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Cong X, Zhang T, Li Z, Luo X, Hu L, Liu W. Prenatal diagnosis of a trisomy 7 mosaic case: CMA, CNV-seq, karyotyping, interphase FISH, and MS-MLPA, which technique to choose? BMC Pregnancy Childbirth 2024; 24:338. [PMID: 38702634 PMCID: PMC11067092 DOI: 10.1186/s12884-024-06522-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 04/15/2024] [Indexed: 05/06/2024] Open
Abstract
OBJECTIVE This study aims to perform a prenatal genetic diagnosis of a high-risk fetus with trisomy 7 identified by noninvasive prenatal testing (NIPT) and to evaluate the efficacy of different genetic testing techniques for prenatal diagnosis of trisomy mosaicism. METHODS For prenatal diagnosis of a pregnant woman with a high risk of trisomy 7 suggested by NIPT, karyotyping and chromosomal microarray analysis (CMA) were performed on an amniotic fluid sample. Low-depth whole-genome copy number variation sequencing (CNV-seq) and fluorescence in situ hybridization (FISH) were used to clarify the results further. In addition, methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) was performed to analyze the possibility of uniparental disomy(UPD). RESULTS Amniotic fluid karyotype analysis revealed a 46, XX result. Approximately 20% mosaic trisomy 7 was detected according to the CMA result. About 16% and 4% of mosaicism was detected by CNV-seq and FISH, respectively. MS-MLPA showed no methylation abnormalities. The fetal ultrasound did not show any detectable abnormalities except for mild intrauterine growth retardation seen at 39 weeks of gestation. After receiving genetic counseling, the expectant mother decided to continue the pregnancy, and follow-up within three months of delivery was normal. CONCLUSION In high-risk NIPT diagnosis, a combination of cytogenetic and molecular genetic techniques proves fruitful in detecting low-level mosaicism. Furthermore, the exclusion of UPD on chromosome 7 remains crucial when NIPT indicates a positive prenatal diagnosis of trisomy 7.
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Affiliation(s)
- Xiaoyi Cong
- Longgang District Maternity & Child Healthcare Hospital of Shenzhen City (Longgang Maternity and Child Institute of Shantou University Medical College), Shenzhen, 518172, China
- Longgang District Key Laboratory for Birth Defects Prevention, Shenzhen, 518172, China
| | - Tong Zhang
- Longgang District Maternity & Child Healthcare Hospital of Shenzhen City (Longgang Maternity and Child Institute of Shantou University Medical College), Shenzhen, 518172, China
- Longgang District Key Laboratory for Birth Defects Prevention, Shenzhen, 518172, China
| | - Zhenming Li
- Longgang District Maternity & Child Healthcare Hospital of Shenzhen City (Longgang Maternity and Child Institute of Shantou University Medical College), Shenzhen, 518172, China
- Longgang District Key Laboratory for Birth Defects Prevention, Shenzhen, 518172, China
| | - Xiaojin Luo
- Longgang District Maternity & Child Healthcare Hospital of Shenzhen City (Longgang Maternity and Child Institute of Shantou University Medical College), Shenzhen, 518172, China
- Longgang District Key Laboratory for Birth Defects Prevention, Shenzhen, 518172, China
| | - Liang Hu
- Longgang District Maternity & Child Healthcare Hospital of Shenzhen City (Longgang Maternity and Child Institute of Shantou University Medical College), Shenzhen, 518172, China
- Longgang District Key Laboratory for Birth Defects Prevention, Shenzhen, 518172, China
| | - Weiqiang Liu
- Longgang District Maternity & Child Healthcare Hospital of Shenzhen City (Longgang Maternity and Child Institute of Shantou University Medical College), Shenzhen, 518172, China.
- Longgang District Key Laboratory for Birth Defects Prevention, Shenzhen, 518172, China.
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Yang Y, Jiang S, Nie M, Jiang Y, Li M, Xia W, Xing X, Wang O, Pan H. Novel 4.18 Mb deletion resulting in 2q37 microdeletion syndrome combined with PTH resistance found in one Chinese patient. Endocrine 2024:10.1007/s12020-024-03740-4. [PMID: 38393510 DOI: 10.1007/s12020-024-03740-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 02/09/2024] [Indexed: 02/25/2024]
Abstract
BACKGROUND 2q37 microdeletion syndrome is a rare clinical condition characterized by a series of physical abnormalities. Its Albright hereditary osteodystrophy (AHO)-like manifestations and possible complication of biochemical abnormalities indicating PTH resistance greatly increased the likelihood of misdiagnosis with classic pseudohypoparathyroidism (PHP) caused by GNAS mutation or methylation alteration, even though there have only been six reports of such clinical occasions. PURPOSE to investigate the underlying genetic defect in a male patient presenting hypocalcemia, elevated PTH and with a history of kyphosis. METHOD clinical information was collected, while the DNA was extracted from peripheral blood and subjected to methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) and exome sequencing. RESULT Physical characteristics featuring short stature, obesity, round face, short neck, and shortened 4th metacarpal and laboratory examination of the patient suggested the presence of PTH resistance, which is indicative of PHP. MS-MLPA did not reveal methylation alterations or deletions of GNAS, STX16 or other monogenetic alterations responsible for iPPSDs, but WES revealed a long-range deletion of approximately 4.18 Mb of the 2q37 region that spanned AGAP1 to NDUFA10, indicating that the patient had 2q37 microdeletion syndrome with PTH resistance. CONCLUSION After undergoing MS-MLPA and exome sequencing, a novel deletion spanning 4.18 Mb on the 2q37 region was identified in one male patient, clarifying the diagnosis of 2q37 microdeletion syndrome with PTH resistance. The new genetic discovery added to our understanding of the molecular defects that cause inactivating PTH/PTH-related protein signaling disorders (iPPSDs).
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Affiliation(s)
- Yi Yang
- Department of Endocrinology, Key Laboratory of Endocrinology, National Health Commission, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Siqi Jiang
- Department of Endocrinology, Key Laboratory of Endocrinology, National Health Commission, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Min Nie
- Department of Endocrinology, Key Laboratory of Endocrinology, National Health Commission, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Yan Jiang
- Department of Endocrinology, Key Laboratory of Endocrinology, National Health Commission, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Mei Li
- Department of Endocrinology, Key Laboratory of Endocrinology, National Health Commission, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Weibo Xia
- Department of Endocrinology, Key Laboratory of Endocrinology, National Health Commission, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Xiaoping Xing
- Department of Endocrinology, Key Laboratory of Endocrinology, National Health Commission, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Ou Wang
- Department of Endocrinology, Key Laboratory of Endocrinology, National Health Commission, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China.
| | - Hui Pan
- Department of Endocrinology, Key Laboratory of Endocrinology, National Health Commission, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China.
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Prapasrat C, Onsod P, Korkiatsakul V, Rerkamnuaychoke B, Wattanasirichaigoon D, Chareonsirisuthigul T. The Utilization of MS-MLPA as the First-Line Test for the Diagnosis of Prader-Willi Syndrome in Thai Patients. J Pediatr Genet 2023; 12:273-279. [PMID: 38162164 PMCID: PMC10756717 DOI: 10.1055/s-0041-1741008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 11/22/2021] [Indexed: 10/19/2022]
Abstract
Prader-Willi syndrome (PWS) is a genetic disorder caused by the expression disruption of genes on the paternally inherited allele of chromosome 15q11.2-q13. Apart from clinical diagnostic criteria, PWS is confirmed by genetic testing. Methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) is one of the molecular techniques used to analyze this syndrome. This study aimed to evaluate the concordance of the test results of MS-MLPA with conventional techniques in the diagnosis of PWS in Thai patients. Forty leftover specimens from routine genetic testing (MS-PCR and FISH) were tested to obtain MS-MLPA results. By comparison, perfect concordance was shown between the result of MS-MLPA and those of conventional techniques. In conclusion, MS-MLPA is an accurate and cost-effective assay that can be used to confirm PWS diagnosis with explicit deletion of affected genes.
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Affiliation(s)
- Chanita Prapasrat
- Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Preyaporn Onsod
- Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Veerawat Korkiatsakul
- Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Budsaba Rerkamnuaychoke
- Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Duangrurdee Wattanasirichaigoon
- Department of Pediatrics, Division of Medical Genetics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Takol Chareonsirisuthigul
- Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Tüysüz B, Kasap B, Uludağ Alkaya D, Alp Ünkar Z, Köseoğlu P, Geyik F, Özer E, Önal H, Gezdirici A, Ercan O. Investigation of (Epi)genetic causes in syndromic short children born small for gestational age. Eur J Med Genet 2023; 66:104854. [PMID: 37758162 DOI: 10.1016/j.ejmg.2023.104854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 08/08/2023] [Accepted: 09/24/2023] [Indexed: 10/03/2023]
Abstract
Intrauterine onset syndromic short stature constitutes a group of diseases that pose challenges in differential diagnosis due to their rarity and clinical as well as molecular heterogeneity. The aim of this study was to investigate the presence of (epi)genetic causes in children born small for gestational age (SGA) and manifesting clinically undiagnosed syndromic short stature. The study group comprised twenty-nine cases selected from the syndromic SGA cohort. Various analyses were performed, including chromosomal microarray (CMA), methylation-specific-multiple ligation probe amplification for chromosomes 6,14 and 20, and whole exome sequencing (WES). Pathogenic copy number variants (CNVs) on chromosomes 2q13, 22q11.3, Xp22.33, 17q21.31, 19p13.13 and 4p16.31 causing syndromic growth disturbance were detected in six patients. Maternal uniparental disomy 14 was identified in a patient. WES was performed in the remaining 22 patients, revealing pathogenic variants in nine cases; six were monoallelic (ACAN, ARID2, NIPBL, PIK3R1, SMAD4, BRIP1), two were biallelic (BRCA2, RFWD3) and one was hemizygous (HUWE1). Seven of these were novel. Craniofacial dysmorphism, which is an important clue for the diagnosis of syndromes, was very mild in all patients. This study unveiled, for the first time, that ARID2 mutatios can cause syndromic SGA. In conclusion, a high (55.2%) diagnosis rate was achieved through the utilization of CMA, epigenetic and WES analyzes; 15 rare syndromes were defined, who were born with SGA and had atypical and/or mild dysmorphic findings. This study not only drew attention to the association of some rare syndromes with SGA, but also introduced novel genes and CNVs as potential contributors to syndromic SGA.
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Affiliation(s)
- Beyhan Tüysüz
- Department of Pediatric Genetics, Istanbul University-Cerrahpaşa, Cerrahpaşa Medical Faculty, Istanbul, Turkey.
| | - Büşra Kasap
- Department of Pediatric Genetics, Istanbul University-Cerrahpaşa, Cerrahpaşa Medical Faculty, Istanbul, Turkey
| | - Dilek Uludağ Alkaya
- Department of Pediatric Genetics, Istanbul University-Cerrahpaşa, Cerrahpaşa Medical Faculty, Istanbul, Turkey
| | - Zeynep Alp Ünkar
- Department of Neonatology, Istanbul University-Cerrahpaşa, Cerrahpaşa Medical Faculty, Istanbul, Turkey
| | - Pınar Köseoğlu
- Department of Genetics, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Filiz Geyik
- Department of Genetics, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Emre Özer
- Department of Pediatric Genetics, Istanbul University-Cerrahpaşa, Cerrahpaşa Medical Faculty, Istanbul, Turkey
| | - Hasan Önal
- Department of Pediatric Endocrinology, University of Health Sciences Turkey, Başakşehir Çam ve Sakura City Hospital, Istanbul, Turkey
| | - Alper Gezdirici
- Department of Medical Genetic, University of Health Sciences Turkey, Başakşehir Çam ve Sakura City Hospital, Istanbul, Turkey
| | - Oya Ercan
- Department of Pediatric Endocrinology, Istanbul University-Cerrahpaşa, Cerrahpaşa Medical Faculty, Istanbul, Turkey
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Manero-Azua A, Pereda A, Llano-Rivas I, Garin I, Perez de Nanclares G. Incidental finding at methylation-specific multiplex ligation-dependent probe amplification ( MS-MLPA): how to proceed? Front Genet 2023; 14:1274056. [PMID: 37854056 PMCID: PMC10580081 DOI: 10.3389/fgene.2023.1274056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 09/19/2023] [Indexed: 10/20/2023] Open
Abstract
Introduction: Since the advent of new generation sequencing, professionals are aware of the possibility of obtaining findings unrelated to the pathology under study. However, this possibility is usually forgotten in the case of studies aimed at a single gene or region. We report a case of a 16-month-old girl with clinical suspicion of Silver-Russell syndrome (SRS). Methods: Following the international SRS consensus, methylation alterations and copy number variations (CNVs) at 11p15 region and maternal uniparental disomy of chromosome 7 were analysed and discarded by MS-MLPA. Results: Unexpectedly, the 11p15 region MS-MLPA showed a decrease in the signal of a copy number reference probe. Deletions affecting a single probe are inconclusive. So, we faced the ethical dilemma of whether it was appropriate to confirm this alteration with independent techniques and to offer a diagnostic possibility that was in no way related to clinical suspicion. Fortunately, in this particular case, the informed consent had not been specific to a particular pathology but to any disorder associated with growth failure. Performed alternative studies allowed the final diagnosis of 22q deletion syndrome. Conclusion: We demonstrate the importance of informing patients about the possibility of obtaining incidental findings in genetic techniques (not only in next generation sequencing) during pre-test genetic counselling consultations. In addition, we highlight the relevance of including in the informed consent the option of knowing these unexpected incidental findings as in some cases, this will help to elucidate the definitive diagnosis and provide the correct follow-up and treatment.
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Affiliation(s)
- Africa Manero-Azua
- Rare Diseases Research Group, Molecular (Epi) Genetics Laboratory, Bioaraba Health Research Institute, Araba University Hospital-Txagorritxu, Vitoria-Gasteiz, Araba, Spain
| | - Arrate Pereda
- Rare Diseases Research Group, Molecular (Epi) Genetics Laboratory, Bioaraba Health Research Institute, Araba University Hospital-Txagorritxu, Vitoria-Gasteiz, Araba, Spain
| | - Isabel Llano-Rivas
- Service of Genetics, Hospital Universitario Cruces, Barakaldo, Bizkaia, Spain
| | - Intza Garin
- Service of Genetics, Hospital Universitario Cruces, Barakaldo, Bizkaia, Spain
| | - Guiomar Perez de Nanclares
- Rare Diseases Research Group, Molecular (Epi) Genetics Laboratory, Bioaraba Health Research Institute, Araba University Hospital-Txagorritxu, Vitoria-Gasteiz, Araba, Spain
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Mastromoro G, Guadagnolo D, Marchionni E, Torres B, Goldoni M, Onori A, Bernardini L, De Luca A, Torrente I, Pizzuti A. Mosaic genome-wide paternal uniparental disomy after discordant results from primary fetal samples and cultured cells. Am J Med Genet A 2023; 191:1101-1106. [PMID: 36598152 DOI: 10.1002/ajmg.a.63112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 12/15/2022] [Accepted: 12/21/2022] [Indexed: 01/05/2023]
Abstract
Mosaic genome-wide paternal uniparental disomy (GWpUPD) is a rare condition in which two euploid cell lines coexist in the same individual, one with biparental content and one with genome-wide paternal isodisomy. We report a complex prenatal diagnosis with discordant results from cultured and uncultured samples. A pregnant woman was referred for placental mesenchymal dysplasia and fetal omphalocele. Karyotype, array-CGH and Beckwith-Wiedemann Syndrome (BWS) testing (methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) of 11p15) performed on amniocytes were negative. After intrauterine fetal demise, the clinical suspicion persisted and BWS MS-MLPA was repeated on cultured cells from umbilical cord and amniotic fluid, revealing a mosaicism for KvH19 hypermethylation/KCNQ1OT1:TSS:DMR hypomethylation. These results, along with microsatellite analysis of the BWS region, were consistent with mosaic paternal 11p15 isodisomy. A concurrent maternal contamination exclusion test, analyzing polymorphic microsatellite markers on multiple chromosomes, showed an imbalance in favor of paternal alleles at all examined loci on cultured amniocytes and umbilical cord samples. This led to suspicion of mosaic GWpUPD, later confirmed by SNP-array, identifying a mosaic genome-wide paternal isodisomy affecting 60% of fetal cells. The assessment of mosaic GWpUPD requires multiple approaches beyond the current established diagnostic processes, also entertaining possible low-rate mosaicism. Clinical acumen and an integrated testing approach are the key to a successful diagnosis.
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Affiliation(s)
- Gioia Mastromoro
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Daniele Guadagnolo
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Enrica Marchionni
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Barbara Torres
- Medical Genetics Division, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy
| | - Marina Goldoni
- Medical Genetics Division, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy
| | - Annamaria Onori
- Medical Genetics Division, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy
| | - Laura Bernardini
- Medical Genetics Division, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy
| | - Alessandro De Luca
- Medical Genetics Division, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy
| | - Isabella Torrente
- Medical Genetics Division, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy
| | - Antonio Pizzuti
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy.,Medical Genetics Division, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Punatar R, Egense A, Mao R, Procter M, Bosworth M, Quigley DI, Angkustsiri K, Shankar SP. Atypical presentation of Angelman syndrome with intact expressive language due to low-level mosaicism. Mol Genet Genomic Med 2022; 10:e2018. [PMID: 35929060 PMCID: PMC9544204 DOI: 10.1002/mgg3.2018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 07/08/2022] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND Angelman syndrome (AS) occurs due to a lack of expression or function of the maternally inherited UBE3A gene. Individuals with AS typically have significant developmental delay, severe speech impairment with absent to minimal verbal language, gait abnormalities including ataxia, and an incongruous happy demeanor. The majority of individuals with AS also have seizures and microcephaly. Some individuals with mosaic AS have been reported to have expressive language and milder levels of developmental delay. CASE REPORT We report a male patient presenting with mild to moderate intellectual disability, hyperphagia, obesity, and the ability to communicate verbally. His phenotype was suggestive of Prader-Willi syndrome. However, methylation testing was positive for Angelman syndrome and additional methylation specific multiplex ligation-dependent amplification (MS-MLPA) study revealed low-level mosaicism for AS. CONCLUSION A broader phenotypic spectrum should be considered for AS as patients with atypical presentations may otherwise elude diagnosis.
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Affiliation(s)
- Ruchi Punatar
- Division of Developmental Behavioral Pediatrics, Department of Pediatrics, University of California Davis, Sacramento, California, USA.,MIND Institute, University of California Davis, Sacramento, California, USA
| | - Alena Egense
- MIND Institute, University of California Davis, Sacramento, California, USA.,Division of Genomic Medicine, Department of Pediatrics, University of California Davis, Sacramento, California, USA
| | - Rong Mao
- ARUP Laboratories, Salt Lake City, Utah, USA.,Department of Pathology, University of Utah, Salt Lake City, Utah, USA
| | | | | | | | - Kathleen Angkustsiri
- Division of Developmental Behavioral Pediatrics, Department of Pediatrics, University of California Davis, Sacramento, California, USA.,MIND Institute, University of California Davis, Sacramento, California, USA
| | - Suma P Shankar
- MIND Institute, University of California Davis, Sacramento, California, USA.,Division of Genomic Medicine, Department of Pediatrics, University of California Davis, Sacramento, California, USA
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10
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Zhang Q, Zhang C, Wang Y, Hao S, Shi J, Feng X, Zheng L, Wang X, Xue C, Zhou B, Liu F, Zhao F, Li X, Deng L, Hou J, Meng Z. Identification of a novel ANK1 mutation in hereditary spherocytosis co-existing with BWS. Mol Genet Genomic Med 2022; 10:e1903. [PMID: 35218326 PMCID: PMC9000940 DOI: 10.1002/mgg3.1903] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 01/24/2022] [Accepted: 02/02/2022] [Indexed: 02/02/2023] Open
Abstract
Background Beckwith–Wiedemann syndrome (BWS) is an inherited disorder affecting 1 in 10,500 to 13,700 newborns worldwide. The disease is caused in a vast majority of patients by a molecular defect in the imprinted chromosome 11p15.5. Hereditary spherocytosis (HS) is a form of hemolytic anemia associated with a variety of mutations leading to congenital red blood cell (RBC) membrane defects. The prevalence of HS varies by geographic regions around the world, ranging from 1.2 in 100,000 in Asia to 1 in 2000 in Northern Europe. Methods and Results Herein, we report for the first time a rare case diagnosed with co‐existing BWS and HS. Based on the classical presentations, including macroglossia, hepatosplenomegaly, and macrosomia, the patient was first suspected with BWS. MS‐MLPA confirmed the BWS diagnosis based on hypomethylation of maternal 11p15.5 (KCNQ1OT1), but no copy number variations in chromosome 11 was detected by CNV‐seq. Nevertheless, to scrutinize molecular causes of other symptoms of the patient, including anemia, hyperbilirubinemia, and jaundice, a whole exome sequencing (WES) was performed. We identified a novel and de novo mutation in ANK1 gene (c.520delC). This frameshift mutation of ANK1 gene results in a truncated protein without important functional domains and impaired membrane stability and structure of the resultant red blood cells (RBCs), leading to a definitive diagnosis of HS. Conclusion The present case demonstrated that multiple genetic and epigenetic aberrations might co‐exist in the complex genetic diseases. For such kind of complicated cases, the different types of molecular tests, such as WES and MS‐MLPA, should be utilized in combination to reveal independent causal molecular events. The identifications from this study added new insights into the understanding of molecular mechanisms underlying the co‐existing HS and BWS.
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Affiliation(s)
- Qinghua Zhang
- Gansu Province Medical Genetics Center, Gansu Province Maternal and Child Health Care Hospital, Lanzhou, China
| | - Chuan Zhang
- Gansu Province Medical Genetics Center, Gansu Province Maternal and Child Health Care Hospital, Lanzhou, China
| | - Yupei Wang
- Gansu Province Medical Genetics Center, Gansu Province Maternal and Child Health Care Hospital, Lanzhou, China
| | - Shengjv Hao
- Gansu Province Medical Genetics Center, Gansu Province Maternal and Child Health Care Hospital, Lanzhou, China
| | - Jingyun Shi
- Department of Neonatal Intensive Care Unit, Gansu Province Maternal and Child Health Care Hospital, Lanzhou, China
| | - Xuan Feng
- Gansu Province Medical Genetics Center, Gansu Province Maternal and Child Health Care Hospital, Lanzhou, China
| | - Lei Zheng
- Gansu Province Medical Genetics Center, Gansu Province Maternal and Child Health Care Hospital, Lanzhou, China
| | - Xin Wang
- Gansu Province Medical Genetics Center, Gansu Province Maternal and Child Health Care Hospital, Lanzhou, China
| | - Chen Xue
- Gansu Province Medical Genetics Center, Gansu Province Maternal and Child Health Care Hospital, Lanzhou, China
| | - Bingbo Zhou
- Gansu Province Medical Genetics Center, Gansu Province Maternal and Child Health Care Hospital, Lanzhou, China
| | - Furong Liu
- Gansu Province Medical Genetics Center, Gansu Province Maternal and Child Health Care Hospital, Lanzhou, China
| | - Fangping Zhao
- Department of Neonatal Intensive Care Unit, Gansu Province Maternal and Child Health Care Hospital, Lanzhou, China
| | - Xuetao Li
- The Laboratory of Computational Medicine and Systems Biology, School of Medicine, South China University of Technology, Guangzhou, China.,Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, School of Medicine, South China University of Technology, Guangzhou, China
| | - Liangyuan Deng
- The Laboratory of Computational Medicine and Systems Biology, School of Medicine, South China University of Technology, Guangzhou, China
| | - Jun Hou
- The Laboratory of Computational Medicine and Systems Biology, School of Medicine, South China University of Technology, Guangzhou, China
| | - Zhaoyan Meng
- Department of Obstetrics, Gansu Province Maternal and Child Health Care Hospital, Lanzhou, China
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11
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Rios-Flores IM, Bobadilla-Morales L, Peña Padilla C, Corona-Rivera A, Acosta-Fernández E, Santana-Hernández J, Brukman-Jiménez SA, Corona Rivera JR. [Prader-Willi and Angelman syndromes: case series diagnosed by MS-MLPA assay]. Rev Med Inst Mex Seguro Soc 2021; 59:170-178. [PMID: 34232598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 02/20/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Prader Willi syndrome (PWS) and Angelman syndrome (AS) are neurodevelopmental disorders caused by deletions or methylation defects, making a loss of expression of imprinted genes located in the 15q11-q13 region, and these can be assessed by different cytogenomic and molecular techniques. We report a case series of patients with PWS and AS evaluated through the MS-MLPA assay. CLINICAL CASES We studied four patients with a clinical diagnosis of PWS and another with AS, evaluated as far as possible with karyotype and FISH, and with MS-MLPA assay for the 15q11-q13 region in all cases. In patients with PWS, neonatal hypotonia was the main reason for consultation and in three of them we identified a deletion of 15q11-q13 by MS-MLPA, also confirmed by FISH; and in the other one, an abnormal methylation pattern consistent with a maternal uniparental disomy. The patient with AS presented with a typical picture which led to the identification of a deletion in 15q11-q13 by MS-MLPA, also confirmed by FISH. CONCLUSIONS The use of the MS-MLPA assay for the 15q11-q13 region was very useful for the diagnosis and identification of the genomic and epigenetic defects involved in either PWS and AS.
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Affiliation(s)
| | - Lucina Bobadilla-Morales
- Hospital Civil de Guadalajara "Dr. Juan I. Menchaca", División de Auxiliares de Diagnóstico y Paramédicos, Unidad de Citogenética. Guadalajara, Jalisco, México
| | - Christian Peña Padilla
- Hospital Civil de Guadalajara "Dr. Juan I. Menchaca", División de Pediatría, Servicio de Genética. Guadalajara, Jalisco, México
| | - Alfredo Corona-Rivera
- Hospital Civil de Guadalajara "Dr. Juan I. Menchaca", División de Auxiliares de Diagnóstico y Paramédicos, Unidad de Citogenética. Guadalajara, Jalisco, México
| | - Elizabeth Acosta-Fernández
- Hospital Civil de Guadalajara "Dr. Juan I. Menchaca", División de Pediatría, Servicio de Genética. Guadalajara, Jalisco, México
| | - Jennifer Santana-Hernández
- Hospital Civil de Guadalajara "Dr. Juan I. Menchaca", División de Auxiliares de Diagnóstico y Paramédicos, Unidad de Citogenética. Guadalajara, Jalisco, México
| | - Sinhue Alejandro Brukman-Jiménez
- Hospital Civil de Guadalajara "Dr. Juan I. Menchaca", División de Auxiliares de Diagnóstico y Paramédicos, Unidad de Citogenética. Guadalajara, Jalisco, México
| | - Jorge Román Corona Rivera
- Universidad de Guadalajara, Centro Universitario de Ciencias de la Salud, Departamento de Biología Molecular y Genómica, Instituto de Genética Humana "Dr. Enrique Corona Rivera". Guadalajara, Jalisco, México
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12
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Mercado M. [Epigenetics of Prader-Willi Syndrome: A good example of translational medicine]. Rev Med Inst Mex Seguro Soc 2021; 59:106-107. [PMID: 34231979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
In this editorial the author presents a study, concerning Prader-Willi syndrome, which is paradigmatic for translational medicine, given that it creates a synergy between genetics and molecular biology, in order to improve the care for patients suffering from this syndrome.
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Affiliation(s)
- Moisés Mercado
- Instituto Mexicano del Seguro Social, Centro Médico Nacional Siglo XXI, Hospital de Especialidades "Dr. Bernardo Sepúlveda Gutiérrez", Unidad de Investigación Médica en Enfermedades Endocrinas. Ciudad de México, México
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13
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Massalska D, Ozdarska K, Roszkowski T, Bijok J, Kucińska-Chahwan A, Panek GM, Zimowski JG. Distribution of diandric and digynic triploidy depending on gestational age. J Assist Reprod Genet 2021; 38:2391-2395. [PMID: 33982170 PMCID: PMC8490569 DOI: 10.1007/s10815-021-02202-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 04/19/2021] [Indexed: 11/18/2022] Open
Abstract
Purpose To establish the distribution of diandric and digynic triploidy depending on gestational age. Methods 107 triploid samples tested prospectively in a single genetic department during a four-year period were analyzed for parental origin of triploidy by Quantitative Fluorescent Polymerase Chain Reaction (QF-PCR) (n=95) with the use of matching parental samples or by MS-MLPA (n=12), when parental samples were unavailable. Tested pregnancies were divided into three subgroups with regard to the gestational age at spontaneous pregnancy loss: <11 gestational weeks, 11–14 gestational weeks, and >14 gestational weeks. Results Diandric triploidy constituted overall 44.9% (46.5% in samples miscarried <11 gestational weeks, 64.3% in samples miscarried between 11 and 14 gestational weeks, and 27.8% in pregnancies which survived >14 gestational weeks). Conclusions The distribution of diandric and digynic triploidy depends on gestational age. The majority of diandric triploid pregnancies is lost in the first trimester of pregnancy. In the second trimester, diandric cases are at least twice less frequent than digynic ones.
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Affiliation(s)
- Diana Massalska
- Department of Gynecologic Oncology and Obstetrics, Centre of Postgraduate Medical Education, Czerniakowska 231, 00-416, Warsaw, Poland.
| | - Katarzyna Ozdarska
- Department of Genetics, Institute of Psychiatry and Neurology, Sobieskiego 9, 02-957, Warsaw, Poland
| | - Tomasz Roszkowski
- Department of Gynecologic Oncology and Obstetrics, Centre of Postgraduate Medical Education, Czerniakowska 231, 00-416, Warsaw, Poland
| | - Julia Bijok
- Department of Gynecologic Oncology and Obstetrics, Centre of Postgraduate Medical Education, Czerniakowska 231, 00-416, Warsaw, Poland
| | - Anna Kucińska-Chahwan
- Department of Gynecologic Oncology and Obstetrics, Centre of Postgraduate Medical Education, Czerniakowska 231, 00-416, Warsaw, Poland
| | - Grzegorz Mieczysław Panek
- Department of Gynecologic Oncology and Obstetrics, Centre of Postgraduate Medical Education, Czerniakowska 231, 00-416, Warsaw, Poland
| | - Janusz Grzegorz Zimowski
- Department of Genetics, Institute of Psychiatry and Neurology, Sobieskiego 9, 02-957, Warsaw, Poland
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14
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Correa ARE, Mishra P, Kabra M, Gupta N. Epigenetic Abnormalities of 11p15.5 Region in Beckwith-Wiedemann Syndrome - A Report of Eight Indian Cases. Indian J Pediatr 2020; 87:175-178. [PMID: 31997239 DOI: 10.1007/s12098-019-03148-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 11/27/2019] [Indexed: 12/14/2022]
Abstract
OBJECTIVES To report a phenotypic series of eight patients of Beckwith-Wiedemann Syndrome (BWS) with abnormalities of 11p15.5 region to highlight the spectrum of phenotypic manifestations. METHODS All the cases were evaluated using Methylation Specific Multiplex Ligation Dependent Probe Amplification (MS-MLPA) of 11p15.5 region to detect the abnormal methylation status of ICR1 (H19DR) and ICR2 (KvDMR) regions. RESULTS The median age at diagnosis was 5.7 mo (range 1.5-13 mo) with female preponderance. Macroglossia, ear creases and abdominal wall defects were the major features. Hypomethylation at ICR2 and hypermethylation at ICR1 was observed in 6/8 and 2/8 patients respectively. No specific genotype and phenotype correlation was observed. CONCLUSIONS This report highlights the major clinical features of BWS that should prompt pediatricians to offer genetic testing to evaluate the epigenetic abnormalities using MS-MLPA, as it not only helps in appropriate counseling but also provides further guidance about the tumor risk surveillance.
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Affiliation(s)
- Alec Reginald Errol Correa
- Department of Pediatrics, Division of Genetics, All India Institute of Medical Sciences, New Delhi, India
| | - Puneeta Mishra
- Department of Pediatrics, Division of Genetics, All India Institute of Medical Sciences, New Delhi, India
| | - Madhulika Kabra
- Department of Pediatrics, Division of Genetics, All India Institute of Medical Sciences, New Delhi, India
| | - Neerja Gupta
- Department of Pediatrics, Division of Genetics, All India Institute of Medical Sciences, New Delhi, India.
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15
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Vermeulen MA, van Deurzen CHM, Doebar SC, de Leng WWJ, Martens JWM, van Diest PJ, Moelans CB. Promoter hypermethylation in ductal carcinoma in situ of the male breast. Endocr Relat Cancer 2019; 26:575-584. [PMID: 30921768 DOI: 10.1530/erc-18-0485] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 03/26/2019] [Indexed: 12/26/2022]
Abstract
Ductal carcinoma in situ (DCIS) of the male breast is very rare and has hardly been studied molecularly. In males, we compared methylation status of 25 breast cancer-related genes in pure DCIS (n = 18) and invasive breast carcinoma (IBC) with adjacent DCIS (DCIS-AIC) (n = 44) using methylation-specific multiplex ligation-dependent probe amplification. Results were compared to female breast cancer (BC). There were no significant differences in methylation features between male pure DCIS, DCIS-AIC and IBC after correction for multiple comparisons. In paired analysis of IBC and adjacent DCIS, CADM1 showed a significantly higher absolute methylation percentage in DCIS (P = 0.002). In cluster analysis, two clusters stood out with respectively infrequent and frequent methylation (GATA5, KLLN, PAX6, PAX5, CDH13, MSH6 and WT1 were frequently methylated). Compared to female DCIS, methylation was in general much less common in male DCIS, especially for VHL, ESR1, CDKN2A, CD44, CHFR, BRCA2, RB1 and STK11. In contrast, THBS1 and GATA5 were more frequently methylated in male DCIS. In conclusion, there is frequent methylation of GATA5, KLLN, PAX6, PAX5, CDH13, MSH6 and WT1 in male DCIS. Since there was little change in the methylation status for the studied genes from pure male DCIS to DCIS-AIC and IBC, methylation of these seven genes is more likely to occur early in male breast carcinogenesis. Based on the current markers male DCIS seems to be an epigenetically more advanced precursor of male BC, although in comparison to its female counterpart it appears that fewer loci harbor methylation, pointing to differences between male and female breast carcinogenesis with regard to the studied loci.
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MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Biomarkers, Tumor/genetics
- Breast Neoplasms/genetics
- Breast Neoplasms/metabolism
- Breast Neoplasms/pathology
- Breast Neoplasms, Male/genetics
- Breast Neoplasms, Male/metabolism
- Breast Neoplasms, Male/pathology
- Carcinoma, Ductal, Breast/genetics
- Carcinoma, Ductal, Breast/metabolism
- Carcinoma, Ductal, Breast/pathology
- Carcinoma, Intraductal, Noninfiltrating/genetics
- Carcinoma, Intraductal, Noninfiltrating/metabolism
- Carcinoma, Intraductal, Noninfiltrating/pathology
- Carcinoma, Lobular/genetics
- Carcinoma, Lobular/metabolism
- Carcinoma, Lobular/pathology
- DNA Methylation
- Female
- Follow-Up Studies
- Gene Expression Regulation, Neoplastic
- Humans
- Inflammatory Breast Neoplasms/genetics
- Inflammatory Breast Neoplasms/metabolism
- Inflammatory Breast Neoplasms/pathology
- Male
- Middle Aged
- Prognosis
- Promoter Regions, Genetic
- Receptor, ErbB-2/metabolism
- Receptors, Estrogen/metabolism
- Receptors, Progesterone/metabolism
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Affiliation(s)
- Marijn A Vermeulen
- Department of Pathology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Carolien H M van Deurzen
- Department of Pathology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
- BOOG Study Center/Dutch Breast Cancer Research Group, Amsterdam, The Netherlands
| | - Shusma C Doebar
- Department of Pathology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Wendy W J de Leng
- Department of Pathology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - John W M Martens
- BOOG Study Center/Dutch Breast Cancer Research Group, Amsterdam, The Netherlands
- Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Paul J van Diest
- Department of Pathology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Cathy B Moelans
- Department of Pathology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
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16
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Maleva Kostovska I, Jakimovska M, Popovska-Jankovic K, Kubelka-Sabit K, Karagjozov M, Plaseska-Karanfilska D. TIMP3 Promoter Methylation Represents an Epigenetic Marker of BRCA1ness Breast Cancer Tumours. Pathol Oncol Res 2018. [PMID: 29524167 DOI: 10.1007/s12253-018-0398-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Tumours presenting BRCAness profile behave more aggressively and are more invasive as a consequence of their complex genetic and epigenetic alterations, caused by impaired fidelity of the DNA repair processes. Methylation of promoter CpG islands represents an alternative mechanism to inactivate DNA repair and tumour suppressor genes. In our study, we analyzed the frequency of methylation changes of 24 tumour suppressor genes and explored their association with BRCAness profile. BRCA1ness profile and aberrant methylation were studied in 233 fresh frozen breast tumour tissues by Multiplex Ligation-dependent Probe Amplification (MLPA) and Methylation Specific (MS)-MLPA methods, respectively. Our analyses revealed that 12.4% of the breast cancer (BC) patients had tumours with a BRCA1ness profile. TIMP3 showed significantly higher (p = 5.8х10-5) methylation frequency in tumours with BRCA1ness, while methylation of APC, GSTP1 and RASSF1 promoters was negatively associated with BRCA1ness (р = 0.0017, р = 0.007 and р = 0.046, respectively). TIMP3 methylation was also associated with triple negative (TN) BC. Furthermore, TN tumours showing BRCA1ness showed stronger association with TIMP3 methylation (p = 0.0008) in comparison to TN tumours without BRCA1ness (p = 0.009). In conclusion, we confirmed that TIMP3 methylation is a marker for TN tumours and furthermore we showed for the first time that TIMP3 promoter methylation is an epigenetic marker of BRCA1ness tumours.
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Affiliation(s)
- Ivana Maleva Kostovska
- Research Centre for Genetic Engineering and Biotechnology "Georgi D. Efremov", Macedonian Academy of Sciences and Arts, KrsteMisirkov 2, Skopje, Republic of Macedonia
| | - Milena Jakimovska
- Research Centre for Genetic Engineering and Biotechnology "Georgi D. Efremov", Macedonian Academy of Sciences and Arts, KrsteMisirkov 2, Skopje, Republic of Macedonia
| | - Katerina Popovska-Jankovic
- Research Centre for Genetic Engineering and Biotechnology "Georgi D. Efremov", Macedonian Academy of Sciences and Arts, KrsteMisirkov 2, Skopje, Republic of Macedonia
| | | | - Mitko Karagjozov
- Clinical Hospital Acibadem Sistina, Skopje, Republic of Macedonia
| | - Dijana Plaseska-Karanfilska
- Research Centre for Genetic Engineering and Biotechnology "Georgi D. Efremov", Macedonian Academy of Sciences and Arts, KrsteMisirkov 2, Skopje, Republic of Macedonia.
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Laurito S, Roqué M. [Variation analysis of the number of copies and methylene patterns in region 15q11-q13]. Medicina (B Aires) 2018; 78:1-5. [PMID: 29360068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023] Open
Abstract
Human chromosome 15q11-q13 region is prone to suffer genetic alterations. Some genes of this region have a differential monoallelic imprinting-regulated expression pattern. Defects in imprinting regulation (IE), uniparental disomy (UPD) or copy number variation (CNV) due to chromosomal breakpoints (BP) in 15q11-q13 region, are associated with several diseases. The most frequent are Prader-Willi syndrome, Angelman syndrome and 15q11-q13 microduplication syndrome. In this work, we analyzed DNA samples from 181 patients with phenotypes which were compatible with the above-mentioned diseases, using Methyl specific-multiplex ligation-dependent probe amplification (MS-MLPA). We show that, of the 181 samples, 39 presented alterations detectable by MS-MLPA. Of those alterations, 61.5% (24/39) were deletions, 5.1% (2/39) duplications and 33.3% (13/39) UPD/IE. The CNV cases were 4 times more frequent than UPD/IE (OR= 4; IC 95%: 1.56-10.25), consistent with the literature. Among the CNVs, two atypical cases allow to postulate new possible BP sites that have not been reported previously in the literature.
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Affiliation(s)
- Sergio Laurito
- Instituto de Histología y Embriología (IHEM), Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, CONICET, Mendoza, Argentina
| | - María Roqué
- Instituto de Histología y Embriología (IHEM), Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo,CONICET, Mendoza, Argentina. E-mail:
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Abstract
This chapter describes a method for the rapid assessment of promoter hypermethylation levels or methylation of imprinted regions in human genomic DNA extracted from various sources using methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA). Multiplex ligation-dependent probe amplification (MLPA) is a powerful and easy-to-perform PCR-based technique that can identify gains, amplifications, losses, deletions, methylation and mutations of up to 55 targets in a single reaction, while requiring only minute quantities of DNA (about 50 ng) extracted from blood, fresh frozen or formalin-fixed paraffin-embedded materials. Methylation-specific MLPA (MS-MLPA) is a variant of MLPA, which does not require sodium bisulfite conversion of unmethylated cytosine residues, but instead makes use of the methylation-sensitive endonuclease HhaI. MS-MLPA probes are designed to contain a HhaI recognition site (GCGC) and thus target one CpG dinucleotide within a CpG island. If the HhaI recognition site is not methylated, HhaI will cut the probe-sample DNA hybrid and no PCR product will be formed. If the target DNA is methylated, HhaI is not able to cut, and the fragment will be amplified during subsequent PCR. For data analysis, MS-MLPA peak patterns of the HhaI-treated and -untreated reactions are compared, leading to calculation of a methylation percentage. The methylation profile of a test sample is assessed by comparing the probe methylation percentages obtained on the test sample to the percentages of the reference samples. MS-MLPA can be combined with copy number and point mutation detection in the same reaction.
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19
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Vos S, Moelans CB, van Diest PJ. BRCA promoter methylation in sporadic versus BRCA germline mutation-related breast cancers. Breast Cancer Res 2017; 19:64. [PMID: 28569220 PMCID: PMC5452400 DOI: 10.1186/s13058-017-0856-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 05/16/2017] [Indexed: 02/08/2023] Open
Abstract
Background In breast cancer, BRCA promoter hypermethylation and BRCA germline mutations are said to occur together rarely, but this property has not yet been translated into a clinical test. Our aim in this study was to investigate the diagnostic value of BRCA1/2 methylation in distinguishing breast carcinomas of BRCA1 and BRCA2 germline mutation carriers from sporadic breast carcinomas using a recently developed BRCA methylation assay based on methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA). Methods MS-MLPAs were performed to assess BRCA1 and BRCA2 methylation in breast carcinoma tissues from 39 BRCA1 and 33 BRCA2 germline mutation carriers, 80 patients with sporadic breast cancer, and normal breast tissues from 5 BRCA1 and 4 BRCA2 mutation carriers and 5 nonmutation carriers. Results Methylation frequencies varied considerably between CpG sites across the BRCA1 and BRCA2 promoters. Some CpG sites were methylated more frequently in BRCA1/2-related than in sporadic carcinomas, whereas other CpG sites were methylated more frequently in sporadic carcinomas, with large variances in sensitivity and specificity as a consequence. Conclusions The diagnostic value of BRCA promoter methylation analysis in distinguishing BRCA1/2-related from sporadic breast carcinomas seems to be considerably dependent on the targeted CpG sites. These findings are important for adequate use of BRCA methylation analysis as a prescreening tool for BRCA germline genetic testing or to identify BRCAness patients who may benefit from targeted therapies such as poly(adenosine diphosphate-ribose) polymerase inhibitors.
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Affiliation(s)
- Shoko Vos
- Department of Pathology, University Medical Center Utrecht, Heidelberglaan 100, 3584, CX, Utrecht, The Netherlands.
| | - Cathy Beatrice Moelans
- Department of Pathology, University Medical Center Utrecht, Heidelberglaan 100, 3584, CX, Utrecht, The Netherlands
| | - Paul Joannes van Diest
- Department of Pathology, University Medical Center Utrecht, Heidelberglaan 100, 3584, CX, Utrecht, The Netherlands
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Cao Y, AlHumaidi SS, Faqeih EA, Pitel BA, Lundquist P, Aypar U. A novel deletion of SNURF/SNRPN exon 1 in a patient with Prader-Willi-like phenotype. Eur J Med Genet 2017; 60:416-420. [PMID: 28554868 DOI: 10.1016/j.ejmg.2017.05.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 05/24/2017] [Accepted: 05/25/2017] [Indexed: 02/07/2023]
Abstract
Here we report the smallest deletion involving SNURF/SNRPN that causes major symptoms of Prader-Willi syndrome (PWS), including hypotonia, dysmorphic features, intellectual disability, and obesity. A female patient with the aforementioned and additional features was referred to the Mayo Clinic Cytogenetics laboratory for genetic testing. Chromosomal microarray analysis and subsequent Sanger sequencing identified a de novo 6.4 kb deletion at 15q11.2, containing exon 1 of the SNURF gene and exon 1 of the shortest isoform of the SNRPN gene. SNURF/SNRPN exon 1, which is methylated on the silent maternal allele, is associated with acetylated histones on the expressed paternal allele. This region also overlaps with the PWS-imprinting center (IC). Subsequent molecular methylation analysis was performed using methylation-specific MLPA (MS-MLPA), which characterized that the deletion of SNURF/SNRPN exon 1 was paternal in origin, consistent with the PWS-like phenotype. Since SNURF/SNRPN gene and the PWS-IC are known to regulate snoRNAs, it is likely that the PWS-like phenotype observed in patients with paternal SNURF/SNRPN deletion is due to the disrupted expression of SNORD116 snoRNAs.
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Affiliation(s)
- Yang Cao
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Susan S AlHumaidi
- Section of Medical Genetics, Children's Specialist Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Eissa A Faqeih
- Section of Medical Genetics, Children's Specialist Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Beth A Pitel
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Patrick Lundquist
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Umut Aypar
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States.
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Gurioli G, Salvi S, Martignano F, Foca F, Gunelli R, Costantini M, Cicchetti G, De Giorgi U, Sbarba PD, Calistri D, Casadio V. Methylation pattern analysis in prostate cancer tissue: identification of biomarkers using an MS-MLPA approach. J Transl Med 2016; 14:249. [PMID: 27576364 PMCID: PMC5006561 DOI: 10.1186/s12967-016-1014-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 08/16/2016] [Indexed: 12/21/2022] Open
Abstract
Background Epigenetic silencing mediated by CpG island methylation is a common feature of many cancers. Characterizing aberrant DNA methylation changes associated with prostate carcinogenesis could potentially identify a tumour-specific methylation pattern, facilitating the early diagnosis of prostate cancer. The objective of the study was to assess the methylation status of 40 tumour suppressor genes in prostate cancer and healthy prostatic tissues. Methods We used methylation specific-multiplex ligation probe amplification (MS-MLPA) assay in two independent case series (training and validation set). The training set comprised samples of prostate cancer tissue (n = 40), healthy prostatic tissue adjacent to the tumor (n = 26), and healthy non prostatic tissue (n = 23), for a total of 89 DNA samples; the validation set was composed of 40 prostate cancer tissue samples and their adjacent healthy prostatic tissue, for a total of 80 DNA samples. Methylation specific-polymerase chain reaction (MSP) was used to confirm the results obtained in the validation set. Results We identified five highly methylated genes in prostate cancer: GSTP1, RARB, RASSF1, SCGB3A1, CCND2 (P < 0.0001), with an area under the ROC curve varying between 0.89 (95 % CI 0.82–0.97) and 0.95 (95 % CI 0.90–1.00). Diagnostic accuracy ranged from 80 % (95 % CI 70–88) to 90 % (95 % CI 81–96). Moreover, a concordance rate ranging from 83 % (95 % CI 72–90) to 89 % (95 % CI 80–95) was observed between MS-MLPA and MSP. Conclusions Our preliminary results highlighted that hypermethylation of GSTP1, RARB, RASSF1, SCGB3A1 and CCND2 was highly tumour-specific in prostate cancer tissue. Electronic supplementary material The online version of this article (doi:10.1186/s12967-016-1014-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Giorgia Gurioli
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Via P. Maroncelli 40, 47014, Meldola, Italy
| | - Samanta Salvi
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Via P. Maroncelli 40, 47014, Meldola, Italy
| | - Filippo Martignano
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Via P. Maroncelli 40, 47014, Meldola, Italy
| | - Flavia Foca
- Unit of Biostatistics and Clinical Trials, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Via P. Maroncelli 40, 47014, Meldola, Italy
| | - Roberta Gunelli
- Department of Urology, Morgagni Pierantoni Hospital, Forlì, Italy
| | | | | | - Ugo De Giorgi
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Via P. Maroncelli 40, 47014, Meldola, Italy
| | - Persio Dello Sbarba
- Dipartimento di Scienze Biomediche, Sperimentali e Cliniche, University of Florence, Florence, Italy
| | - Daniele Calistri
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Via P. Maroncelli 40, 47014, Meldola, Italy
| | - Valentina Casadio
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Via P. Maroncelli 40, 47014, Meldola, Italy.
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López F, Sampedro T, Llorente JL, Hermsen M, Álvarez-Marcos C. Alterations of p14 ARF , p15 INK4b , and p16 INK4a Genes in Primary Laryngeal Squamous Cell Carcinoma. Pathol Oncol Res 2017; 23:63-71. [PMID: 27377733 DOI: 10.1007/s12253-016-0083-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 06/28/2016] [Indexed: 10/21/2022]
Abstract
The 9p21 gene cluster, harboring growth suppressive genes p14 ARF , p15 INK4b , and p16 INK4a , is one of the major aberration hotspots in head and neck cancers. We try to elucidate specific aberrations affecting this region, throughout methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) assay. Methylation of the gene was investigated by MS-MLPA in a well-characterized series of 27 laryngeal squamous cell carcinomas and 20 samples of healthy mucosa. Aberrant promoter hypermethylation was confirmed using and methylation-specific. All samples studied except 3 (11 %) presented losses at 9p21 segment. The most common finding was the small deletion (exon 1α) of the p16 INK4a locus (44 %). Deletion of the 9p21 gene cluster was identified in 5 cases (18 %). We only found methylation in 8 samples (30 %) for p15 IK4b -exon 1. Promoter methylation of p14 ARF , p15 IK4b and p16 INK4a was not detected in any tumor sample. Methylation-specific polymerase chain reaction confirmed the results. Our data indicate that there may be a subgroup of patients in which epigenetic regulation of 9p21 segment might have little relevance. Nevertheless, MS-MLPA could not be suitable for the study of methylation at this region and further research is required.
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Aypar U, Hoppman NL, Thorland EC, Dawson DB. Patients with mosaic methylation patterns of the Prader-Willi/Angelman Syndrome critical region exhibit AS-like phenotypes with some PWS features. Mol Cytogenet 2016; 9:26. [PMID: 27006693 PMCID: PMC4802915 DOI: 10.1186/s13039-016-0233-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 03/09/2016] [Indexed: 01/29/2023] Open
Abstract
Background Loss of expression of imprinted genes in the 15q11.2-q13 region is known to cause either Prader-Willi syndrome (PWS) or Angelman syndrome (AS), depending on the parent of origin. In some patients (1 % in PWS and 2–4 % in AS), the disease is due to aberrant imprinting or gene silencing, or both. Results We report here a 4-year-old boy on whom a chromosomal microarray (CMA) was performed due to mild hand tremors, mild developmental delays, and clumsiness. CMA revealed absence of heterozygosity (AOH) spanning the entire chromosome 15, suggesting uniparental isodisomy 15. The patient had no definitive phenotypic features of PWS or AS. Methylation-sensitive multiplex ligation-dependent probe amplification (MS-MLPA) was performed to determine the parent of origin of the uniparental disomy (UPD) by examining methylation status at maternally imprinted sites. Interestingly, our patient had a mosaic methylation pattern. We identified nine additional previously tested patients with a similar mosaic methylation pattern. CMA was performed on these individuals retrospectively to test whether patients with mosaic methylation are more likely to have UPD of chromosome 15. Of the nine patients, only one had regions of AOH on chromosome 15; however, this patient had numerous regions of AOH on multiple chromosomes suggestive of consanguinity. Conclusion The patients with mosaic methylation had milder or atypical features of AS, and the majority also had some features characteristic of PWS. We suggest that quantitative methylation analysis be performed for cases of atypical PWS or AS. It is also important to follow up with methylation testing when whole-chromosome isodisomy is detected.
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Affiliation(s)
- Umut Aypar
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905 USA
| | - Nicole L Hoppman
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905 USA
| | - Erik C Thorland
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905 USA
| | - D Brian Dawson
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905 USA
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Russo S, Calzari L, Mussa A, Mainini E, Cassina M, Di Candia S, Clementi M, Guzzetti S, Tabano S, Miozzo M, Sirchia S, Finelli P, Prontera P, Maitz S, Sorge G, Calcagno A, Maghnie M, Divizia MT, Melis D, Manfredini E, Ferrero GB, Pecile V, Larizza L. A multi-method approach to the molecular diagnosis of overt and borderline 11p15.5 defects underlying Silver-Russell and Beckwith-Wiedemann syndromes. Clin Epigenetics 2016; 8:23. [PMID: 26933465 PMCID: PMC4772365 DOI: 10.1186/s13148-016-0183-8] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 02/08/2016] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Multiple (epi)genetic defects affecting the expression of the imprinted genes within the 11p15.5 chromosomal region underlie Silver-Russell (SRS) and Beckwith-Wiedemann (BWS) syndromes. The molecular diagnosis of these opposite growth disorders requires a multi-approach flowchart to disclose known primary and secondary (epi)genetic alterations; however, up to 20 and 30 % of clinically diagnosed BWS and SRS cases remain without molecular diagnosis. The complex structure of the 11p15 region with variable CpG methylation and low-rate mosaicism may account for missed diagnoses. Here, we demonstrate the relevance of complementary techniques for the assessment of different CpGs and the importance of testing multiple tissues to increase the SRS and BWS detection rate. RESULTS Molecular testing of 147 and 450 clinically diagnosed SRS and BWS cases provided diagnosis in 34 SRS and 185 BWS patients, with 9 SRS and 21 BWS cases remaining undiagnosed and herein referred to as "borderline." A flowchart including complementary techniques and, when applicable, the analysis of buccal swabs, allowed confirmation of the molecular diagnosis in all borderline cases. Comparison of methylation levels by methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) in borderline and control cases defined an interval of H19/IGF2:IG-DMR loss of methylation that was distinct between "easy to diagnose" and "borderline" cases, which were characterized by values ≤mean -3 standard deviations (SDs) compared to controls. Values ≥mean +1 SD at H19/IGF2: IG-DMR were assigned to borderline hypermethylated BWS cases and those ≤mean -2 SD at KCNQ1OT1: TSS-DMR to hypomethylated BWS cases; these were supported by quantitative pyrosequencing or Southern blot analysis. Six BWS cases suspected to carry mosaic paternal uniparental disomy of chromosome 11 were confirmed by SNP array, which detected mosaicism till 10 %. Regarding the clinical presentation, borderline SRS were representative of the syndromic phenotype, with exception of one patient, whereas BWS cases showed low frequency of the most common features except hemihyperplasia. CONCLUSIONS A conclusive molecular diagnosis was reached in borderline methylation cases, increasing the detection rate by 6 % for SRS and 5 % for BWS cases. The introduction of complementary techniques and additional tissue analyses into routine diagnostic work-up should facilitate the identification of cases undiagnosed because of mosaicism, a distinctive feature of epigenetic disorders.
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Affiliation(s)
- Silvia Russo
- Human Molecular Genetics Laboratory, IRCCS Istituto Auxologico Italiano, Milano, Italy
| | - Luciano Calzari
- Human Molecular Genetics Laboratory, IRCCS Istituto Auxologico Italiano, Milano, Italy
| | - Alessandro Mussa
- Department of Pediatric and Public Health Sciences, University of Turin, Torino, Italy
| | - Ester Mainini
- Human Molecular Genetics Laboratory, IRCCS Istituto Auxologico Italiano, Milano, Italy
| | - Matteo Cassina
- Clinical Genetics Unit, Department of Women's and Children's Health, University of Padua, Padova, Italy
| | - Stefania Di Candia
- Department of Pediatrics, San Raffaele Scientific Institute, Milano, Italy
| | - Maurizio Clementi
- Clinical Genetics Unit, Department of Women's and Children's Health, University of Padua, Padova, Italy
| | - Sara Guzzetti
- Human Molecular Genetics Laboratory, IRCCS Istituto Auxologico Italiano, Milano, Italy
| | - Silvia Tabano
- Division of Pathology - Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Department of Pathophysiology and Transplantation, University of Milan, Milano, Italy
| | - Monica Miozzo
- Division of Pathology - Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Department of Pathophysiology and Transplantation, University of Milan, Milano, Italy
| | - Silvia Sirchia
- Department of Health Sciences, University of Milan, Milano, Italy
| | - Palma Finelli
- Human Molecular Genetics Laboratory, IRCCS Istituto Auxologico Italiano, Milano, Italy
| | - Paolo Prontera
- Medical Genetics Unit, Department of Surgical and Biomedical Sciences, University of Perugia, Hospital "S. M. della Misericordia", Perugia, Italy
| | - Silvia Maitz
- Clinical Pediatric Genetics Unit, Pediatrics Clinics, MBBM Foundation, S. Gerardo Hospital, Monza, Italy
| | - Giovanni Sorge
- Department of Pediatrics and Medical Sciences, AO "Policlinico Vittorio Emanuele", Catania, Italy
| | - Annalisa Calcagno
- Pediatric Endocrine Unit, Department of Pediatrics, IRCCS, Children's Hospital Giannina Gaslini, Genova, Italy
| | - Mohamad Maghnie
- Pediatric Endocrine Unit, Department of Pediatrics, IRCCS, Children's Hospital Giannina Gaslini, Genova, Italy
| | - Maria Teresa Divizia
- Department of Medical Genetics, IRCCS, Children's Hospital Giannina Gaslini, Genova, Italy
| | - Daniela Melis
- Clinical Pediatric Genetics, Department of Pediatrics, University "Federico II", Napoli, Italy
| | - Emanuela Manfredini
- Medical Genetics Unit, Department of Laboratory Medicine, Niguarda Ca' Granda Hospital, Milano, Italy
| | | | - Vanna Pecile
- Institute for Maternal and Child Health, Foundation IRCCS Burlo Garofolo Institute, Trieste, Italy
| | - Lidia Larizza
- Human Molecular Genetics Laboratory, IRCCS Istituto Auxologico Italiano, Milano, Italy
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Shakeri H, Gharesouran J, Fakhrjou A, Esfahani A, Mohaddes Ardebili SM. DNA methylation assessment as a prognostic factor in invasive breast cancer using methylation-specific multiplex ligation dependent probe amplification. EXCLI J 2016; 15:11-20. [PMID: 27065772 PMCID: PMC4822054 DOI: 10.17179/excli2015-485] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 12/05/2015] [Indexed: 12/17/2022]
Abstract
DNA methylation of promoter regions is a common molecular mechanism for inactivation of tumor suppressor genes that participates in carcinogenesis. Determining the methylation status of genes in cancer and their association with clinical features play an essential role in early diagnosis, prognosis and determine appropriate treatment for patients. The purpose of the present study was to evaluate the methylation of tumor suppressor genes in patients with invasive ductal carcinoma (IDC). Furthermore, we evaluated the association between clinical parameters and DNA methylation as a biomarker in diagnostic IDC patients. The methylation-specific multiplex ligation dependent probe amplification (MS-MLPA) assay was used to analyze the methylation profile of 24 genes in formalin-fixed paraffin embedded (FFPE) tissue samples from 75 patients with IDC. Each of the patients showed a distinctive methylation profile. We observed higher methylation in the RASSF1 (48 %), CDH13 (44 %) and GSTP1 (36 %) genes. Some of the methylated genes were associated with clinical features. Methylation of GSTP1 (P=0.028) and RASSF1 (P=0.012) were related with lymph node metastasis. Methylation of GSTP1 (P=0.005) was associated with high histological grade. Moreover, concurrent methylation of GSTP1 and CDH13 was observed in IDC patients (p<0.001). Hierarchical cluster analysis based on the methylation profile revealed two main clusters of patients, the highly methylated cluster being significantly associated with high histological grade and lymph node metastasis. The results of this study indicate that the methylation status of RASSF1 and CDH13 and GSTP1 can be a prognostic marker to better management of IDC patients.
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Affiliation(s)
- Halaleh Shakeri
- Hematology & Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Biochemistry and Clinical Laboratories, Division of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Jalal Gharesouran
- Department of Biochemistry and Clinical Laboratories, Division of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ashraf Fakhrjou
- Department of Pathology, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ali Esfahani
- Hematology & Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Seyyed Mojtaba Mohaddes Ardebili
- Hematology & Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Biochemistry and Clinical Laboratories, Division of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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26
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Moelans CB, Vlug EJ, Ercan C, Bult P, Buerger H, Cserni G, van Diest PJ, Derksen PWB. Methylation biomarkers for pleomorphic lobular breast cancer - a short report. Cell Oncol (Dordr) 2015; 38:397-405. [PMID: 26392358 PMCID: PMC4602117 DOI: 10.1007/s13402-015-0241-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/17/2015] [Indexed: 12/17/2022] Open
Abstract
Background Pleomorphic invasive lobular cancer (pleomorphic ILC) is a rare variant of ILC that is characterized by a classic ILC-like growth pattern combined with an infiltrative ductal cancer (IDC)-like high nuclear atypicality. There is an ongoing discussion whether pleomorphic ILC is a dedifferentiated form of ILC or in origin an IDC with a secondary loss of cohesion. Since gene promoter hypermethylation is an early event in breast carcinogenesis and thus may provide information on tumor progression, we set out to compare the methylation patterns of pleomorphic ILC, classic ILC and IDC. In addition, we aimed at analyzing the methylation status of pleomorphic ILC. Methods We performed promoter methylation profiling of 24 established and putative tumor suppressor genes by methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) analysis in 20 classical ILC, 16 pleomorphic ILC and 20 IDC cases. Results We found that pleomorphic ILC showed relatively low TP73 and MLH1 methylation levels and relatively high RASSF1A methylation levels compared to classic ILC. Compared to IDC, pleomorphic ILC showed relatively low MLH1 and BRCA1 methylation levels. Hierarchical cluster analysis revealed a similar methylation pattern for pleomorphic ILC and IDC, while the methylation pattern of classic ILC was different. Conclusion This is the first report to identify TP73, RASSF1A, MLH1 and BRCA1 as possible biomarkers to distinguish pleomorphic ILC from classic ILC and IDC.
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MESH Headings
- Adaptor Proteins, Signal Transducing/genetics
- Analysis of Variance
- BRCA1 Protein/genetics
- Biomarkers, Tumor/classification
- Biomarkers, Tumor/genetics
- Breast Neoplasms/diagnosis
- Breast Neoplasms/genetics
- Carcinoma, Ductal, Breast/diagnosis
- Carcinoma, Ductal, Breast/genetics
- Carcinoma, Lobular/diagnosis
- Carcinoma, Lobular/genetics
- Cluster Analysis
- DNA Methylation
- DNA-Binding Proteins/genetics
- Diagnosis, Differential
- Female
- Humans
- Logistic Models
- Multiplex Polymerase Chain Reaction/methods
- MutL Protein Homolog 1
- Nuclear Proteins/genetics
- Promoter Regions, Genetic/genetics
- ROC Curve
- Tumor Protein p73
- Tumor Suppressor Proteins/classification
- Tumor Suppressor Proteins/genetics
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Affiliation(s)
- Cathy B Moelans
- Department of Pathology, University Medical Center Utrecht, PO Box 85500, 3508 GA, Utrecht, The Netherlands.
| | - Eva J Vlug
- Department of Pathology, University Medical Center Utrecht, PO Box 85500, 3508 GA, Utrecht, The Netherlands
| | - Cigdem Ercan
- Department of Pathology, University Medical Center Utrecht, PO Box 85500, 3508 GA, Utrecht, The Netherlands
| | - Peter Bult
- Department of Pathology, Radboud University Nijmegen, Nijmegen, The Netherlands
| | | | - Gabor Cserni
- Department of Pathology, Bács-Kiskun County Teaching Hospital, Kecskemét, Hungary
| | - Paul J van Diest
- Department of Pathology, University Medical Center Utrecht, PO Box 85500, 3508 GA, Utrecht, The Netherlands
| | - Patrick W B Derksen
- Department of Pathology, University Medical Center Utrecht, PO Box 85500, 3508 GA, Utrecht, The Netherlands.
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Trabelsi S, Mama N, Ladib M, Karmeni N, Haddaji Mastouri M, Chourabi M, Mokni M, Tlili K, Krifa H, Yacoubi MT, Saad A, H'mida Ben Brahim D. MGMT methylation assessment in glioblastoma: MS-MLPA versus human methylation 450K beadchip array and immunohistochemistry. Clin Transl Oncol 2016; 18:391-7. [PMID: 26289551 DOI: 10.1007/s12094-015-1381-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2015] [Accepted: 08/05/2015] [Indexed: 10/23/2022]
Abstract
PURPOSE The MGMT gene encodes a DNA repair enzyme that counteracts with chemotherapy efficiency, specifically with alkylating agents such as temozolomide (TMZ). It is well established that MGMT methylation should be screened as a predictive marker for TMZ in glioblastoma, and we thus aimed to determine a reliable and practical diagnostic method of MGMT methylation detection. PATIENTS AND METHODS 55 glioblastomas were investigated for MGMT methylation status using methylation-specific multiplexed ligation probe amplification (MS-MLPA), illumina human methylation 450K BeadChip array (HM450 K) analysis, and compared to MGMT protein expression by immunohistochemistry (IHC) staining. The methylation status of promoter, intron and all MGMT CpG targeted sites were separately correlated to patient's survival. RESULTS In addition to MS-MLPA and 450 K concordance, our results showed significantly higher overall survival (OS) of patients receiving TMZ and presenting MGMT methylated promoter (mean OS = 21.5 months, p = 0.046). Including all glioblastoma cases and regardless of chemotherapy, MS-MLPA showed significant survival difference between MGMT methylated and unmethylated cases (mean OS = 13, p = 0.021). CONCLUSION We concluded that in glioblastoma, MGMT promoter methylation predicts TMZ sensitivity. This current comparative analysis leads to consider that MS-MLPA is a valuable as HM450 K array for MGMT methylation status screening.
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Valo S, Kaur S, Ristimäki A, Renkonen-Sinisalo L, Järvinen H, Mecklin JP, Nyström M, Peltomäki P. DNA hypermethylation appears early and shows increased frequency with dysplasia in Lynch syndrome-associated colorectal adenomas and carcinomas. Clin Epigenetics 2015. [PMID: 26203307 PMCID: PMC4511034 DOI: 10.1186/s13148-015-0102-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Lynch syndrome (LS) is associated with germline mutations in DNA mismatch repair (MMR) genes. The first "hit" to inactivate one allele of the predisposing MMR gene is present in every cell, contributing to accelerated tumorigenesis. Less information is available of the nature, timing, and order of other molecular "hits" required for tumor development. To this end, MMR protein expression and coordinated promoter methylation were examined in colorectal specimens prospectively collected from LS mutation carriers (n = 55) during colonoscopy surveillance (10/2011-5/2013), supplemented with retrospective specimens. RESULTS Loss of MMR protein corresponding to the gene mutated in the germline increased with dysplasia, with frequency of 0 % in normal mucosa, 50-68 % in low-grade dysplasia adenomas, and 100 % in high-grade dysplasia adenomas and carcinomas. Promoter methylation as a putative "second hit" occurred in 1/56 (2 %) of tumors with silenced MMR protein. A general hypermethylation tendency was evaluated by two gene sets, eight CpG island methylator phenotype (CIMP) genes, and seven candidate tumor suppressor genes linked to colorectal carcinoma (CRC). Hypermethylation followed the same trend as MMR protein loss and was present in some low-grade dysplasia adenomas that still expressed MMR protein suggesting the absence of a "second hit." To assess prospectively collected normal mucosa for carcinogenic "fields," the specimen donors were stratified according to age at biopsy (50 years or below vs. above 50 years) and further according to the absence vs. presence of a (previous or concurrent) diagnosis of CRC. In mutation carriers over 50 years old, two markers from the candidate gene panel (SFRP1 and SLC5A8) revealed a significantly elevated average degree of methylation in individuals with CRC diagnosis vs. those without. CONCLUSIONS Our findings emphasize the importance and early appearance of epigenetic alterations in LS-associated tumorigenesis. The results serve early detection and assessment of progression of CRC.
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Affiliation(s)
- Satu Valo
- Division of Genetics, Department of Biosciences, University of Helsinki, Helsinki, Finland ; Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
| | - Sippy Kaur
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
| | - Ari Ristimäki
- Genome-Scale Biology, Research Programs Unit, University of Helsinki, Helsinki, Finland ; Department of Pathology, HUSLAB, Helsinki University Central Hospital and University of Helsinki, Helsinki, Finland
| | - Laura Renkonen-Sinisalo
- Department of Gastrointestinal and General Surgery, Helsinki University Central Hospital, Helsinki, Finland
| | - Heikki Järvinen
- Department of Gastrointestinal and General Surgery, Helsinki University Central Hospital, Helsinki, Finland
| | - Jukka-Pekka Mecklin
- Department of Surgery, Jyväskylä Central Hospital, University of Eastern Finland, Jyväskylä, Finland
| | - Minna Nyström
- Division of Genetics, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Päivi Peltomäki
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
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Fairbrother LC, Cytrynbaum C, Boutis P, Buiting K, Weksberg R, Williams C. Mild Angelman syndrome phenotype due to a mosaic methylation imprinting defect. Am J Med Genet A 2015; 167:1565-9. [PMID: 25899869 DOI: 10.1002/ajmg.a.37058] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 02/22/2015] [Indexed: 12/31/2022]
Abstract
Angelman syndrome (AS) is a neurogenetic disorder causing severe to profound intellectual disability, absent or very limited speech and a high risk for seizures. AS is caused by a loss of function of the maternally-derived UBE3A allele due to one of several mechanisms including imprinting defects (ImpDs). We present a girl with AS due to a mosaic ImpD who has relatively high developmental function (VABS-II composite score of 76) and communication skills (as demonstrated in supplemental video links). Given the patient's relatively mild developmental impairment, without clinical evidence of seizures, gait disturbance or inappropriate laughter, the diagnosis of AS was not initially suspected. Initial laboratory testing for AS was inconclusive but additional studies suggested mosaic ImpD and characteristic EEG findings provided further support for the clinical diagnosis. Our patient, along with other case reports of children with AS and relatively mild phenotypes, raises the question as to whether there exists an undiagnosed group of individuals with mild intellectual disability and expressive speech delays due to mosaic methylation defects of the chromosome 15q11.2-13 region. Population studies may be needed to determine if such an undiagnosed group exists.
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Affiliation(s)
- Laura C Fairbrother
- Division of Genetics and Metabolism, Department of Pediatrics, University of Florida, Raymond C. Philips Unit, Gainesville, Florida
| | - Cheryl Cytrynbaum
- Division of Clinical and Metabolic Genetics, Department of Pediatrics and Genetics and Genome Biology, Research Institute, Hospital for Sick Children, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Ontario, Canada
| | | | - Karin Buiting
- Institut f, ü, r Humangenetik, Universit, ä, tsklinikum Essen, Essen, Germany
| | - Rosanna Weksberg
- Division of Clinical and Metabolic Genetics, Department of Pediatrics and Genetics and Genome Biology, Research Institute, Hospital for Sick Children, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Ontario, Canada
| | - Charles Williams
- Division of Genetics and Metabolism, Department of Pediatrics, University of Florida, Raymond C. Philips Unit, Gainesville, Florida
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López F, Sampedro T, Llorente JL, Domínguez F, Hermsen M, Suárez C, Alvarez-Marcos C. Utility of MS-MLPA in DNA methylation profiling in primary laryngeal squamous cell carcinoma. Oral Oncol 2014; 50:291-7. [PMID: 24444674 DOI: 10.1016/j.oraloncology.2014.01.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Accepted: 01/04/2014] [Indexed: 01/14/2023]
Abstract
OBJECTIVES Methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) assay is a method that has rarely been exploited in DNA methylation profiling of laryngeal squamous cell carcinoma (LSCC). MATERIAL AND METHODS Methylation of the gene was investigated by MS-MLPA in a well-characterized series of 53 LSCC and 30 samples of healthy mucosa. Aberrant promoter hypermethylation was confirmed using bisulfite pyrosequencing, and methylation-specific. RESULTS Promoter hypermethylation was observed in 36 of the 53 patients (68%). CDKN2B (28%), APC (17%), RARβ (15%), DAPK1 (11%) and CHFR (11%) were most frequently hypermethylated. Aberrant methylation of CHFR was mainly a late-stage event. Methylation-specific polymerase chain reaction and bisulfite pyrosequencing confirmed aberrant methylation for CDKN2B, APC and DAPK1. CONCLUSION Promoter methylation profiling of LSCC using MS-MLPA identified CDKN2B, DAPK1, RARβ, APC, and CHFR as frequent epigenetic events. The clinical implications of these genes as biomarkers are highly relevant as attractive targets for cancer therapy, given the reversible nature of epigenetic gene silencing.
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Affiliation(s)
- Fernando López
- Department of Otorhinolaryngology and Instituto Universitario de Oncología del Principado de Asturias, Hospital Universitario Central de Asturias, Oviedo, Asturias, Spain.
| | - Teresa Sampedro
- Department of Medical Oncology, Hospital San Agustín, Avilés, Asturias, Spain
| | - José L Llorente
- Department of Otorhinolaryngology and Instituto Universitario de Oncología del Principado de Asturias, Hospital Universitario Central de Asturias, Oviedo, Asturias, Spain
| | | | - Mario Hermsen
- Department of Otorhinolaryngology and Instituto Universitario de Oncología del Principado de Asturias, Hospital Universitario Central de Asturias, Oviedo, Asturias, Spain
| | - Carlos Suárez
- Department of Otorhinolaryngology and Instituto Universitario de Oncología del Principado de Asturias, Hospital Universitario Central de Asturias, Oviedo, Asturias, Spain
| | - César Alvarez-Marcos
- Department of Otorhinolaryngology and Instituto Universitario de Oncología del Principado de Asturias, Hospital Universitario Central de Asturias, Oviedo, Asturias, Spain
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García-Baquero R, Puerta P, Beltran M, Alvarez M, Sacristan R, Alvarez-Ossorio JL, Sánchez-Carbayo M. Methylation of a novel panel of tumor suppressor genes in urine moves forward noninvasive diagnosis and prognosis of bladder cancer: a 2-center prospective study. J Urol 2013; 190:723-30. [PMID: 23485510 DOI: 10.1016/j.juro.2013.01.105] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/29/2013] [Indexed: 12/29/2022]
Abstract
PURPOSE Changes in DNA methylation of tumor suppressor genes early in carcinogenesis represent potential indicators of cancer detection and disease evolution. We examined the diagnostic, stratification and prognostic biomarker roles in urine of the methylation of a novel panel of tumor suppressor genes in bladder cancer. MATERIAL AND METHODS We evaluated the methylation of 18 tumor suppressor genes in 2 prospective, independent sets of urine samples (training set of 120 preparations and validation set of 128) from patients with bladder cancer (170) and controls (78) using methylation specific multiplex ligation-dependent probe amplification. Diagnostic performance was evaluated with ROC curves. Recurrence, progression and disease specific survival were analyzed using univariate and multivariate Cox models. RESULTS PRDM2, HLTF, ID4, DLC1, BNIP3, H2AFX, CACNA1G, TGIF and CACNA1A were methylated in bladder cancer. CCND2, SCGB3A1, BNIP3, ID4 and RUNX3 were the most frequently methylated tumor suppressor genes in each urine set. Methylation of several tumor suppressor genes correlated with clinicopathological variables, such as stage, tumor grade, focality or age. ROC analysis revealed significant diagnostic accuracy for RUNX3 and CACNA1A in the training set, and for RUNX3 and ID4 in the validation set. On univariate and multivariate analysis CACNA1A methylation correlated with recurrence in the training set, while in the validation set PRDM2 and BNIP3 were significantly associated with recurrence and disease specific survival, respectively. CONCLUSIONS Tumor suppressor gene methylation allowed for histopathological and clinical stratification. Urine methylation has noninvasive usefulness not only for diagnostic assessment but also as independent bladder cancer prognosticators.
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Affiliation(s)
- Rodrigo García-Baquero
- Tumor Markers Group, Molecular Pathology Program, Spanish National Cancer Center, Madrid, Spain; Urology Department, Hospital Puerta del Mar, Cadiz, Spain
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Cardoso LCA, Tenorio Castaño JA, Pereira HS, Lima MADFD, Dos Santos ACE, de Faria PS, Ferman S, Seuánez HN, Nevado JB, de Almeida JCC, Lapunzina P, Vargas FR. Constitutional and somatic methylation status of DMRH19 and KvDMR in Wilms tumor patients. Genet Mol Biol 2012; 35:714-24. [PMID: 23271929 PMCID: PMC3526076 DOI: 10.1590/s1415-47572012005000073] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Accepted: 07/24/2012] [Indexed: 12/18/2022] Open
Abstract
The most frequent epigenetic alterations in Wilms tumor (WT) occur at WT2, assigned to 11p15. WT2 consists of two domains: telomeric domain 1 (DMRH19) that contains the IGF2 gene and an imprinted maternally expressed transcript (H19) and centromeric domain 2 (KvDMR) that contains the genes KCNQ1, KCNQ1OT1 and CDKN1C. In this work, we used pyrosequencing and MS-MLPA to compare the methylation patterns of DMRH19/KvDMR in blood and tumor samples from 40 WT patients. Normal constitutional KvDMR methylation indicated that most of the epigenetic alterations in WT occur at DMRH19. Constitutional DMRH19 hypermethylation (HM DMRH19) was observed in two patients with Beckwith-Wiedemann syndrome. Pyrosequencing and MS-MLPA showed HM DMRH19 in 28/34 tumor samples: 16/34 with isolated HM DMRH19 and 12/34 with concomitant HM DMRH19 and KvDMR hypomethylation, indicating paternal uniparental disomy. With the exception of one blood sample, the MS-MLPA and pyrosequencing findings were concordant. Diffuse or focal anaplasia was present in five tumor samples and was associated with isolated somatic HM DMRH19 in four of them. Constitutional 11p15 methylation abnormalities were present in 5% of the samples and somatic abnormalities in the majority of tumors. Combined analysis of DMRH19/KvDMR by pyrosequencing and MS-MLPA is beneficial for characterizing epigenetic anomalies in WT, and MS-MLPA is useful and reliable for estimation of DNA methylation in a clinical setting.
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Affiliation(s)
- Leila C A Cardoso
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil. ; Programa de Genética, Instituto Nacional de Câncer, Rio de Janeiro, RJ, Brazil
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Tran HTT, Kim HN, Lee IK, Kim YK, Ahn JS, Yang DH, Lee JJ, Kim HJ. DNA methylation changes following 5-azacitidine treatment in patients with myelodysplastic syndrome. J Korean Med Sci 2011; 26:207-13. [PMID: 21286011 PMCID: PMC3031004 DOI: 10.3346/jkms.2011.26.2.207] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2010] [Accepted: 11/09/2010] [Indexed: 12/24/2022] Open
Abstract
DNA methyltransferase inhibitor, 5-azacitidine (AC) is effective in myelodysplastic syndromes (MDS) and can induce re-expression in cancer. We analyzed the methylation of 25 tumor suppressor genes in AC-treated MDS. Hypermethylation of CDKN2B, FHIT, ESR1, and IGSF4 gene was detected in 9/44 patients. In concordance with the clinical response, a lack of or decreased methylation in 4 patients with hematologic improvements and persistent methylation in 4 others with no response was observed. The mRNA expression of CDKN2B, IGSF4, and ESR1 was significantly reduced in MDS. Our results suggest that methylation changes contribute to disease pathogenesis and may serve as marker to monitor the efficacy of treatments.
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Affiliation(s)
- Huong Thi Thanh Tran
- Genome Research Center for Hematopoietic Diseases, Chonnam National University Hwasun Hospital, Hwasun, Korea
| | - Hee Nam Kim
- Genome Research Center for Hematopoietic Diseases, Chonnam National University Hwasun Hospital, Hwasun, Korea
| | - Il-Kwon Lee
- Genome Research Center for Hematopoietic Diseases, Chonnam National University Hwasun Hospital, Hwasun, Korea
| | - Yeo-Kyeoung Kim
- Department of Hematology-Oncology, Chonnam National University Medical School, Gwangju, Korea
| | - Jae-Sook Ahn
- Department of Hematology-Oncology, Chonnam National University Medical School, Gwangju, Korea
| | - Deok-Hwan Yang
- Department of Hematology-Oncology, Chonnam National University Medical School, Gwangju, Korea
| | - Je-Jung Lee
- Department of Hematology-Oncology, Chonnam National University Medical School, Gwangju, Korea
| | - Hyeoung-Joon Kim
- Genome Research Center for Hematopoietic Diseases, Chonnam National University Hwasun Hospital, Hwasun, Korea
- Department of Hematology-Oncology, Chonnam National University Medical School, Gwangju, Korea
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