1
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Giaccari C, Cecere F, Argenziano L, Pagano A, Galvao A, Acampora D, Rossi G, Hay Mele B, Acurzio B, Coonrod S, Cubellis MV, Cerrato F, Andrews S, Cecconi S, Kelsey G, Riccio A. A maternal-effect Padi6 variant causes nuclear and cytoplasmic abnormalities in oocytes, as well as failure of epigenetic reprogramming and zygotic genome activation in embryos. Genes Dev 2024; 38:131-150. [PMID: 38453481 PMCID: PMC10982689 DOI: 10.1101/gad.351238.123] [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: 10/09/2023] [Accepted: 02/15/2024] [Indexed: 03/09/2024]
Abstract
Maternal inactivation of genes encoding components of the subcortical maternal complex (SCMC) and its associated member, PADI6, generally results in early embryo lethality. In humans, SCMC gene variants were found in the healthy mothers of children affected by multilocus imprinting disturbances (MLID). However, how the SCMC controls the DNA methylation required to regulate imprinting remains poorly defined. We generated a mouse line carrying a Padi6 missense variant that was identified in a family with Beckwith-Wiedemann syndrome and MLID. If homozygous in female mice, this variant resulted in interruption of embryo development at the two-cell stage. Single-cell multiomic analyses demonstrated defective maturation of Padi6 mutant oocytes and incomplete DNA demethylation, down-regulation of zygotic genome activation (ZGA) genes, up-regulation of maternal decay genes, and developmental delay in two-cell embryos developing from Padi6 mutant oocytes but little effect on genomic imprinting. Western blotting and immunofluorescence analyses showed reduced levels of UHRF1 in oocytes and abnormal localization of DNMT1 and UHRF1 in both oocytes and zygotes. Treatment with 5-azacytidine reverted DNA hypermethylation but did not rescue the developmental arrest of mutant embryos. Taken together, this study demonstrates that PADI6 controls both nuclear and cytoplasmic oocyte processes that are necessary for preimplantation epigenetic reprogramming and ZGA.
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Affiliation(s)
- Carlo Giaccari
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania "Luigi Vanvitelli," Caserta 81100, Italy
| | - Francesco Cecere
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania "Luigi Vanvitelli," Caserta 81100, Italy
| | - Lucia Argenziano
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania "Luigi Vanvitelli," Caserta 81100, Italy
| | - Angela Pagano
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania "Luigi Vanvitelli," Caserta 81100, Italy
| | - Antonio Galvao
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, United Kingdom
- Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, United Kingdom
- Institute of Animal Reproduction and Food Research of the Polish Academy of Sciences, Olsztyn 10-748, Poland
| | - Dario Acampora
- Institute of Genetics and Biophysics (IGB) "Adriano Buzzati-Traverso," Consiglio Nazionale delle Ricerche (CNR), Naples 80131, Italy
| | - Gianna Rossi
- Department of Life, Health, and Environmental Sciences, Università dell'Aquila, L'Aquila 67100, Italy
| | - Bruno Hay Mele
- Department of Biology, University of Naples "Federico II," Napoli 80126, Italy
| | - Basilia Acurzio
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania "Luigi Vanvitelli," Caserta 81100, Italy
| | - Scott Coonrod
- Baker Institute for Animal Health, Cornell University, Ithaca, New York 14853, USA
| | | | - Flavia Cerrato
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania "Luigi Vanvitelli," Caserta 81100, Italy
| | - Simon Andrews
- Bioinformatics Unit, The Babraham Institute, Cambridge CB22 3AT, United Kingdom
| | - Sandra Cecconi
- Department of Life, Health, and Environmental Sciences, Università dell'Aquila, L'Aquila 67100, Italy
| | - Gavin Kelsey
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, United Kingdom;
- Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, United Kingdom
- Wellcome-MRC Institute of Metabolic Science-Metabolic Research Laboratories, Cambridge CB2 0QQ, United Kingdom
| | - Andrea Riccio
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania "Luigi Vanvitelli," Caserta 81100, Italy;
- Institute of Genetics and Biophysics (IGB) "Adriano Buzzati-Traverso," Consiglio Nazionale delle Ricerche (CNR), Naples 80131, Italy
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2
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Eggermann T. Human Reproduction and Disturbed Genomic Imprinting. Genes (Basel) 2024; 15:163. [PMID: 38397153 PMCID: PMC10888310 DOI: 10.3390/genes15020163] [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: 01/02/2024] [Revised: 01/23/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
Genomic imprinting is a specific mode of gene regulation which particularly accounts for the factors involved in development. Its disturbance affects the fetus, the course of pregnancy and even the health of the mother. In children, aberrant imprinting signatures are associated with imprinting disorders (ImpDis). These alterations also affect the function of the placenta, which has consequences for the course of the pregnancy. The molecular causes of ImpDis comprise changes at the DNA level and methylation disturbances (imprinting defects/ImpDefs), and there is an increasing number of reports of both pathogenic fetal and maternal DNA variants causing ImpDefs. These ImpDefs can be inherited, but prediction of the pregnancy complications caused is difficult, as they can cause miscarriages, aneuploidies, health issues for the mother and ImpDis in the child. Due to the complexity of imprinting regulation, each pregnancy or patient with suspected altered genomic imprinting requires a specific workup to identify the precise molecular cause and also careful clinical documentation. This review will cover the current knowledge on the molecular causes of aberrant imprinting signatures and illustrate the need to identify this basis as the prerequisite for personalized genetic and reproductive counselling of families.
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Affiliation(s)
- Thomas Eggermann
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH University Aachen, Pauwelsstr. 3, D-52074 Aachen, Germany
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3
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Maksiutenko EM, Barbitoff YA, Nasykhova YA, Pachuliia OV, Lazareva TE, Bespalova ON, Glotov AS. The Landscape of Point Mutations in Human Protein Coding Genes Leading to Pregnancy Loss. Int J Mol Sci 2023; 24:17572. [PMID: 38139401 PMCID: PMC10743817 DOI: 10.3390/ijms242417572] [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: 10/23/2023] [Revised: 12/01/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023] Open
Abstract
Pregnancy loss is the most frequent complication of a pregnancy which is devastating for affected families and poses a significant challenge for the health care system. Genetic factors are known to play an important role in the etiology of pregnancy loss; however, despite advances in diagnostics, the causes remain unexplained in more than 30% of cases. In this review, we aggregated the results of the decade-long studies into the genetic risk factors of pregnancy loss (including miscarriage, termination for fetal abnormality, and recurrent pregnancy loss) in euploid pregnancies, focusing on the spectrum of point mutations associated with these conditions. We reviewed the evolution of molecular genetics methods used for the genetic research into causes of pregnancy loss, and collected information about 270 individual genetic variants in 196 unique genes reported as genetic cause of pregnancy loss. Among these, variants in 18 genes have been reported by multiple studies, and two or more variants were reported as causing pregnancy loss for 57 genes. Further analysis of the properties of all known pregnancy loss genes showed that they correspond to broadly expressed, highly evolutionary conserved genes involved in crucial cell differentiation and developmental processes and related signaling pathways. Given the features of known genes, we made an effort to construct a list of candidate genes, variants in which may be expected to contribute to pregnancy loss. We believe that our results may be useful for prediction of pregnancy loss risk in couples, as well as for further investigation and revealing genetic etiology of pregnancy loss.
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Affiliation(s)
| | - Yury A. Barbitoff
- Department of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology and Reproductology, Mendeleevskaya Line 3, 199034 St. Petersburg, Russia; (E.M.M.); (Y.A.N.); (O.V.P.); (T.E.L.); (O.N.B.)
| | | | | | | | | | - Andrey S. Glotov
- Department of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology and Reproductology, Mendeleevskaya Line 3, 199034 St. Petersburg, Russia; (E.M.M.); (Y.A.N.); (O.V.P.); (T.E.L.); (O.N.B.)
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4
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Schlaich E, Hubens WHG, Eggermann T. First-time application of droplet digital PCR for methylation testing of the 11p15.5 imprinting regions. Mol Genet Genomic Med 2023; 11:e2264. [PMID: 37519217 PMCID: PMC10724498 DOI: 10.1002/mgg3.2264] [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: 04/20/2023] [Revised: 06/20/2023] [Accepted: 07/20/2023] [Indexed: 08/01/2023] Open
Abstract
BACKGROUND Beckwith-Wiedemann syndrome and Silver-Russel syndrome are two imprinting disorders caused by opposite molecular alterations in 11p15.5. With the current diagnostic tests, their molecular diagnosis is challenging due to molecular heterogeneity and mosaic occurrence of the most frequent alterations. As the determination of precise (epi)genotype of patients is relevant as the basis for a personalized treatment, different approaches are needed to increase the sensitivity of diagnostic testing of imprinting disorders. METHODS We established methylation-specific droplet digital PCR approaches (MS-ddPCR) for the two imprinting centers in 11p15.5, and analyzed patients with paternal uniparental disomy of chromosome 11p15.5 (upd(11)pat) and other imprinting defects in the region. The results were compared to those from MS-MLPA (multiplex ligation-dependent probe amplification) and MS-pyrosequencing. RESULTS MS-ddPCR confirmed the molecular alterations in all patients and the results matched well with MS-MLPA. The results of MS-pyrosequencing varied between different runs, whereas MS-ddPCR results were reproducible. CONCLUSION We show for the first time that MS-ddPCR is a reliable and easy applicable method for determination of MS-associated changes in imprinting disorders. It is therefore an additional tool for multimethod diagnostics of imprinting disorders suitable to improve the diagnostic yield.
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Affiliation(s)
- Elia Schlaich
- Institute for Human Genetics and Genome Medicine, Medical Faculty, RWTH Aachen UniversityAachenGermany
| | - Wouter H. G. Hubens
- Institute for Stem Cell Biology, Medical Faculty, RWTH Aachen UniversityAachenGermany
- Helmholtz Institute for Biomedical Engineering, RWTH Aachen UniversityAachenGermany
| | - Thomas Eggermann
- Institute for Human Genetics and Genome Medicine, Medical Faculty, RWTH Aachen UniversityAachenGermany
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5
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Jentoft IMA, Bäuerlein FJB, Welp LM, Cooper BH, Petrovic A, So C, Penir SM, Politi AZ, Horokhovskyi Y, Takala I, Eckel H, Moltrecht R, Lénárt P, Cavazza T, Liepe J, Brose N, Urlaub H, Fernández-Busnadiego R, Schuh M. Mammalian oocytes store proteins for the early embryo on cytoplasmic lattices. Cell 2023; 186:5308-5327.e25. [PMID: 37922900 DOI: 10.1016/j.cell.2023.10.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 08/01/2023] [Accepted: 10/02/2023] [Indexed: 11/07/2023]
Abstract
Mammalian oocytes are filled with poorly understood structures called cytoplasmic lattices. First discovered in the 1960s and speculated to correspond to mammalian yolk, ribosomal arrays, or intermediate filaments, their function has remained enigmatic to date. Here, we show that cytoplasmic lattices are sites where oocytes store essential proteins for early embryonic development. Using super-resolution light microscopy and cryoelectron tomography, we show that cytoplasmic lattices are composed of filaments with a high surface area, which contain PADI6 and subcortical maternal complex proteins. The lattices associate with many proteins critical for embryonic development, including proteins that control epigenetic reprogramming of the preimplantation embryo. Loss of cytoplasmic lattices by knocking out PADI6 or the subcortical maternal complex prevents the accumulation of these proteins and results in early embryonic arrest. Our work suggests that cytoplasmic lattices enrich maternally provided proteins to prevent their premature degradation and cellular activity, thereby enabling early mammalian development.
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Affiliation(s)
- Ida M A Jentoft
- Department of Meiosis, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Felix J B Bäuerlein
- Institute for Neuropathology, University Medical Center Göttingen, 37077 Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, 37077 Göttingen, Germany
| | - Luisa M Welp
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany; Institute of Clinical Chemistry, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Benjamin H Cooper
- Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, 37075 Göttingen, Germany
| | - Arsen Petrovic
- Institute for Neuropathology, University Medical Center Göttingen, 37077 Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, 37077 Göttingen, Germany
| | - Chun So
- Department of Meiosis, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Sarah Mae Penir
- Department of Meiosis, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Antonio Z Politi
- Facility for Light Microscopy, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Yehor Horokhovskyi
- Quantitative and Systems Biology Group, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Iina Takala
- Quantitative and Systems Biology Group, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Heike Eckel
- Kinderwunschzentrum Göttingen, 37081 Göttingen, Germany
| | | | - Peter Lénárt
- Facility for Light Microscopy, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Tommaso Cavazza
- Department of Meiosis, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Juliane Liepe
- Quantitative and Systems Biology Group, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Nils Brose
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, 37077 Göttingen, Germany; Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, 37075 Göttingen, Germany
| | - Henning Urlaub
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, 37077 Göttingen, Germany; Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany; Institute of Clinical Chemistry, University Medical Center Göttingen, 37075 Göttingen, Germany; Göttingen Center for Molecular Biosciences, Georg-August University Göttingen, 37077 Göttingen, Germany
| | - Rubén Fernández-Busnadiego
- Institute for Neuropathology, University Medical Center Göttingen, 37077 Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, 37077 Göttingen, Germany; Faculty of Physics, Georg-August-Universität Göttingen, 37077 Göttingen, Germany
| | - Melina Schuh
- Department of Meiosis, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, 37077 Göttingen, Germany.
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6
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Williams JPC, Walport LJ. PADI6: What we know about the elusive fifth member of the peptidyl arginine deiminase family. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220242. [PMID: 37778376 PMCID: PMC10542454 DOI: 10.1098/rstb.2022.0242] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 03/05/2023] [Indexed: 10/03/2023] Open
Abstract
Peptidyl arginine deiminase 6 (PADI6) is a maternal factor that is vital for early embryonic development. Deletion and mutations of its encoding gene in female mice or women lead to early embryonic developmental arrest, female infertility, maternal imprinting defects and hyperproliferation of the trophoblast. PADI6 is the fifth and least well-characterized member of the peptidyl arginine deiminases (PADIs), which catalyse the post-translational conversion of arginine to citrulline. It is less conserved than the other PADIs, and currently has no reported catalytic activity. While there are many suggested functions of PADI6 in the early mouse embryo, including in embryonic genome activation, cytoplasmic lattice formation, maternal mRNA and ribosome regulation, and organelle distribution, the molecular mechanisms of its function remain unknown. In this review, we discuss what is known about the function of PADI6 and highlight key outstanding questions that must be answered if we are to understand the crucial role it plays in early embryo development and female fertility. This article is part of the Theo Murphy meeting issue 'The virtues and vices of protein citrullination'.
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Affiliation(s)
| | - Louise J. Walport
- Imperial College of Science Technology and Medicine, London, W12 0BZ, UK
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7
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Cecere F, Pignata L, Hay Mele B, Saadat A, D'Angelo E, Palumbo O, Palumbo P, Carella M, Scarano G, Rossi GB, Angelini C, Sparago A, Cerrato F, Riccio A. Co-Occurrence of Beckwith-Wiedemann Syndrome and Early-Onset Colorectal Cancer. Cancers (Basel) 2023; 15:cancers15071944. [PMID: 37046605 PMCID: PMC10093120 DOI: 10.3390/cancers15071944] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/20/2023] [Accepted: 03/21/2023] [Indexed: 04/14/2023] Open
Abstract
CRC is an adult-onset carcinoma representing the third most common cancer and the second leading cause of cancer-related deaths in the world. EO-CRC (<45 years of age) accounts for 5% of the CRC cases and is associated with cancer-predisposing genetic factors in half of them. Here, we describe the case of a woman affected by BWSp who developed EO-CRC at age 27. To look for a possible molecular link between BWSp and EO-CRC, we analysed her whole-genome genetic and epigenetic profiles in blood, and peri-neoplastic and neoplastic colon tissues. The results revealed a general instability of the tumor genome, including copy number and methylation changes affecting genes of the WNT signaling pathway, CRC biomarkers and imprinted loci. At the germline level, two missense mutations predicted to be likely pathogenic were found in compound heterozygosity affecting the Cystic Fibrosis (CF) gene CFTR that has been recently classified as a tumor suppressor gene, whose dysregulation represents a severe risk factor for developing CRC. We also detected constitutional loss of methylation of the KCNQ1OT1:TSS-DMR that leads to bi-allelic expression of the lncRNA KCNQ1OT1 and BWSp. Our results support the hypothesis that the inherited CFTR mutations, together with constitutional loss of methylation of the KCNQ1OT1:TSS-DMR, initiate the tumorigenesis process. Further somatic genetic and epigenetic changes enhancing the activation of the WNT/beta-catenin pathway likely contributed to increase the growth advantage of cancer cells. Although this study does not provide any conclusive cause-effect relationship between BWSp and CRC, it is tempting to speculate that the imprinting defect of BWSp might accelerate tumorigenesis in adult cancer in the presence of predisposing genetic variants.
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Affiliation(s)
- Francesco Cecere
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania "Luigi Vanvitelli", 81100 Caserta, Italy
| | - Laura Pignata
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania "Luigi Vanvitelli", 81100 Caserta, Italy
| | - Bruno Hay Mele
- Department of Biology, Università degli Studi di Napoli "Federico II", 80126 Napoli, Italy
| | - Abu Saadat
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania "Luigi Vanvitelli", 81100 Caserta, Italy
| | - Emilia D'Angelo
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania "Luigi Vanvitelli", 81100 Caserta, Italy
| | - Orazio Palumbo
- Division of Medical Genetics, Fondazione IRCCS "Casa Sollievo della Sofferenza", 71013 San Giovanni Rotondo, Italy
| | - Pietro Palumbo
- Division of Medical Genetics, Fondazione IRCCS "Casa Sollievo della Sofferenza", 71013 San Giovanni Rotondo, Italy
| | - Massimo Carella
- Division of Medical Genetics, Fondazione IRCCS "Casa Sollievo della Sofferenza", 71013 San Giovanni Rotondo, Italy
| | - Gioacchino Scarano
- Medical Genetics Unit, Azienda Ospedaliera "San Pio" P."Gaetano Rummo", 82100 Benevento, Italy
| | | | - Claudia Angelini
- Istituto per le Applicazioni del Calcolo (IAC) "Mauro Picone", Consiglio Nazionale delle Ricerche (CNR), 80131 Napoli, Italy
| | - Angela Sparago
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania "Luigi Vanvitelli", 81100 Caserta, Italy
| | - Flavia Cerrato
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania "Luigi Vanvitelli", 81100 Caserta, Italy
| | - Andrea Riccio
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania "Luigi Vanvitelli", 81100 Caserta, Italy
- Institute of Genetics and e Biophysics (IGB) "Adriano Buzzati-Traverso", Consiglio Nazionale delle Ricerche (CNR), 80131 Napoli, Italy
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8
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Bilo L, Ochoa E, Lee S, Dey D, Kurth I, Kraft F, Rodger F, Docquier F, Toribio A, Bottolo L, Binder G, Fekete G, Elbracht M, Maher ER, Begemann M, Eggermann T. Molecular characterisation of 36 multilocus imprinting disturbance (MLID) patients: a comprehensive approach. Clin Epigenetics 2023; 15:35. [PMID: 36859312 PMCID: PMC9979536 DOI: 10.1186/s13148-023-01453-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 02/20/2023] [Indexed: 03/03/2023] Open
Abstract
BACKGROUND Imprinting disorders (ImpDis) comprise diseases which are caused by aberrant regulation of monoallelically and parent-of-origin-dependent expressed genes. A characteristic molecular change in ImpDis patients is aberrant methylation signatures at disease-specific loci, without an obvious DNA change at the specific differentially methylated region (DMR). However, there is a growing number of reports on multilocus imprinting disturbances (MLIDs), i.e. aberrant methylation at different DMRs in the same patient. These MLIDs account for a significant number of patients with specific ImpDis, and several reports indicate a central role of pathogenic maternal effect variants in their aetiology by affecting the maturation of the oocyte and the early embryo. Though several studies on the prevalence and the molecular causes of MLID have been conducted, homogeneous datasets comprising both genomic and methylation data are still lacking. RESULTS Based on a cohort of 36 MLID patients, we here present both methylation data obtained from next-generation sequencing (NGS, ImprintSeq) approaches and whole-exome sequencing (WES). The compilation of methylation data did not reveal a disease-specific MLID episignature, and a predisposition for the phenotypic modification was not obvious as well. In fact, this lack of epigenotype-phenotype correlation might be related to the mosaic distribution of imprinting defects and their functional relevance in specific tissues. CONCLUSIONS Due to the higher sensitivity of NGS-based approaches, we suggest that ImprintSeq might be offered at reference centres in case of ImpDis patients with unusual phenotypes but MLID negative by conventional tests. By WES, additional MLID causes than the already known maternal effect variants could not be identified, neither in the patients nor in the maternal exomes. In cases with negative WES results, it is currently unclear to what extent either environmental factors or undetected genetic variants contribute to MLID.
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Affiliation(s)
- Larissa Bilo
- Medical Faculty, Institute for Human Genetics and Genome Medicine, RWTH Aachen University, Pauwelsstr. 30, 52074, Aachen, Germany
| | - Eguzkine Ochoa
- Department of Medical Genetics, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Sunwoo Lee
- Department of Medical Genetics, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Daniela Dey
- Medical Faculty, Institute for Human Genetics and Genome Medicine, RWTH Aachen University, Pauwelsstr. 30, 52074, Aachen, Germany
| | - Ingo Kurth
- Medical Faculty, Institute for Human Genetics and Genome Medicine, RWTH Aachen University, Pauwelsstr. 30, 52074, Aachen, Germany
| | - Florian Kraft
- Medical Faculty, Institute for Human Genetics and Genome Medicine, RWTH Aachen University, Pauwelsstr. 30, 52074, Aachen, Germany
| | - Fay Rodger
- Department of Medical Genetics, University of Cambridge, Cambridge, CB2 0QQ, UK
- Stratified Medicine Core Laboratory NGS Hub, Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - France Docquier
- Department of Medical Genetics, University of Cambridge, Cambridge, CB2 0QQ, UK
- Stratified Medicine Core Laboratory NGS Hub, Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Ana Toribio
- Department of Medical Genetics, University of Cambridge, Cambridge, CB2 0QQ, UK
- Stratified Medicine Core Laboratory NGS Hub, Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Leonardo Bottolo
- Department of Medical Genetics, University of Cambridge, Cambridge, CB2 0QQ, UK
- MRC Biostatistics Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- The Alan Turing Institute, London, UK
| | - Gerhard Binder
- Pediatric Endocrinology, University Children's Hospital, Universiy of Tuebingen, Tuebingen, Germany
| | - György Fekete
- Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Miriam Elbracht
- Medical Faculty, Institute for Human Genetics and Genome Medicine, RWTH Aachen University, Pauwelsstr. 30, 52074, Aachen, Germany
| | - Eamonn R Maher
- Department of Medical Genetics, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Matthias Begemann
- Medical Faculty, Institute for Human Genetics and Genome Medicine, RWTH Aachen University, Pauwelsstr. 30, 52074, Aachen, Germany
| | - Thomas Eggermann
- Medical Faculty, Institute for Human Genetics and Genome Medicine, RWTH Aachen University, Pauwelsstr. 30, 52074, Aachen, Germany.
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9
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Zhu C, Liu C, Chai Z. Role of the PADI family in inflammatory autoimmune diseases and cancers: A systematic review. Front Immunol 2023; 14:1115794. [PMID: 37020554 PMCID: PMC10067674 DOI: 10.3389/fimmu.2023.1115794] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 02/08/2023] [Indexed: 04/07/2023] Open
Abstract
The peptidyl arginine deiminase (PADI) family is a calcium ion-dependent group of isozymes with sequence similarity that catalyze the citrullination of proteins. Histones can serve as the target substrate of PADI family isozymes, and therefore, the PADI family is involved in NETosis and the secretion of inflammatory cytokines. Thus, the PADI family is associated with the development of inflammatory autoimmune diseases and cancer, reproductive development, and other related diseases. In this review, we systematically discuss the role of the PADI family in the pathogenesis of various diseases based on studies from the past decade to provide a reference for future research.
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Affiliation(s)
- Changhui Zhu
- Department of Plastic Surgery, Shandong Provincial Qianfoshan Hospital, School of Basic Medical Sciences, Weifang Medical University, Weifang, Shandong, China
- Shandong Provincial Key Laboratory for Rheumatic Disease and Translational Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, China
| | - Chunyan Liu
- Shandong Provincial Key Laboratory for Rheumatic Disease and Translational Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, China
- *Correspondence: Chunyan Liu, ; Zhengbin Chai,
| | - Zhengbin Chai
- Department of Clinical Laboratory Medicine, Shandong Public Health Clinical Center, Shandong University, Jinan, China
- *Correspondence: Chunyan Liu, ; Zhengbin Chai,
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10
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Grolaux R, Hardy A, Olsen C, Van Dooren S, Smits G, Defrance M. Identification of differentially methylated regions in rare diseases from a single-patient perspective. Clin Epigenetics 2022; 14:174. [PMID: 36527161 PMCID: PMC9758859 DOI: 10.1186/s13148-022-01403-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 12/07/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND DNA methylation (5-mC) is being widely recognized as an alternative in the detection of sequence variants in the diagnosis of some rare neurodevelopmental and imprinting disorders. Identification of alterations in DNA methylation plays an important role in the diagnosis and understanding of the etiology of those disorders. Canonical pipelines for the detection of differentially methylated regions (DMRs) usually rely on inter-group (e.g., case versus control) comparisons. However, these tools might perform suboptimally in the context of rare diseases and multilocus imprinting disturbances due to small cohort sizes and inter-patient heterogeneity. Therefore, there is a need to provide a simple but statistically robust pipeline for scientists and clinicians to perform differential methylation analyses at the single patient level as well as to evaluate how parameter fine-tuning may affect differentially methylated region detection. RESULT We implemented an improved statistical method to detect differentially methylated regions in correlated datasets based on the Z-score and empirical Brown aggregation methods from a single-patient perspective. To accurately assess the predictive power of our method, we generated semi-simulated data using a public control population of 521 samples and investigated how the size of the control population, methylation difference, and region size affect DMR detection. In addition, we validated the detection of methylation events in patients suffering from rare multi-locus imprinting disturbance and evaluated how this method could complement existing tools in the context of clinical diagnosis. CONCLUSION In this study, we present a robust statistical method to perform differential methylation analysis at the single patient level and describe its optimal parameters to increase DMRs identification performance. Finally, we show its diagnostic utility when applied to rare disorders.
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Affiliation(s)
- Robin Grolaux
- grid.4989.c0000 0001 2348 0746Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles, Brussels, Belgium
| | - Alexis Hardy
- grid.4989.c0000 0001 2348 0746Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles, Brussels, Belgium
| | - Catharina Olsen
- grid.8767.e0000 0001 2290 8069Clinical Sciences, Research Group Reproduction and Genetics, Brussels Interuniversity Genomics High Throughput Core (BRIGHTcore), Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium ,grid.8767.e0000 0001 2290 8069Clinical Sciences, Research Group Reproduction and Genetics, Centre for Medical Genetics, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium ,grid.8767.e0000 0001 2290 8069Interuniversity Institute of Bioinformatics in Brussels, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Sonia Van Dooren
- grid.8767.e0000 0001 2290 8069Clinical Sciences, Research Group Reproduction and Genetics, Brussels Interuniversity Genomics High Throughput Core (BRIGHTcore), Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium ,grid.8767.e0000 0001 2290 8069Clinical Sciences, Research Group Reproduction and Genetics, Centre for Medical Genetics, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium ,grid.8767.e0000 0001 2290 8069Interuniversity Institute of Bioinformatics in Brussels, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Guillaume Smits
- grid.4989.c0000 0001 2348 0746Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles, Brussels, Belgium ,grid.4989.c0000 0001 2348 0746Center of Human Genetics, Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Matthieu Defrance
- grid.4989.c0000 0001 2348 0746Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles, Brussels, Belgium
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11
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Christensen AO, Li G, Young CH, Snow B, Khan SA, DeVore SB, Edwards S, Bouma GJ, Navratil AM, Cherrington BD, Rothfuss HM. Peptidylarginine deiminase enzymes and citrullinated proteins in female reproductive physiology and associated diseases†. Biol Reprod 2022; 107:1395-1410. [PMID: 36087287 PMCID: PMC10248218 DOI: 10.1093/biolre/ioac173] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/30/2022] [Accepted: 09/07/2022] [Indexed: 09/15/2023] Open
Abstract
Citrullination, the post-translational modification of arginine residues, is catalyzed by the four catalytically active peptidylarginine deiminase (PAD or PADI) isozymes and alters charge to affect target protein structure and function. PADs were initially characterized in rodent uteri and, since then, have been described in other female tissues including ovaries, breast, and the lactotrope and gonadotrope cells of the anterior pituitary gland. In these tissues and cells, estrogen robustly stimulates PAD expression resulting in changes in levels over the course of the female reproductive cycle. The best-characterized targets for PADs are arginine residues in histone tails, which, when citrullinated, alter chromatin structure and gene expression. Methodological advances have allowed for the identification of tissue-specific citrullinomes, which reveal that PADs citrullinate a wide range of enzymes and structural proteins to alter cell function. In contrast to their important physiological roles, PADs and citrullinated proteins are also involved in several female-specific diseases including autoimmune disorders and reproductive cancers. Herein, we review current knowledge regarding PAD expression and function and highlight the role of protein citrullination in both normal female reproductive tissues and associated diseases.
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Affiliation(s)
- Amanda O Christensen
- Department of Zoology and Physiology, University of Wyoming, Laramie, WY 82071, USA
| | - Guangyuan Li
- Department of Zoology and Physiology, University of Wyoming, Laramie, WY 82071, USA
| | - Coleman H Young
- Department of Zoology and Physiology, University of Wyoming, Laramie, WY 82071, USA
| | - Bryce Snow
- Department of Zoology and Physiology, University of Wyoming, Laramie, WY 82071, USA
| | | | - Stanley B DeVore
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Sydney Edwards
- Animal Reproduction and Biotechnology Laboratory, Department of Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Gerrit J Bouma
- Animal Reproduction and Biotechnology Laboratory, Department of Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Amy M Navratil
- Department of Zoology and Physiology, University of Wyoming, Laramie, WY 82071, USA
| | - Brian D Cherrington
- Department of Zoology and Physiology, University of Wyoming, Laramie, WY 82071, USA
| | - Heather M Rothfuss
- Department of Zoology and Physiology, University of Wyoming, Laramie, WY 82071, USA
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12
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Solovova OA, Chernykh VB. Genetics of Oocyte Maturation Defects and Early Embryo Development Arrest. Genes (Basel) 2022; 13:1920. [PMID: 36360157 PMCID: PMC9689903 DOI: 10.3390/genes13111920] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 10/18/2022] [Accepted: 10/19/2022] [Indexed: 08/08/2023] Open
Abstract
Various pathogenic factors can lead to oogenesis failure and seriously affect both female reproductive health and fertility. Genetic factors play an important role in folliculogenesis and oocyte maturation but still need to be clarified. Oocyte maturation is a well-organized complex process, regulated by a large number of genes. Pathogenic variants in these genes as well as aneuploidy, defects in mitochondrial genome, and other genetic and epigenetic factors can result in unexplained infertility, early pregnancy loss, and recurrent failures of IVF/ICSI programs due to poor ovarian response to stimulation, oocyte maturation arrest, poor gamete quality, fertilization failure, or early embryonic developmental arrest. In this paper, we review the main genes, as well as provide a description of the defects in the mitochondrial genome, associated with female infertility.
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13
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Different Mechanisms Cause Hypomethylation of Both H19 and KCNQ1OT1 Imprinted Differentially Methylated Regions in Two Cases of Silver-Russell Syndrome Spectrum. Genes (Basel) 2022; 13:genes13101875. [PMID: 36292759 PMCID: PMC9602374 DOI: 10.3390/genes13101875] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/27/2022] [Accepted: 10/13/2022] [Indexed: 11/04/2022] Open
Abstract
Silver–Russell syndrome is an imprinting disorder characterised by pre- and post-natal growth retardation and several heterogeneous molecular defects affecting different human genomic loci. In the majority of cases, the molecular defect is the loss of methylation (LOM) of the H19/IGF2 differentially methylated region (DMR, also known as IC1) at the telomeric domain of the 11p15.5 imprinted genes cluster, which causes the altered expression of the growth controlling genes, IGF2 and H19. Very rarely, the LOM also affects the KCNQ1OT1 DMR (also known as IC2) at the centromeric domain, resulting in an SRS phenotype by an unknown mechanism. In this study, we report on two cases with SRS features and a LOM of either IC1 and IC2. In one case, this rare and complex epimutation was secondary to a de novo mosaic in cis maternal duplication, involving the entire telomeric 11p15.5 domain and part of the centromeric domain but lacking CDKN1C. In the second case, neither the no 11p15.5 copy number variant nor the maternal-effect subcortical maternal complex (SCMC) variant were found to be associated with the epimutation, suggesting that it arose as a primary event. Our findings further add to the complexity of the molecular genetics of SRS and indicate how the LOM in both 11p15.5 DMRs may result from different molecular mechanisms.
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14
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Wang X, Zhu H, He Y, Zeng J, Zhao J, Xia Q, Wu L, Yao Z, Li Y. A novel homozygous mutation in the PADI6 gene causes early embryo arrest. Reprod Health 2022; 19:190. [PMID: 36088419 PMCID: PMC9463787 DOI: 10.1186/s12978-022-01495-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 08/30/2022] [Indexed: 11/12/2022] Open
Abstract
Background It has been proved that mutations in the PADI6 gene can cause early embryo arrest. This study describes a newly discovered mutation in PADI6 that expands the genetic spectrum of early embryo arrest. Methods Peripheral blood of a patient diagnosed with early embryo arrest was collected for whole-exome sequencing. Sanger sequencing was performed to confirm this mutation. The effects of the variant were investigated in human embryonic kidney 293T (HEK293T) cells using western blotting, real-time quantitative polymerase chain reaction, and immunofluorescence. Results A novel homozygous mutation in PADI6 was identified in the proband. The patient carried a frameshift insertion mutation c.558dupA (p.Thr187Asnfs*48), which was located in the protein arginine deiminase middle domain. The variant destroyed PADI6 protein expression and reduced PADI6 mRNA expression in HEK293T cells. Conclusions The newly identified mutation in PADI6 accounts for early embryo arrest. It expands the spectrum of genetic causes and phenotypes of infertility in humans. These findings also provide an additional possible diagnostic marker for patients with recurrent in vitro fertilization/intracytoplasmic sperm injection failure. Supplementary Information The online version contains supplementary material available at 10.1186/s12978-022-01495-7. Some infertile patients experience multiple in vitro fertilization/intracytoplasmic sperm injection (IVF/ICSI) failure owing to recurrent early embryo arrest. However, the underlying mechanisms remain largely unknown. Due to the development of whole-exome sequencing, early embryo arrest has been confirmed as a type of Mendelian disease. This study aimed to identify the genetic cause of early embryo arrest in patients and to expand the genetic spectrum. Furthermore, it can help doctors offer better suggestions to such patients and prevent patients from suffering from multiple IVF/ICSI failures.
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15
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Bińkowski J, Taryma-Leśniak O, Łuczkowska K, Niedzwiedź A, Lechowicz K, Strapagiel D, Jarczak J, Davalos V, Pujol A, Esteller M, Kotfis K, Machaliński B, Parczewski M, Wojdacz TK. Epigenetic activation of antiviral sensors and effectors of interferon response pathways during SARS-CoV-2 infection. Biomed Pharmacother 2022; 153:113396. [PMID: 36076479 PMCID: PMC9271528 DOI: 10.1016/j.biopha.2022.113396] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 07/01/2022] [Accepted: 07/07/2022] [Indexed: 12/15/2022] Open
Abstract
Recent studies have shown that methylation changes identified in blood cells of COVID-19 patients have a potential to be used as biomarkers of SARS-CoV-2 infection outcomes. However, different studies have reported different subsets of epigenetic lesions that stratify patients according to the severity of infection symptoms, and more importantly, the significance of those epigenetic changes in the pathology of the infection is still not clear. We used methylomics and transcriptomics data from the largest so far cohort of COVID-19 patients from four geographically distant populations, to identify casual interactions of blood cells’ methylome in pathology of the COVID-19 disease. We identified a subset of methylation changes that is uniformly present in all COVID-19 patients regardless of symptoms. Those changes are not present in patients suffering from upper respiratory tract infections with symptoms similar to COVID-19. Most importantly, the identified epigenetic changes affect the expression of genes involved in interferon response pathways and the expression of those genes differs between patients admitted to intensive care units and only hospitalized. In conclusion, the DNA methylation changes involved in pathophysiology of SARS-CoV-2 infection, which are specific to COVID-19 patients, can not only be utilized as biomarkers in the disease management but also present a potential treatment target.
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16
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Pignata L, Cecere F, Verma A, Hay Mele B, Monticelli M, Acurzio B, Giaccari C, Sparago A, Hernandez Mora JR, Monteagudo-Sánchez A, Esteller M, Pereda A, Tenorio-Castano J, Palumbo O, Carella M, Prontera P, Piscopo C, Accadia M, Lapunzina P, Cubellis MV, de Nanclares GP, Monk D, Riccio A, Cerrato F. Novel genetic variants of KHDC3L and other members of the subcortical maternal complex associated with Beckwith-Wiedemann syndrome or Pseudohypoparathyroidism 1B and multi-locus imprinting disturbances. Clin Epigenetics 2022; 14:71. [PMID: 35643636 PMCID: PMC9148495 DOI: 10.1186/s13148-022-01292-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 05/16/2022] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Beckwith-Wiedemann syndrome (BWS) and Pseudohypoparathyroidism type 1B (PHP1B) are imprinting disorders (ID) caused by deregulation of the imprinted gene clusters located at 11p15.5 and 20q13.32, respectively. In both of these diseases a subset of the patients is affected by multi-locus imprinting disturbances (MLID). In several families, MLID is associated with damaging variants of maternal-effect genes encoding protein components of the subcortical maternal complex (SCMC). However, frequency, penetrance and recurrence risks of these variants are still undefined. In this study, we screened two cohorts of BWS patients and one cohort of PHP1B patients for the presence of MLID, and analysed the positive cases for the presence of maternal variants in the SCMC genes by whole exome-sequencing and in silico functional studies. RESULTS We identified 10 new cases of MLID associated with the clinical features of either BWS or PHP1B, in which segregate 13 maternal putatively damaging missense variants of the SCMC genes. The affected genes also included KHDC3L that has not been associated with MLID to date. Moreover, we highlight the possible relevance of relatively common variants in the aetiology of MLID. CONCLUSION Our data further add to the list of the SCMC components and maternal variants that are involved in MLID, as well as of the associated clinical phenotypes. Also, we propose that in addition to rare variants, common variants may play a role in the aetiology of MLID and imprinting disorders by exerting an additive effect in combination with rarer putatively damaging variants. These findings provide useful information for the molecular diagnosis and recurrence risk evaluation of MLID-associated IDs in genetic counselling.
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Affiliation(s)
- Laura Pignata
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università Degli Studi Della Campania "Luigi Vanvitelli", Caserta, Italy
| | - Francesco Cecere
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università Degli Studi Della Campania "Luigi Vanvitelli", Caserta, Italy
- Institute of Genetics and Biophysics (IGB), "Adriano Buzzati-Traverso", Consiglio Nazionale Delle Ricerche (CNR), Naples, Italy
| | - Ankit Verma
- Institute of Genetics and Biophysics (IGB), "Adriano Buzzati-Traverso", Consiglio Nazionale Delle Ricerche (CNR), Naples, Italy
| | - Bruno Hay Mele
- Department of Biology, Università Degli Studi Di Napoli "Federico II", Naples, Italy
| | - Maria Monticelli
- Department of Biology, Università Degli Studi Di Napoli "Federico II", Naples, Italy
| | - Basilia Acurzio
- Institute of Genetics and Biophysics (IGB), "Adriano Buzzati-Traverso", Consiglio Nazionale Delle Ricerche (CNR), Naples, Italy
| | - Carlo Giaccari
- Institute of Genetics and Biophysics (IGB), "Adriano Buzzati-Traverso", Consiglio Nazionale Delle Ricerche (CNR), Naples, Italy
| | - Angela Sparago
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università Degli Studi Della Campania "Luigi Vanvitelli", Caserta, Italy
| | - Jose Ramon Hernandez Mora
- Cancer Epigenetic and Biology Program (PEBC), Imprinting and Cancer Group, Institut d'Investigació Biomedica de Bellvitge (IDIBELL), Avinguda Granvia, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Ana Monteagudo-Sánchez
- Cancer Epigenetic and Biology Program (PEBC), Imprinting and Cancer Group, Institut d'Investigació Biomedica de Bellvitge (IDIBELL), Avinguda Granvia, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Manel Esteller
- Josep Carreras Leukeamia Research Institute, Can Ruti, Cami de les Escoles, Badalona, Barcelona, Spain
- Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain
- Institucio Catalana de Recerca I Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Catalonia, Spain
| | - Arrate Pereda
- Molecular (Epi)Genetics Laboratory, Rare Diseases Research Group, Bioaraba Health Research Institute, Araba University Hospital-Txagorritxu, C/Jose Atxotegi s/n, 01009, Vitoria-Gasteiz, Spain
| | - Jair Tenorio-Castano
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain
- Institute of Medical and Molecular Genetics, INGEMM-Idipaz, Madrid, Spain
- ITHACA, European Reference Network, Brussels, Belgium
| | - Orazio Palumbo
- Division of Medical Genetics, Fondazione IRCCS "Casa Sollievo Della Sofferenza", 71013, San Giovanni Rotondo, FG, Italy
| | - Massimo Carella
- Division of Medical Genetics, Fondazione IRCCS "Casa Sollievo Della Sofferenza", 71013, San Giovanni Rotondo, FG, Italy
| | - Paolo Prontera
- Medical Genetics Unit, University and Hospital of Perugia, Perugia, Italy
| | - Carmelo Piscopo
- Medical and Laboratory Genetics Unit, "Antonio Cardarelli" Hospital, 80131, Naples, Italy
| | - Maria Accadia
- Medical Genetics Service, Hospital "Cardinale G. Panico", 73039, Tricase, Lecce, Italy
| | - Pablo Lapunzina
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain
- Institute of Medical and Molecular Genetics, INGEMM-Idipaz, Madrid, Spain
- ITHACA, European Reference Network, Brussels, Belgium
| | | | - Guiomar Perez de Nanclares
- Molecular (Epi)Genetics Laboratory, Rare Diseases Research Group, Bioaraba Health Research Institute, Araba University Hospital-Txagorritxu, C/Jose Atxotegi s/n, 01009, Vitoria-Gasteiz, Spain
| | - David Monk
- Cancer Epigenetic and Biology Program (PEBC), Imprinting and Cancer Group, Institut d'Investigació Biomedica de Bellvitge (IDIBELL), Avinguda Granvia, L'Hospitalet de Llobregat, Barcelona, Spain
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TG, UK
| | - Andrea Riccio
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università Degli Studi Della Campania "Luigi Vanvitelli", Caserta, Italy.
- Institute of Genetics and Biophysics (IGB), "Adriano Buzzati-Traverso", Consiglio Nazionale Delle Ricerche (CNR), Naples, Italy.
| | - Flavia Cerrato
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università Degli Studi Della Campania "Luigi Vanvitelli", Caserta, Italy.
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Nowacka-Woszuk J, Stachowiak M, Szczerbal I, Szydlowski M, Szabelska-Beresewicz A, Zyprych-Walczak J, Krzeminska P, Nowak T, Lukomska A, Ligocka Z, Biezynski J, Dzimira S, Nizanski W, Switonski M. Whole genome sequencing identifies a missense polymorphism in PADI6 associated with testicular/ovotesticular XX disorder of sex development in dogs. Genomics 2022; 114:110389. [PMID: 35597501 DOI: 10.1016/j.ygeno.2022.110389] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 04/07/2022] [Accepted: 05/11/2022] [Indexed: 12/17/2022]
Abstract
Disorders of sex development (DSDs) are congenital malformations defined as discrepancies between sex chromosomes and phenotypical sex. Testicular or ovotesticular XX DSDs are frequently observed in female dogs, while monogenic XY DSDs are less frequent. Here, we applied whole genome sequencing (WGS) to search for causative mutations in XX DSD females in French Bulldogs (FB) and American Staffordshire Terries (AST) and in XY DSD Yorkshire Terries (YT). The WGS results were validated by Sanger sequencing and ddPCR. It was shown that a missense SNP of the PADI6 gene, is significantly associated with the XX DSD (SRY-negative) phenotype in AST (P = 0.0051) and FB (P = 0.0306). On the contrary, we did not find any associated variant with XY DSD in YTs. Our study suggests that the genetic background of the XX DSD may be more complex and breed-specific.
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Affiliation(s)
- Joanna Nowacka-Woszuk
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, 60-637 Poznan, Poland
| | - Monika Stachowiak
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, 60-637 Poznan, Poland
| | - Izabela Szczerbal
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, 60-637 Poznan, Poland
| | - Maciej Szydlowski
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, 60-637 Poznan, Poland
| | - Alicja Szabelska-Beresewicz
- Department of Mathematical and Statistical Methods, Poznan University of Life Sciences, Wojska Polskiego 28, 60-637 Poznan, Poland
| | - Joanna Zyprych-Walczak
- Department of Mathematical and Statistical Methods, Poznan University of Life Sciences, Wojska Polskiego 28, 60-637 Poznan, Poland
| | - Paulina Krzeminska
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, 60-637 Poznan, Poland
| | - Tomasz Nowak
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, 60-637 Poznan, Poland
| | - Anna Lukomska
- Department of Preclinical Sciences and Infectious Diseases, Poznan University of Life Sciences, Wolynska 35, 60-637 Poznan, Poland
| | - Zuzanna Ligocka
- Department of Reproduction and Clinic of Farm Animals, Wroclaw University of Environmental and Life Sciences, Pl. Grunwaldzki 49, 50-366 Wroclaw, Poland
| | - Janusz Biezynski
- Department of Surgery, Wroclaw University of Environmental and Life Sciences, Pl. Grunwaldzki 51, 50-366 Wroclaw, Poland
| | - Stanislaw Dzimira
- Department of Pathology, Wroclaw University of Environmental and Life Sciences, C. K. Norwida 31, 50-375 Wroclaw, Poland
| | - Wojciech Nizanski
- Department of Reproduction and Clinic of Farm Animals, Wroclaw University of Environmental and Life Sciences, Pl. Grunwaldzki 49, 50-366 Wroclaw, Poland
| | - Marek Switonski
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, 60-637 Poznan, Poland.
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18
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Capalbo A, Buonaiuto S, Figliuzzi M, Damaggio G, Girardi L, Caroselli S, Poli M, Patassini C, Cetinkaya M, Yuksel B, Azad A, Grøndahl M, Hoffmann E, Simón C, Colonna V, Kahraman S. A standardized approach for case selection and genomic data analysis of maternal exomes for the diagnosis of oocyte maturation and early embryonic developmental arrest in IVF. Reprod Biomed Online 2022; 45:508-518. [DOI: 10.1016/j.rbmo.2022.05.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 05/17/2022] [Indexed: 11/15/2022]
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19
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Tannorella P, Calzari L, Daolio C, Mainini E, Vimercati A, Gentilini D, Soli F, Pedrolli A, Bonati MT, Larizza L, Russo S. Germline variants in genes of the subcortical maternal complex and Multilocus Imprinting Disturbance are associated with miscarriage/infertility or Beckwith-Wiedemann progeny. Clin Epigenetics 2022; 14:43. [PMID: 35317853 PMCID: PMC8941822 DOI: 10.1186/s13148-022-01262-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 03/09/2022] [Indexed: 12/30/2022] Open
Abstract
Beckwith–Wiedemann syndrome (BWS, OMIM # 130650) is an imprinting disorder, associated with overgrowth and increased risk of embryonal tumors. Patients carrying hypomethylation in the KCNQ1OT1:TSS DMR (11p15.5) show MLID (Multilocus Imprinting Disturbance) upon epimutations at other imprinted regions. Few cases of BWS MLID’s mothers with biallelic pathogenetic variants in maternal effect genes, mainly components of the subcortical maternal complex, are reported. We describe two families, one with a history of conception difficulties with a novel homozygous nonsense NLRP2 variant and another experiencing 8 miscarriages with a compound heterozygous PADI6 variant.
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Affiliation(s)
- Pierpaola Tannorella
- Research Laboratory of Medical Cytogenetics and Molecular Genetics, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Luciano Calzari
- Research Laboratory of Medical Cytogenetics and Molecular Genetics, IRCCS Istituto Auxologico Italiano, Milan, Italy.,Bioinformatics and Statistical Genomics Unit, Istituto Auxologico Italiano IRCCS, Milan, Italy
| | | | - Ester Mainini
- Research Laboratory of Medical Cytogenetics and Molecular Genetics, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Alessandro Vimercati
- Research Laboratory of Medical Cytogenetics and Molecular Genetics, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Davide Gentilini
- Bioinformatics and Statistical Genomics Unit, Istituto Auxologico Italiano IRCCS, Milan, Italy.,Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
| | - Fiorenza Soli
- Medical Genetic Unit, S. Chiara Hospital APSS, Trento, Italy
| | | | - Maria Teresa Bonati
- Clinic of Medical Genetics, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Lidia Larizza
- Research Laboratory of Medical Cytogenetics and Molecular Genetics, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Silvia Russo
- Research Laboratory of Medical Cytogenetics and Molecular Genetics, IRCCS Istituto Auxologico Italiano, Milan, Italy.
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20
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Eggermann T, Yapici E, Bliek J, Pereda A, Begemann M, Russo S, Tannorella P, Calzari L, de Nanclares GP, Lombardi P, Temple IK, Mackay D, Riccio A, Kagami M, Ogata T, Lapunzina P, Monk D, Maher ER, Tümer Z. Trans-acting genetic variants causing multilocus imprinting disturbance (MLID): common mechanisms and consequences. Clin Epigenetics 2022; 14:41. [PMID: 35296332 PMCID: PMC8928698 DOI: 10.1186/s13148-022-01259-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 02/28/2022] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Imprinting disorders are a group of congenital diseases which are characterized by molecular alterations affecting differentially methylated regions (DMRs). To date, at least twelve imprinting disorders have been defined with overlapping but variable clinical features including growth and metabolic disturbances, cognitive dysfunction, abdominal wall defects and asymmetry. In general, a single specific DMR is affected in an individual with a given imprinting disorder, but there are a growing number of reports on individuals with so-called multilocus imprinting disturbances (MLID), where aberrant imprinting marks (most commonly loss of methylation) occur at multiple DMRs. However, as the literature is fragmented, we reviewed the molecular and clinical data of 55 previously reported or newly identified MLID families with putative pathogenic variants in maternal effect genes (NLRP2, NLRP5, NLRP7, KHDC3L, OOEP, PADI6) and in other candidate genes (ZFP57, ARID4A, ZAR1, UHRF1, ZNF445). RESULTS In 55 families, a total of 68 different candidate pathogenic variants were identified (7 in NLRP2, 16 in NLRP5, 7 in NLRP7, 17 in PADI6, 15 in ZFP57, and a single variant in each of the genes ARID4A, ZAR1, OOEP, UHRF1, KHDC3L and ZNF445). Clinical diagnoses of affected offspring included Beckwith-Wiedemann syndrome spectrum, Silver-Russell syndrome spectrum, transient neonatal diabetes mellitus, or they were suspected for an imprinting disorder (undiagnosed). Some families had recurrent pregnancy loss. CONCLUSIONS Genomic maternal effect and foetal variants causing MLID allow insights into the mechanisms behind the imprinting cycle of life, and the spatial and temporal function of the different factors involved in oocyte maturation and early development. Further basic research together with identification of new MLID families will enable a better understanding of the link between the different reproductive issues such as recurrent miscarriages and preeclampsia in maternal effect variant carriers/families and aneuploidy and the MLID observed in the offsprings. The current knowledge can already be employed in reproductive and genetic counselling in specific situations.
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Affiliation(s)
- Thomas Eggermann
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Pauwelsstr. 30, 52074, Aachen, Germany.
| | - Elzem Yapici
- grid.1957.a0000 0001 0728 696XInstitute of Human Genetics, Medical Faculty, RWTH Aachen University, Pauwelsstr. 30, 52074 Aachen, Germany
| | - Jet Bliek
- grid.509540.d0000 0004 6880 3010Department of Human Genetics, Laboratory for Genome Diagnostics, Amsterdam UMC, Amsterdam, Netherlands
| | - Arrate Pereda
- grid.468902.10000 0004 1773 0974Molecular (Epi)Genetics Laboratory, Bioaraba Health Research Institute, Hospital Universitario Araba-Txagorritxu, Vitoria-Gasteiz, Alava Spain
| | - Matthias Begemann
- grid.1957.a0000 0001 0728 696XInstitute of Human Genetics, Medical Faculty, RWTH Aachen University, Pauwelsstr. 30, 52074 Aachen, Germany
| | - Silvia Russo
- grid.418224.90000 0004 1757 9530Research Laboratory of Medical Cytogenetics and Molecular Genetics, Istituto Auxologico Italiano, IRCCS, Milan, Italy
| | - Pierpaola Tannorella
- grid.418224.90000 0004 1757 9530Research Laboratory of Medical Cytogenetics and Molecular Genetics, Istituto Auxologico Italiano, IRCCS, Milan, Italy
| | - Luciano Calzari
- grid.418224.90000 0004 1757 9530Research Laboratory of Medical Cytogenetics and Molecular Genetics, Istituto Auxologico Italiano, IRCCS, Milan, Italy
| | - Guiomar Perez de Nanclares
- grid.468902.10000 0004 1773 0974Molecular (Epi)Genetics Laboratory, Bioaraba Health Research Institute, Hospital Universitario Araba-Txagorritxu, Vitoria-Gasteiz, Alava Spain
| | - Paola Lombardi
- grid.509540.d0000 0004 6880 3010Department of Human Genetics, Laboratory for Genome Diagnostics, Amsterdam UMC, Amsterdam, Netherlands
| | - I. Karen Temple
- grid.123047.30000000103590315Wessex Clinical Genetics Service, University Hospital Southampton, Southampton, UK ,grid.430506.40000 0004 0465 4079Wessex Clinical Genetics Service, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Deborah Mackay
- grid.430506.40000 0004 0465 4079Wessex Clinical Genetics Service, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Andrea Riccio
- grid.9841.40000 0001 2200 8888Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania ‘Luigi Vanvitelli’, Caserta, Italy ,grid.419869.b0000 0004 1758 2860Institute of Genetics and Biophysics ‘Adriano Buzzati–Traverso’ CNR, Naples, Italy
| | - Masayo Kagami
- grid.63906.3a0000 0004 0377 2305Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Ohkura, Setagayaku, Tokyo, Japan
| | - Tsutomu Ogata
- grid.413553.50000 0004 1772 534XDepartment of Pediatrics, Hamamatsu Medical Center, Hamamatsu, Japan ,grid.505613.40000 0000 8937 6696Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Pablo Lapunzina
- grid.81821.320000 0000 8970 9163CIBERER-ISCIII and INGEMM, Institute of Medical and Molecular Genetics, Hospital Universitario La Paz, Madrid, Spain ,ERN-Ithaca, European Reference Networks, Madrid, Spain
| | - David Monk
- grid.8273.e0000 0001 1092 7967School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Eamonn R. Maher
- grid.24029.3d0000 0004 0383 8386Department of Medical Genetics, University of Cambridge and Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ UK ,grid.24029.3d0000 0004 0383 8386Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ UK
| | - Zeynep Tümer
- grid.475435.4Department of Clinical Genetics, Kennedy Center, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark ,grid.5254.60000 0001 0674 042XDepartment of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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21
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Grosvenor SE, Davies JH, Lever M, Sillibourne J, Mackay DJG, Temple IK. A patient with multilocus imprinting disturbance involving hypomethylation at 11p15 and 14q32, and phenotypic features of Beckwith-Wiedemann and Temple syndromes. Am J Med Genet A 2022; 188:1896-1903. [PMID: 35266280 PMCID: PMC9310769 DOI: 10.1002/ajmg.a.62717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 11/15/2021] [Accepted: 11/30/2021] [Indexed: 11/26/2022]
Abstract
Beckwith‐Wiedemann syndrome (BWS) and Temple syndrome (TS) are classical imprinting disorders (IDs) with nonconfluent clinical features. We report here on a patient with clinical features of both syndromes, in whom epimutations were found at the BWS and TS imprinted regions, consistent with multilocus imprinting disturbance (MLID). This is the first case report of a patient with clinical features of both conditions who was found to have loss of methylation (LOM) of KCNQ1OT1: TSS‐DMR (ICR2) in the 11p15 imprinted region associated with BWS and LOM of MEG3: TSS‐DMR in the 14q32 imprinted region associated with TS. The report draws attention to the importance of testing for MLID as a cause of atypical clinical presentations of patients with IDs.
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Affiliation(s)
- Sarah E Grosvenor
- Human Development and Health, Faculty of Medicine, University of Southampton, Tremona Road, Southampton, UK
| | - Justin H Davies
- Human Development and Health, Faculty of Medicine, University of Southampton, Tremona Road, Southampton, UK.,Department of Paediatric Endocrinology, University Hospital Southampton NHS Foundation Trusts, Southampton, UK
| | - Margaret Lever
- Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust, Salisbury, UK
| | - Julie Sillibourne
- Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust, Salisbury, UK
| | - Deborah J G Mackay
- Human Development and Health, Faculty of Medicine, University of Southampton, Tremona Road, Southampton, UK.,Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust, Salisbury, UK
| | - I Karen Temple
- Human Development and Health, Faculty of Medicine, University of Southampton, Tremona Road, Southampton, UK.,Wessex Clinical Genetics Service, University Hospital Southampton NHS Foundation Trusts, Southampton, UK
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22
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Picchetta L, Caroselli S, Figliuzzi M, Cogo F, Zambon P, Costa M, Pergher I, Patassini C, Cortellessa F, Zuccarello D, Poli M, Capalbo A. Molecular tools for the genomic assessment of oocyte’s reproductive competence. J Assist Reprod Genet 2022; 39:847-860. [PMID: 35124783 PMCID: PMC9050973 DOI: 10.1007/s10815-022-02411-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 01/24/2022] [Indexed: 12/15/2022] Open
Abstract
The most important factor associated with oocytes' developmental competence has been widely identified as the presence of chromosomal abnormalities. However, growing application of genome-wide sequencing (GS) in population diagnostics has enabled the identification of multifactorial genetic predispositions to sub-lethal pathologies, including those affecting IVF outcomes and reproductive fitness. Indeed, GS analysis in families with history of isolated infertility has recently led to the discovery of new genes and variants involved in specific human infertility endophenotypes that impact the availability and the functionality of female gametes by altering unique mechanisms necessary for oocyte maturation and early embryo development. Ongoing advancements in analytical and bioinformatic pipelines for the study of the genetic determinants of oocyte competence may provide the biological evidence required not only for improving the diagnosis of isolated female infertility but also for the development of novel preventive and therapeutic approaches for reproductive failure. Here, we provide an updated discussion and review of the progresses made in preconception genomic medicine in the identification of genetic factors associated with oocyte availability, function, and competence.
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23
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Ochoa E, Lee S, Lan-Leung B, Dias RP, Ong KK, Radley JA, Pérez de Nanclares G, Martinez R, Clark G, Martin E, Castaño L, Bottolo L, Maher ER. ImprintSeq, a novel tool to interrogate DNA methylation at human imprinted regions and diagnose multilocus imprinting disturbance. Genet Med 2022; 24:463-474. [PMID: 34906518 DOI: 10.1016/j.gim.2021.10.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 10/19/2021] [Indexed: 01/14/2023] Open
Abstract
PURPOSE Disruptions of genomic imprinting are associated with congenital imprinting disorders (CIDs) and other disease states, including cancer. CIDs are most often associated with altered methylation at imprinted differentially methylated regions (iDMRs). In some cases, multiple iDMRs are affected causing multilocus imprinting disturbances (MLIDs). The availability of accurate, quantitative, and scalable high-throughput methods to interrogate multiple iDMRs simultaneously would enhance clinical diagnostics and research. METHODS We report the development of a custom targeted methylation sequencing panel that covered most relevant 63 iDMRs for CIDs and the detection of MLIDs. We tested it in 70 healthy controls and 147 individuals with CIDs. We distinguished loss and gain of methylation per differentially methylated region and classified high and moderate methylation alterations. RESULTS Across a range of CIDs with a variety of molecular mechanisms, ImprintSeq performed at 98.4% sensitivity, 99.9% specificity, and 99.9% accuracy (when compared with previous diagnostic testing). ImprintSeq was highly sensitive for detecting MLIDs and enabled diagnostic criteria for MLID to be proposed. In a child with extreme MLID profile a probable genetic cause was identified. CONCLUSION ImprintSeq provides a novel assay for clinical diagnostic and research studies of CIDs, MLIDs, and the role of disordered imprinting in human disease states.
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Affiliation(s)
- Eguzkine Ochoa
- Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Sunwoo Lee
- Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Benoit Lan-Leung
- Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Renuka P Dias
- Department of Endocrinology and Diabetes, Birmingham Children's Hospital, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, United Kingdom; Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Ken K Ong
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom; Department of Paediatrics, School of Clinical Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Jessica A Radley
- West Midlands Regional Clinical Genetics Service and Birmingham Health Partners, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, United Kingdom; London North West Regional Genetics Service, St. Mark's and Northwick Park hospitals, Harrow, Middlesex, United Kingdom
| | - Gustavo Pérez de Nanclares
- Biocruces Bizkaia Health Research Institute, Hospital Universitario Cruces, CIBERDEM, CIBERER, Endo-ERN, University of the Basque Country (UPV-EHU), Bizkaia, Spain
| | - Rosa Martinez
- Biocruces Bizkaia Health Research Institute, Hospital Universitario Cruces, CIBERDEM, CIBERER, Endo-ERN, University of the Basque Country (UPV-EHU), Bizkaia, Spain
| | - Graeme Clark
- Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, United Kingdom; Stratified Medicine Core Laboratory NGS Hub, Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Ezequiel Martin
- Stratified Medicine Core Laboratory NGS Hub, Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Luis Castaño
- Biocruces Bizkaia Health Research Institute, Hospital Universitario Cruces, CIBERDEM, CIBERER, Endo-ERN, University of the Basque Country (UPV-EHU), Bizkaia, Spain
| | - Leonardo Bottolo
- Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, United Kingdom; The Alan Turing Institute, London, United Kingdom; MRC Biostatistics Unit, School of Clinical Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Eamonn R Maher
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom.
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24
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Novel biallelic mutations in PADI6 in patients with early embryonic arrest. J Hum Genet 2022; 67:285-293. [PMID: 34987164 DOI: 10.1038/s10038-021-00998-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 11/02/2021] [Accepted: 11/21/2021] [Indexed: 01/08/2023]
Abstract
Peptidyl arginine deiminase, type VI (PADI6) is a member of the subcortical maternal complex (SCMC), which plays vital roles in mammalian embryogenesis. Most mutations in SCMC members have been reported to cause human embryonic arrest, and a total of 15 mutations in PADI6 have been shown to be responsible for early embryonic arrest according to previous studies. However, the genetic factors behind this phenotype remain to be understood in further detail. Here, we identified 13 novel mutations and 4 previously reported mutations of PADI6 in 14 patients who were diagnosed with abnormal embryonic development caused by early arrest, embryonic fragmentation, and recurrent implantation failure. Most of the mutations were predicted by in silico analysis to be deleterious or damaging to the function of PADI6. In addition, the total and East Asian population frequencies of the mutations were low or absent in the gnomAD database. Our study expands the mutational spectrum in PADI6 and will provide precise targets for genetic counseling in the future.
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25
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Anvar Z, Chakchouk I, Demond H, Sharif M, Kelsey G, Van den Veyver IB. DNA Methylation Dynamics in the Female Germline and Maternal-Effect Mutations That Disrupt Genomic Imprinting. Genes (Basel) 2021; 12:genes12081214. [PMID: 34440388 PMCID: PMC8394515 DOI: 10.3390/genes12081214] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/30/2021] [Accepted: 08/03/2021] [Indexed: 11/16/2022] Open
Abstract
Genomic imprinting is an epigenetic marking process that results in the monoallelic expression of a subset of genes. Many of these ‘imprinted’ genes in mice and humans are involved in embryonic and extraembryonic growth and development, and some have life-long impacts on metabolism. During mammalian development, the genome undergoes waves of (re)programming of DNA methylation and other epigenetic marks. Disturbances in these events can cause imprinting disorders and compromise development. Multi-locus imprinting disturbance (MLID) is a condition by which imprinting defects touch more than one locus. Although most cases with MLID present with clinical features characteristic of one imprinting disorder. Imprinting defects also occur in ‘molar’ pregnancies-which are characterized by highly compromised embryonic development-and in other forms of reproductive compromise presenting clinically as infertility or early pregnancy loss. Pathogenic variants in some of the genes encoding proteins of the subcortical maternal complex (SCMC), a multi-protein complex in the mammalian oocyte, are responsible for a rare subgroup of moles, biparental complete hydatidiform mole (BiCHM), and other adverse reproductive outcomes which have been associated with altered imprinting status of the oocyte, embryo and/or placenta. The finding that defects in a cytoplasmic protein complex could have severe impacts on genomic methylation at critical times in gamete or early embryo development has wider implications beyond these relatively rare disorders. It signifies a potential for adverse maternal physiology, nutrition, or assisted reproduction to cause epigenetic defects at imprinted or other genes. Here, we review key milestones in DNA methylation patterning in the female germline and the embryo focusing on humans. We provide an overview of recent findings regarding DNA methylation deficits causing BiCHM, MLID, and early embryonic arrest. We also summarize identified SCMC mutations with regard to early embryonic arrest, BiCHM, and MLID.
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Affiliation(s)
- Zahra Anvar
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX 77030, USA; (Z.A.); (I.C.); (M.S.)
- Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Imen Chakchouk
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX 77030, USA; (Z.A.); (I.C.); (M.S.)
- Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Hannah Demond
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK;
| | - Momal Sharif
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX 77030, USA; (Z.A.); (I.C.); (M.S.)
- Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Gavin Kelsey
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK;
- Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, UK
- Correspondence: (G.K.); (I.B.V.d.V.); Tel.: +44-1223-496332 (G.K.); +832-824-8125 (I.B.V.d.V.)
| | - Ignatia B. Van den Veyver
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX 77030, USA; (Z.A.); (I.C.); (M.S.)
- Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Correspondence: (G.K.); (I.B.V.d.V.); Tel.: +44-1223-496332 (G.K.); +832-824-8125 (I.B.V.d.V.)
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26
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Eggermann T. Maternal Effect Mutations: A Novel Cause for Human Reproductive Failure. Geburtshilfe Frauenheilkd 2021; 81:780-788. [PMID: 34294945 PMCID: PMC8288500 DOI: 10.1055/a-1396-4390] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 02/19/2021] [Indexed: 12/12/2022] Open
Abstract
Genetic alterations significantly contribute to the aetiology of reproductive failure and comprise monogenic, chromosomal and epigenetic disturbances. The implementation of next-generation sequencing (NGS) based approaches in research and diagnostics allows the comprehensive analysis of these genetic causes, and the increasing detection rates of genetic mutations causing reproductive complications confirm the potential of the new techniques. Whereas mutations affecting the fetal genome are well known to affect pregnancies and their outcome, the contribution of alterations of the maternal genome was widely unclear. With the recent mainly NGS-based identification of maternal effect variants, a new cause of human reproductive failure has been identified. Maternal effect mutations affect the expression of subcortical maternal complex (SCMC) proteins from the maternal genome, and thereby disturb oocyte maturation and progression of the early embryo. They cause a broad range of reproductive failures and pregnancy complications, including infertility, miscarriages, hydatidiform moles, aneuploidies and imprinting disturbances in the fetus. The identification of women carrying these molecular alterations in SCMC encoding genes is therefore essential for a personalised reproductive and genetic counselling. The diagnostic application of new NGS-based assays allows the comprehensive analysis of these factors, and helps to further decipher these functional links between the factors and their disturbances. A close interdisciplinary collaboration between different disciplines is definitely required to further decipher the complex regulation of early embryo development, and to translate the basic research results into clinical practice.
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Affiliation(s)
- Thomas Eggermann
- Institute of Human Genetics, RWTH Aachen University, Aachen, Germany
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27
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Drugs and Epigenetic Molecular Functions. A Pharmacological Data Scientometric Analysis. Int J Mol Sci 2021; 22:ijms22147250. [PMID: 34298869 PMCID: PMC8311652 DOI: 10.3390/ijms22147250] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 06/25/2021] [Accepted: 06/30/2021] [Indexed: 12/14/2022] Open
Abstract
Interactions of drugs with the classical epigenetic mechanism of DNA methylation or histone modification are increasingly being elucidated mechanistically and used to develop novel classes of epigenetic therapeutics. A data science approach is used to synthesize current knowledge on the pharmacological implications of epigenetic regulation of gene expression. Computer-aided knowledge discovery for epigenetic implications of current approved or investigational drugs was performed by querying information from multiple publicly available gold-standard sources to (i) identify enzymes involved in classical epigenetic processes, (ii) screen original biomedical scientific publications including bibliometric analyses, (iii) identify drugs that interact with epigenetic enzymes, including their additional non-epigenetic targets, and (iv) analyze computational functional genomics of drugs with epigenetic interactions. PubMed database search yielded 3051 hits on epigenetics and drugs, starting in 1992 and peaking in 2016. Annual citations increased to a plateau in 2000 and show a downward trend since 2008. Approved and investigational drugs in the DrugBank database included 122 compounds that interacted with 68 unique epigenetic enzymes. Additional molecular functions modulated by these drugs included other enzyme interactions, whereas modulation of ion channels or G-protein-coupled receptors were underrepresented. Epigenetic interactions included (i) drug-induced modulation of DNA methylation, (ii) drug-induced modulation of histone conformations, and (iii) epigenetic modulation of drug effects by interference with pharmacokinetics or pharmacodynamics. Interactions of epigenetic molecular functions and drugs are mutual. Recent research activities on the discovery and development of novel epigenetic therapeutics have passed successfully, whereas epigenetic effects of non-epigenetic drugs or epigenetically induced changes in the targets of common drugs have not yet received the necessary systematic attention in the context of pharmacological plasticity.
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28
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Bebbere D, Albertini DF, Coticchio G, Borini A, Ledda S. The subcortical maternal complex: emerging roles and novel perspectives. Mol Hum Reprod 2021; 27:6311673. [PMID: 34191027 DOI: 10.1093/molehr/gaab043] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/19/2021] [Indexed: 11/13/2022] Open
Abstract
Since its recent discovery, the subcortical maternal complex (SCMC) is emerging as a maternally inherited and crucial biological structure for the initial stages of embryogenesis in mammals. Uniquely expressed in oocytes and preimplantation embryos, where it localizes to the cell subcortex, this multiprotein complex is essential for early embryo development in the mouse and is functionally conserved across mammalian species, including humans. The complex has been linked to key processes leading the transition from oocyte to embryo, including meiotic spindle formation and positioning, regulation of translation, organelle redistribution, and epigenetic reprogramming. Yet, the underlying molecular mechanisms for these diverse functions are just beginning to be understood, hindered by unresolved interplay of SCMC components and variations in early lethal phenotypes. Here we review recent advances confirming involvement of the SCMC in human infertility, revealing an unexpected relationship with offspring health. Moreover, SCMC organization is being further revealed in terms of novel components and interactions with additional cell constituents. Collectively, this evidence prompts new avenues of investigation into possible roles during the process of oogenesis and the regulation of maternal transcript turnover during the oocyte to embryo transition.
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Affiliation(s)
- Daniela Bebbere
- Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | | | | | | | - Sergio Ledda
- Department of Veterinary Medicine, University of Sassari, Sassari, Italy
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29
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Alhendi ASN, Lim D, McKee S, McEntagart M, Tatton-Brown K, Temple IK, Davies JH, Mackay DJG. Whole-genome analysis as a diagnostic tool for patients referred for diagnosis of Silver-Russell syndrome: a real-world study. J Med Genet 2021; 59:613-622. [PMID: 34135092 DOI: 10.1136/jmedgenet-2021-107699] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 05/06/2021] [Indexed: 02/01/2023]
Abstract
BACKGROUND Silver-Russell syndrome (SRS) is an imprinting disorder characterised by prenatal and postnatal growth restriction, but its clinical features are non-specific and its differential diagnosis is broad. Known molecular causes of SRS include imprinting disturbance, single nucleotide variant (SNV), CNV or UPD affecting several genes; however, up to 40% of individuals with a clinical diagnosis of SRS currently receive no positive molecular diagnosis. METHODS To determine whether whole-genome sequencing (WGS) could uncover pathogenic variants missed by current molecular testing, we analysed data of 72 participants recruited to the 100,000 Genomes Project within the clinical category of SRS. RESULTS In 20 participants (27% of the cohort) we identified genetic variants plausibly accounting for SRS. Coding SNVs were identified in genes including CDKN1C, IGF2, IGF1R and ORC1. Maternal-effect variants were found in mothers of five participants, including two participants with imprinting disturbance and one with multilocus imprinting disorder. Two regions of homozygosity were suggestive of UPD involving imprinted regions implicated in SRS and Temple syndrome, and three plausibly pathogenic CNVs were found, including a paternal deletion of PLAGL1. In 48 participants with no plausible pathogenic variant, unbiased analysis of SNVs detected a potential association with STX4. CONCLUSION WGS analysis can detect UPD, CNV and SNV and is potentially a valuable addition to diagnosis of SRS and related growth-restricting disorders.
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Affiliation(s)
- Ahmed S N Alhendi
- Human Genetics and Genomic Medicine, Faculty of Medicine, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Derek Lim
- Department of Clinical Genetics, Birmingham Women's and Children's Hospital, Birmingham, UK
| | - Shane McKee
- Department of Genetic Medicine, Belfast City Hospital, Belfast, UK
| | - Meriel McEntagart
- Department of Clinical Genetics, St George's Healthcare NHS Trust, London, UK
| | | | - I Karen Temple
- Human Genetics and Genomic Medicine, Faculty of Medicine, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Justin H Davies
- Human Genetics and Genomic Medicine, Faculty of Medicine, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Deborah J G Mackay
- Human Genetics and Genomic Medicine, Faculty of Medicine, University Hospital Southampton NHS Foundation Trust, Southampton, UK .,Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust, Salisbury, UK
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NLRP7 Promotes Choriocarcinoma Growth and Progression through the Establishment of an Immunosuppressive Microenvironment. Cancers (Basel) 2021; 13:cancers13122999. [PMID: 34203890 PMCID: PMC8232770 DOI: 10.3390/cancers13122999] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/08/2021] [Accepted: 06/12/2021] [Indexed: 12/14/2022] Open
Abstract
The inflammatory gene NLRP7 is the major gene responsible for recurrent complete hydatidiform moles (CHM), an abnormal pregnancy that can develop into gestational choriocarcinoma (CC). However, the role of NLRP7 in the development and immune tolerance of CC has not been investigated. Three approaches were employed to define the role of NLRP7 in CC development: (i) a clinical study that analyzed human placenta and sera collected from women with normal pregnancies, CHM or CC; (ii) an in vitro study that investigated the impact of NLRP7 knockdown on tumor growth and organization; and (iii) an in vivo study that used two CC mouse models, including an orthotopic model. NLRP7 and circulating inflammatory cytokines were upregulated in tumor cells and in CHM and CC. In tumor cells, NLRP7 functions in an inflammasome-independent manner and promoted their proliferation and 3D organization. Gravid mice placentas injected with CC cells invalidated for NLRP7, exhibited higher maternal immune response, developed smaller tumors, and displayed less metastases. Our data characterized the critical role of NLRP7 in CC and provided evidence of its contribution to the development of an immunosuppressive maternal microenvironment that not only downregulates the maternal immune response but also fosters the growth and progression of CC.
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Kagami M, Hara-Isono K, Matsubara K, Nakabayashi K, Narumi S, Fukami M, Ohkubo Y, Saitsu H, Takada S, Ogata T. ZNF445: a homozygous truncating variant in a patient with Temple syndrome and multilocus imprinting disturbance. Clin Epigenetics 2021; 13:119. [PMID: 34039421 PMCID: PMC8157728 DOI: 10.1186/s13148-021-01106-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 05/18/2021] [Indexed: 11/12/2022] Open
Abstract
Background ZNF445, as well as ZFP57, is involved in the postfertilization methylation maintenance of multiple imprinting-associated differentially methylated regions (iDMRs). Thus, ZNF445 pathogenic variants are predicted to cause multilocus imprinting disturbances (MLIDs), as do ZFP57 pathogenic variants. In particular, the MEG3/DLK1:IG-DMR would be affected, because the postzygotic methylation imprint of the MEG3/DLK1:IG-DMR is maintained primarily by ZNF445, whereas that of most iDMRs is preserved by both ZFP57 and ZNF445 or primarily by ZFP57. Results We searched for a ZNF445 variant(s) in six patients with various imprinting disorders (IDs) caused by epimutations and MLIDs revealed by pyrosequencing for nine iDMRs, without a selection for the original IDs. Re-analysis of the previously obtained whole exome sequencing data identified a homozygous ZNF445 variant (NM_181489.6:c.2803C>T:p.(Gln935*)) producing a truncated protein missing two of 14 zinc finger domains in a patient with Temple syndrome and MLID. In this patient, array-based genomewide methylation analysis revealed severe hypomethylation of most CpGs at the MEG3:TSS-DMR, moderate hypomethylation of roughly two-thirds of CpGs at the H19/IGF2:IG-DMR, and mild-to-moderate hypomethylation of a few CpGs at the DIRAS3:TSS-DMR, MEST:alt-TSS-DMR, IGF2:Ex9-DMR, IGF2:alt-TSS, and GNAS-AS1:TSS-DMR. Furthermore, bisulfite sequencing analysis for the MEG3/DLK1:IG-DMR delineated a markedly hypomethylated segment (CG-A). The heterozygous parents were clinically normal and had virtually no aberrant methylation pattern. Conclusions We identified a ZNF445 pathogenic variant for the first time. Since ZNF445 binds to the MEG3/DLK1:IG-DMR and other iDMRs affected in this patient, the development of Temple syndrome and MLID would primarily be explained by the ZNF445 variant. Furthermore, CG-A may be the target site for ZNF445 within the MEG3/DLK1:IG-DMR. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01106-5.
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Affiliation(s)
- Masayo Kagami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan.
| | - Kaori Hara-Isono
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan
| | - Keiko Matsubara
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal Fetal Biology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan
| | - Satoshi Narumi
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan
| | - Maki Fukami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan
| | - Yumiko Ohkubo
- Department of Pediatrics, Shizuoka Saiseikai Hospital, Oshika 1-1-1, Suruga-ku, Shizuoka, 422-8527, Japan
| | - Hirotomo Saitsu
- Department of Biochemistry, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, 431-3192, Japan
| | - Shuji Takada
- Department of Systems BioMedicine, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan
| | - Tsutomu Ogata
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan. .,Department of Pediatrics, Shizuoka Saiseikai Hospital, Oshika 1-1-1, Suruga-ku, Shizuoka, 422-8527, Japan. .,Department of Biochemistry, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, 431-3192, Japan. .,Department of Pediatrics, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, 431-3192, Japan. .,Department of Pediatrics, Hamamatsu Medical Center, Tomitsuka 328, Naka-ku, Hamamatsu, 432-8580, Japan.
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Pignata L, Sparago A, Palumbo O, Andreucci E, Lapi E, Tenconi R, Carella M, Riccio A, Cerrato F. Mosaic Segmental and Whole-Chromosome Upd(11)mat in Silver-Russell Syndrome. Genes (Basel) 2021; 12:genes12040581. [PMID: 33923683 PMCID: PMC8073375 DOI: 10.3390/genes12040581] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 03/26/2021] [Accepted: 03/26/2021] [Indexed: 12/14/2022] Open
Abstract
Molecular defects altering the expression of the imprinted genes of the 11p15.5 cluster are responsible for the etiology of two congenital disorders characterized by opposite growth disturbances, Silver-Russell syndrome (SRS), associated with growth restriction, and Beckwith-Wiedemann syndrome (BWS), associated with overgrowth. At the molecular level, SRS and BWS are characterized by defects of opposite sign, including loss (LoM) or gain (GoM) of methylation at the H19/IGF2:intergenic differentially methylated region (H19/IGF2:IG-DMR), maternal or paternal duplication (dup) of 11p15.5, maternal (mat) or paternal (pat) uniparental disomy (upd), and gain or loss of function mutations of CDKN1C. However, while upd(11)pat is found in 20% of BWS cases and in the majority of them it is segmental, upd(11)mat is extremely rare, being reported in only two SRS cases to date, and in both of them is extended to the whole chromosome. Here, we report on two novel cases of mosaic upd(11)mat with SRS phenotype. The upd is mosaic and isodisomic in both cases but covers the entire chromosome in one case and is restricted to 11p14.1-pter in the other case. The segmental upd(11)mat adds further to the list of molecular defects of opposite sign in SRS and BWS, making these two imprinting disorders even more specular than previously described.
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Affiliation(s)
- Laura Pignata
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania “Luigi Vanvitelli”, 81100 Caserta, Italy; (L.P.); (A.S.); (F.C.)
| | - Angela Sparago
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania “Luigi Vanvitelli”, 81100 Caserta, Italy; (L.P.); (A.S.); (F.C.)
| | - Orazio Palumbo
- Division of Medical Genetics, Fondazione IRCCS “Casa Sollievo della Sofferenza”, 71013 San Giovanni Rotondo, Italy; (O.P.); (M.C.)
| | - Elena Andreucci
- Medical Genetics Unit, Meyer Children’s Hospital, 50139 Firenze, Italy; (E.A.); (E.L.)
| | - Elisabetta Lapi
- Medical Genetics Unit, Meyer Children’s Hospital, 50139 Firenze, Italy; (E.A.); (E.L.)
| | - Romano Tenconi
- Department of Pediatrics, Clinical Genetics, Università di Padova, 35122 Padova, Italy;
| | - Massimo Carella
- Division of Medical Genetics, Fondazione IRCCS “Casa Sollievo della Sofferenza”, 71013 San Giovanni Rotondo, Italy; (O.P.); (M.C.)
| | - Andrea Riccio
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania “Luigi Vanvitelli”, 81100 Caserta, Italy; (L.P.); (A.S.); (F.C.)
- Institute of Genetics and Biophysics (IGB) “Adriano Buzzati-Traverso”, Consiglio Nazionale delle Ricerche (CNR), 80131 Napoli, Italy
- Correspondence:
| | - Flavia Cerrato
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania “Luigi Vanvitelli”, 81100 Caserta, Italy; (L.P.); (A.S.); (F.C.)
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The genetics of recurrent hydatidiform moles in Mexico: further evidence of a strong founder effect for one mutation in NLRP7 and its widespread. J Assist Reprod Genet 2021; 38:1879-1886. [PMID: 33751332 DOI: 10.1007/s10815-021-02132-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 02/24/2021] [Indexed: 12/11/2022] Open
Abstract
PURPOSE To investigate the frequency of a founder mutation in NLRP7, L750V, in independent cohorts of Mexican patients with recurrent hydatidiform moles (RHMs). METHODS Mutation analysis was performed by Sanger sequencing on DNA from 44 unrelated Mexican patients with RHMs and seven molar tissues from seven additional unrelated patients. RESULTS L750V was present in homozygous or heterozygous state in 37 (86%) patients and was transmitted on the same haplotype to patients from different states of Mexico. We also identified a second founder mutation, c.2810+2T>G in eight (18.1%) patients, and a novel premature stop-codon mutation W653*. CONCLUSION Our data confirm the strong founder effect for L750V, which appears to be the most common mutation in NLRP7. We also report on six healthy live births to five patients with biallelic NLRP7 mutations, two from spontaneous conceptions and four from donated ovum and discuss our recommendations for DNA testing and genetic counseling.
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Rezaei M, Suresh B, Bereke E, Hadipour Z, Aguinaga M, Qian J, Bagga R, Fardaei M, Hemida R, Jagadeesh S, Majewski J, Slim R. Novel pathogenic variants in NLRP7, NLRP5, and PADI6 in patients with recurrent hydatidiform moles and reproductive failure. Clin Genet 2021; 99:823-828. [PMID: 33583041 DOI: 10.1111/cge.13941] [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: 01/25/2021] [Revised: 02/07/2021] [Accepted: 02/10/2021] [Indexed: 12/26/2022]
Abstract
Recurrent hydatidiform moles (RHMs) are human pregnancies with abnormal embryonic development and hyperproliferating trophoblast. Biallelic mutations in NLRP7 and KHDC3L, members of the subcortical maternal complex (SCMC), explain the etiology of RHMs in only 60% of patients. Here we report the identification of seven functional variants in a recessive state in three SCMC members, five in NLRP7, one in NLRP5, and one in PADI6. In NLRP5, we report the first patient with RHMs and biallelic mutations. In PADI6, the patient had four molar pregnancies, two of which had fetuses with various abnormalities including placental mesenchymal dysplasia and intra-uterine growth restriction, which are features of Beckwith-Wiedemann syndrome and Silver Russell syndrome, respectively. Our findings corroborate recent studies and highlight the common oocyte origin of all these conditions and the continuous spectrum of abnormalities associated with deficiencies in the SCMC genes.
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Affiliation(s)
- Maryam Rezaei
- Department of Human Genetics, McGill University Health Centre Research Institute, Montreal, Quebec, Canada
| | - Beena Suresh
- Department of Clinical Genetics & Genetic counselling, Mediscan Systems, Chennai, India
| | - Eric Bereke
- Department of Human Genetics, McGill University Health Centre Research Institute, Montreal, Quebec, Canada.,Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Zahra Hadipour
- Medical Genetics Department, Atieh Research Center and Hospital, Tehran, Iran
| | - Monica Aguinaga
- Genetics and Genomics Department, Instituto Nacional de Perinatologia, Mexico City, Mexico
| | - Jianhua Qian
- Department of Gynecology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Rashmi Bagga
- Department of Obstetrics & Gynecology, Post Graduate Institute of Medical, Education and Research, PGIMER, Chandigarh, India
| | - Majid Fardaei
- Department of Medical Genetics, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Reda Hemida
- Obstetrics and Gynecology, Mansoura University, Mansoura, Egypt
| | - Sujatha Jagadeesh
- Department of Clinical Genetics & Genetic counselling, Mediscan Systems, Chennai, India
| | - Jacek Majewski
- Department of Human Genetics, McGill University Health Centre Research Institute, Montreal, Quebec, Canada.,Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Rima Slim
- Department of Human Genetics, McGill University Health Centre Research Institute, Montreal, Quebec, Canada.,Departments of Obstetrics and Gynecology, McGill University Health Centre, Montreal, Quebec, Canada
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35
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Choufani S, Ko JM, Lou Y, Shuman C, Fishman L, Weksberg R. Paternal Uniparental Disomy of the Entire Chromosome 20 in a Child with Beckwith-Wiedemann Syndrome. Genes (Basel) 2021; 12:genes12020172. [PMID: 33513760 PMCID: PMC7911624 DOI: 10.3390/genes12020172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 01/22/2021] [Accepted: 01/25/2021] [Indexed: 12/14/2022] Open
Abstract
Epigenetic alterations at imprinted genes on different chromosomes have been linked to several imprinting disorders (IDs) such as Beckwith-Wiedemann syndrome (BWS) and pseudohypoparathyroidism type 1b (PHP1b). Here, we present a male patient with these two distinct IDs caused by two independent mechanisms-loss of methylation (LOM) at chromosome 11p15.5 associated with multi-locus imprinting disturbances (MLID and paternal uniparental disomy of chromosome 20 (patUPD20). A clinical diagnosis of BWS was made based on the clinical features of macrosomia, macroglossia, and umbilical hernia. The diagnosis of PHP1b was supported by the presence of reduced growth velocity and mild learning disability as well as hypocalcemia and hyperphosphatemia at 14 years of age. Molecular analyses, including genome-wide DNA methylation (Illumina 450k array), bisulfite pyrosequencing, single nucleotide polymorphism (SNP) array and microsatellite analysis, demonstrated loss of methylation (LOM) at IC2 on chromosome 11p15.5, and paternal isodisomy of the entire chromosome 20. In addition, imprinting disturbances were noted at the differentially methylated regions (DMRs) associated with DIRAS3 on chromosome 1 and PLAGL1 on chromosome 6. This is the first case report of PHP1b due to patUPD20 diagnosed in a BWS patient with LOM at IC2 demonstrating etiologic heterogeneity for multiple imprinting disorders in a single individual.
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Affiliation(s)
- Sanaa Choufani
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; (S.C.); (J.M.K.); (Y.L.)
| | - Jung Min Ko
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; (S.C.); (J.M.K.); (Y.L.)
- Department of Pediatrics, Seoul National University Children’s Hospital, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Youliang Lou
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; (S.C.); (J.M.K.); (Y.L.)
| | - Cheryl Shuman
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1X8, Canada;
| | - Leona Fishman
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada;
- Department of Pediatrics, University of Toronto, Toronto, ON M5S 1A1, Canada
| | - Rosanna Weksberg
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; (S.C.); (J.M.K.); (Y.L.)
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1X8, Canada;
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada;
- Department of Pediatrics, University of Toronto, Toronto, ON M5S 1A1, Canada
- Correspondence:
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Pignata L, Palumbo O, Cerrato F, Acurzio B, de Álava E, Roma J, Gallego S, Mora J, Carella M, Riccio A, Verde G. Both Epimutations and Chromosome Aberrations Affect Multiple Imprinted Loci in Aggressive Wilms Tumors. Cancers (Basel) 2020; 12:cancers12113411. [PMID: 33217932 PMCID: PMC7698742 DOI: 10.3390/cancers12113411] [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: 10/26/2020] [Revised: 11/11/2020] [Accepted: 11/16/2020] [Indexed: 12/21/2022] Open
Abstract
The embryonal renal cancer Wilms tumor (WT) accounts for 7% of all children's malignancies. Its most frequent molecular defect is represented by DNA methylation abnormalities at the imprinted 11p15.5 region. Multiple imprinted methylation alterations dictated by chromosome copy-number variations have been recently demonstrated in adult cancers, raising the question of whether multiple imprinted loci were also affected in WT. To address this issue, we analyzed DNA methylation and chromosome profiles of 7 imprinted loci in 48 WT samples. The results demonstrated that methylation abnormalities of multiple imprinted loci occurred in 35% of the cases, but that they were associated with either chromosome aberrations or normal chromosome profiles. Multiple imprinted methylation changes were correlated with tumor stage and presence of metastasis, indicating that these epimutations were more frequent in highly aggressive tumors. When chromosome profiles were affected, these alterations were extended to flanking cancer driver genes. Overall, this study demonstrates the presence of multiple imprinted methylation defects in aggressive WTs and suggests that the mechanism by which they arise in embryonal and adult cancers is different.
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Affiliation(s)
- Laura Pignata
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies, University of Campania ‘Luigi Vanvitelli’, 81100 Caserta, Italy; (L.P.); (F.C.)
- Institute of Genetics and Biophysics ‘Adriano Buzzati-Traverso’ CNR, 80131-Napoli, Italy;
| | - Orazio Palumbo
- Division of Medical Genetics, Fondazione IRCCS “Casa Sollievo della Sofferenza”, 71013 San Giovanni Rotondo (FG), Italy; (O.P.); (M.C.)
| | - Flavia Cerrato
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies, University of Campania ‘Luigi Vanvitelli’, 81100 Caserta, Italy; (L.P.); (F.C.)
| | - Basilia Acurzio
- Institute of Genetics and Biophysics ‘Adriano Buzzati-Traverso’ CNR, 80131-Napoli, Italy;
| | - Enrique de Álava
- Department of Pathology, Institute of Biomedicine of Sevilla (IBiS), Virgen del Rocio University Hospital/CSIC/University of Sevilla/CIBERONC, 41013 Seville, Spain;
- Department of Normal and Pathological Cytology and Histology, School of Medicine, University of Seville, 08035 Seville, Spain
| | - Josep Roma
- Group of Translational Research in Child and Adolescent Cancer, Vall d’Hebron Research Institute-Universitat Autònoma de Barcelona, 08193 Barcelona, Spain; (J.R.); (S.G.)
| | - Soledad Gallego
- Group of Translational Research in Child and Adolescent Cancer, Vall d’Hebron Research Institute-Universitat Autònoma de Barcelona, 08193 Barcelona, Spain; (J.R.); (S.G.)
| | - Jaume Mora
- Pediatric Cancer Center Barcelona (PCCB), Hospital Sant Joan de Déu, Esplugues de Llobregat, 08950 Barcelona, Spain;
| | - Massimo Carella
- Division of Medical Genetics, Fondazione IRCCS “Casa Sollievo della Sofferenza”, 71013 San Giovanni Rotondo (FG), Italy; (O.P.); (M.C.)
| | - Andrea Riccio
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies, University of Campania ‘Luigi Vanvitelli’, 81100 Caserta, Italy; (L.P.); (F.C.)
- Institute of Genetics and Biophysics ‘Adriano Buzzati-Traverso’ CNR, 80131-Napoli, Italy;
- Correspondence: (A.R.); (G.V.)
| | - Gaetano Verde
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies, University of Campania ‘Luigi Vanvitelli’, 81100 Caserta, Italy; (L.P.); (F.C.)
- Institute of Genetics and Biophysics ‘Adriano Buzzati-Traverso’ CNR, 80131-Napoli, Italy;
- Correspondence: (A.R.); (G.V.)
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