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Shiek SS, Mani MS, Kabekkodu SP, Dsouza HS. Health repercussions of environmental exposure to lead: Methylation perspective. Toxicology 2021; 461:152927. [PMID: 34492314 DOI: 10.1016/j.tox.2021.152927] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 07/23/2021] [Accepted: 09/01/2021] [Indexed: 12/15/2022]
Abstract
Lead (Pb) exposure has been a major public health concern for a long time now due to its permanent adverse effects on the human body. The process of lead toxicity has still not been fully understood, but recent advances in Omics technology have enabled researchers to evaluate lead-mediated alterations at the epigenome-wide level. DNA methylation is one of the widely studied and well-understood epigenetic modifications. Pb has demonstrated its ability to induce not just acute deleterious health consequences but also alters the epi-genome such that the disease manifestation happens much later in life as supported by Barkers Hypothesis of the developmental origin of health and diseases. Furthermore, these alterations are passed on to the next generation. Based on previous in-vivo, in-vitro, and human studies, this review provides an insight into the role of Pb in the development of several human disorders.
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Affiliation(s)
- Sadiya Sadiq Shiek
- Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | - Monica Shirley Mani
- Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | - Shama Prasada Kabekkodu
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India.
| | - Herman S Dsouza
- Department of Radiation Biology and Toxicology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India.
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2
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Lecaudey LA, Singh P, Sturmbauer C, Duenser A, Gessl W, Ahi EP. Transcriptomics unravels molecular players shaping dorsal lip hypertrophy in the vacuum cleaner cichlid, Gnathochromis permaxillaris. BMC Genomics 2021; 22:506. [PMID: 34225643 PMCID: PMC8256507 DOI: 10.1186/s12864-021-07775-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 05/18/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Teleosts display a spectacular diversity of craniofacial adaptations that often mediates ecological specializations. A considerable amount of research has revealed molecular players underlying skeletal craniofacial morphologies, but less is known about soft craniofacial phenotypes. Here we focus on an example of lip hypertrophy in the benthivorous Lake Tangnayika cichlid, Gnathochromis permaxillaris, considered to be a morphological adaptation to extract invertebrates out of the uppermost layer of mud bottom. We investigate the molecular and regulatory basis of lip hypertrophy in G. permaxillaris using a comparative transcriptomic approach. RESULTS We identified a gene regulatory network involved in tissue overgrowth and cellular hypertrophy, potentially associated with the formation of a locally restricted hypertrophic lip in a teleost fish species. Of particular interest were the increased expression level of apoda and fhl2, as well as reduced expression of cyp1a, gimap8, lama5 and rasal3, in the hypertrophic lip region which have been implicated in lip formation in other vertebrates. Among the predicted upstream transcription factors, we found reduced expression of foxp1 in the hypertrophic lip region, which is known to act as repressor of cell growth and proliferation, and its function has been associated with hypertrophy of upper lip in human. CONCLUSION Our results provide a genetic foundation for future studies of molecular players shaping soft and exaggerated, but locally restricted, craniofacial morphological changes in fish and perhaps across vertebrates. In the future, we advocate integrating gene regulatory networks of various craniofacial phenotypes to understand how they collectively govern trophic and behavioural adaptations.
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Affiliation(s)
- Laurène Alicia Lecaudey
- Institute of Biology, University of Graz, Universitätsplatz 2, A-8010 Graz, Austria
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | - Pooja Singh
- Institute of Biology, University of Graz, Universitätsplatz 2, A-8010 Graz, Austria
- Department of Biological Sciences, University of Calgary, 2500 University Dr NW, Calgary, AB T2N 1N4 Canada
| | - Christian Sturmbauer
- Institute of Biology, University of Graz, Universitätsplatz 2, A-8010 Graz, Austria
| | - Anna Duenser
- Institute of Biology, University of Graz, Universitätsplatz 2, A-8010 Graz, Austria
| | - Wolfgang Gessl
- Institute of Biology, University of Graz, Universitätsplatz 2, A-8010 Graz, Austria
| | - Ehsan Pashay Ahi
- Institute of Biology, University of Graz, Universitätsplatz 2, A-8010 Graz, Austria
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Viikinkaari 9, 00014 Helsinki, Finland
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3
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Liao J, Zeng TB, Pierce N, Tran DA, Singh P, Mann JR, Szabó PE. Prenatal correction of IGF2 to rescue the growth phenotypes in mouse models of Beckwith-Wiedemann and Silver-Russell syndromes. Cell Rep 2021; 34:108729. [PMID: 33567274 PMCID: PMC7968144 DOI: 10.1016/j.celrep.2021.108729] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 12/02/2020] [Accepted: 01/15/2021] [Indexed: 12/19/2022] Open
Abstract
Beckwith-Wiedemann syndrome (BWS) and Silver-Russell syndrome (SRS) are imprinting disorders manifesting as aberrant fetal growth and severe postnatal-growth-related complications. Based on the insulator model, one-third of BWS cases and two-thirds of SRS cases are consistent with misexpression of insulin-like growth factor 2 (IGF2), an important facilitator of fetal growth. We propose that the IGF2-dependent BWS and SRS cases can be identified by prenatal diagnosis and can be prevented by prenatal intervention targeting IGF2. We test this hypothesis using our mouse models of IGF2-dependent BWS and SRS. We find that genetically normalizing IGF2 levels in a double rescue experiment corrects the fetal overgrowth phenotype in the BWS model and the growth retardation in the SRS model. In addition, we pharmacologically rescue the BWS growth phenotype by reducing IGF2 signaling during late gestation. This animal study encourages clinical investigations to target IGF2 for prenatal diagnosis and prenatal prevention in human BWS and SRS. Liao et al. use mouse models to test a prenatal approach for correcting growth anomalies in two imprinting diseases, BWS and SRS. They find that cases where the fetal growth factor IGF2 is misregulated can be diagnosed, and growth can be corrected by prenatally adjusting IGF2 or its signaling output.
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Affiliation(s)
- Ji Liao
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Tie-Bo Zeng
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Nicholas Pierce
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Diana A Tran
- Division of Molecular and Cellular Biology, City of Hope Cancer Center, Duarte, CA 91010, USA; Irell and Manella Graduate School, City of Hope, Duarte, CA 91010, USA
| | - Purnima Singh
- Division of Molecular and Cellular Biology, City of Hope Cancer Center, Duarte, CA 91010, USA
| | - Jeffrey R Mann
- Division of Molecular and Cellular Biology, City of Hope Cancer Center, Duarte, CA 91010, USA
| | - Piroska E Szabó
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA.
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4
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Zhang C, Hao S, Zhang Q, Liu F, Zhou B, Xuan F, Xing W, Chen X, Wang Y, Ma P, Cao Z, Ma X. Maternal UPD of chromosome 7 in a patient with Silver-Russell syndrome and Pendred syndrome. J Clin Lab Anal 2020; 34:e23407. [PMID: 32666542 PMCID: PMC7521231 DOI: 10.1002/jcla.23407] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 04/28/2020] [Accepted: 05/09/2020] [Indexed: 01/16/2023] Open
Abstract
Background Silver‐Russell syndrome (SRS) is a heterogeneous imprinting disorder featuring severe intrauterine and postnatal growth retardation and dysmorphic features. Pendred syndrome (PDS) is an autosomal recessive disorder caused by mutations in the SLC26A4 gene characterized by sensorineural hearing loss. Methods Karyotyping analysis was performed to investigate any chromosomal abnormalities. Whole‐genome copy number variation and loss of heterozygosity were analyzed using an Affymetrix CytoScan 750 K Microarray. Variant screening was performed by targeted next‐generation sequencing on all known deafness‐causing genes. Results The proband was a patient with SRS caused by maternal uniparental disomy 7. The PDS of the proband was caused by homozygous variant c.919‐2A > G of SLC26A4; both mutated alleles were inherited from his mother. Conclusion This is the first report of uniparental disomy 7 leading to SRS and Pendred syndrome. Patients with intrauterine growth retardation or those born small for gestational age and exhibiting postnatal growth failure should undergo molecular testing to reach a clinical diagnosis.
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Affiliation(s)
- Chuan Zhang
- Graduate School of Peking Union Medical College, Beijing, China.,National Research Institute for Family Planning, National Human Genetic Resources Center, Beijing, China.,Gansu Province Medical Genetics Center, Gansu Province Maternal and Child Health Care Hospital, Lanzhou, China
| | - Shengju Hao
- Gansu Province Medical Genetics Center, Gansu Province Maternal and Child Health Care Hospital, Lanzhou, China
| | - Qinghua Zhang
- Gansu Province Medical Genetics Center, Gansu Province Maternal and Child Health Care Hospital, Lanzhou, China
| | - Furong Liu
- Gansu Province Medical Genetics Center, Gansu Province Maternal and Child Health Care Hospital, Lanzhou, China
| | - Bingbo Zhou
- Gansu Province Medical Genetics Center, Gansu Province Maternal and Child Health Care Hospital, Lanzhou, China
| | - Feng Xuan
- Gansu Province Medical Genetics Center, Gansu Province Maternal and Child Health Care Hospital, Lanzhou, China
| | - Wang Xing
- Gansu Province Medical Genetics Center, Gansu Province Maternal and Child Health Care Hospital, Lanzhou, China
| | - Xue Chen
- Gansu Province Medical Genetics Center, Gansu Province Maternal and Child Health Care Hospital, Lanzhou, China
| | - Yan Wang
- Gansu Province Medical Genetics Center, Gansu Province Maternal and Child Health Care Hospital, Lanzhou, China
| | - Panpan Ma
- Gansu Province Medical Genetics Center, Gansu Province Maternal and Child Health Care Hospital, Lanzhou, China
| | - Zongfu Cao
- Graduate School of Peking Union Medical College, Beijing, China.,National Research Institute for Family Planning, National Human Genetic Resources Center, Beijing, China
| | - Xu Ma
- Graduate School of Peking Union Medical College, Beijing, China.,National Research Institute for Family Planning, National Human Genetic Resources Center, Beijing, China
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Kahila H, Marjonen H, Auvinen P, Avela K, Riikonen R, Kaminen‐Ahola N. 18q12.3-q21.1 microdeletion detected in the prenatally alcohol-exposed dizygotic twin with discordant fetal alcohol syndrome phenotype. Mol Genet Genomic Med 2020; 8:e1192. [PMID: 32096599 PMCID: PMC7196488 DOI: 10.1002/mgg3.1192] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 11/21/2019] [Accepted: 12/10/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND A pair of dizygotic twins discordantly affected by heavy prenatal alcohol exposure (PAE) was reported previously by Riikonen, suggesting the role of genetic risk or protective factors in the etiology of alcohol-induced developmental disorders. Now, we have re-examined these 25-year-old twins and explored genetic origin of the phenotypic discordancy reminiscent with fetal alcohol syndrome (FAS). Furthermore, we explored alterations in DNA methylation profile of imprinting control region at growth-related insulin-like growth factor 2 (IGF2)/H19 locus in twins' white blood cells (WBC), which have been associated earlier with alcohol-induced genotype-specific changes in placental tissue. METHODS Microarray-based comparative genomic hybridization (aCGH) was used to detect potential submicroscopic chromosomal abnormalities, and developmental as well as phenotypic information about twins were collected. Traditional bisulfite sequencing was used for DNA methylation analysis. RESULTS Microarray-based comparative genomic hybridization revealed a microdeletion 18q12.3-q21.1. in affected twin, residing in a known 18q deletion syndrome region. This syndrome has been associated with growth restriction, developmental delay or intellectual deficiency, and abnormal facial features in previous studies, and thus likely explains the phenotypic discordancy between the twins. We did not observe association between WBCs' DNA methylation profile and PAE, but interestingly, a trend of decreased DNA methylation at the imprinting control region was seen in the twin with prenatal growth retardation at birth. CONCLUSIONS The microdeletion emphasizes the importance of adequate chromosomal testing in examining the etiology of complex alcohol-induced developmental disorders. Furthermore, the genotype-specific decreased DNA methylation at the IGF2/H19 locus cannot be considered as a biological mark for PAE in adult WBCs.
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Affiliation(s)
- Hanna Kahila
- Department of Obstetrics and GynecologyHelsinki University Hospital and University of HelsinkiHelsinkiFinland
| | - Heidi Marjonen
- Department of Medical and Clinical GeneticsMedicumUniversity of HelsinkiHelsinkiFinland
| | - Pauliina Auvinen
- Department of Medical and Clinical GeneticsMedicumUniversity of HelsinkiHelsinkiFinland
| | - Kristiina Avela
- Department of Clinical GeneticsHelsinki University HospitalHUSLABHelsinkiFinland
| | - Raili Riikonen
- Children's HospitalKuopio University HospitalUniversity of Eastern FinlandKuopioFinland
| | - Nina Kaminen‐Ahola
- Department of Medical and Clinical GeneticsMedicumUniversity of HelsinkiHelsinkiFinland
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Imprinted genes in clinical exome sequencing: Review of 538 cases and exploration of mouse-human conservation in the identification of novel human disease loci. Eur J Med Genet 2020; 63:103903. [PMID: 32169557 DOI: 10.1016/j.ejmg.2020.103903] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 01/20/2020] [Accepted: 03/09/2020] [Indexed: 01/01/2023]
Abstract
Human imprinting disorders cause a range of dysmorphic and neurocognitive phenotypes, and they may elude traditional molecular diagnosis such exome sequencing. The discovery of novel disorders related to imprinted genes has lagged behind traditional Mendelian disorders because current diagnostic technology, especially unbiased testing, has limited utility in their discovery. To identify novel imprinting disorders, we reviewed data for every human gene hypothesized to be imprinted, identified each mouse ortholog, determined its imprinting status in the mouse, and analyzed its function in humans and mice. We identified 17 human genes that are imprinted in both humans and mice, and have functional data in mice or humans to suggest that dysregulated expression would lead to an abnormal phenotype in humans. These 17 genes, along with known imprinted genes, were preferentially flagged 538 clinical exome sequencing tests. The identified genes were: DIRAS3 [1p31.3], TP73 [1p36.32], SLC22A3 [6q25.3], GRB10 [7p12.1], DDC [7p12.2], MAGI2 [7q21.11], PEG10 [7q21.3], PPP1R9A [7q21.3], CALCR [7q21.3], DLGAP2 [8p23.3], GLIS3 [9p24.2], INPP5F [10q26.11], ANO1 [11q13.3], SLC38A4 [12q13.11], GATM [15q21.1], PEG3 [19q13.43], and NLRP2 [19q13.42]. In the 538 clinical cases, eight cases (1.7%) reported variants in a causative known imprinted gene. There were 367/758 variants (48.4%) in imprinted genes that were not known to cause disease, but none of those variants met the criteria for clinical reporting. Imprinted disorders play a significant role in human disease, and additional human imprinted disorders remain to be discovered. Therefore, evolutionary conservation is a potential tool to identify novel genes involved in human imprinting disorders and to identify them in clinical testing.
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7
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Jiménez-Romero MS, Barcos-Martínez M, Espejo-Portero I, Benítez-Burraco A. Language Impairment Resulting from a de novo Deletion of 7q32.1q33. Mol Syndromol 2016; 7:292-298. [PMID: 27867345 DOI: 10.1159/000448208] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/20/2016] [Indexed: 12/17/2022] Open
Abstract
We report on a girl who presents with hearing loss, behavioral disturbances (according to the Inventory for Client and Agency Planning) as well as motor and cognitive delay (according to Battelle Developmental Inventories) which have a significant impact on her speech and language abilities [according to the Peabody Picture Vocabulary Test (ed 3), and the Prueba de Lenguaje Oral de Navarra-Revisada (Navarra Oral Language Test, Revised)]. Five copy number variations (CNVs) were identified in the child: arr[hg18] 7q32.1q33(127109685-132492196)×1, 8p23.1(7156900-7359099) ×1, 15q13.1(26215673-26884937)×1, Xp22.33(17245- 102434)×3, and Xp22.33(964441-965024)×3. The pathogenicity of similar CNVs is mostly reported as unknown. The largest deletion is found in a hot spot for cognitive disease and language impairment and contains several genes involved in brain development and function, many of which have been related to developmental disorders encompassing language deficits (dyslexia, speech-sound disorder, and autism). Some of these genes interact with FOXP2. The proband's phenotype may result from a reduced expression of some of these genes.
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Affiliation(s)
- María S Jiménez-Romero
- Department of Psychology, University of Córdoba, Córdoba, Spain; Maimónides Institute of Biomedical Research, University Hospital 'Reina Sofía', Córdoba, Spain
| | - Montserrat Barcos-Martínez
- Maimónides Institute of Biomedical Research, University Hospital 'Reina Sofía', Córdoba, Spain; Laboratory of Molecular Genetics, University Hospital 'Reina Sofía', Córdoba, Spain
| | - Isabel Espejo-Portero
- Maimónides Institute of Biomedical Research, University Hospital 'Reina Sofía', Córdoba, Spain; Laboratory of Molecular Genetics, University Hospital 'Reina Sofía', Córdoba, Spain
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Vincent RN, Gooding LD, Louie K, Chan Wong E, Ma S. Altered DNA methylation and expression of PLAGL1 in cord blood from assisted reproductive technology pregnancies compared with natural conceptions. Fertil Steril 2016; 106:739-748.e3. [PMID: 27178226 DOI: 10.1016/j.fertnstert.2016.04.036] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2016] [Revised: 04/24/2016] [Accepted: 04/25/2016] [Indexed: 11/30/2022]
Abstract
OBJECTIVE To investigate DNA methylation and expression of imprinted genes and an imprinted gene network (IGN) in neonates conceived via assisted reproductive technology (ART). DESIGN Case control. SETTING Research institution. PATIENT(S) Two hundred sixty-four cases of cord blood and/or placental villi from neonates (101 IVF, 81 ICSI, 82 naturally conceived). INTERVENTION(S) Placentas were obtained at birth for biopsy and cord blood extraction. MAIN OUTCOME MEASURE(S) DNA methylation and expression of imprinted genes. RESULT(S) DNA methylation at the PLAGL1 differentially methylated region (DMR) was significantly higher in IVF cord blood (48.0%) compared with controls (46.0%). No differences were found in DNA methylation between conception modes for KvDMR1 and LINE-1 in cord blood and placenta as well as PLAGL1 and PEG10 in placenta villi. PLAGL1 expression was lower in both IVF and ICSI cord blood groups than in controls (relative quantification of 0.65, 0.74, 0.89, respectively). Analyzing the expression of 3 genes in a PLAGL1 regulated IGN revealed different expression between conception modes and a significant correlation to PLAGL1 expression in only one (KCNQ1OT1). CONCLUSION(S) Our results suggest a stability of DNA methylation at imprinted DMRs; however, we show PLAGL1 methylation/expression to be altered after ART. As PLAGL1 expression correlated with only one of the three IGN genes in cord blood, we propose there is a more complex mechanism of regulating the IGN that may involve other genes and epigenetic modifications in this tissue. Further research investigating IGN-implicated genes in various neonatal tissues is warranted to elucidate the full effects ART-induced alterations to PLAGL1 and the IGN may have on fetal growth/development.
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Affiliation(s)
- Rebecca N Vincent
- Department of Obstetrics and Gynaecology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Luke D Gooding
- Department of Obstetrics and Gynaecology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kenny Louie
- Department of Obstetrics and Gynaecology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Edgar Chan Wong
- Department of Obstetrics and Gynaecology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sai Ma
- Department of Obstetrics and Gynaecology, University of British Columbia, Vancouver, British Columbia, Canada.
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Wit JM, Oostdijk W, Losekoot M, van Duyvenvoorde HA, Ruivenkamp CAL, Kant SG. MECHANISMS IN ENDOCRINOLOGY: Novel genetic causes of short stature. Eur J Endocrinol 2016; 174:R145-73. [PMID: 26578640 DOI: 10.1530/eje-15-0937] [Citation(s) in RCA: 111] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 11/16/2015] [Indexed: 12/17/2022]
Abstract
The fast technological development, particularly single nucleotide polymorphism array, array-comparative genomic hybridization, and whole exome sequencing, has led to the discovery of many novel genetic causes of growth failure. In this review we discuss a selection of these, according to a diagnostic classification centred on the epiphyseal growth plate. We successively discuss disorders in hormone signalling, paracrine factors, matrix molecules, intracellular pathways, and fundamental cellular processes, followed by chromosomal aberrations including copy number variants (CNVs) and imprinting disorders associated with short stature. Many novel causes of GH deficiency (GHD) as part of combined pituitary hormone deficiency have been uncovered. The most frequent genetic causes of isolated GHD are GH1 and GHRHR defects, but several novel causes have recently been found, such as GHSR, RNPC3, and IFT172 mutations. Besides well-defined causes of GH insensitivity (GHR, STAT5B, IGFALS, IGF1 defects), disorders of NFκB signalling, STAT3 and IGF2 have recently been discovered. Heterozygous IGF1R defects are a relatively frequent cause of prenatal and postnatal growth retardation. TRHA mutations cause a syndromic form of short stature with elevated T3/T4 ratio. Disorders of signalling of various paracrine factors (FGFs, BMPs, WNTs, PTHrP/IHH, and CNP/NPR2) or genetic defects affecting cartilage extracellular matrix usually cause disproportionate short stature. Heterozygous NPR2 or SHOX defects may be found in ∼3% of short children, and also rasopathies (e.g., Noonan syndrome) can be found in children without clear syndromic appearance. Numerous other syndromes associated with short stature are caused by genetic defects in fundamental cellular processes, chromosomal abnormalities, CNVs, and imprinting disorders.
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Affiliation(s)
- Jan M Wit
- Departments of PaediatricsClinical GeneticsLeiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Wilma Oostdijk
- Departments of PaediatricsClinical GeneticsLeiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Monique Losekoot
- Departments of PaediatricsClinical GeneticsLeiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Hermine A van Duyvenvoorde
- Departments of PaediatricsClinical GeneticsLeiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Claudia A L Ruivenkamp
- Departments of PaediatricsClinical GeneticsLeiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Sarina G Kant
- Departments of PaediatricsClinical GeneticsLeiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands
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Vals MA, Yakoreva M, Kahre T, Mee P, Muru K, Joost K, Teek R, Soellner L, Eggermann T, Õunap K. The Frequency of Methylation Abnormalities Among Estonian Patients Selected by Clinical Diagnostic Scoring Systems for Silver-Russell Syndrome and Beckwith-Wiedemann Syndrome. Genet Test Mol Biomarkers 2015; 19:684-91. [PMID: 26505556 DOI: 10.1089/gtmb.2015.0163] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
AIMS To study the frequency of methylation abnormalities among Estonian patients selected according to published clinical diagnostic scoring systems for Silver-Russell syndrome (SRS) and Beckwith-Wiedemann syndrome (BWS). MATERIALS AND METHODS Forty-eight patients with clinical suspicion of SRS (n = 20) or BWS (n = 28) were included in the study group, to whom methylation-specific multiplex ligation-dependant probe amplification analysis of 11p15 region was made. In addition, to patients with minimal diagnostic score for either SRS or BWS, multilocus methylation-specific single nucleotide primer extension assay was performed. RESULTS Five (38%) SRS patients with positive clinical scoring had abnormal methylation pattern at chromosome 11p15, whereas in the BWS group, only one patient was diagnosed with imprinting control region 2 (ICR2) hypomethylation (8%). An unexpected hypomethylation of the PLAGL1 (6q24) and IGF2R (6q25) genes in the patient with the highest BWS scoring was found. CONCLUSIONS Compared to BWS, diagnostic criteria used for selecting SRS patients gave us a similar detection rate of 11p15 imprinting disorders as seen in other studies. A more careful selection of patients with possible BWS should be considered to improve the detection of molecularly confirmed cases. Genome-wide multilocus methylation tests could be used in routine clinical practice as it increases the detection rates of imprinting disorders.
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Affiliation(s)
- Mari-Anne Vals
- 1 Department of Genetics, United Laboratories, Tartu University Hospital , Tartu, Estonia .,2 Department of Pediatrics, University of Tartu , Tartu, Estonia .,3 Children's Clinic, Tartu University Hospital , Tartu, Estonia
| | - Maria Yakoreva
- 1 Department of Genetics, United Laboratories, Tartu University Hospital , Tartu, Estonia .,2 Department of Pediatrics, University of Tartu , Tartu, Estonia
| | - Tiina Kahre
- 1 Department of Genetics, United Laboratories, Tartu University Hospital , Tartu, Estonia .,2 Department of Pediatrics, University of Tartu , Tartu, Estonia
| | - Pille Mee
- 4 United Laboratories, Tartu University Hospital , Tartu, Estonia
| | - Kai Muru
- 1 Department of Genetics, United Laboratories, Tartu University Hospital , Tartu, Estonia .,2 Department of Pediatrics, University of Tartu , Tartu, Estonia
| | - Kairit Joost
- 1 Department of Genetics, United Laboratories, Tartu University Hospital , Tartu, Estonia
| | - Rita Teek
- 1 Department of Genetics, United Laboratories, Tartu University Hospital , Tartu, Estonia .,2 Department of Pediatrics, University of Tartu , Tartu, Estonia
| | - Lukas Soellner
- 5 Institute of Human Genetics , RWTH Aachen, Aachen, Germany
| | | | - Katrin Õunap
- 1 Department of Genetics, United Laboratories, Tartu University Hospital , Tartu, Estonia .,2 Department of Pediatrics, University of Tartu , Tartu, Estonia
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Arcos-Machancoses JV, Reina PM, Martinez F, Busselo MJ, Perez-Aytes A. Silver-Rusell syndrome caused by epigenetic alteration in a child conceived by intrauterine insemination from donor sperm. Am J Med Genet A 2015; 167A:2861-4. [PMID: 26238787 DOI: 10.1002/ajmg.a.37265] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 07/13/2015] [Indexed: 01/20/2023]
Affiliation(s)
| | | | - Francisco Martinez
- Unidad de Genetica, Hospital Universitari i Politécnic La Fe, Valencia, Spain
| | | | - Antonio Perez-Aytes
- Dismorfologia y Genetica Reproductiva, Grupo de Investigacion en Perinatologia, Instituto de Investigacion Sanitaria Hospital Universitari i Politécnic La Fe, Valencia, Spain
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Angrand PO, Vennin C, Le Bourhis X, Adriaenssens E. The role of long non-coding RNAs in genome formatting and expression. Front Genet 2015; 6:165. [PMID: 25972893 PMCID: PMC4413816 DOI: 10.3389/fgene.2015.00165] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Accepted: 04/12/2015] [Indexed: 12/14/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are transcripts without protein-coding potential but having a pivotal role in numerous biological functions. Long non-coding RNAs act as regulators at different levels of gene expression including chromatin organization, transcriptional regulation, and post-transcriptional control. Misregulation of lncRNAs expression has been found to be associated to cancer and other human disorders. Here, we review the different types of lncRNAs, their mechanisms of action on genome formatting and expression and emphasized on the multifaceted action of the H19 lncRNA.
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Affiliation(s)
| | - Constance Vennin
- Cell Plasticity and Cancer - Inserm U908, University of Lille Lille, France
| | - Xuefen Le Bourhis
- Cell Plasticity and Cancer - Inserm U908, University of Lille Lille, France
| | - Eric Adriaenssens
- Cell Plasticity and Cancer - Inserm U908, University of Lille Lille, France
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13
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Genome-wide methylation analysis in Silver-Russell syndrome patients. Hum Genet 2015; 134:317-332. [PMID: 25563730 DOI: 10.1007/s00439-014-1526-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 12/29/2014] [Indexed: 01/09/2023]
Abstract
Silver-Russell syndrome (SRS) is a clinically heterogeneous disorder characterised by severe in utero growth restriction and poor postnatal growth, body asymmetry, irregular craniofacial features and several additional minor malformations. The aetiology of SRS is complex and current evidence strongly implicates imprinted genes. Approximately, half of all patients exhibit DNA hypomethylation at the H19/IGF2 imprinted domain, and around 10% have maternal uniparental disomy of chromosome 7. We measured DNA methylation in 18 SRS patients at >485,000 CpG sites using DNA methylation microarrays. Using a novel bioinformatics methodology specifically designed to identify subsets of patients with a shared epimutation, we analysed methylation changes genome-wide as well as at known imprinted regions to identify SRS-associated epimutations. Our analysis identifies epimutations at the previously characterised domains of H19/IGF2 and at imprinted regions on chromosome 7, providing proof of principle that our methodology can detect DNA methylation changes at imprinted loci. In addition, we discovered two novel epimutations associated with SRS and located at imprinted loci previously linked to relevant mouse and human phenotypes. We identify RB1 as an additional imprinted locus associated with SRS, with a region near the RB1 differentially methylated region hypermethylated in 13/18 (~70%) patients. We also report 6/18 (~33%) patients were hypermethylated at a CpG island near the ANKRD11 gene. We do not observe consistent co-occurrence of epimutations at multiple imprinted loci in single SRS individuals. SRS is clinically heterogeneous and the absence of multiple imprinted loci epimutations reflects the heterogeneity at the molecular level. Further stratification of SRS patients by molecular phenotypes might aid the identification of disease causes.
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Filges I, Manokhina I, Peñaherrera MS, McFadden DE, Louie K, Nosova E, Friedman JM, Robinson WP. Recurrent triploidy due to a failure to complete maternal meiosis II: whole-exome sequencing reveals candidate variants. Mol Hum Reprod 2014; 21:339-46. [PMID: 25504873 DOI: 10.1093/molehr/gau112] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 12/05/2014] [Indexed: 01/16/2023] Open
Abstract
Triploidy is a relatively common cause of miscarriage; however, recurrent triploidy has rarely been reported. A healthy 34-year-old woman was ascertained because of 18 consecutive miscarriages with triploidy found in all 5 karyotyped losses. Molecular results in a sixth loss were also consistent with triploidy. Genotyping of markers near the centromere on multiple chromosomes suggested that all six triploid conceptuses occurred as a result of failure to complete meiosis II (MII). The proband's mother had also experienced recurrent miscarriage, with a total of 18 miscarriages. Based on the hypothesis that an inherited autosomal-dominant maternal predisposition would explain the phenotype, whole-exome sequencing of the proband and her parents was undertaken to identify potential candidate variants. After filtering for quality and rarity, potentially damaging variants shared between the proband and her mother were identified in 47 genes. Variants in genes coding for proteins implicated in oocyte maturation, oocyte activation or polar body extrusion were then prioritized. Eight of the most promising candidate variants were confirmed by Sanger sequencing. These included a novel change in the PLCD4 gene, and a rare variant in the OSBPL5 gene, which have been implicated in oocyte activation upon fertilization and completion of MII. Several variants in genes coding proteins playing a role in oocyte maturation and early embryonic development were also identified. The genes identified may be candidates for the study in other women experiencing recurrent triploidy or recurrent IVF failure.
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Affiliation(s)
- I Filges
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada V6T 1Z3 Child and Family Research Institute, Vancouver, BC, Canada V5Z 4H4 Medical Genetics, Department of Biomedicine, University Hospital Basel, Basel 4031, Switzerland
| | - I Manokhina
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada V6T 1Z3 Child and Family Research Institute, Vancouver, BC, Canada V5Z 4H4
| | - M S Peñaherrera
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada V6T 1Z3 Child and Family Research Institute, Vancouver, BC, Canada V5Z 4H4
| | - D E McFadden
- Child and Family Research Institute, Vancouver, BC, Canada V5Z 4H4 Department of Pathology, University of British Columbia, Vancouver, BC, Canada V6T 2B5
| | - K Louie
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada V6T 1Z3 Child and Family Research Institute, Vancouver, BC, Canada V5Z 4H4
| | - E Nosova
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC, Canada V5Z 4H4 Centre for Applied Neurogenetics, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
| | - J M Friedman
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada V6T 1Z3 Child and Family Research Institute, Vancouver, BC, Canada V5Z 4H4
| | - W P Robinson
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada V6T 1Z3 Child and Family Research Institute, Vancouver, BC, Canada V5Z 4H4
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Huang Y, Zhang P, Zheng S, Dong R. Hypermethylation of SHH in the pathogenesis of congenital anorectal malformations. J Pediatr Surg 2014; 49:1400-4. [PMID: 25148746 DOI: 10.1016/j.jpedsurg.2014.03.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 02/15/2014] [Accepted: 03/11/2014] [Indexed: 01/11/2023]
Abstract
OBJECTIVE This study sought to examine promoter methylation and expression of the identified sonic hedgehog (SHH) gene in terminal rectal tissues of children with congenital anorectal malformations (ARMs). METHODS Tissue samples from the terminal rectum of pediatric patients with ARMs (five cases each of high and intermediate malformation - two cases of rectovesical fistula, two cases of rectourethral prostatic fistula, one case of cloaca with >3cm common channel, four cases of rectourethral bulbar fistula and one case of imperforate anus without fistula, respectively, and ten cases of low malformation - five cases of perineal fistula and five cases of vestibular fistula, respectively), and patients with non-gastrointestinal tract malformation (six cases, anal fistula) were collected and divided into three groups: high-intermediate ARM (ARMhi-int), low ARM (ARMlo), and control (Cont.). Real-time RT-PCR was used to detect mRNA expression levels of the verified differentially methylated gene SHH, and bisulfite genomic sequencing was performed to evaluate DNA methylation in the SHH promoter region. RESULTS The average methylation levels of the SHH promoter were significantly higher in ARMhi-int (0.850±0.030, P=0.0036) and ARMlo (0.540±0.053, P=0.0087) groups than in Cont. group (0.280±0.032). SHH mRNA expression levels were lower in ARMhi-int (0.340±0.015, P=0.0065) and ARMlo (0.530±0.042, P=0.0156) groups than in Cont. group (0.870±0.046). The average methylation levels of the SHH promoter were higher in ARMhi-int group than in ARMlo group (0.850±0.030 vs. 0.540±0.053, P=0.0095), while SHH expression was significantly reduced in ARMhi-int group compared to ARMlo group (0.340±0.15 vs. 0.530±0.042, P=0.0252). The methylation levels of the SHH promoter in ARMhi-int group were negatively correlated with SHH gene expression (r=-0.89, P<0.01). CONCLUSIONS The SHH gene, which plays a major role in the development of the anorectum and enteric nervous system, is hypermethylated at its promoter, and this is correlated with low levels of SHH gene expression. This epigenetic modification may therefore be responsible for the observed changes in SHH expression, which could in turn underlie the pathogenesis of congenital ARMs.
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Affiliation(s)
- Yanlei Huang
- Department of Pediatric Surgery, Children's Hospital of Fudan University, Shanghai 201102, P.R. China.
| | - Pei Zhang
- Department of Pediatric Surgery, Children's Hospital of Fudan University, Shanghai 201102, P.R. China
| | - Shan Zheng
- Department of Pediatric Surgery, Children's Hospital of Fudan University, Shanghai 201102, P.R. China.
| | - Rui Dong
- Department of Pediatric Surgery, Children's Hospital of Fudan University, Shanghai 201102, P.R. China
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Abstract
Genome‐wide SNP analyses have identified genomic variants associated with adult human height. However, these only explain a fraction of human height variation, suggesting that significant information might have been systematically missed by SNP sequencing analysis. A candidate for such non‐SNP‐linked information is DNA methylation. Regulation by DNA methylation requires the presence of CpG islands in the promoter region of candidate genes. Seventy two of 87 (82.8%), height‐associated genes were indeed found to contain CpG islands upstream of the transcription start site (USC CpG island searcher; validation: UCSC Genome Browser), which were shown to correlate with gene regulation. Consistent with this, DNA hypermethylation modules were detected in 42 height‐associated genes, versus 1.5% of control genes (P = 8.0199e−17), as were dynamic methylation changes and gene imprinting. Epigenetic heredity thus appears to be a determinant of adult human height. Major findings in mouse models and in human genetic diseases support this model. Modulation of DNA methylation are candidate to mediate environmental influence on epigenetic traits. This may help to explain progressive height changes over multiple generations, through trans‐generational heredity of progressive DNA methylation patterns. Epigenetic heredity appears to be a determinant of adult human height. Major findings in mouse models and in human genetic diseases support this model. Modulation of DNA methylation is candidate to mediate environmental influence on epigenetic traits.
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Affiliation(s)
- Pasquale Simeone
- Unit of Cancer Pathology, Department of Neuroscience and Imaging and CeSI, University "G. d'Annunzio" Foundation, Chieti Scalo, Italy
| | - Saverio Alberti
- Unit of Cancer Pathology, Department of Neuroscience and Imaging and CeSI, University "G. d'Annunzio" Foundation, Chieti Scalo, Italy
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17
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Brown LA, Rupps R, Peñaherrera MS, Robinson WP, Patel MS, Eydoux P, Boerkoel CF. A cryptic familial rearrangement of 11p15.5, involving both imprinting centers, in a family with a history of short stature. Am J Med Genet A 2014; 164A:1587-94. [DOI: 10.1002/ajmg.a.36490] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 01/14/2014] [Indexed: 01/08/2023]
Affiliation(s)
- Lindsay A. Brown
- Department of Pathology and Laboratory Medicine; University of British Columbia; Vancouver Canada
| | - Rosemarie Rupps
- Department of Medical Genetics; University of British Columbia; Vancouver Canada
| | - Maria S. Peñaherrera
- Department of Medical Genetics; University of British Columbia; Vancouver Canada
- Child & Family Research Institute; Vancouver Canada
| | - Wendy P. Robinson
- Department of Medical Genetics; University of British Columbia; Vancouver Canada
- Child & Family Research Institute; Vancouver Canada
| | - Millan S. Patel
- Department of Medical Genetics; University of British Columbia; Vancouver Canada
| | - Patrice Eydoux
- Department of Pathology and Laboratory Medicine; University of British Columbia; Vancouver Canada
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Skaar DA, Li Y, Bernal AJ, Hoyo C, Murphy SK, Jirtle RL. The human imprintome: regulatory mechanisms, methods of ascertainment, and roles in disease susceptibility. ILAR J 2014; 53:341-58. [PMID: 23744971 DOI: 10.1093/ilar.53.3-4.341] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Imprinted genes form a special subset of the genome, exhibiting monoallelic expression in a parent-of-origin-dependent fashion. This monoallelic expression is controlled by parental-specific epigenetic marks, which are established in gametogenesis and early embryonic development and are persistent in all somatic cells throughout life. We define this specific set of cis-acting epigenetic regulatory elements as the imprintome, a distinct and specially tasked subset of the epigenome. Imprintome elements contain DNA methylation and histone modifications that regulate monoallelic expression by affecting promoter accessibility, chromatin structure, and chromatin configuration. Understanding their regulation is critical because a significant proportion of human imprinted genes are implicated in complex diseases. Significant species variation in the repertoire of imprinted genes and their epigenetic regulation, however, will not allow model organisms solely to be used for this crucial purpose. Ultimately, only the human will suffice to accurately define the human imprintome.
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Affiliation(s)
- David A Skaar
- Department of Oncology, Duke University Medical Center, Durham, North Carolina, USA
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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.
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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
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20
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Lee BH, Kim GH, Oh TJ, Kim JH, Lee JJ, Choi SH, Lee JY, Kim JM, Choi IH, Kim YM, Choi JH, Yoo HW. Quantitative analysis of methylation status at 11p15 and 7q21 for the genetic diagnosis of Beckwith-Wiedemann syndrome and Silver-Russell syndrome. J Hum Genet 2013; 58:604-10. [PMID: 23803580 DOI: 10.1038/jhg.2013.67] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Revised: 04/19/2013] [Accepted: 05/06/2013] [Indexed: 01/09/2023]
Abstract
Methylation-specific (MS) multiplex ligation-dependent probe amplification (MLPA) at two differentially methylated regions (DMRs) at chromosome 11p15, H19-DMR and LIT1-DMR, and microsatellite analysis for uniparental disomy (UPD) at chromosome 7 or 11, have been recommended for the genetic diagnosis of the Beckwith-Wiedemann syndrome (BWS) and the Silver-Russell syndrome (SRS). In this study, the efficacy of the MS pyrosequencing method at H19-DMR and LIT1-DMR at 11p15 and SGCE-DMR at 7q21 was evaluated for the genetic diagnosis of BWS (n=18) and SRS (n=20) patients. Epigenetic alterations or UPD were detected in 83% of BWS and 50% of SRS individuals by MS-MLPA, but the detection rate increased to 95% of BWS and 70% of SRS by MS pyrosequencing. Thirteen BWS patients (72%) harbored loss-of-methylation (LOM) at LIT1-DMR and two patients (11%) harbored gain-of-methylation (GOM) at H19-DMR, whereas two patients (11%) had both LOM at LIT1-DMR and GOM at H19-DMR, reflecting paternal UPD 11. Thirteen SRS patients (65%) harbored LOM at H19-DMR, whereas one patient (5%) had GOM at SGCE-DMR, reflecting maternal UPD 7. Birth anthropometric profiles were significantly correlated to methylation scores at either H19-DMR or LIT1-DMR. In conclusion, MS pyrosequencing enhanced the detection rate of molecular defects in BWS and SRS. Moreover, it indicates that methylation status at 11p15.5 might have an important role in fetal growth.
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Affiliation(s)
- Beom Hee Lee
- 1] Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul, Korea [2] Genome Research Center for Birth Defects and Genetic Disorders, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul, Korea [3] Medical Genetics Center, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul, Korea
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Hanna CW, McFadden DE, Robinson WP. DNA methylation profiling of placental villi from karyotypically normal miscarriage and recurrent miscarriage. THE AMERICAN JOURNAL OF PATHOLOGY 2013; 182:2276-84. [PMID: 23583422 DOI: 10.1016/j.ajpath.2013.02.021] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Revised: 01/31/2013] [Accepted: 02/12/2013] [Indexed: 12/20/2022]
Abstract
Miscarriage occurs in 15% of clinical pregnancies. Although chromosomal errors are observed in >50%, causes of karyotypically normal losses are poorly understood. DNA methylation undergoes reprogramming during development and must be appropriately set to maintain a healthy pregnancy. We hypothesize that aberrant DNA methylation may cause karyotypically normal miscarriage, particularly among women experiencing recurrent miscarriage (RM). DNA methylation in first-trimester chorionic villi was assessed in chromosomally normal miscarriages from women with RM (N = 33) or isolated miscarriage (M; N = 21) and elective terminations (TA; N = 16). Differentially methylated candidate loci were identified using the Illumina Infinium HumanMethylation27 BeadChip array. Follow-up bisulfite pyrosequencing at promoter regions showed an increase in methylation in M compared with TA at cytochrome P450, subfamily 1A, polypeptide 2 (CYP1A2; P = 0.002) and RM compared with TA at AXL receptor tyrosine kinase (P = 0.02), and a decrease in RM and M compared with TA at defensin β 1 (DEFB1; P = 0.008). Gene ontology analysis showed an enrichment of imprinted genes (P = 9.53 × 10(-10)) and genes previously associated with RM (P = 9.51 × 10(-6)). An increase of outliers at seven imprinted loci was observed in RM (3.9%) compared with M (0%) and TA (0.9%) (P = 0.02), with increased average methylation at H19/IGF2 ICR1 in M samples (P < 0.0001). Altered DNA methylation in the placenta at specific loci, and global dysregulation in specific cases, may contribute to or be a consequence of poor placental function in karyotypically normal miscarriage.
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Affiliation(s)
- Courtney W Hanna
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
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22
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Niederhoffer KY, Peñaherrera M, Pugash D, Rupps R, Arbour L, Tessier F, Choufani S, Zhao C, Manokhina I, Shuman C, Robinson WP, Weksberg R, Boerkoel CF. Beckwith-Wiedemann syndrome in sibs discordant for IC2 methylation. Am J Med Genet A 2012; 158A:1662-9. [PMID: 22615066 DOI: 10.1002/ajmg.a.35377] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2011] [Accepted: 02/19/2012] [Indexed: 11/10/2022]
Abstract
Genetically heterogeneous imprinting disorders include Beckwith-Wiedemann syndrome (BWS) and multiple maternal hypomethylation syndrome (MMHS). Using DNA sequencing, quantitative PCR, SNuPE, pyrosequencing, and hybridization to the Illumina GoldenGate Methylation Cancer Panel 1 array, we characterized the genomic DNA of two brothers with BWS who were discordant for loss of methylation at several differentially methylated regions (DMR), including imprinting center 2 (IC2) on chromosome band 11p15.5, which is often hypomethylated in BWS. In keeping with MMHS, the elder child had hypomethylation of SGCE and PLAGL1 as well as of IC2, whereas the younger brother demonstrated no loss of methylation at these DMRs. Although this discordance is consistent with the observation that 15-20% of individuals with BWS do not have detectable genetic or epigenetic alterations of 11p15.5, this is the first report of familial recurrence of BWS with discordance for chromosomal 11p15.5 alterations. We hypothesize that this apparent discordance arises either from mosaicism precluding identification of IC2 hypomethylation in blood or buccal mucosa DNA of the younger child, or from hypomethylation at a site not interrogated by our molecular studies.
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Affiliation(s)
- Karen Y Niederhoffer
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
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23
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Saenger P, Reiter E. Genetic factors associated with small for gestational age birth and the use of human growth hormone in treating the disorder. INTERNATIONAL JOURNAL OF PEDIATRIC ENDOCRINOLOGY 2012; 2012:12. [PMID: 22587301 PMCID: PMC3511163 DOI: 10.1186/1687-9856-2012-12] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2011] [Accepted: 03/19/2012] [Indexed: 12/31/2022]
Abstract
The term small for gestational age (SGA) refers to infants whose birth weights and/or lengths are at least two standard deviation (SD) units less than the mean for gestational age. This condition affects approximately 3%–10% of newborns. Causes for SGA birth include environmental factors, placental factors such as abnormal uteroplacental blood flow, and inherited genetic mutations. In the past two decades, an enhanced understanding of genetics has identified several potential causes for SGA. These include mutations that affect the growth hormone (GH)/insulin-like growth factor (IGF)-1 axis, including mutations in the IGF-1 gene and acid-labile subunit (ALS) deficiency. In addition, select polymorphisms observed in patients with SGA include those involved in genes associated with obesity, type 2 diabetes, hypertension, ischemic heart disease and deletion of exon 3 growth hormone receptor (d3-GHR) polymorphism. Uniparental disomy (UPD) and imprinting effects may also underlie some of the phenotypes observed in SGA individuals. The variety of genetic mutations associated with SGA births helps explain the diversity of phenotype characteristics, such as impaired motor or mental development, present in individuals with this disorder. Predicting the effectiveness of recombinant human GH (hGH) therapy for each type of mutation remains challenging. Factors affecting response to hGH therapy include the dose and method of hGH administration as well as the age of initiation of hGH therapy. This article reviews the results of these studies and summarizes the success of hGH therapy in treating this difficult and genetically heterogenous disorder.
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Affiliation(s)
- Paul Saenger
- Albert Einstein College of Medicine, Winthrop University Hospital, 120 Mineola Boulevard, Mineola, NY, 13501, USA.
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24
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Kannenberg K, Urban C, Binder G. Increased incidence of aberrant DNA methylation within diverse imprinted gene loci outside of IGF2/H19 in Silver-Russell syndrome. Clin Genet 2012; 81:366-77. [DOI: 10.1111/j.1399-0004.2012.01844.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Abstract
Normally, one inherits one chromosome of each pair from one parent and the second chromosome from the other parent. Uniparental disomy (UPD) describes the inheritance of both homologues of a chromosome pair from the same parent. The biological basis of UPD syndromes is disturbed genomic imprinting. The consequences of UPD depend on the specific chromosome/segment involved and its parental origin. Phenotypes range from unapparent to unmasking of an autosomal-recessive disease to presentation as a syndromic imprinting disorder. Whilst paternal UPD(7) is clinically unapparent, maternal UPD(7) is one of several causes of Silver-Russell syndrome. Presentation of paternal UPD(14) ("Kagami syndrome") is a thoracic dysplasia syndrome with mental retardation and limited survival. Findings in maternal UPD(14) ("Temple") syndrome show an age-dependent overlap with the well-known maternal UPD(15) (Prader-Willi) syndrome and are dominated by initial failure to thrive followed by obesity, learning difficulties and precocious puberty. Diagnostic strategies to tackle the genetic heterogeneity of UPD(7) and UPD(14) syndromes will be explained. Management issues in UPD(7) and UPD(14) patients will be discussed, and finally areas requiring further research will be outlined.
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Affiliation(s)
- Katrin Hoffmann
- Institute of Medical Genetics, Campus Virchow-Klinikum, Charité, Augustenburger Platz 1, Berlin, Germany.
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26
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Wilkins JF, Úbeda F. Diseases associated with genomic imprinting. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2011; 101:401-45. [PMID: 21507360 DOI: 10.1016/b978-0-12-387685-0.00013-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Genomic imprinting is the phenomenon where the expression of a locus differs between the maternally and paternally inherited alleles. Typically, this manifests as transcriptional silencing of one of the alleles, although many genes are imprinted in a tissue- or isoform-specific manner. Diseases associated with imprinted genes include various cancers, disorders of growth and metabolism, and disorders in neurodevelopment, cognition, and behavior, including certain major psychiatric disorders. In many cases, the disease phenotypes associated with dysfunction at particular imprinted loci can be understood in terms of the evolutionary processes responsible for the origin of imprinting. Imprinted gene expression represents the outcome of an intragenomic evolutionary conflict, where natural selection favors different expression strategies for maternally and paternally inherited alleles. This conflict is reasonably well understood in the context of the early growth effects of imprinted genes, where paternally inherited alleles are selected to place a greater demand on maternal resources than are maternally inherited alleles. Less well understood are the origins of imprinted gene expression in the brain, and their effects on cognition and behavior. This chapter reviews the genetic diseases that are associated with imprinted genes, framed in terms of the evolutionary pressures acting on gene expression at those loci. We begin by reviewing the phenomenon and evolutionary origins of genomic imprinting. We then discuss diseases that are associated with genetic or epigenetic defects at particular imprinted loci, many of which are associated with abnormalities in growth and/or feeding behaviors that can be understood in terms of the asymmetric pressures of natural selection on maternally and paternally inherited alleles. We next described the evidence for imprinted gene effects on adult cognition and behavior, and the possible role of imprinted genes in the etiology of certain major psychiatric disorders. Finally, we conclude with a discussion of how imprinting, and the evolutionary-genetic conflicts that underlie it, may enhance both the frequency and morbidity of certain types of diseases.
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