1
|
Higashimoto K, Sun F, Imagawa E, Saida K, Miyake N, Hara S, Yatsuki H, Kubiura-Ichimaru M, Fujita A, Mizuguchi T, Matsumoto N, Soejima H. Whole-exome sequencing reveals causative genetic variants for several overgrowth syndromes in molecularly negative Beckwith-Wiedemann spectrum. J Med Genet 2024; 61:590-594. [PMID: 38228391 DOI: 10.1136/jmg-2023-109621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 01/03/2024] [Indexed: 01/18/2024]
Abstract
Background Beckwith-Wiedemann syndrome (BWS) is an imprinting disorder caused by (epi)genetic alterations at 11p15. Because approximately 20% of patients test negative via molecular testing of peripheral blood leukocytes, the concept of Beckwith-Wiedemann spectrum (BWSp) was established to encompass a broader cohort with diverse and overlapping phenotypes. The prevalence of other overgrowth syndromes concealed within molecularly negative BWSp remains unexplored. Methods We conducted whole-exome sequencing (WES) on 69 singleton patients exhibiting molecularly negative BWSp. Variants were confirmed by Sanger sequencing or quantitative genomic PCR. We compared BWSp scores and clinical features between groups with classical BWS (cBWS), atypical BWS or isolated lateralised overgrowth (aBWS+ILO) and overgrowth syndromes identified via WES. Results Ten patients, one classified as aBWS and nine as cBWS, showed causative gene variants for Simpson-Golabi-Behmel syndrome (five patients), Sotos syndrome (two), Imagawa-Matsumoto syndrome (one), glycosylphosphatidylinositol biosynthesis defect 11 (one) or 8q duplication/9p deletion (one). BWSp scores did not distinguish between cBWS and other overgrowth syndromes. Birth weight and height in other overgrowth syndromes were significantly larger than in aBWS+ILO and cBWS, with varying intergroup frequencies of clinical features. Conclusion Molecularly negative BWSp encapsulates other syndromes, and considering both WES and clinical features may facilitate accurate diagnosis.
Collapse
Affiliation(s)
- Ken Higashimoto
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Saga University Faculty of Medicine, Saga, Japan
| | - Feifei Sun
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Saga University Faculty of Medicine, Saga, Japan
- Department of Ultrasound, Shengjing Hospital of China Medical University, Shenyang, China
| | - Eri Imagawa
- Department of Pediatrics, The Jikei University School of Medicine, Tokyo, Japan
| | - Ken Saida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
- Department of Human Genetics, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Satoshi Hara
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Saga University Faculty of Medicine, Saga, Japan
| | - Hitomi Yatsuki
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Saga University Faculty of Medicine, Saga, Japan
| | - Musashi Kubiura-Ichimaru
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Saga University Faculty of Medicine, Saga, Japan
| | - Atsushi Fujita
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Hidenobu Soejima
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Saga University Faculty of Medicine, Saga, Japan
| |
Collapse
|
2
|
Alhendi ASN, Gazdagh G, Lim D, McMullan D, Wright M, Temple IK, Davies JH, Mackay DJG. A case of mosaic deletion of paternally-inherited PLAGL1 and two cases of upd(6)mat add to evidence for PLAGL1 under-expression as a cause of growth restriction. Am J Med Genet A 2024; 194:383-388. [PMID: 37850521 DOI: 10.1002/ajmg.a.63448] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 09/18/2023] [Accepted: 10/06/2023] [Indexed: 10/19/2023]
Abstract
PLAGL1 is one of a group of imprinted genes, whose altered expression causes imprinting disorders impacting growth, development, metabolism, and behavior. PLAGL1 over-expression causes transient neonatal diabetes mellitus (TNDM type 1) and, based on murine models, under-expression would be expected to cause growth restriction. However, only some reported individuals with upd(6)mat have growth restriction, giving rise to uncertainty about the role of PLAGL1 in human growth. Here we report three individuals investigated for growth restriction, two with upd(6)mat and one with a mosaic deletion of the paternally-inherited allele of PLAGL1. These cases add to evidence of its involvement in pre- and early post-natal human growth.
Collapse
Affiliation(s)
| | - Gabriella Gazdagh
- Faculty of Medicine, University of Southampton, UK
- University Hospital Southampton, UK
| | - Derek Lim
- Birmingham Women's and Children's Foundation Trust, UK
| | | | | | - I Karen Temple
- Faculty of Medicine, University of Southampton, UK
- University Hospital Southampton, UK
| | - Justin H Davies
- Faculty of Medicine, University of Southampton, UK
- University Hospital Southampton, UK
| | | |
Collapse
|
3
|
Pignata L, Cecere F, Acquaviva F, D’Angelo E, Cioffi D, Pellino V, Palumbo O, Palumbo P, Carella M, Sparago A, De Brasi D, Cerrato F, Riccio A. Co-occurrence of Beckwith-Wiedemann syndrome and pseudohypoparathyroidism type 1B: coincidence or common molecular mechanism? Front Cell Dev Biol 2023; 11:1237629. [PMID: 37635873 PMCID: PMC10448386 DOI: 10.3389/fcell.2023.1237629] [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: 06/09/2023] [Accepted: 07/31/2023] [Indexed: 08/29/2023] Open
Abstract
Imprinting disorders are congenital diseases caused by dysregulation of genomic imprinting, affecting growth, neurocognitive development, metabolism and cancer predisposition. Overlapping clinical features are often observed among this group of diseases. In rare cases, two fully expressed imprinting disorders may coexist in the same patient. A dozen cases of this type have been reported so far. Most of them are represented by individuals affected by Beckwith-Wiedemann spectrum (BWSp) and Transient Neonatal Diabetes Mellitus (TNDM) or BWSp and Pseudo-hypoparathyroidism type 1B (PHP1B). All these patients displayed Multilocus imprinting disturbances (MLID). Here, we report the first case of co-occurrence of BWS and PHP1B in the same individual in absence of MLID. Genome-wide methylation and SNP-array analyses demonstrated loss of methylation of the KCNQ1OT1:TSS-DMR on chromosome 11p15.5 as molecular cause of BWSp, and upd(20)pat as cause of PHP1B. The absence of MLID and the heterodisomy of chromosome 20 suggests that BWSp and PHP1B arose through distinct and independent mechanism in our patient. However, we cannot exclude that the rare combination of the epigenetic defect on chromosome 11 and the UPD on chromosome 20 may originate from a common so far undetermined predisposing molecular lesion. A better comprehension of the molecular mechanisms underlying the co-occurrence of two imprinting disorders will improve genetic counselling and estimate of familial recurrence risk of these rare cases. Furthermore, our study also supports the importance of multilocus molecular testing for revealing MLID as well as complex cases of imprinting disorders.
Collapse
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
| | - Fabio Acquaviva
- UOSD Genetica Medica, Dipartimento di Pediatria Generale e d’Urgenza, AORN Santobono-Pausilipon, Naples, Italy
| | - Emilia D’Angelo
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania “Luigi Vanvitelli”, Caserta, Italy
| | - Daniela Cioffi
- UOSD Auxologia e Endocrinologia Pediatrica, Dipartimento di Pediatria Specialistica, AORN Santobono-Pausilipon, Naples, Italy
| | - Valeria Pellino
- UOSD Auxologia e Endocrinologia Pediatrica, Dipartimento di Pediatria Specialistica, AORN Santobono-Pausilipon, Naples, Italy
| | - Orazio Palumbo
- Division of Medical Genetics, Fondazione IRCCS “Casa Sollievo della Sofferenza”, San Giovanni Rotondo, Italy
| | - Pietro Palumbo
- Division of Medical Genetics, Fondazione IRCCS “Casa Sollievo della Sofferenza”, San Giovanni Rotondo, Italy
| | - Massimo Carella
- Division of Medical Genetics, Fondazione IRCCS “Casa Sollievo della Sofferenza”, San Giovanni Rotondo, Italy
| | - Angela Sparago
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania “Luigi Vanvitelli”, Caserta, Italy
| | - Daniele De Brasi
- UOSD Genetica Medica, Dipartimento di Pediatria Generale e d’Urgenza, AORN Santobono-Pausilipon, Naples, Italy
| | - Flavia Cerrato
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania “Luigi Vanvitelli”, Caserta, Italy
| | - Andrea Riccio
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania “Luigi Vanvitelli”, Caserta, Italy
- Istituto di Genetica e Biofisica “Adriano Buzzati Traverso” Consiglio Nazionale delle Ricerche, Naples, Italy
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
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.
Collapse
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.
| |
Collapse
|
6
|
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.
Collapse
|