA4 downregulation may induce apoptosis and G1-S arrest by suppressing the protein kinase B/c-MYC pathway. These results suggest that CPA4 has an oncogenic effect on lung cancer growth. Taken together, we identified a novel gene in lung cancer that might provide a basis for new therapeutic targets.
Collapse
Affiliation(s)
- Yangyang Fu
- Division of Pulmonary Medicine, Key Laboratory of Heart and Lung, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Lihuang Su
- Division of Pulmonary Medicine, Key Laboratory of Heart and Lung, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Mengsi Cai
- Division of Pulmonary Medicine, Key Laboratory of Heart and Lung, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Boyang Yao
- Division of Pulmonary Medicine, Key Laboratory of Heart and Lung, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Sisi Xiao
- Division of Pulmonary Medicine, Key Laboratory of Heart and Lung, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Qinlian He
- Division of Pulmonary Medicine, Key Laboratory of Heart and Lung, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Le Xu
- Division of Pulmonary Medicine, Key Laboratory of Heart and Lung, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Lehe Yang
- Division of Pulmonary Medicine, Key Laboratory of Heart and Lung, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Chengguang Zhao
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Tingting Wan
- Division of Pulmonary Medicine, Key Laboratory of Heart and Lung, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Lianyou Shao
- Division of Pulmonary Medicine, Key Laboratory of Heart and Lung, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Liangxing Wang
- Division of Pulmonary Medicine, Key Laboratory of Heart and Lung, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xiaoying Huang
- Division of Pulmonary Medicine, Key Laboratory of Heart and Lung, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| |
Collapse
|
7
|
Everson TM, Marable C, Deyssenroth MA, Punshon T, Jackson BP, Lambertini L, Karagas MR, Chen J, Marsit CJ. Placental Expression of Imprinted Genes, Overall and in Sex-Specific Patterns, Associated with Placental Cadmium Concentrations and Birth Size. ENVIRONMENTAL HEALTH PERSPECTIVES 2019; 127:57005. [PMID: 31082282 PMCID: PMC6791491 DOI: 10.1289/ehp4264] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 04/09/2019] [Accepted: 04/22/2019] [Indexed: 05/04/2023]
Abstract
BACKGROUND Prenatal cadmium (Cd) exposure has been recognized to restrict growth, and male and female fetuses may have differential susceptibility to the developmental toxicity of Cd. Imprinted genes, which exhibit monoallelic expression based on parent of origin, are highly expressed in placental tissues. The function of these genes is particularly critical to fetal growth and development, and some are expressed in sex-specific patterns. OBJECTIVES We aimed to examine whether prenatal Cd associates with the expression of imprinted placental genes, overall or in fetal sex-specific patterns, across two independent epidemiologic studies. METHODS We tested for Cd–sex interactions in association with gene expression, then regressed the placental expression levels of 74 putative imprinted genes on placental log-Cd concentrations while adjusting for maternal age, sex, smoking history, and educational attainment. These models were performed within study- and sex-specific strata in the New Hampshire Birth Cohort Study (NHBCS; [Formula: see text]) and the Rhode Island Child Health Study (RICHS; [Formula: see text]). We then used fixed-effects models to estimate the sex-specific and overall associations across strata and then examine heterogeneity in the associations by fetal sex. RESULTS We observed that higher Cd concentrations were associated with higher expression of distal-less homeobox 5 (DLX5) ([Formula: see text]), and lower expression of h19 imprinted maternally expressed transcript (H19) ([Formula: see text]) and necdin, MAGE family member (NDN) ([Formula: see text]) across study and sex-specific strata, while three other genes [carboxypeptidase A4 (CPA4), growth factor receptor bound protein 10 (GRB10), and integrin-linked kinase (ILK)] were significantly associated with Cd concentrations, but only among female placenta ([Formula: see text]). Additionally, the expression of DLX5, H19, and NDN, the most statistically significant Cd-associated genes, were also associated with standardized birth weight z-scores. DISCUSSION The differential regulation of a set of imprinted genes, particularly DLX5, H19, and NDN, in association with prenatal Cd exposure may be involved in overall developmental toxicity, and some imprinted genes may respond to Cd exposure in a manner that is specific to infant gender. https://doi.org/10.1289/EHP4264.
Collapse
Affiliation(s)
- Todd M. Everson
- Department of Environmental Health, Rollins School of Public Health at Emory University, Atlanta, Georgia, USA
| | - Carmen Marable
- Department of Environmental Health, Rollins School of Public Health at Emory University, Atlanta, Georgia, USA
| | - Maya A. Deyssenroth
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Tracy Punshon
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, USA
| | - Brian P. Jackson
- Department of Earth Sciences, Dartmouth College, Hanover, New Hampshire, USA
| | - Luca Lambertini
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Margaret R. Karagas
- Department of Epidemiology, Geisel School of Medicine at Dartmouth College, Hanover, New Hampshire, USA
- Children’s Environmental Health and Disease Prevention Research Center at Dartmouth Geisel School of Medicine, Lebanon, New Hampshire, USA
| | - Jia Chen
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Carmen J. Marsit
- Department of Environmental Health, Rollins School of Public Health at Emory University, Atlanta, Georgia, USA
- Department of Epidemiology, Rollins School of Public Health at Emory University, Atlanta, Georgia, USA
| |
Collapse
|
8
|
Mai Q, Mai X, Huang X, Zhang D, Huang K, Zhou C. Imprinting Status in Two Human Parthenogenetic Embryonic Stem Cell Lines: Analysis of 63 Imprinted Gene Expression Levels in Undifferentiated and Early Differentiated Stages. Stem Cells Dev 2018; 27:430-439. [PMID: 29402175 DOI: 10.1089/scd.2017.0247] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Human parthenogenetic embryonic stem cells (hPESCs) represent a source of histocompatible tissues for transplantation and carry two copies of the maternal genome, but lack the paternal genome. In this study, we selected 63 known human imprinted genes to investigate the imprinting status of hPESC. The expression level of these genes, including 27 maternally and 36 paternally imprinted were illustrated in hPESC and human embryonic stem cells (hESCs) derived from fertilized embryo lines. The expression activity changes of these genes were analyzed in undifferentiated and early differentiated hPESC lines. In addition, the methylation status of four differentially methylated regions (DMRs) of the imprinted genes was analyzed in undifferentiated and early differentiated hPESC and hESC lines. As a result, we found that all the maternally imprinted genes were expressed at similar levels in the undifferentiated hPESC lines and the hESC lines, except ZNF264 and ATP10A. Twenty-one analyzed paternal imprinted genes were expressed at the same level in two separated hPESC lines as well as compared with the hESC lines, whereas 15 other paternal imprinted genes were significantly downregulated or inactivated in hPESC lines as compared with the hESC line. During prolonged passage, the expression levels of the majority of imprinted genes remained stable in two hPESC lines. The four DMRs, including PEG3/ZIM2 (DMRs), SNURF/SNRPN DMRs, and KVDMR1 DMRs are highly methylated in the genes of two undifferentiated hPESCs and its embryonic bodies (EBs), whereas the genes of the undifferentiated hESCs and its EBs are half methylated. During the early differentiation stage, the imprinted genes showed the same expression trend and the expression levels of H19, IGF2, SLC22A2, SLC22A3/SLC22A18, and CPA4 were significantly upregulated in both hPESC lines. As conclusion, hPESCs show a substantial degree of epigenetic stability with respect to some imprinted genes.
Collapse
Affiliation(s)
- Qingyun Mai
- 1 Reproductive Medical Center, The First Affiliated Hospital of Sun Yat-sen University , Guangzhou, China
| | - Xiuyun Mai
- 1 Reproductive Medical Center, The First Affiliated Hospital of Sun Yat-sen University , Guangzhou, China .,2 Reproductive Medical Center , Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Xin Huang
- 1 Reproductive Medical Center, The First Affiliated Hospital of Sun Yat-sen University , Guangzhou, China
| | - Dan Zhang
- 1 Reproductive Medical Center, The First Affiliated Hospital of Sun Yat-sen University , Guangzhou, China
| | - Kejun Huang
- 1 Reproductive Medical Center, The First Affiliated Hospital of Sun Yat-sen University , Guangzhou, China
| | - Canquan Zhou
- 1 Reproductive Medical Center, The First Affiliated Hospital of Sun Yat-sen University , Guangzhou, China
| |
Collapse
|
9
|
White MJ, Kodaman NM, Harder RH, Asselbergs FW, Vaughan DE, Brown NJ, Moore JH, Williams SM. Genetics of Plasminogen Activator Inhibitor-1 (PAI-1) in a Ghanaian Population. PLoS One 2015; 10:e0136379. [PMID: 26322636 PMCID: PMC4556460 DOI: 10.1371/journal.pone.0136379] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 08/03/2015] [Indexed: 11/18/2022] Open
Abstract
Plasminogen activator inhibitor 1 (PAI-1), a major modulator of the fibrinolytic system, is an important factor in cardiovascular disease (CVD) susceptibility and severity. PAI-1 is highly heritable, but the few genes associated with it explain only a small portion of its variation. Studies of PAI-1 typically employ linear regression to estimate the effects of genetic variants on PAI-1 levels, but PAI-1 is not normally distributed, even after transformation. Therefore, alternative statistical methods may provide greater power to identify important genetic variants. Additionally, most genetic studies of PAI-1 have been performed on populations of European descent, limiting the generalizability of their results. We analyzed >30,000 variants for association with PAI-1 in a Ghanaian population, using median regression, a non-parametric alternative to linear regression. Three variants associated with median PAI-1, the most significant of which was in the gene arylsulfatase B (ARSB) (p = 1.09 x 10−7). We also analyzed the upper quartile of PAI-1, the most clinically relevant part of the distribution, and found 19 SNPs significantly associated in this quartile. Of note an association was found in period circadian clock 3 (PER3). Our results reveal novel associations with median and elevated PAI-1 in an understudied population. The lack of overlap between the two analyses indicates that the genetic effects on PAI-1 are not uniform across its distribution. They also provide evidence of the generalizability of the circadian pathway’s effect on PAI-1, as a recent meta-analysis performed in Caucasian populations identified another circadian clock gene (ARNTL).
Collapse
Affiliation(s)
- Marquitta J. White
- Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Genetics and Institute of Quantitative Biomedical Sciences, Dartmouth College, Hanover, New Hampshire, United States of America
| | - Nuri M. Kodaman
- Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Genetics and Institute of Quantitative Biomedical Sciences, Dartmouth College, Hanover, New Hampshire, United States of America
| | - Reed H. Harder
- Department of Genetics and Institute of Quantitative Biomedical Sciences, Dartmouth College, Hanover, New Hampshire, United States of America
| | - Folkert W. Asselbergs
- Department Heart & Lungs, University Medical Center Utrecht, Heidelberglaan 100, 3584CX, Utrecht, the Netherlands
- Institute of Cardiovascular Science, University College London, 222 Euston Road, London, United Kingdom
- Durrer Center for Cardiogenetic Research, ICIN-Netherlands Heart Institute, Utrecht, The Netherlands
| | - Douglas E. Vaughan
- Department of Medicine, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Nancy J. Brown
- Department of Medicine Vanderbilt University, Nashville, Tennessee, United States of America
| | - Jason H. Moore
- Department of Genetics and Institute of Quantitative Biomedical Sciences, Dartmouth College, Hanover, New Hampshire, United States of America
| | - Scott M. Williams
- Department of Genetics and Institute of Quantitative Biomedical Sciences, Dartmouth College, Hanover, New Hampshire, United States of America
- * E-mail:
| |
Collapse
|
10
|
Green BB, Kappil M, Lambertini L, Armstrong DA, Guerin DJ, Sharp AJ, Lester BM, Chen J, Marsit CJ. Expression of imprinted genes in placenta is associated with infant neurobehavioral development. Epigenetics 2015. [PMID: 26198301 DOI: 10.1080/15592294.2015.1073880] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Genomic imprinting disorders often exhibit delayed neurobehavioral development, suggesting this unique mechanism of epigenetic regulation plays a role in mental and neurological health. While major errors in imprinting have been linked to adverse health outcomes, there has been little research conducted on how moderate variability in imprinted gene expression within a population contributes to differences in neurobehavioral outcomes, particularly at birth. Here, we profiled the expression of 108 known and putative imprinted genes in human placenta samples from 615 infants assessed by the Neonatal Intensive Care Unit (NICU) Network Neurobehavioral Scales (NNNS). Data reduction identified 10 genes (DLX5, DHCR24, VTRNA2-1, PHLDA2, NPAP1, FAM50B, GNAS-AS1, PAX8-AS1, SHANK2, and COPG2IT1) whose expression could distinguish between newborn neurobehavioral profiles derived from the NNNS. Clustering infants based on the expression pattern of these genes identified 2 groups of infants characterized by reduced quality of movement, increased signs of asymmetrical and non-optimal reflexes, and increased odds of demonstrating increased signs of physiologic stress and abstinence. Overall, these results suggest that common variation in placental imprinted gene expression is linked to suboptimal performance on scales of neurological functioning as well as with increased signs of physiologic stress, highlighting the central importance of the control of expression of these genes in the placenta for neurobehavioral development.
Collapse
Affiliation(s)
- Benjamin B Green
- a Department of Epidemiology and Department of Pharmacology and Toxicology ; Geisel School of Medicine at Dartmouth College ; Hanover , NH USA
| | | | | | | | | | | | | | | | | |
Collapse
|
11
|
Hannula-Jouppi K, Muurinen M, Lipsanen-Nyman M, Reinius LE, Ezer S, Greco D, Kere J. Differentially methylated regions in maternal and paternal uniparental disomy for chromosome 7. Epigenetics 2013; 9:351-65. [PMID: 24247273 PMCID: PMC4053454 DOI: 10.4161/epi.27160] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
DNA methylation is a hallmark of genomic imprinting and differentially methylated regions (DMRs) are found near and in imprinted genes. Imprinted genes are expressed only from the maternal or paternal allele and their normal balance can be disrupted by uniparental disomy (UPD), the inheritance of both chromosomes of a chromosome pair exclusively from only either the mother or the father. Maternal UPD for chromosome 7 (matUPD7) results in Silver-Russell syndrome (SRS) with typical features and growth retardation, but no gene has been conclusively implicated in SRS. In order to identify novel DMRs and putative imprinted genes on chromosome 7, we analyzed eight matUPD7 patients, a segmental matUPD7q31-qter, a rare patUPD7 case and ten controls on the Infinium HumanMethylation450K BeadChip with 30 017 CpG methylation probes for chromosome 7. Genome-scale analysis showed highly significant clustering of DMRs only on chromosome 7, including the known imprinted loci GRB10, SGCE/PEG10, and PEG/MEST. We found ten novel DMRs on chromosome 7, two DMRs for the predicted imprinted genes HOXA4 and GLI3 and one for the disputed imprinted gene PON1. Quantitative RT-PCR on blood RNA samples comparing matUPD7, patUPD7, and controls showed differential expression for three genes with novel DMRs, HOXA4, GLI3, and SVOPL. Allele specific expression analysis confirmed maternal only expression of SVOPL and imprinting of HOXA4 was supported by monoallelic expression. These results present the first comprehensive map of parent-of-origin specific DMRs on human chromosome 7, suggesting many new imprinted sites.
Collapse
Affiliation(s)
- Katariina Hannula-Jouppi
- Department of Medical Genetics; Haartman Institute; Molecular Neurology Program; Research Program's Unit; Folkhälsan Institute of Genetics; University of Helsinki; Helsinki, Finland; Department of Dermatology and Allergology; Skin and Allergy Hospital; Helsinki University Central Hospital; Helsinki University Hospital; Helsinki, Finland
| | - Mari Muurinen
- Department of Medical Genetics; Haartman Institute; Molecular Neurology Program; Research Program's Unit; Folkhälsan Institute of Genetics; University of Helsinki; Helsinki, Finland
| | - Marita Lipsanen-Nyman
- Children's Hospital; University of Helsinki and Helsinki University Central Hospital; Helsinki University Hospital; Helsinki, Finland
| | - Lovisa E Reinius
- Department of Biosciences and Nutrition; Center for Biosciences; Karolinska Institutet; Stockholm, Sweden
| | - Sini Ezer
- Department of Medical Genetics; Haartman Institute; Molecular Neurology Program; Research Program's Unit; Folkhälsan Institute of Genetics; University of Helsinki; Helsinki, Finland
| | - Dario Greco
- Department of Medical Genetics; Haartman Institute; Molecular Neurology Program; Research Program's Unit; Folkhälsan Institute of Genetics; University of Helsinki; Helsinki, Finland; Department of Biosciences and Nutrition; Center for Biosciences; Karolinska Institutet; Stockholm, Sweden; Unit of Systems Toxicology; Finnish Institute of Occupational Health (FIOH); Helsinki, Finland
| | - Juha Kere
- Department of Medical Genetics; Haartman Institute; Molecular Neurology Program; Research Program's Unit; Folkhälsan Institute of Genetics; University of Helsinki; Helsinki, Finland; Department of Biosciences and Nutrition; Center for Biosciences; Karolinska Institutet; Stockholm, Sweden; Science for Life Laboratory; Karolinska Institutet; Solna, Sweden
| |
Collapse
|
12
|
Diagnostic value of DNA alteration: loss of heterozygosity or allelic imbalance-promising for molecular staging of prostate cancers. Med Oncol 2013; 30:391. [PMID: 23288724 PMCID: PMC3586396 DOI: 10.1007/s12032-012-0391-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2012] [Accepted: 11/21/2012] [Indexed: 01/12/2023]
Abstract
The biological behavior of prostate cancer is uncertain, and therefore, search for molecular prognostic markers associated with disease progression seems to be essential. We performed microsatellite allelotyping of DNA isolated from primary prostate tumors biopsies (prostate adenocarcinoma, PCa). We evaluated the frequency of allelic imbalance (AI), including loss of heterozygosity and/or microsatellite imbalance (LOH/MSI) as well as the association of these DNA alterations with clinicopathological variables. We assessed the significance of LOH/MSI alterations in selected imprinted and non-imprinted chromosomal regions (IR and NIR) in PCa. A total of 50 biopsies of prostate tumor (containing >75 % tumor cells) were histologically examined confirming prostate carcinoma. Microsatellite allelotyping using 16 microsatellite markers linked to the following chromosomal regions: 1p31.2, 3p21.3–25.3, 7q32.2, 9p21.3, 11p15.5, 12q23.2, and 16q22.1 was performed. The incidence of LOH/MSI alterations in prostate tumor cells was the highest for chromosomal regions 7q32.2 and 16q22.1 (31.25 and 26.60 %, respectively), followed by 1p31.2 and 3p21.3–25.3 (26.50 and 17.40 %, respectively). Statistically significant increase in LOH/MSI alterations has been observed for markers: D1S2137 (1p region; p = 0.00032), D9S974 (9p region; p = 0.0017), and D16S3025 (16q region; p = 0.0017). Statistically significant differences in frequency of LOH/MSI alterations in particular chromosomal regions have been found for 1p31.2, 7q32.2 and 16q22.1 (p = 0.027, p = 0.012 and p = 0.031, respectively). We documented statistically significant association between Fractional Allele Loss (FAL) index and advanced tumor stage (p < 0.05). We suggest that genomic instability of LOH/MSI type is a frequent event in prostate carcinogenesis and assessed as FAL index has clinical value for the molecular staging of prostate cancer in (TRUS)-guided prostate biopsy material.
Collapse
|
13
|
Morcos L, Ge B, Koka V, Lam KCL, Pokholok DK, Gunderson KL, Montpetit A, Verlaan DJ, Pastinen T. Genome-wide assessment of imprinted expression in human cells. Genome Biol 2011; 12:R25. [PMID: 21418647 PMCID: PMC3129675 DOI: 10.1186/gb-2011-12-3-r25] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Revised: 01/21/2011] [Accepted: 03/21/2011] [Indexed: 01/19/2023] Open
Abstract
Background Parent-of-origin-dependent expression of alleles, imprinting, has been suggested to impact a substantial proportion of mammalian genes. Its discovery requires allele-specific detection of expressed transcripts, but in some cases detected allelic expression bias has been interpreted as imprinting without demonstrating compatible transmission patterns and excluding heritable variation. Therefore, we utilized a genome-wide tool exploiting high density genotyping arrays in parallel measurements of genotypes in RNA and DNA to determine allelic expression across the transcriptome in lymphoblastoid cell lines (LCLs) and skin fibroblasts derived from families. Results We were able to validate 43% of imprinted genes with previous demonstration of compatible transmission patterns in LCLs and fibroblasts. In contrast, we only validated 8% of genes suggested to be imprinted in the literature, but without clear evidence of parent-of-origin-determined expression. We also detected five novel imprinted genes and delineated regions of imprinted expression surrounding annotated imprinted genes. More subtle parent-of-origin-dependent expression, or partial imprinting, could be verified in four genes. Despite higher prevalence of monoallelic expression, immortalized LCLs showed consistent imprinting in fewer loci than primary cells. Random monoallelic expression has previously been observed in LCLs and we show that random monoallelic expression in LCLs can be partly explained by aberrant methylation in the genome. Conclusions Our results indicate that widespread parent-of-origin-dependent expression observed recently in rodents is unlikely to be captured by assessment of human cells derived from adult tissues where genome-wide assessment of both primary and immortalized cells yields few new imprinted loci.
Collapse
Affiliation(s)
- Lisanne Morcos
- McGill University and Genome Quebec Innovation Centre, 740 Dr Penfield Avenue, Montreal, Quebec, H3A 1A4, Canada
| | | | | | | | | | | | | | | | | |
Collapse
|
14
|
Mai X, Mai Q, Li T, Zhou C. Dynamic expression patterns of imprinted genes in human embryonic stem cells following prolonged passaging and differentiation. J Assist Reprod Genet 2010; 28:315-23. [PMID: 21161363 DOI: 10.1007/s10815-010-9524-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2010] [Accepted: 12/01/2010] [Indexed: 11/26/2022] Open
Abstract
PURPOSE To evaluate the overall expression patterns of imprinted genes in human embryonic stem cells following long term culture and differentiation. MATERIALS AND METHODS Expression levels of 65 imprinted genes determined by PCR array were analyzed in one human embryonic stem cell line (cHES1) following prolonged passaging and differentiation. RESULTS Transcripts of 63 imprinted genes were detected in cHES1 cells. Expression levels of all but 5 imprinted genes did not correlate with passage numbers or differ in cells after passage 50 compared with those before passage 50. SLC22A2, SLC22A3, CPA, H19, COPG2IT1 and IGF2 expression were significantly increased in embryoid bodies compared with undifferentiated cells. CONCLUSIONS The global expression profiles of imprinted genes are generally stable in human embryonic stem cells after prolonged passaging and differentiation.
Collapse
Affiliation(s)
- Xiuyun Mai
- Reproductive Medical Center, The First Affiliated Hospital of Sun Yat-Sen University, 58 Zhongshan 2nd Avenue, Yuexiu, 510080, Guangzhou, China
| | | | | | | |
Collapse
|
15
|
Carboxypeptidase A6 in zebrafish development and implications for VIth cranial nerve pathfinding. PLoS One 2010; 5:e12967. [PMID: 20885977 PMCID: PMC2945764 DOI: 10.1371/journal.pone.0012967] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2010] [Accepted: 09/03/2010] [Indexed: 02/01/2023] Open
Abstract
Carboxypeptidase A6 (CPA6) is an extracellular protease that cleaves carboxy-terminal hydrophobic amino acids and has been implicated in the defective innervation of the lateral rectus muscle by the VIth cranial nerve in Duane syndrome. In order to investigate the role of CPA6 in development, in particular its potential role in axon guidance, the zebrafish ortholog was identified and cloned. Zebrafish CPA6 was secreted and interacted with the extracellular matrix where it had a neutral pH optimum and specificity for C-terminal hydrophobic amino acids. Transient mRNA expression was found in newly formed somites, pectoral fin buds, the stomodeum and a conspicuous condensation posterior to the eye. Markers showed this tissue was not myogenic in nature. Rather, the CPA6 localization overlapped with a chondrogenic site which subsequently forms the walls of a myodome surrounding the lateral rectus muscle. No other zebrafish CPA gene exhibited a similar expression profile. Morpholino-mediated knockdown of CPA6 combined with retrograde labeling and horizontal eye movement analyses demonstrated that deficiency of CPA6 alone did not affect either VIth nerve development or function in the zebrafish. We suggest that mutations in other genes and/or enhancer elements, together with defective CPA6 expression, may be required for altered VIth nerve pathfinding. If mutations in CPA6 contribute to Duane syndrome, our results also suggest that Duane syndrome can be a chondrogenic rather than a myogenic or neurogenic developmental disorder.
Collapse
|
16
|
Tanco S, Zhang X, Morano C, Avilés FX, Lorenzo J, Fricker LD. Characterization of the substrate specificity of human carboxypeptidase A4 and implications for a role in extracellular peptide processing. J Biol Chem 2010; 285:18385-96. [PMID: 20385563 DOI: 10.1074/jbc.m109.060350] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
CPA4 (carboxypeptidase A4) is a member of the metallocarboxypeptidase family. CPA4 was originally found in a screen of mRNAs up-regulated by sodium butyrate-induced differentiation of cancer cells. Further studies suggested a relation between CPA4 and prostate cancer aggressiveness. In the present study, we determined that CPA4 is secreted from cells as a soluble proenzyme (pro-CPA4) that can be activated by endoproteases, such as trypsin. Three complementary approaches were used to study the substrate specificity of CPA4; kinetic analysis was performed using a new series of chromogenic substrates and some biologically relevant peptides, the cleavage of synthetic peptides was tested individually, and the cleavage of a mixture of >100 mouse brain peptides was examined using a quantitative peptidomics mass spectrometry-based approach. CPA4 was able to cleave hydrophobic C-terminal residues with a preference for Phe, Leu, Ile, Met, Tyr, and Val. However, not all peptides with C-terminal hydrophobic residues were cleaved, indicating the importance of additional residues within the peptide. Aliphatic, aromatic, and basic residues in the P1 position have a positive influence on the cleavage specificity. In contrast, acidic residues, Pro, and Gly have a negative influence in the P1 position. Some of the peptides identified as CPA4 substrates (such as neurotensin, granins, and opioid peptides) have been previously shown to function in cell proliferation and differentiation, potentially explaining the link between CPA4 and cancer aggressiveness. Taken together, these studies suggest that CPA4 functions in neuropeptide processing and regulation in the extracellular environment.
Collapse
Affiliation(s)
- Sebastian Tanco
- Departament de Bioquimica, Institut de Biotecnologia i de Biomedicina, Universitat Autonoma de Barcelona, Bellaterra, Barcelona, Spain
| | | | | | | | | | | |
Collapse
|
17
|
Detection of allelic imbalance in MLH1 expression by pyrosequencing serves as a tool for the identification of germline defects in Lynch syndrome. Fam Cancer 2010; 9:345-56. [DOI: 10.1007/s10689-009-9314-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
|
18
|
Masuo Y, Imai T, Shibato J, Hirano M, Jones OAH, Maguire ML, Satoh K, Kikuchi S, Rakwal R. Omic analyses unravels global molecular changes in the brain and liver of a rat model for chronic Sake (Japanese alcoholic beverage) intake. Electrophoresis 2009; 30:1259-75. [PMID: 19382137 DOI: 10.1002/elps.200900045] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The effects of chronic administration of Sake (Japanese alcoholic beverage, Nihonshu) on brain and liver of female F334 (Fisher) rats were surveyed via global omic analyses using DNA microarray, 2-DE, and proton nuclear magnetic resonance. Rats weaned at 4 wk of age were given free access to Sake (15% alcohol), instead of water. At 13 months of age, and 24 h after withdrawal of Sake supply, rats were sacrificed, and the whole brain and liver tissues dissected for analyses. In general, molecular changes in brain were found to be less than those in liver. Transcriptomics data revealed 36 and 9, and 80 and 62 up- and down-regulated genes, in the brain and liver, respectively, with binding and catalytic activity gene categories the most prominently changed. Results suggested Sake-induced fragility of brain and liver toxicity/damage, though no significant abnormalities in growth were seen. At protein level, a striking decrease was found in the expression of NADH dehydrogenase (ubiquinone) Fe-S protein 1 in brain, suggesting attenuation of mitochondrial metabolism. In liver, results again suggested an attenuation of mitochondrial function and, in addition, glycoproteins with unknown function were induced at protein and gene levels, suggesting possible changes in glycoprotein binding in that organ. Metabolomic analysis of brain revealed significant increases in valine, arginine/ornithine, alanine, glutamine, and choline with decreases in isoleucine, N-acetyl aspartate, taurine, glutamate, and gamma aminobutyric acid. Our results provide a detailed inventory of molecular components of both brain and liver after Sake intake, and may help to better understand effects of chronic Sake drinking.
Collapse
Affiliation(s)
- Yoshinori Masuo
- Health Technology Research Center (HTRC), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Méreau A, Anquetil V, Cibois M, Noiret M, Primot A, Vallée A, Paillard L. Analysis of splicing patterns by pyrosequencing. Nucleic Acids Res 2009; 37:e126. [PMID: 19671523 PMCID: PMC2770645 DOI: 10.1093/nar/gkp626] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Several different mRNAs can be produced from a given pre-mRNA by regulated alternative splicing, or as the result of deregulations that may lead to pathological states. Analysing splicing patterns is therefore of importance to describe and understand developmental programs, cellular responses to internal or external cues, or human diseases. We describe here a method, Pyrosequencing Analysis of Splicing Patterns (PASP), that combines RT–PCR and pyrosequencing of PCR products. We demonstrated that: (i) Ratios of two pure RNAs mixed in various proportions were accurately measured by PASP; (ii) PASP can be adapted to virtually any splicing event, including mutually exclusive exons, complex patterns of exon skipping or inclusion, and alternative 3′ terminal exons; (iii) In extracts from different organs, the proportions of RNA isoforms measured by PASP reflected those measured by other methods. The PASP method is therefore reliable for analysing splicing patterns. All steps are done in 96-wells microplates, without gel electrophoresis, opening the way to high-throughput comparisons of RNA from several sources.
Collapse
Affiliation(s)
- Agnès Méreau
- Institut de Génétique et Développement de Rennes, Université de Rennes 1, IFR 140, CNRS, UMR6061, Equipe Expression Génétique et Développement, Université Européenne de Bretagne, F-35000 Rennes, France
| | | | | | | | | | | | | |
Collapse
|
20
|
Abstract
Silver-Russell syndrome (SRS) is a clinically heterogeneous syndrome characterized by intra-uterine and postnatal growth retardation with spared cranial growth, dysmorphic features and frequent body asymmetry. Various cytogenetic abnormalities have been described in a small number of SRS or SRS-like cases involving chromosomes 7, 8, 11, 15, 17 and 18. However, until recent data became available involving imprinted genes on chromosome 7 and chromosome 11p15, the molecular cause of the syndrome was unknown in most cases. Genomic imprinting is the best example of transcriptional control of genes by epigenetic modifications. Many imprinted genes play key roles in fetal and placental growth and behaviour. This is illustrated in SRS, which can now be considered as a new imprinting disease model. These new findings in the pathophysiology of SRS allow long-term follow-up studies to be performed based on molecular diagnosis. This could help to define appropriate clinical guidelines regarding growth and feeding difficulties.
Collapse
Affiliation(s)
- Sylvie Rossignol
- Explorations fonctionnelles endocriniennes, Hôpital Trousseau (APHP); INSERM U515; Université Pierre et Marie Curie-Paris6, 26 avenue du Dr Netter, 75012 Paris, France.
| | | | | | | |
Collapse
|
21
|
Ruf N, Bähring S, Galetzka D, Pliushch G, Luft FC, Nürnberg P, Haaf T, Kelsey G, Zechner U. Sequence-based bioinformatic prediction and QUASEP identify genomic imprinting of the KCNK9 potassium channel gene in mouse and human. Hum Mol Genet 2007; 16:2591-9. [PMID: 17704508 DOI: 10.1093/hmg/ddm216] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Genomic imprinting is the epigenetic marking of gene subsets resulting in monoallelic or predominant expression of one of the two parental alleles according to their parental origin. We describe the systematic experimental verification of a prioritized 16 candidate imprinted gene set predicted by sequence-based bioinformatic analyses. We used Quantification of Allele-Specific Expression by Pyrosequencing (QUASEP) and discovered maternal-specific imprinted expression of the Kcnk9 gene as well as strain-dependent preferential expression of the Rarres1 gene in E11.5 (C57BL/6 x Cast/Ei)F1 and informative (C57BL/6 x Cast/Ei) x C57BL/6 backcross mouse embryos. For the remaining 14 candidate imprinted genes, we observed biallelic expression. In adult mouse tissues, we found that Kcnk9 expression was restricted to the brain and also was maternal-specific. QUASEP analysis of informative human fetal brain samples further demonstrated maternal-specific imprinted expression of the human KCNK9 orthologue. The CpG islands associated with the mouse and human Kcnk9/KCNK9 genes were not differentially methylated, but strongly hypomethylated. Thus, we speculate that mouse Kcnk9 imprinting may be regulated by the maternal germline differentially methylated region in Peg13, an imprinted non-coding RNA gene in close proximity to Kcnk9 on distal mouse chromosome 15. Our data have major implications for the proposed role of Kcnk9 in neurodevelopment, apoptosis and tumourigenesis, as well as for the efficiency of sequence-based bioinformatic predictions of novel imprinted genes.
Collapse
Affiliation(s)
- Nico Ruf
- Max-Delbrueck-Center for Molecular Medicine, D-13125 Berlin, Germany
| | | | | | | | | | | | | | | | | |
Collapse
|
22
|
Fernández D, Vendrell J, Avilés FX, Fernández-Recio J. Structural and functional characterization of binding sites in metallocarboxypeptidases based on Optimal Docking Area analysis. Proteins 2007; 68:131-44. [PMID: 17407161 DOI: 10.1002/prot.21390] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The metallocarboxypeptidases (MCPs) belonging to the clan MC were studied by the Optimal Docking Area (ODA) method to evaluate protein-protein binding sites and to provide a basis for the identification of binding partners for this class of enzymes. The ODA method identifies surface patches with optimal desolvation energy based on the selection of low-energy docking regions, generated from a set of surface points around the protein. With few exceptions, the ODA method identified surface patches with a significant low-energy docking surface for all the MCPs with known three-dimensional structure. Overall, in 14 out of 24 cases, the detected ODA patches were correctly located (i.e. more than 50% of the predicted residues were in known protein-protein binding sites), yielding a global success rate of 58%. More specifically, the success rate increased up to 80% on the ODA patches detected for the catalytic domains of the M14A subfamily, independently on the partner. Interestingly, the ODA residues on the catalytic domain were correctly located in the interface with the N-terminal pro domain in all MCPs. The spatial distribution of the ODA patches for the different members of the family is in relation to the origin and function of the particular MCP, which allowed distinguishing between them. In good agreement with the experimentally characterized protein interfaces, the total average surface area of the theoretically derived ODA patches for the catalytic domain of MCPs is around 1700 A2 and their content in hydrophobic residues is about 40%. As a particular case, the average surface area of the ODA patches in MCPs of crop insect pests is about twice that of the MCPs of vertebrates, which might be related to their particular function. We recognized two binding regions for the catalytic domain of the MCPs, one of them accounting for nearly all the known intermolecular interactions made up by the enzymes. Protein inhibitors seem to have evolved to dock on this subset of ODA patches, evoking the binding mode of the N-terminal pro domains. The second binding region detected, for which no ligands have been identified so far, seems to be related to the acquisition/maintenance of the native structure of the peptidase. Overall, the ODA method has been successful in identifying low-energy docking areas in a set of structurally and functionally related proteins, suggesting that it can be easily extended to other families in the search for protein-protein binding sites and for their functional significance.
Collapse
Affiliation(s)
- Daniel Fernández
- Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | | | | | | |
Collapse
|
23
|
Parker-Katiraee L, Carson AR, Yamada T, Arnaud P, Feil R, Abu-Amero SN, Moore GE, Kaneda M, Perry GH, Stone AC, Lee C, Meguro-Horike M, Sasaki H, Kobayashi K, Nakabayashi K, Scherer SW. Identification of the imprinted KLF14 transcription factor undergoing human-specific accelerated evolution. PLoS Genet 2007; 3:e65. [PMID: 17480121 PMCID: PMC1865561 DOI: 10.1371/journal.pgen.0030065] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2006] [Accepted: 03/12/2007] [Indexed: 12/22/2022] Open
Abstract
Imprinted genes are expressed in a parent-of-origin manner and are located in clusters throughout the genome. Aberrations in the expression of imprinted genes on human Chromosome 7 have been suggested to play a role in the etiologies of Russell-Silver Syndrome and autism. We describe the imprinting of KLF14, an intronless member of the Krüppel-like family of transcription factors located at Chromosome 7q32. We show that it has monoallelic maternal expression in all embryonic and extra-embryonic tissues studied, in both human and mouse. We examine epigenetic modifications in the KLF14 CpG island in both species and find this region to be hypomethylated. In addition, we perform chromatin immunoprecipitation and find that the murine Klf14 CpG island lacks allele-specific histone modifications. Despite the absence of these defining features, our analysis of Klf14 in offspring from DNA methyltransferase 3a conditional knockout mice reveals that the gene's expression is dependent upon a maternally methylated region. Due to the intronless nature of Klf14 and its homology to Klf16, we suggest that the gene is an ancient retrotransposed copy of Klf16. By sequence analysis of numerous species, we place the timing of this event after the divergence of Marsupialia, yet prior to the divergence of the Xenarthra superclade. We identify a large number of sequence variants in KLF14 and, using several measures of diversity, we determine that there is greater variability in the human lineage with a significantly increased number of nonsynonymous changes, suggesting human-specific accelerated evolution. Thus, KLF14 may be the first example of an imprinted transcript undergoing accelerated evolution in the human lineage. Imprinted genes are expressed in a parent-of-origin manner, where one of the two inherited copies of the imprinted gene is silenced. Aberrations in the expression of these genes, which generally regulate growth, are associated with various developmental disorders, emphasizing the importance of their discovery and analysis. In this study, we identify a novel imprinted gene, named KLF14, on human Chromosome 7. It is predicted to bind DNA and regulate transcription and was shown to be expressed from the maternally inherited chromosome in all human and mouse tissues examined. Surprisingly, we did not identify molecular signatures generally associated with imprinted regions, such as DNA methylation. Additionally, the identification of numerous DNA sequence variants led to an in-depth analysis of the gene's evolution. It was determined that there is greater variability in KLF14 in the human lineage, when compared to other primates, with a significantly increased number of polymorphisms encoding for changes at the protein level, suggesting human-specific accelerated evolution. As the first example of an imprinted transcript undergoing accelerated evolution in the human lineage, we propose that the accumulation of polymorphisms in KLF14 may be aided by the silencing of the inactive allele, allowing for stronger selection.
Collapse
Affiliation(s)
- Layla Parker-Katiraee
- Program in Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular and Medical Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Andrew R Carson
- Program in Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular and Medical Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Takahiro Yamada
- Program in Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Philippe Arnaud
- Institute of Molecular Genetics (IGMM), CNRS UMR5535, Montpellier, France
- University of Montpellier II, Montpellier, France
| | - Robert Feil
- Institute of Molecular Genetics (IGMM), CNRS UMR5535, Montpellier, France
- University of Montpellier II, Montpellier, France
| | - Sayeda N Abu-Amero
- Institute of Child Health, University College London, London, United Kingdom
| | - Gudrun E Moore
- Institute of Child Health, University College London, London, United Kingdom
| | - Masahiro Kaneda
- Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Research Organization of Information and Systems, Mishima, Japan
| | - George H Perry
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, United States of America
| | - Anne C Stone
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, United States of America
| | - Charles Lee
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | - Makiko Meguro-Horike
- Program in Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Hiroyuki Sasaki
- Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Research Organization of Information and Systems, Mishima, Japan
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (Sokendai), Mishima, Japan
| | - Keiko Kobayashi
- Department of Molecular Metabolism and Biochemical Genetics, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Kazuhiko Nakabayashi
- Program in Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Research Organization of Information and Systems, Mishima, Japan
| | - Stephen W Scherer
- Program in Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular and Medical Genetics, University of Toronto, Toronto, Ontario, Canada
- * To whom correspondence should be addressed. E-mail:
| |
Collapse
|
24
|
Abstract
The autism spectrum disorders (ASD) comprise a complex group of behaviorally related disorders that are primarily genetic in origin. Involvement of epigenetic regulatory mechanisms in the pathogenesis of ASD has been suggested by the occurrence of ASD in patients with disorders arising from epigenetic mutations (fragile X syndrome) or that involve key epigenetic regulatory factors (Rett syndrome). Moreover, the most common recurrent cytogenetic abnormalities in ASD involve maternally derived duplications of the imprinted domain on chromosome 15q11-13. Thus, parent of origin effects on sharing and linkage to imprinted regions on chromosomes 15q and 7q suggest that these regions warrant specific examination from an epigenetic perspective, particularly because epigenetic modifications do not change the primary genomic sequence, allowing risk epialleles to evade detection using standard screening strategies. This review examines the potential role of epigenetic factors in the etiology of ASD.
Collapse
Affiliation(s)
- N Carolyn Schanen
- Center for Pediatric Research, Nemours Biomedical Research, Wilmington, DE 19803, USA.
| |
Collapse
|
25
|
Reboul MP, Tandonnet O, Biteau N, Belet-de Putter C, Rebouissoux L, Moradkhani K, Vu PY, Saura R, Arveiler B, Lacombe D, Taine L, Iron A. Mosaic maternal uniparental isodisomy for chromosome 7q21-qter. Clin Genet 2006; 70:207-13. [PMID: 16922723 DOI: 10.1111/j.1399-0004.2006.00664.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Uniparental disomy (UPD) for several human chromosomes is associated with clinical abnormalities. We report the case of a 2-year-old boy with severe intrauterine and post-natal growth retardation (IUGR/PNGR) and highly variable sweat chloride concentrations. The patient was identified as heterozygous for the F508del mutation of the CFTR (cystic fibrosis transmembrane conductance regulator) gene. Unexpectedly, the signal corresponding to the maternally inherited F508del allele appeared much more intense than the paternally derived wild allele. Molecular analysis including polymorphic marker studies, microsatellites and single-nucleotide polymorphisms subsequently showed that the boy was a carrier of a de novo mosaic maternal isodisomy of a chromosome 7 segment while there was a biparental inheritance of the rest of the chromosome. This is the first report of a mosaic partial UPD7. The matUPD7 segment at 7q21-qter extends for 72.7 Mb. The karyotype (550 bands) of our patient was normal, and fluorescence in situ hybridization with probes mapping around the CFTR gene allowed us to rule out a partial duplication. The detection of this chromosomal rearrangement confirms the hypothesis that the 7q31-qter segment is a candidate for the localization of human imprinted genes involved in the control of IUGR and PNGR. It also emphasizes the importance of searching for UPD7 in severe, isolated and unexplained IUGR and PNGR.
Collapse
Affiliation(s)
- M-P Reboul
- Service de Génétique Médicale, Hopital Pellegrin, Laboratoire de Génétique Humaine, Développement et Cancer, Université Victor Segalen Bordeaux 2, France.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
26
|
Abu-Amero S, Monk D, Apostolidou S, Stanier P, Moore G. Imprinted genes and their role in human fetal growth. Cytogenet Genome Res 2006; 113:262-70. [PMID: 16575189 DOI: 10.1159/000090841] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2005] [Accepted: 07/06/2005] [Indexed: 01/16/2023] Open
Abstract
Growth is defined as the progressive increase in size and is listed as one of the eight main characteristics of life. In human gestation the most rapid growth phase is from 16 to 32 weeks when first there is both cell number and size increase and then from 32 weeks onwards there is continued size increase (Pollack and Divon, 1992). The mechanism of growth in utero is of fundamental interest to clinicians and scientists because of its implications for neonatal health. Growth is multifactorial in origin with both genetics and environment contributing equally large parts. Despite this complexity analysis of the candidate genes involved is possible using simple tissue biopsies at the relevant stages of development. Of particular interest in understanding fetal growth is the analysis of a group of genes that show a parent-of-origin effect known as genomic imprinting. Imprinted genes are not only found in eutherian (placental) and metatherian (marsupial) mammals but surprisingly also in plants. Nevertheless, their evolution in mammals appears to be linked primarily to placentation. It is thought to result from a potential conflict between the parents in terms of the drive to successfully propagate their own separate genes and the mother's added drive for her survival through the pregnancy to reproduce again. This means that the mother wants to restrict fetal growth and the father to enhance it.
Collapse
Affiliation(s)
- S Abu-Amero
- Institute of Reproductive and Developmental Biology, Faculty of Medicine, Imperial College, London Hammersmith Campus, London, UK
| | | | | | | | | |
Collapse
|
27
|
Luedi PP, Hartemink AJ, Jirtle RL. Genome-wide prediction of imprinted murine genes. Genome Res 2005; 15:875-84. [PMID: 15930497 PMCID: PMC1142478 DOI: 10.1101/gr.3303505] [Citation(s) in RCA: 213] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2004] [Accepted: 03/22/2005] [Indexed: 01/06/2023]
Abstract
Imprinted genes are epigenetically modified genes whose expression is determined according to their parent of origin. They are involved in embryonic development, and imprinting dysregulation is linked to cancer, obesity, diabetes, and behavioral disorders such as autism and bipolar disease. Herein, we train a statistical model based on DNA sequence characteristics that not only identifies potentially imprinted genes, but also predicts the parental allele from which they are expressed. Of 23,788 annotated autosomal mouse genes, our model identifies 600 (2.5%) to be potentially imprinted, 64% of which are predicted to exhibit maternal expression. These predictions allowed for the identification of putative candidate genes for complex conditions where parent-of-origin effects are involved, including Alzheimer disease, autism, bipolar disorder, diabetes, male sexual orientation, obesity, and schizophrenia. We observe that the number, type, and relative orientation of repeated elements flanking a gene are particularly important in predicting whether a gene is imprinted.
Collapse
Affiliation(s)
- Philippe P Luedi
- Center for Bioinformatics and Computational Biology, Duke University, Durham, North Carolina 27708, USA
| | | | | |
Collapse
|
28
|
Flori E, Girodon E, Samama B, Becmeur F, Viville B, Girard-Lemaire F, Doray B, Schluth C, Marcellin L, Boehm N, Goossens M, Pingault V. Trisomy 7 mosaicism, maternal uniparental heterodisomy 7 and Hirschsprung's disease in a child with Silver–Russell syndrome. Eur J Hum Genet 2005; 13:1013-8. [PMID: 15915162 DOI: 10.1038/sj.ejhg.5201442] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Prenatal trisomy 7 is usually a cell culture artifact in amniocytes with normal diploid karyotype at birth and normal fetal outcome. In the same way, true prenatal trisomy 7 mosaicism usually results in a normal child except when trisomic cells persist after birth or when trisomy rescue leads to maternal uniparental disomy, which is responsible for 5.5-7% of patients with Silver-Russell syndrome (SRS). We report here on the unusual association of SRS and Hirschsprung's disease (HSCR) in a patient with maternal uniparental heterodisomy 7 and trisomy 7 mosaicism in intestine and skin fibroblasts. HSCR may be fortuitous given its frequency, multifactorial inheritance and genetic heterogeneity. However, the presence of the trisomy 7 mosaicism in intestine as well as in skin fibroblasts suggests that SRS and HSCR might possibly be related. Such an association might result from either an increased dosage of a nonimprinted gene due to trisomy 7 mosaicism in skin fibroblasts (leading to SRS) and in intestine (leading to HSCR), or from an overexpression, through genomic imprinting, of maternally expressed imprinted allele(s) in skin fibroblasts and intestine or from a combination of trisomy 7 mosaicism and genomic imprinting. This report suggests that the SRS phenotype observed in maternal uniparental disomy 7 (mUPD(7)) patients might also result from an undetected low level of trisomy 7 mosaicism. In order to validate this hypothesis, we propose to perform a conventional and molecular cytogenetic analysis in different tissues every time mUPD7 is displayed.
Collapse
Affiliation(s)
- Elisabeth Flori
- Service de Cytogénétique, Fédération de Génétique, Hôpitaux Universitaires de Strasbourg, Strasbourg, France.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
29
|
Yamada T, Mitsuya K, Kayashima T, Yamasaki K, Ohta T, Yoshiura KI, Matsumoto N, Yamada H, Minakami H, Oshimura M, Niikawa N, Kishino T. Imprinting analysis of 10 genes and/or transcripts in a 1.5-Mb MEST-flanking region at human chromosome 7q32. Genomics 2004; 83:402-12. [PMID: 14962666 DOI: 10.1016/j.ygeno.2003.08.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2003] [Accepted: 08/14/2003] [Indexed: 12/21/2022]
Abstract
MEST is one of the imprinted genes in human. With the assistance of our integration map and the complete sequence in the registry, we mapped a total of 16 genes/transcripts at the 1.5-Mb MEST-flanking region at 7q32. This region has been suggested to form an imprinted gene cluster, because MEST and its three flanking genes/transcripts (MESTIT1, CPA4, and COPG2IT1) were reported to be imprinted, although two (TSGA14 and COPG2) were shown to escape imprinting. In this study, 10 other genes/transcripts were examined for their imprinting status in human fetal tissues. The results indicated that 8 genes/transcripts (NRF1, UBE2H, HSPC216, KIAA0265, FLJ14803, CPA2, CPA1, and DKFZp667F0312) were expressed biallelically. The imprinting status of two (TSGA13 and CPA5) was not conclusive, because of their weak and/or tissue-specific expression and inconstant results. These findings provided evidence that only 4 of the 16 genes/transcripts located to the region show monoallelic expression, while others are not involved in imprinting. Therefore, it is less likely that the MEST-flanking 7q32 region forms a large imprinted domain.
Collapse
Affiliation(s)
- Takahiro Yamada
- Reproductive and Developmental Medicine, Division of Pathophysiological Science, Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|