1
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Cevik SE, Skaar DA, Jima DD, Liu AJ, Østbye T, Whitson HE, Jirtle RL, Hoyo C, Planchart A. DNA methylation of imprint control regions associated with Alzheimer's disease in non-Hispanic Blacks and non-Hispanic Whites. Clin Epigenetics 2024; 16:58. [PMID: 38658973 PMCID: PMC11043040 DOI: 10.1186/s13148-024-01672-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 04/13/2024] [Indexed: 04/26/2024] Open
Abstract
Alzheimer's disease (AD) prevalence is twice as high in non-Hispanic Blacks (NHBs) as in non-Hispanic Whites (NHWs). The objective of this study was to determine whether aberrant methylation at imprint control regions (ICRs) is associated with AD. Differentially methylated regions (DMRs) were bioinformatically identified from whole-genome bisulfite sequenced DNA derived from brain tissue of 9 AD (5 NHBs and 4 NHWs) and 8 controls (4 NHBs and 4 NHWs). We identified DMRs located within 120 regions defined as candidate ICRs in the human imprintome ( https://genome.ucsc.edu/s/imprintome/hg38.AD.Brain_track ). Eighty-one ICRs were differentially methylated in NHB-AD, and 27 ICRs were differentially methylated in NHW-AD, with two regions common to both populations that are proximal to the inflammasome gene, NLRP1, and a known imprinted gene, MEST/MESTIT1. These findings indicate that early developmental alterations in DNA methylation of regions regulating genomic imprinting may contribute to AD risk and that this epigenetic risk differs between NHBs and NHWs.
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Affiliation(s)
- Sebnem E Cevik
- Toxicology Program, North Carolina State University, Raleigh, NC, USA
| | - David A Skaar
- Toxicology Program, North Carolina State University, Raleigh, NC, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Dereje D Jima
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Andy J Liu
- Department of Neurology, School of Medicine, Duke University, Durham, NC, USA
| | - Truls Østbye
- Department of Family Medicine and Community Health, Duke University, Durham, NC, USA
| | - Heather E Whitson
- Department of Medicine, School of Medicine, Duke University, Durham, NC, USA
- Duke Center for the Study of Aging and Human Development, Durham, NC, USA
- Duke/UNC Alzheimer's Disease Research Center (ADRC), Durham, NC, USA
| | - Randy L Jirtle
- Toxicology Program, North Carolina State University, Raleigh, NC, USA.
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA.
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.
| | - Cathrine Hoyo
- Toxicology Program, North Carolina State University, Raleigh, NC, USA.
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA.
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.
| | - Antonio Planchart
- Toxicology Program, North Carolina State University, Raleigh, NC, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
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2
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Ishihara T, Suzuki S, Newman TA, Fenelon JC, Griffith OW, Shaw G, Renfree MB. Marsupials have monoallelic MEST expression with a conserved antisense lncRNA but MEST is not imprinted. Heredity (Edinb) 2024; 132:5-17. [PMID: 37952041 PMCID: PMC10798977 DOI: 10.1038/s41437-023-00656-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 10/16/2023] [Accepted: 10/17/2023] [Indexed: 11/14/2023] Open
Abstract
The imprinted isoform of the Mest gene in mice is involved in key mammalian traits such as placental and fetal growth, maternal care and mammary gland maturation. The imprinted isoform has a distinct differentially methylated region (DMR) at its promoter in eutherian mammals but in marsupials, there are no differentially methylated CpG islands between the parental alleles. Here, we examined similarities and differences in the MEST gene locus across mammals using a marsupial, the tammar wallaby, a monotreme, the platypus, and a eutherian, the mouse, to investigate how imprinting of this gene evolved in mammals. By confirming the presence of the short isoform in all mammalian groups (which is imprinted in eutherians), this study suggests that an alternative promoter for the short isoform evolved at the MEST gene locus in the common ancestor of mammals. In the tammar, the short isoform of MEST shared the putative promoter CpG island with an antisense lncRNA previously identified in humans and an isoform of a neighbouring gene CEP41. The antisense lncRNA was expressed in tammar sperm, as seen in humans. This suggested that the conserved lncRNA might be important in the establishment of MEST imprinting in therian mammals, but it was not imprinted in the tammar. In contrast to previous studies, this study shows that MEST is not imprinted in marsupials. MEST imprinting in eutherians, therefore must have occurred after the marsupial-eutherian split with the acquisition of a key epigenetic imprinting control region, the differentially methylated CpG islands between the parental alleles.
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Affiliation(s)
- Teruhito Ishihara
- School of BioSciences, The University of Melbourne, Melbourne, VIC, 3010, Australia
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - Shunsuke Suzuki
- Department of Agricultural and Life Sciences, Shinshu University, Nagano, Japan
| | - Trent A Newman
- School of BioSciences, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Jane C Fenelon
- School of BioSciences, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Oliver W Griffith
- Department of Biological Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Geoff Shaw
- School of BioSciences, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Marilyn B Renfree
- School of BioSciences, The University of Melbourne, Melbourne, VIC, 3010, Australia.
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3
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Narusawa H, Sasaki S, Hara-Isono K, Matsubara K, Fukami M, Nagasaki K, Kagami M. A boy with overgrowth caused by multi-locus imprinting disturbance including hypomethylation of MEST:alt-TSS-DMR. Eur J Med Genet 2022; 65:104502. [DOI: 10.1016/j.ejmg.2022.104502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/07/2022] [Accepted: 04/09/2022] [Indexed: 11/03/2022]
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4
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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.
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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
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Kaur P, Chaudhry C, Kaur A, Panigrahi I, Srivastava P. Case Studies of Two Classical Imprinting Growth Disorders: Silver–Russell and Beckwith–Wiedemann Syndromes. J Pediatr Genet 2021. [DOI: 10.1055/s-0041-1739388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
AbstractThe genetic influences on human growth are being increasingly deciphered. Silver–Russell and Beckwith–Wiedemann syndromes (SRS; BWS) are two relatively common genetic syndromes with under- and overgrowth-related issues being the reason for referral. Aberration in genomic imprinting is the underlying genetic pathomechanism behind these syndromes. Herein, we described a series of children with these two growth disorders and give an orientation to the reader of the concept of imprinting as well as the genetic testing strategy and counseling to be offered in these syndromes.
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Affiliation(s)
- Parminder Kaur
- Department of Pediatrics, Genetic and Metabolic Unit, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Chakshu Chaudhry
- Department of Pediatrics, Genetic and Metabolic Unit, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Anupriya Kaur
- Department of Pediatrics, Genetic and Metabolic Unit, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Inusha Panigrahi
- Department of Pediatrics, Genetic and Metabolic Unit, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Priyanka Srivastava
- Department of Pediatrics, Genetic and Metabolic Unit, Postgraduate Institute of Medical Education and Research, Chandigarh, India
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Ye M, Yang ZY, Zhang Y, Xing YX, Xie QG, Zhou JH, Wang L, Xie W, Kee K, Chian RC. Single-cell multiomic analysis of in vivo and in vitro matured human oocytes. Hum Reprod 2021; 35:886-900. [PMID: 32325493 DOI: 10.1093/humrep/deaa044] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 02/03/2020] [Indexed: 12/11/2022] Open
Abstract
STUDY QUESTION Are there any differences between in vivo (IVV) and in vitro (IVT) matured metaphase II (MII) oocytes at the molecular level? SUMMARY ANSWER Between IVV and IVT oocytes, 507 differentially expressed genes (DEGs) were identified; the non-CpG methylomes were significantly different, but the CpG methylomes and genomic copy number variations (CNVs) were similar. WHAT IS KNOWN ALREADY A previous study using microarray and single-cell RNA-seq analysis revealed that numerous genes were differentially expressed between IVV and IVT oocytes. Independent studies of DNA methylation profiling in human oocytes have revealed negative correlations between gene transcription and the DNA methylation level at gene promoter regions. No study has compared global CpG or non-CpG methylation between these two groups of oocytes. Although a high level of aneuploidy has been reported in MII oocytes, no direct comparison of IVV and IVT oocytes based on single-cell sequencing data has been performed. STUDY DESIGN, SIZE, DURATION We collected eight IVV oocytes from six patients and seven IVT oocytes from seven patients and then analysed each oocyte using the previously established single-cell triple omics sequencing (scTrioseq) analysis to determine associations among the transcriptome, DNA methylome and chromosome ploidy in the oocytes. PARTICIPANTS/MATERIALS, SETTING, METHODS All IVV oocytes were donated by patients who received 150 IU gonadotropin per day from the third day of their menstrual cycle, followed by GnRH antagonist after 5 days of gonadotropin stimulation. All IVT oocytes were from immature oocytes which were donated by volunteers undergoing delivery by caesarean section then cultured in oocyte maturation medium containing 75 mIU/ml hMG for 24 to 48 h. Every single oocyte was analysed using the previously established single-cell multiomic sequencing analysis. MAIN RESULTS AND THE ROLE OF CHANCE There were 507 genes differentially expressed between the IVV (n = 8) and IVT (n = 7) oocytes, even though their global transcriptome profiles were similar. The enriched genes in IVV oocytes were related to the cell cycle process while those in IVT oocytes were related to mitochondrial respiration biogenesis. Although the global CpG methylation of the two groups of oocytes was similar, the non-CpG methylation level in IVV oocytes was higher than that in IVT oocytes. A high aneuploidy ratio was found in both groups, but the aneuploidy did not affect transcription according to the correlation analysis. LARGE-SCALE DATA N/A. LIMITATIONS AND REASONS FOR CAUTION Due to the difficulty in collecting MII oocytes, especially IVV matured oocytes, the sample size was limited. WIDER IMPLICATIONS OF THE FINDINGS Our findings indicate that single-cell multiomic sequencing can be utilised to examine the similarity and differences between IVV and IVT matured MII oocytes. STUDY FUNDING/COMPETING INTEREST(S) This work was supported by the Ministry of Science and Technology of China, National Key R&D Program of China (No. 2017YFC1001601). The donated oocytes were collected by Shanghai Tenth People's Hospital. The authors declare no competing interests.
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Affiliation(s)
- Min Ye
- Center for Stem Cell Biology and Regenerative Medicine, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, 100084, P. R. of China
| | - Zhi-Yong Yang
- Center for Reproductive Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, 200072, P. R. of China.,Tongji University School of Medicine, Shanghai, 200092, P. R. of China
| | - Yu Zhang
- Center for Stem Cell Biology and Regenerative Medicine, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, 100084, P. R. of China.,MOE Key Laboratory of Bioinformatics, School of Life Sciences, THU-PKU Center for Life Science, Tsinghua University, Beijing 100084, China
| | - Ya-Xin Xing
- Center for Reproductive Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, 200072, P. R. of China
| | - Qi-Gui Xie
- Center for Reproductive Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, 200072, P. R. of China
| | - Jian-Hong Zhou
- Center for Reproductive Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, 200072, P. R. of China
| | - Ling Wang
- Center for Reproductive Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, 200072, P. R. of China
| | - Wei Xie
- Center for Stem Cell Biology and Regenerative Medicine, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, 100084, P. R. of China.,MOE Key Laboratory of Bioinformatics, School of Life Sciences, THU-PKU Center for Life Science, Tsinghua University, Beijing 100084, China
| | - KehKooi Kee
- Center for Stem Cell Biology and Regenerative Medicine, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, 100084, P. R. of China
| | - Ri-Cheng Chian
- Center for Reproductive Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, 200072, P. R. of China
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7
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Chalas C, Receveur A, Frydman N, Massin N, Tachdjian G, Drouineaud V, Benachi A, Patrat C, Petit FM. A case of germline mosaicism for a 7q32.1q33 deletion in a sperm donor: consequences on pregnancy follow-up and recommendations. Basic Clin Androl 2020; 30:14. [PMID: 33024563 PMCID: PMC7532087 DOI: 10.1186/s12610-020-00113-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 08/24/2020] [Indexed: 01/23/2023] Open
Abstract
Background Germline mosaicism is considered to be a rare event. However, its occurrence is underestimated due to the limited availability of germ cells. The genomic variations that underlie this phenomenon comprise single nucleotide polymorphism (SNPs), copy number variations (CNVs) and aneuploidies. In the case of CNVs, deletions are more frequent in the paternal germline while duplications are more commonly maternal in origin. Germline mosaicism increases with paternal age as the risk of SNPs increase with the number of germ cell divisions. We here report a case of germline mosaicism in the spermatozoa of a donor that resulted in one pathological pregnancy. Results Straws from the same sperm donor were provided to seven recipient couples, resulting in four pregnancies. Second trimester ultrasound analysis revealed bilateral talipes equinovarus associated with growth retardation in one of these pregnancies. Array-comparative genomic hybridization (CGH) carried out after amniocentesis revealed a 4 Mb deletion in the 7q32.1q33 region. The blood karyotypes and array-CGHs were normal in the mother, as well as in the donor. However, the microsatellite profile indicated a paternal origin. Fluorescent in situ hybridization (FISH) analysis of the donor’s spermatozoa revealed the same chromosomal rearrangements in 12% of the spermatozoa population. Due to the documented risk of mental retardation associated with genomic rearrangements in the same region, the couple decided to terminate the pregnancy. Amniocentesis was performed in the other couples, which yielded normal FISH analysis results. Conclusions Several cases of germline mosaicism have been reported to date, but their frequency is probably underestimated. Moreover, it is important to note that germline mosaicism cannot be ruled out by conventional cytogenetic screening of blood cells. This case highlights the need for close follow-up of every pregnancy obtained through gamete donation, given that the occurrence of germline mosaicism may have major consequences when multiple pregnancies are obtained concomitantly.
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Affiliation(s)
- Celine Chalas
- Laboratoire d'Histologie-Embryologie-Biologie de la Reproduction - CECOS, Hôpital Cochin, AP-HP, Centre Université de Paris, F-75014 Paris, France
| | - Aline Receveur
- Laboratoire de cytogénomique, Hôpital Antoine Béclère, AP-HP, Université Paris Saclay, cedex, F-92141 Clamart, France
| | - Nelly Frydman
- Laboratoire d'Histologie-Embryologie-Cytogenetique- CECOS, Hôpital Antoine Béclère, AP-HP, Université Paris Saclay, cedex, F-92141 Clamart, France.,Faculté de médecine de Bicêtre, Université Paris-Saclay, F-94270 Le Kremlin Bicêtre, France
| | - Nathalie Massin
- Service de gynécologie et obstétrique, Centre Hospitalier Intercommunal, F-94010 Créteil, France
| | - Gerard Tachdjian
- Laboratoire de cytogénomique, Hôpital Antoine Béclère, AP-HP, Université Paris Saclay, cedex, F-92141 Clamart, France.,Laboratoire d'Histologie-Embryologie-Cytogenetique- CECOS, Hôpital Antoine Béclère, AP-HP, Université Paris Saclay, cedex, F-92141 Clamart, France.,Faculté de médecine de Bicêtre, Université Paris-Saclay, F-94270 Le Kremlin Bicêtre, France
| | - Veronique Drouineaud
- Laboratoire d'Histologie-Embryologie-Biologie de la Reproduction - CECOS, Hôpital Cochin, AP-HP, Centre Université de Paris, F-75014 Paris, France
| | - Alexandra Benachi
- Faculté de médecine de Bicêtre, Université Paris-Saclay, F-94270 Le Kremlin Bicêtre, France.,Service de gynécologie et obstétrique, Hôpital Antoine Béclère, AP-HP, Université Paris Saclay, cedex, F-92141 Clamart, France
| | - Catherine Patrat
- Laboratoire d'Histologie-Embryologie-Biologie de la Reproduction - CECOS, Hôpital Cochin, AP-HP, Centre Université de Paris, F-75014 Paris, France.,Université de Paris, U 1016, Institut Cochin, F-75014 Paris, France
| | - Francois Michael Petit
- Laboratoire de génétique moléculaire, Hôpital Antoine Béclère, AP-HP, Université Paris Saclay, cedex, F-92141 Clamart, France
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Chang S, Bartolomei MS. Modeling human epigenetic disorders in mice: Beckwith-Wiedemann syndrome and Silver-Russell syndrome. Dis Model Mech 2020; 13:dmm044123. [PMID: 32424032 PMCID: PMC7272347 DOI: 10.1242/dmm.044123] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Genomic imprinting, a phenomenon in which the two parental alleles are regulated differently, is observed in mammals, marsupials and a few other species, including seed-bearing plants. Dysregulation of genomic imprinting can cause developmental disorders such as Beckwith-Wiedemann syndrome (BWS) and Silver-Russell syndrome (SRS). In this Review, we discuss (1) how various (epi)genetic lesions lead to the dysregulation of clinically relevant imprinted loci, and (2) how such perturbations may contribute to the developmental defects in BWS and SRS. Given that the regulatory mechanisms of most imprinted clusters are well conserved between mice and humans, numerous mouse models of BWS and SRS have been generated. These mouse models are key to understanding how mutations at imprinted loci result in pathological phenotypes in humans, although there are some limitations. This Review focuses on how the biological findings obtained from innovative mouse models explain the clinical features of BWS and SRS.
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Affiliation(s)
- Suhee Chang
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Marisa S Bartolomei
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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Nakamura A, Muroya K, Ogata-Kawata H, Nakabayashi K, Matsubara K, Ogata T, Kurosawa K, Fukami M, Kagami M. A case of paternal uniparental isodisomy for chromosome 7 associated with overgrowth. J Med Genet 2018; 55:567-570. [DOI: 10.1136/jmedgenet-2017-104986] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 01/26/2018] [Accepted: 02/05/2018] [Indexed: 12/31/2022]
Abstract
BackgroundPaternal uniparental disomy for chromosome 7 (upd(7)pat) is extremely rare, and only four cases have been previously reported. As these cases were accompanied by autosomal-recessive disorders which are likely to be involved in growth restriction, the relevance of upd(7)pat to the overgrowth phenotype remains unclear. Here we describe one case of upd(7)pat with no additional genetic diseases, which may answer the question.MethodsA 5-year-old Japanese boy presented with a tall stature of unknown causes. To detect the genetic cause of the tall stature, we performed Sanger sequencing, targeted resequencing, comparative genomic hybridisation and single-nucleotide polymorphism (SNP) array analyses, methylation analysis and microsatellite analysis.ResultsWe could not detect pathogenic variants in causative genes for overgrowth syndrome or apparent copy number alterations. DNA methylation analysis revealed hypomethylation at the GRB10, PEG1 and PEG10 differentially methylated regions. SNP array and microsatellite analyses suggested paternal uniparental isodisomy for chromosome 7. Furthermore, we could not identify homozygous mutations of known causative genes for inherited disorders on chromosome 7.ConclusionWe report the first case of upd(7)pat with an overgrowth phenotype.
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10
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Tümer Z, López-Hernández JA, Netchine I, Elbracht M, Grønskov K, Gede LB, Sachwitz J, den Dunnen JT, Eggermann T. Structural and sequence variants in patients with Silver-Russell syndrome or similar features-Curation of a disease database. Hum Mutat 2018; 39:345-364. [PMID: 29250858 DOI: 10.1002/humu.23382] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 12/08/2017] [Accepted: 12/11/2017] [Indexed: 12/11/2022]
Abstract
Silver-Russell syndrome (SRS) is a clinically and molecularly heterogeneous disorder involving prenatal and postnatal growth retardation, and the term SRS-like is broadly used to describe individuals with clinical features resembling SRS. The main molecular subgroups are loss of methylation of the distal imprinting control region (H19/IGF2:IG-DMR) on 11p15.5 (50%) and maternal uniparental disomy of chromosome 7 (5%-10%). Through a comprehensive literature search, we identified 91 patients/families with various structural and small sequence variants, which were suggested as additional molecular defects leading to SRS/SRS-like phenotypes. However, the molecular and phenotypic data of these patients were not standardized and therefore not comparable, rendering difficulties in phenotype-genotype comparisons. To overcome this challenge, we curated a disease database including (epi)genetic phenotypic data of these patients. The clinical features are scored according to the Netchine-Harbison clinical scoring system (NH-CSS), which has recently been accepted as standard by consensus. The structural and sequence variations are reviewed and where necessary redescribed according to recent recommendations. Our study provides a framework for both research and diagnostic purposes through facilitating a standardized comparison of (epi)genotypes with phenotypes of patients with structural/sequence variants.
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Affiliation(s)
- Zeynep Tümer
- Applied Human Molecular Genetics, Kennedy Centre, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Glostrup, Denmark
| | | | - Irène Netchine
- Sorbonne Universite, INSERM UMR_S 938, CDR Saint-Antoine, Paris, France.,APHP, Armand Trousseau Hospital, Pediatric Endocrinology, Paris, France
| | - Miriam Elbracht
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Karen Grønskov
- Applied Human Molecular Genetics, Kennedy Centre, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Glostrup, Denmark
| | - Lene Bjerring Gede
- Applied Human Molecular Genetics, Kennedy Centre, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Glostrup, Denmark
| | - Jana Sachwitz
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Johan T den Dunnen
- Human Genetics and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Thomas Eggermann
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
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Maternal GRB10 microdeletion is a novel cause of cystic placenta: Spectrum of genomic changes in the etiology of enlarged cystic placenta. Placenta 2017; 57:33-41. [DOI: 10.1016/j.placenta.2017.05.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 05/30/2017] [Accepted: 05/31/2017] [Indexed: 01/30/2023]
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12
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Velker BAM, Denomme MM, Krafty RT, Mann MRW. Maintenance of Mest imprinted methylation in blastocyst-stage mouse embryos is less stable than other imprinted loci following superovulation or embryo culture. ENVIRONMENTAL EPIGENETICS 2017; 3:dvx015. [PMID: 29492315 PMCID: PMC5804554 DOI: 10.1093/eep/dvx015] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 06/07/2017] [Accepted: 07/19/2017] [Indexed: 06/08/2023]
Abstract
Assisted reproductive technologies are fertility treatments used by subfertile couples to conceive their biological child. Although generally considered safe, these pregnancies have been linked to genomic imprinting disorders, including Beckwith-Wiedemann and Silver-Russell Syndromes. Silver-Russell Syndrome is a growth disorder characterized by pre- and post-natal growth retardation. The Mest imprinted domain is one candidate region on chromosome 7 implicated in Silver-Russell Syndrome. We have previously shown that maintenance of imprinted methylation was disrupted by superovulation or embryo culture during pre-implantation mouse development. For superovulation, this disruption did not originate in oogenesis as a methylation acquisition defect. However, in comparison to other genes, Mest exhibits late methylation acquisition kinetics, possibly making Mest more vulnerable to perturbation by environmental insult. In this study, we present a comprehensive evaluation of the effects of superovulation and in vitro culture on genomic imprinting at the Mest gene. Superovulation resulted in disruption of imprinted methylation at the maternal Mest allele in blastocysts with an equal frequency of embryos having methylation errors following low or high hormone treatment. This disruption was not due to a failure of imprinted methylation acquisition at Mest in oocytes. For cultured embryos, both the Fast and Slow culture groups experienced a significant loss of maternal Mest methylation compared to in vivo-derived controls. This loss of methylation was independent of development rates in culture. These results indicate that Mest is more susceptible to imprinted methylation maintenance errors compared to other imprinted genes.
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Affiliation(s)
- Brenna A. M. Velker
- Department of Obstetrics & Gynecology, University of Western Ontario, Schulich School of Medicine and Dentistry, London, ON, Canada
- Department of Biochemistry, University of Western Ontario, Schulich School of Medicine and Dentistry, London, ON, Canada
- Children’s Health Research Institute, London, ON, Canada
| | - Michelle M. Denomme
- Department of Obstetrics & Gynecology, University of Western Ontario, Schulich School of Medicine and Dentistry, London, ON, Canada
- Department of Biochemistry, University of Western Ontario, Schulich School of Medicine and Dentistry, London, ON, Canada
- Children’s Health Research Institute, London, ON, Canada
- Fertility Laboratories Of Colorado, 10290 Ridgegate Circle, Lonetree, CO 80124 USA
| | - Robert T. Krafty
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Mellissa R. W. Mann
- Magee-Womens Research Institute, Pittsburgh, PA, USA
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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13
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Wakeling EL, Brioude F, Lokulo-Sodipe O, O'Connell SM, Salem J, Bliek J, Canton APM, Chrzanowska KH, Davies JH, Dias RP, Dubern B, Elbracht M, Giabicani E, Grimberg A, Grønskov K, Hokken-Koelega ACS, Jorge AA, Kagami M, Linglart A, Maghnie M, Mohnike K, Monk D, Moore GE, Murray PG, Ogata T, Petit IO, Russo S, Said E, Toumba M, Tümer Z, Binder G, Eggermann T, Harbison MD, Temple IK, Mackay DJG, Netchine I. Diagnosis and management of Silver-Russell syndrome: first international consensus statement. Nat Rev Endocrinol 2017; 13:105-124. [PMID: 27585961 DOI: 10.1038/nrendo.2016.138] [Citation(s) in RCA: 296] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
This Consensus Statement summarizes recommendations for clinical diagnosis, investigation and management of patients with Silver-Russell syndrome (SRS), an imprinting disorder that causes prenatal and postnatal growth retardation. Considerable overlap exists between the care of individuals born small for gestational age and those with SRS. However, many specific management issues exist and evidence from controlled trials remains limited. SRS is primarily a clinical diagnosis; however, molecular testing enables confirmation of the clinical diagnosis and defines the subtype. A 'normal' result from a molecular test does not exclude the diagnosis of SRS. The management of children with SRS requires an experienced, multidisciplinary approach. Specific issues include growth failure, severe feeding difficulties, gastrointestinal problems, hypoglycaemia, body asymmetry, scoliosis, motor and speech delay and psychosocial challenges. An early emphasis on adequate nutritional status is important, with awareness that rapid postnatal weight gain might lead to subsequent increased risk of metabolic disorders. The benefits of treating patients with SRS with growth hormone include improved body composition, motor development and appetite, reduced risk of hypoglycaemia and increased height. Clinicians should be aware of possible premature adrenarche, fairly early and rapid central puberty and insulin resistance. Treatment with gonadotropin-releasing hormone analogues can delay progression of central puberty and preserve adult height potential. Long-term follow up is essential to determine the natural history and optimal management in adulthood.
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Affiliation(s)
- Emma L Wakeling
- North West Thames Regional Genetics Service, London North West Healthcare NHS Trust, Watford Road, Harrow HA1 3UJ, UK
| | - Frédéric Brioude
- AP-HP, Hôpitaux Universitaires Paris Est (AP-HP) Hôpital des Enfants Armand Trousseau, Service d'Explorations Fonctionnelles Endocriniennes, 26 avenue du Dr Arnold Netter, 75012 Paris, France
- Centre de Recherche Saint Antoine, INSERM UMR S938, 34 rue Crozatier, 75012 Paris, France
- Sorbonne Universities, UPMC UNIV Paris 06, 4 place Jussieu, 75005 Paris, France
| | - Oluwakemi Lokulo-Sodipe
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton SO17 1BJ, UK
- Wessex Clinical Genetics Service, Princess Anne Hospital, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK
| | - Susan M O'Connell
- Department of Paediatrics and Child Health, Cork University Hospital, Wilton, Cork T12 DC4A, Ireland
| | - Jennifer Salem
- MAGIC Foundation, 6645 W. North Avenue, Oak Park, Illinois 60302, USA
| | - Jet Bliek
- Academic Medical Centre, Department of Clinical Genetics, Laboratory for Genome Diagnostics, Meibergdreef 15, 1105AZ Amsterdam, Netherlands
| | - Ana P M Canton
- Unidade de Endocrinologia Genetica, Laboratorio de Endocrinologia Celular e Molecular LIM/25, Disciplina de Endocrinologia da Faculdade de Medicina da Universidade de Sao Paulo, Av. Dr. Arnaldo, 455 5° andar sala 5340 (LIM25), 01246-000 São Paulo, SP, Brazil
| | - Krystyna H Chrzanowska
- Department of Medical Genetics, The Children's Memorial Health Institute, Al. Dzieci Polskich 20, 04-730 Warsaw, Poland
| | - Justin H Davies
- Department of Paediatric Endocrinology, University Hospital Southampton, Tremona Road, Southampton SO16 6YD, UK
| | - Renuka P Dias
- Institutes of Metabolism and Systems Research, Vincent Drive, University of Birmingham, Birmingham B15 2TT, UK
- Centre for Endocrinology, Diabetes and Metabolism, Vincent Drive, Birmingham Health Partners, Birmingham B15 2TH, UK
- Department of Paediatric Endocrinology and Diabetes, Birmingham Children's Hospital NHS Foundation Trust, Steelhouse Lane, Birmingham B4 6NH, UK
| | - Béatrice Dubern
- AP-HP, Hôpitaux Universitaires Paris Est (AP-HP) Hôpital des Enfants Armand Trousseau, Nutrition and Gastroenterology Department, 26 avenue du Dr Arnold Netter, 75012 Paris, France
- Trousseau Hospital, HUEP, APHP, UPMC, 75012 Paris, France
| | - Miriam Elbracht
- Insitute of Human Genetics, Technical University of Aachen, Pauwelsstr. 30, D-52074 Aachen, Germany
| | - Eloise Giabicani
- AP-HP, Hôpitaux Universitaires Paris Est (AP-HP) Hôpital des Enfants Armand Trousseau, Service d'Explorations Fonctionnelles Endocriniennes, 26 avenue du Dr Arnold Netter, 75012 Paris, France
- Centre de Recherche Saint Antoine, INSERM UMR S938, 34 rue Crozatier, 75012 Paris, France
- Sorbonne Universities, UPMC UNIV Paris 06, 4 place Jussieu, 75005 Paris, France
| | - Adda Grimberg
- Perelman School of Medicine, University of Pennsylvania, The Children's Hospital of Philadelphia, 3401 Civic Center Boulevard, Suite 11NW30, Philadelphia, Pennsylvania 19104, USA
| | - Karen Grønskov
- Applied Human Molecular Genetics, Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Gl. Landevej 7, 2600 Glostrup, Copenhagen, Denmark
| | - Anita C S Hokken-Koelega
- Erasmus University Medical Center, Pediatrics, Subdivision of Endocrinology, Wytemaweg 80, 3015 CN, Rotterdam, Netherlands
| | - Alexander A Jorge
- Unidade de Endocrinologia Genetica, Laboratorio de Endocrinologia Celular e Molecular LIM/25, Disciplina de Endocrinologia da Faculdade de Medicina da Universidade de Sao Paulo, Av. Dr. Arnaldo, 455 5° andar sala 5340 (LIM25), 01246-000 São Paulo, SP, Brazil
| | - Masayo Kagami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, 2-10-1 Ohkura, Setagayaku, Tokyo 157-8535, Japan
| | - Agnes Linglart
- APHP, Department of Pediatric Endocrinology, Reference Center for Rare Disorders of the Mineral Metabolism and Plateforme d'Expertise Paris Sud Maladies Rares, Hospital Bicêtre Paris Sud, 78 Rue du Général Leclerc, 94270 Le Kremlin-Bicêtre, France
| | - Mohamad Maghnie
- IRCCS Istituto Giannina Gaslini, University of Genova, Via Gerolamo Gaslini 5, 16147 Genova, Italy
| | - Klaus Mohnike
- Otto-von-Guericke University, Department of Pediatrics, Leipziger Street 44, 39120 Magdeburg, Germany
| | - David Monk
- Imprinting and Cancer Group, Cancer Epigenetic and Biology Program, Bellvitge Biomedical Research Institute, Gran via 199-203, Hospital Duran i Reynals, 08908, Barcelona, Spain
| | - Gudrun E Moore
- Fetal Growth and Development Group, Institute of Child Health, University College London, 30 Guilford Street, London WC1N 1EH, UK
| | - Philip G Murray
- Centre for Paediatrics and Child Health, Institute of Human Development, Royal Manchester Children's Hospital, Oxford Road, Manchester M13 9WL, UK
| | - Tsutomu Ogata
- Department of Pediatrics, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu 431-3192, Japan
| | - Isabelle Oliver Petit
- Pediatric Endocrinology, Genetic, Bone Disease &Gynecology Unit, Children's Hospital, TSA 70034, 31059 Toulouse, France
| | - Silvia Russo
- Instituto Auxologico Italiano, Cytogenetic and Molecular Genetic Laboratory, via Ariosto 13 20145 Milano, Italy
| | - Edith Said
- Department of Anatomy &Cell Biology, Centre for Molecular Medicine &Biobanking, Faculty of Medicine &Surgery, University of Malta, Msida MSD2090, Malta
- Section of Medical Genetics, Department of Pathology, Mater dei Hospital, Msida MSD2090, Malta
| | - Meropi Toumba
- IASIS Hospital, 8 Voriou Ipirou, 8036, Paphos, Cyprus
- The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Zeynep Tümer
- Applied Human Molecular Genetics, Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Gl. Landevej 7, 2600 Glostrup, Copenhagen, Denmark
| | - Gerhard Binder
- University Children's Hospital, Pediatric Endocrinology, Hoppe-Seyler-Strasse 1, 72070 Tuebingen, Germany
| | - Thomas Eggermann
- Insitute of Human Genetics, Technical University of Aachen, Pauwelsstr. 30, D-52074 Aachen, Germany
| | - Madeleine D Harbison
- Mount Sinai School of Medicine, 5 E 98th Street #1192, New York, New York 10029, USA
| | - I Karen Temple
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton SO17 1BJ, UK
- Wessex Clinical Genetics Service, Princess Anne Hospital, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK
| | - Deborah J G Mackay
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton SO17 1BJ, UK
| | - Irène Netchine
- AP-HP, Hôpitaux Universitaires Paris Est (AP-HP) Hôpital des Enfants Armand Trousseau, Service d'Explorations Fonctionnelles Endocriniennes, 26 avenue du Dr Arnold Netter, 75012 Paris, France
- Centre de Recherche Saint Antoine, INSERM UMR S938, 34 rue Crozatier, 75012 Paris, France
- Sorbonne Universities, UPMC UNIV Paris 06, 4 place Jussieu, 75005 Paris, France
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14
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Ishida M. New developments in Silver-Russell syndrome and implications for clinical practice. Epigenomics 2016; 8:563-80. [PMID: 27066913 DOI: 10.2217/epi-2015-0010] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Silver-Russell syndrome is a clinically and genetically heterogeneous disorder, characterized by prenatal and postnatal growth restriction, relative macrocephaly, body asymmetry and characteristic facial features. It is one of the imprinting disorders, which results as a consequence of aberrant imprinted gene expressions. Currently, maternal uniparental disomy of chromosome 7 accounts for approximately 10% of Silver-Russell syndrome cases, while ~50% of patients have hypomethylation at imprinting control region 1 at chromosome 11p15.5 locus, leaving ~40% of cases with unknown etiologies. This review aims to provide a comprehensive list of molecular defects in Silver-Russell syndrome reported to date and to highlight the importance of multiple-loci/tissue testing and trio (both parents and proband) screening. The epigenetic and phenotypic overlaps with other imprinting disorders will also be discussed.
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Affiliation(s)
- Miho Ishida
- University College London, Institute of Child Health, Genetics & Genomic Medicine programme, Genetics & Epigenetics in Health & Diseases Section, 30 Guilford Street, London, WC1N 1EH, UK
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15
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Carrera IA, de Zaldívar MS, Martín R, Begemann M, Soellner L, Eggermann T. Microdeletions of the 7q32.2 imprinted region are associated with Silver-Russell syndrome features. Am J Med Genet A 2015; 170:743-9. [PMID: 26663145 DOI: 10.1002/ajmg.a.37492] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 11/13/2015] [Indexed: 11/07/2022]
Abstract
The association of maternal uniparental disomy of human chromosome 7 (upd(7) mat) and the growth retardation disorder Silver-Russell syndrome (SRS) is well established, but the causative gene or region is currently unknown. However, several observations indicate that molecular alterations of the genomically imprinted MEST region in 7q32.2 are associated with growth retardation and a phenotype reminiscent to SRS. We now report on a second patient with a similar phenotype and a de novo 7q32.2 microdeletion including MEST affecting the paternal allele. This confirms the central role of imprinted genes in 7q32.2 in the etiology of a growth retardation phenotype associated with SRS features.
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Affiliation(s)
- Ignacio Arroyo Carrera
- Pediatric Service, San Pedro de Alcántara Hospital, Cáceres, Spain.,Center for Biomedical Research on Rare Diseases (CIBERER), Madrid, Spain
| | | | - Rebeca Martín
- Pediatric Service, San Pedro de Alcántara Hospital, Cáceres, Spain
| | - Matthias Begemann
- Institute of Human Genetics, University Hospital, RWTH Aachen University, Aachen, Germany
| | - Lukas Soellner
- Institute of Human Genetics, University Hospital, RWTH Aachen University, Aachen, Germany
| | - Thomas Eggermann
- Institute of Human Genetics, University Hospital, RWTH Aachen University, Aachen, Germany
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16
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Eggermann T, Perez de Nanclares G, Maher ER, Temple IK, Tümer Z, Monk D, Mackay DJG, Grønskov K, Riccio A, Linglart A, Netchine I. Imprinting disorders: a group of congenital disorders with overlapping patterns of molecular changes affecting imprinted loci. Clin Epigenetics 2015; 7:123. [PMID: 26583054 PMCID: PMC4650860 DOI: 10.1186/s13148-015-0143-8] [Citation(s) in RCA: 129] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 09/29/2015] [Indexed: 12/17/2022] Open
Abstract
Congenital imprinting disorders (IDs) are characterised by molecular changes affecting imprinted chromosomal regions and genes, i.e. genes that are expressed in a parent-of-origin specific manner. Recent years have seen a great expansion in the range of alterations in regulation, dosage or DNA sequence shown to disturb imprinted gene expression, and the correspondingly broad range of resultant clinical syndromes. At the same time, however, it has become clear that this diversity of IDs has common underlying principles, not only in shared molecular mechanisms, but also in interrelated clinical impacts upon growth, development and metabolism. Thus, detailed and systematic analysis of IDs can not only identify unifying principles of molecular epigenetics in health and disease, but also support personalisation of diagnosis and management for individual patients and families.
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Affiliation(s)
- Thomas Eggermann
- Department of Human Genetics, RWTH Aachen, Pauwelsstr. 30, Aachen, Germany ; Sorbonne Universites, UPMC Univ Paris 06, UMR_S 938, CDR Saint-Antoine, Paris, France ; 3APHP, Pediatric Endocrinology, Armand Trousseau Hospital, Paris, France
| | - Guiomar Perez de Nanclares
- Molecular (Epi)Genetics Laboratory, BioAraba National Health Institute, Hospital Universitario Araba, Vitoria-Gasteiz, Spain
| | - Eamonn R Maher
- Department of Medical Genetics, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - I Karen Temple
- Human Genetics and Genomic Medicine, Faculty of Medicine University of Southampton, Southampton, UK ; Wessex Clinical Genetics Service, Princess Anne Hospital, Coxford Road, Southampton, UK
| | - Zeynep Tümer
- Clinical Genetic Clinic, Kennedy Center, Rigshospitalet, Copenhagen University Hospital, Glostrup, Denmark
| | - David Monk
- Imprinting and Cancer Group, Cancer Epigenetic and Biology Program (PEBC), Institut d'Investigació Biomedica de Bellvitge (IDIBELL), Hospital Duran i Reynals, Barcelona, Spain
| | - Deborah J G Mackay
- Human Genetics and Genomic Medicine, Faculty of Medicine University of Southampton, Southampton, UK ; Wessex Clinical Genetics Service, Princess Anne Hospital, Coxford Road, Southampton, UK
| | - Karen Grønskov
- Clinical Genetic Clinic, Kennedy Center, Rigshospitalet, Copenhagen University Hospital, Glostrup, Denmark
| | - Andrea Riccio
- DiSTABiF, Seconda Università degli Studi di Napoli, Caserta, Italy
| | - Agnès Linglart
- Institute of Genetics and Biophysics-ABT, CNR, Napoli, Italy
| | - Irène Netchine
- Endocrinology and diabetology for children and reference center for rare disorders of calcium and phosphorus metabolism, Bicêtre Paris Sud, APHP, Le Kremlin-Bicêtre, France ; INSERM U986, INSERM, Le Kremlin-Bicêtre, France ; INSERM, UMR_S 938, CDR Saint-Antoine, Paris, F-75012 France
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17
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Polla DL, Cardoso MTO, Silva MCB, Cardoso ICC, Medina CTN, Araujo R, Fernandes CC, Reis AMM, de Andrade RV, Pereira RW, Pogue R. Use of Targeted Exome Sequencing for Molecular Diagnosis of Skeletal Disorders. PLoS One 2015; 10:e0138314. [PMID: 26380986 PMCID: PMC4575211 DOI: 10.1371/journal.pone.0138314] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 08/28/2015] [Indexed: 01/19/2023] Open
Abstract
Genetic disorders of the skeleton comprise a large group of more than 450 clinically distinct and genetically heterogeneous diseases associated with mutations in more than 300 genes. Achieving a definitive diagnosis is complicated due to the genetic heterogeneity of these disorders, their individual rarity and their diverse radiographic presentations. We used targeted exome sequencing and designed a 1.4Mb panel for simultaneous testing of more than 4,800 exons in 309 genes involved in skeletal disorders. DNA from 69 individuals from 66 families with a known or suspected clinical diagnosis of a skeletal disorder was analyzed. Of 36 cases with a specific clinical hypothesis with a known genetic basis, mutations were identified for eight cases (22%). Of 20 cases with a suspected skeletal disorder but without a specific diagnosis, four causative mutations were identified. Also included were 11 cases with a specific skeletal disorder but for which there was at the time no known associated gene. For these cases, one mutation was identified in a known skeletal disease genes, and re-evaluation of the clinical phenotype in this case changed the diagnoses from osteodysplasia syndrome to Apert syndrome. These results suggest that the NGS panel provides a fast, accurate and cost-effective molecular diagnostic tool for identifying mutations in a highly genetically heterogeneous set of disorders such as genetic skeletal disorders. The data also stress the importance of a thorough clinical evaluation before DNA sequencing. The strategy should be applicable to other groups of disorders in which the molecular basis is largely known.
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Affiliation(s)
- Daniel L. Polla
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Distrito Federal, Brazil
| | - Maria T. O. Cardoso
- Núcleo de Genética da Secretaria de Saúde do Distrito Federal, Brasília, Distrito Federal, Brazil
- Curso de Medicina, Universidade Católica de Brasília, Taguatinga, Distrito Federal, Brazil
| | - Mayara C. B. Silva
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Distrito Federal, Brazil
| | - Isabela C. C. Cardoso
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Distrito Federal, Brazil
| | - Cristina T. N. Medina
- Núcleo de Genética da Secretaria de Saúde do Distrito Federal, Brasília, Distrito Federal, Brazil
| | - Rosenelle Araujo
- Núcleo de Genética da Secretaria de Saúde do Distrito Federal, Brasília, Distrito Federal, Brazil
| | - Camila C. Fernandes
- Departamento de Tecnologia, Laboratório Multiusuário Centralizado para Sequenciamento de DNA em Larga Escala e Análise de Expressão Gênica, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Campus Jaboticabal, Jaboticabal, São Paulo, Brazil
| | - Alessandra M. M. Reis
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Distrito Federal, Brazil
| | - Rosangela V. de Andrade
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Distrito Federal, Brazil
| | - Rinaldo W. Pereira
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Distrito Federal, Brazil
| | - Robert Pogue
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Distrito Federal, Brazil
- * E-mail:
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18
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Eggermann T, Heilsberg AK, Bens S, Siebert R, Beygo J, Buiting K, Begemann M, Soellner L. Additional molecular findings in 11p15-associated imprinting disorders: an urgent need for multi-locus testing. J Mol Med (Berl) 2015; 92:769-77. [PMID: 24658748 DOI: 10.1007/s00109-014-1141-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 02/23/2014] [Accepted: 02/27/2014] [Indexed: 12/26/2022]
Abstract
UNLABELLED The chromosomal region 11p15 contains two imprinting control regions (ICRs) and is a key player in molecular processes regulated by genomic imprinting. Genomic as well as epigenetic changes affecting 11p15 are associated either with Silver-Russell syndrome (SRS) or Beckwith-Wiedemann syndrome (BWS). In the last years, a growing number of patients affected by imprinting disorders (IDs) have reported carrying the disease-specific 11p15 hypomethylation patterns as well as methylation changes at imprinted loci at other chromosomal sites (multi-locus methylation defects, MLMD). Furthermore, in several patients, molecular alterations (e.g., uniparental disomies, UPDs) additional to the primary epimutations have been reported. To determine the frequency and distribution of mutations and epimutations in patients referred as SRS or BWS for genetic testing, we retrospectively ascertained our routine patient cohort consisting of 711 patients (SRS, n = 571; BWS, n = 140). As this cohort represents the typical cohort in a routine diagnostic lab without clinical preselection, the detection rates were much lower than those reported from clinically characterized cohorts in the literature (SRS, 19.9%; BWS, 28.6%). Among the molecular subgroups known to be predisposed to MLMD, the frequencies corresponded to that in the literature (SRS, 7.1% in ICR1 hypomethylation carriers; BWS, 20.8% in ICR2 hypomethylation patients). In several patients, more than one epigenetic or genetic disturbance could be identified. Our study illustrates that the complex molecular alterations as well as the overlapping and sometimes unusual clinical findings in patients with imprinting disorders (IDs) often make the decision for a specific imprinting disorder test difficult. We therefore suggest to implement molecular assays in routine ID diagnostics which allow the detection of a broad range of (epi)mutation types (epimutations, UPDs, chromosomal imbalances) and cover the clinically most relevant known ID loci because of the following: (a) Multi-locus tests increase the detection rates as they cover numerous loci. (b) Patients with unexpected molecular alterations are detected. (c) The testing of rare imprinting disorders becomes more efficient and quality of molecular diagnosis increases. (d) The tests identify MLMDs. In the future, the detailed characterization of clinical and molecular findings in ID patients will help us to decipher the complex regulation of imprinting and thereby providing the basis for more directed genetic counseling and therapeutic managements in IDs. KEY MESSAGE Molecular disturbances in patients with imprinting disorders are often not restricted to the disease-specific locus but also affect other chromosomal regions. These additional disturbances include methylation defects, uniparental disomies as well as chromosomal imbalances. The identification of these additional alterations is mandatory for a well-directed genetic counseling. Furthermore, these findings help to decipher the complex regulation of imprinting.
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19
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Shi X, Chen S, Zheng H, Wang L, Wu Y. Abnormal DNA Methylation of Imprinted Loci in Human Preimplantation Embryos. Reprod Sci 2014; 21:978-983. [PMID: 24406788 DOI: 10.1177/1933719113519173] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
PURPOSE To evaluate the epigenetic risk linked to assisted reproductive technology (ART) at single-embryo level by analyzing the methylation status of imprinted H19, PEG1, and KvDMR1 in human preimplantation embryos. METHODS A total of 254 human day 3 embryos produced by ART procedures were collected. All embryos were normally fertilized but unsuitable for transfer or freezing due to poor quality. Pyrosequencing with confirmatory routine bisulfite sequencing were used to determine the DNA methylation patterns of H19 differentially methylated region (DMR) in 63 embryos, PEG1 DMR in 65 embryos, and KvDMR1 in 67 embryos. RESULTS Aberrant methylation patterns were found in 8.0% embryos at H19 DMR, 16.9% embryos at PEG1 DMR, and 10.4% embryos at KvDMR1. No methylation errors were found in corresponding sperm samples. CONCLUSIONS We hypothesized that the use of poor-quality embryos may increase the risk of imprinting defects because they might have methylation errors.
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Affiliation(s)
- Xiaoyun Shi
- Departments of reproductive Medicine and Obstetrics and Gynecology, The Second People's Hospital of Guiyang, Guiyang, People's Republic of China
| | - Shiling Chen
- Department of Obstetrics and Gynecology, Center for reproductive Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Haiyan Zheng
- Department of Obstetrics and Gynecology, Center for reproductive Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Lele Wang
- Department of Obstetrics and Gynecology, Center for reproductive Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Yaqin Wu
- Department of Obstetrics and Gynecology, Center for reproductive Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
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Jacob KJ, Robinson WP, Lefebvre L. Beckwith-Wiedemann and Silver-Russell syndromes: opposite developmental imbalances in imprinted regulators of placental function and embryonic growth. Clin Genet 2013; 84:326-34. [PMID: 23495910 DOI: 10.1111/cge.12143] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Revised: 03/12/2013] [Accepted: 03/12/2013] [Indexed: 11/29/2022]
Abstract
Beckwith-Wiedemann syndrome (BWS) and Silver-Russell syndrome (SRS) are two congenital disorders with opposite outcomes on fetal growth, overgrowth and growth restriction, respectively. Although both disorders are heterogeneous, most cases of BWS and SRS are associated with opposite epigenetic or genetic abnormalities on 11p15.5 leading to opposite imbalances in the expression levels of imprinted genes. In this article, we review evidence implicating these genes in the developmental regulation of embryonic growth and placental function in mouse models. The emerging picture suggests that both SRS and BWS can be caused by the simultaneous and opposite deregulation of two groups of imprinted genes on 11p15.5. A detailed description of the phenotypic abnormalities associated with each syndrome must take into consideration the developmental functions of each gene involved.
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Affiliation(s)
- K J Jacob
- Department of Medical Genetics; Life Sciences Institute, Molecular Epigenetics Group, University of British Columbia, Vancouver, Canada
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Shi X, Chen S, Zheng H, Wang L, Wu Y. Aberrant DNA methylation of imprinted loci in human in vitro matured oocytes after long agonist stimulation. Eur J Obstet Gynecol Reprod Biol 2013; 167:64-8. [DOI: 10.1016/j.ejogrb.2012.10.037] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Revised: 10/18/2012] [Accepted: 10/30/2012] [Indexed: 11/27/2022]
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Eggermann T, Spengler S, Gogiel M, Begemann M, Elbracht M. Epigenetic and genetic diagnosis of Silver-Russell syndrome. Expert Rev Mol Diagn 2012; 12:459-71. [PMID: 22702363 DOI: 10.1586/erm.12.43] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Silver-Russell syndrome (SRS) is a congenital imprinting disorder characterized by intrauterine and postnatal growth restriction and further characteristic features. SRS is genetically heterogenous: 7-10% of patients carry a maternal uniparental disomy of chromosome 7; >38% show a hypomethylation in imprinting control region 1 in 11p15; and a further class of mutations are copy number variations affecting different chromosomes, but mainly 11p15 and 7. The diagnostic work-up should thus aim to detect these three molecular subtypes. Numerous techniques are currently applied in genetic SRS testing, but none of them covers all known (epi)mutations, and they should therefore be used synergistically. However, future next-generation sequencing approaches will allow a comprehensive analysis of all types of alterations in SRS.
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Affiliation(s)
- Thomas Eggermann
- Institute of Human Genetics, University Hospital Aachen, Pauwelsstr. 30, D-52074 Aachen, Germany.
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Girardot M, Cavaillé J, Feil R. Small regulatory RNAs controlled by genomic imprinting and their contribution to human disease. Epigenetics 2012; 7:1341-8. [PMID: 23154539 PMCID: PMC3528689 DOI: 10.4161/epi.22884] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
More than a hundred protein-coding genes are controlled by genomic imprinting in humans. These atypical genes are organized in chromosomal domains, each of which is controlled by a differentially methylated "imprinting control region" (ICR). How ICRs mediate the parental allele-specific expression of close-by genes is now becoming understood. At several imprinted domains, this epigenetic mechanism involves the action of long non-coding RNAs. It is less well appreciated that imprinted gene domains also transcribe hundreds of microRNA and small nucleolar RNA genes and that these represent the densest clusters of small RNA genes in mammalian genomes. The evolutionary reasons for this remarkable enrichment of small regulatory RNAs at imprinted domains remain unclear. However, recent studies show that imprinted small RNAs modulate specific functions in development and metabolism and also are frequently perturbed in cancer. Here, we review our current understanding of imprinted small RNAs in the human genome and discuss how perturbation of their expression contributes to disease.
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Affiliation(s)
- Michael Girardot
- Institute of Molecular Genetics, CNRS and the University of Montpellier, Montpellier, France.
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Begemann M, Spengler S, Kordaß U, Schröder C, Eggermann T. Segmental maternal uniparental disomy 7q associated with DLK1/GTL2 (14q32) hypomethylation. Am J Med Genet A 2012; 158A:423-8. [DOI: 10.1002/ajmg.a.34412] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2011] [Accepted: 11/10/2011] [Indexed: 12/18/2022]
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