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Qin Y, Touch K, Sha M, Sun Y, Zhang S, Wu J, Wu Y, Feng L, Chen S, Xiao J. The chromosomal characteristics of spontaneous abortion and its potential associated copy number variants and genes. J Assist Reprod Genet 2024; 41:1285-1296. [PMID: 38668959 PMCID: PMC11143157 DOI: 10.1007/s10815-024-03119-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 04/02/2024] [Indexed: 06/01/2024] Open
Abstract
PURPOSE This study aimed to investigate the correlation between chromosomal abnormalities in spontaneous abortion with clinical features and seek copy number variations (CNVs) and genes that might be connected to spontaneous abortion. METHODS Over 7 years, we used CNV-seq and STR analysis to study POCs, comparing chromosomal abnormalities with clinical features and identifying critical CNVs and genes associated with spontaneous abortion. RESULTS Total chromosomal variants in the POCs were identified in 66.8% (2169/3247) of all cases, which included 45.2% (1467/3247) numerical abnormalities and 21.6% (702/3247) copy number variants (CNVs). Chromosome number abnormalities, especially aneuploidy abnormalities, were more pronounced in the group of mothers aged ≥ 35 years, the early miscarriage group, and the chorionic villi group. We further analyzed 212 pathogenic and likely pathogenic CNVs in 146 POCs as well as identified 8 statistically significant SORs through comparison with both a healthy population and a group of non-spontaneously aborted fetuses. Our analysis suggests that these CNVs may play a crucial role in spontaneous abortion. Furthermore, by utilizing the RVIS score and MGI database, we identified 86 genes associated with spontaneous abortion, with particular emphasis on PARP6, ISLR, ULK3, FGFRL1, TBC1D14, SCRIB, and PLEC. CONCLUSION We found variability in chromosomal abnormalities across clinical features, identifying eight crucial copy number variations (CNVs) and multiple key genes that may be linked to spontaneous abortion. This research enhances the comprehension of genetic factors contributing to spontaneous abortion.
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Affiliation(s)
- Yu Qin
- Department of Obstetrics & Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jiefang Avenue 1095, Wuhan, 430030, Hubei, China
| | - Koksear Touch
- Department of Obstetrics & Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jiefang Avenue 1095, Wuhan, 430030, Hubei, China
| | - Menghan Sha
- Department of Obstetrics, Maternal and Child Health Hospital of Hubei Province, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yanan Sun
- Department of Obstetrics & Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jiefang Avenue 1095, Wuhan, 430030, Hubei, China
| | - Shunran Zhang
- Department of Obstetrics & Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jiefang Avenue 1095, Wuhan, 430030, Hubei, China
| | - Jianli Wu
- Department of Obstetrics & Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jiefang Avenue 1095, Wuhan, 430030, Hubei, China
| | - Yuanyuan Wu
- Department of Obstetrics & Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jiefang Avenue 1095, Wuhan, 430030, Hubei, China
| | - Ling Feng
- Department of Obstetrics & Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jiefang Avenue 1095, Wuhan, 430030, Hubei, China
| | - Suhua Chen
- Department of Obstetrics & Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jiefang Avenue 1095, Wuhan, 430030, Hubei, China.
| | - Juan Xiao
- Department of Obstetrics & Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jiefang Avenue 1095, Wuhan, 430030, Hubei, China.
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Almeida VT, Chehimi SN, Carvalho GFS, Gasparini Y, Nascimento AM, Vieira LL, Wolff BM, Montenegro MM, Kulikowski LD. Differences in DNA methylation status explain phenotypic variability in patients with 5p- syndrome. BMC Res Notes 2024; 17:121. [PMID: 38679724 PMCID: PMC11057176 DOI: 10.1186/s13104-024-06734-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 03/01/2024] [Indexed: 05/01/2024] Open
Abstract
Cri Du Chat syndrome, or 5p- syndrome, is characterized by a terminal or interstitial deletion on the short arm of chromosome 5 that causes variable clinical manifestations, including high-pitched cry in newborns, delayed growth, and global development. Different cytogenomic rearrangements, family history, and environmental factors may hinder the genotype-phenotype association. Thus, the phenotypic variability of this syndrome may not be limited only to variations in gene structure, such as deletions and duplications. It is possible that other mechanisms related to the activation or inactivation of promoters and/or exons of actively transcribed genes, such as DNA methylation are involved. Therefore, we studied the genome-wide methylation status profile of peripheral blood samples from fifteen patients with Cri du Chat Syndrome and nine control samples through the array method to look for Differentially Methylated Regions. We found that Differentially Methylated Regions outside the 5p region are mainly associated with regulating gene transcription, splicing, and chromatin remodeling. Most biological pathways are related to transcription, histone and chromatin binding, spliceosome and ribosomal complex, and RNA processing. Our results suggest that changes in the 5p region can cause an imbalance in other chromosomal regions capable of affecting gene modulation and thus explain the phenotypic differences in patients with 5p-.
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Affiliation(s)
- Vanessa Tavares Almeida
- Laboratorio de Citogenomica, Departamento de Patologia, Faculdade de Medicina, Universidade de Sao Paulo, PAMB, 2º Floor, Block 12, Room 07, Dr. Eneas de Carvalho Aguiar Avenue, 155, Cerqueira Cesar, Sao Paulo, 05403-000, Brazil.
| | - Samar N Chehimi
- Laboratorio de Citogenomica, Departamento de Patologia, Faculdade de Medicina, Universidade de Sao Paulo, PAMB, 2º Floor, Block 12, Room 07, Dr. Eneas de Carvalho Aguiar Avenue, 155, Cerqueira Cesar, Sao Paulo, 05403-000, Brazil
| | - Gleyson F S Carvalho
- Laboratorio de Citogenomica, Departamento de Patologia, Faculdade de Medicina, Universidade de Sao Paulo, PAMB, 2º Floor, Block 12, Room 07, Dr. Eneas de Carvalho Aguiar Avenue, 155, Cerqueira Cesar, Sao Paulo, 05403-000, Brazil
| | - Yanca Gasparini
- Laboratorio de Citogenomica, Departamento de Patologia, Faculdade de Medicina, Universidade de Sao Paulo, PAMB, 2º Floor, Block 12, Room 07, Dr. Eneas de Carvalho Aguiar Avenue, 155, Cerqueira Cesar, Sao Paulo, 05403-000, Brazil
| | - Amom M Nascimento
- Laboratorio de Citogenomica, Departamento de Patologia, Faculdade de Medicina, Universidade de Sao Paulo, PAMB, 2º Floor, Block 12, Room 07, Dr. Eneas de Carvalho Aguiar Avenue, 155, Cerqueira Cesar, Sao Paulo, 05403-000, Brazil
| | - Lucas L Vieira
- Laboratorio de Citogenomica, Departamento de Patologia, Faculdade de Medicina, Universidade de Sao Paulo, PAMB, 2º Floor, Block 12, Room 07, Dr. Eneas de Carvalho Aguiar Avenue, 155, Cerqueira Cesar, Sao Paulo, 05403-000, Brazil
| | - Beatriz M Wolff
- Laboratorio de Citogenomica, Departamento de Patologia, Faculdade de Medicina, Universidade de Sao Paulo, PAMB, 2º Floor, Block 12, Room 07, Dr. Eneas de Carvalho Aguiar Avenue, 155, Cerqueira Cesar, Sao Paulo, 05403-000, Brazil
| | - Marília M Montenegro
- Laboratorio de Citogenomica, Departamento de Patologia, Faculdade de Medicina, Universidade de Sao Paulo, PAMB, 2º Floor, Block 12, Room 07, Dr. Eneas de Carvalho Aguiar Avenue, 155, Cerqueira Cesar, Sao Paulo, 05403-000, Brazil
| | - Leslie D Kulikowski
- Laboratorio de Citogenomica, Departamento de Patologia, Faculdade de Medicina, Universidade de Sao Paulo, PAMB, 2º Floor, Block 12, Room 07, Dr. Eneas de Carvalho Aguiar Avenue, 155, Cerqueira Cesar, Sao Paulo, 05403-000, Brazil
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Shastri GG, Sudre G, Ahn K, Jung B, Kolachana B, Auluck PK, Elnitski L, Marenco S, Shaw P. Cortico-striatal differences in the epigenome in attention-deficit/ hyperactivity disorder. Transl Psychiatry 2024; 14:189. [PMID: 38605038 PMCID: PMC11009227 DOI: 10.1038/s41398-024-02896-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 03/20/2024] [Accepted: 04/02/2024] [Indexed: 04/13/2024] Open
Abstract
While epigenetic modifications have been implicated in ADHD through studies of peripheral tissue, to date there has been no examination of the epigenome of the brain in the disorder. To address this gap, we mapped the methylome of the caudate nucleus and anterior cingulate cortex in post-mortem tissue from fifty-eight individuals with or without ADHD. While no single probe showed adjusted significance in differential methylation, several differentially methylated regions emerged. These regions implicated genes involved in developmental processes including neurogenesis and the differentiation of oligodendrocytes and glial cells. We demonstrate a significant association between differentially methylated genes in the caudate and genes implicated by GWAS not only in ADHD but also in autistic spectrum, obsessive compulsive and bipolar affective disorders through GWAS. Using transcriptomic data available on the same subjects, we found modest correlations between the methylation and expression of genes. In conclusion, this study of the cortico-striatal methylome points to gene and gene pathways involved in neurodevelopment, consistent with studies of common and rare genetic variation, as well as the post-mortem transcriptome in ADHD.
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Affiliation(s)
- Gauri G Shastri
- Social and Behavioral Research Branch, National Human Genome Research Institute, NIH, Bethesda, MD, 20892, USA
| | - Gustavo Sudre
- Social and Behavioral Research Branch, National Human Genome Research Institute, NIH, Bethesda, MD, 20892, USA
| | - Kwangmi Ahn
- Social and Behavioral Research Branch, National Human Genome Research Institute, NIH, Bethesda, MD, 20892, USA
| | - Benjamin Jung
- Social and Behavioral Research Branch, National Human Genome Research Institute, NIH, Bethesda, MD, 20892, USA
| | - Bhaskar Kolachana
- Human Brain Collection Core, National Institute of Mental Health, NIH, Bethesda, MD, 20892, USA
| | - Pavan K Auluck
- Human Brain Collection Core, National Institute of Mental Health, NIH, Bethesda, MD, 20892, USA
| | - Laura Elnitski
- Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, 20892, USA
| | - Stefano Marenco
- Human Brain Collection Core, National Institute of Mental Health, NIH, Bethesda, MD, 20892, USA
| | - Philip Shaw
- Social and Behavioral Research Branch, National Human Genome Research Institute, NIH, Bethesda, MD, 20892, USA.
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Danesino C, Gualtierotti M, Origi M, Cistaro A, Malacarne M, Massidda M, Bencardino K, Coviello D, Albani G, Schiera IG, Liava A, Guala A. Esophageal Cancer with Early Onset in a Patient with Cri du Chat Syndrome. Diseases 2023; 12:9. [PMID: 38248360 PMCID: PMC10813838 DOI: 10.3390/diseases12010009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 12/02/2023] [Accepted: 12/19/2023] [Indexed: 01/23/2024] Open
Abstract
BACKGROUND In Cri du Chat (CdC), cancer as comorbidity is extremely rare. In databases from Denmark, Spain, Australia, New Zealand, and Japan, no cancer was reported; in Italy and Germany, four cancers were identified out of 321 CdCs. METHODS In a 29-year-old CdC patient, clinical investigations following hematemesis led to the diagnosis of esophageal adenocarcinoma (EAC). A high pain threshold was also observed. Conventional and molecular cytogenetic defined the size of the deletion, and exome analysis on the trio completed the molecular work. RESULTS Cytogenetic analysis showed a de novo chromosomal alteration: 46,XY,ishdel(5)(p14.3)(D5S28-) and arr[GRCh37] 5p15.33p14.3(1498180_19955760)x1. A quantitative sensory test demonstrated a high heat threshold. A 18f-fluorodeoxyglucose PET/TC scan of the brain failed to detect reduction of metabolism in the somatosensory area or insular cortex. Exome analysis in the trio (patient and parents) failed to identify variants to be interpreted as a likely risk factor for EAC. CONCLUSION We conclude that the presence of well-known risk factors (maleness, obesity, gastroesophageal reflux, and Barrett's metaplasia) in a patient with very limited capability of expressing discomfort or referring clinical symptoms have been the main risk factors for developing EAC. At present, based on the available data, there is no evidence of any increased risk of developing cancer in CdC patients.
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Affiliation(s)
- Cesare Danesino
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Scientific Committee of A.B.C. Associazione Bambini Cri du Chat, 50026 Firenze, Italy; (A.C.); (A.G.)
| | - Monica Gualtierotti
- UOC Chirurgia Generale Oncologica e Mininvasiva, Ospedale Niguarda, 20162 Milano, Italy; (M.G.); (M.O.)
| | - Matteo Origi
- UOC Chirurgia Generale Oncologica e Mininvasiva, Ospedale Niguarda, 20162 Milano, Italy; (M.G.); (M.O.)
| | - Angelina Cistaro
- Scientific Committee of A.B.C. Associazione Bambini Cri du Chat, 50026 Firenze, Italy; (A.C.); (A.G.)
- Nuclear Medicine Unit, Salus Alliance Medical, 16129 Genova, Italy
- Pediatric Study Group Italian Associaton of Nuclear Medicine (AIMN), 20159 Milan, Italy
| | - Michela Malacarne
- UOC Laboratorio di Genetica Umana, IRCCS G. Gaslini, 16147 Genova, Italy; (M.M.); (M.M.); (D.C.)
| | - Matteo Massidda
- UOC Laboratorio di Genetica Umana, IRCCS G. Gaslini, 16147 Genova, Italy; (M.M.); (M.M.); (D.C.)
- Department of Medical, Surgery and Experimental Sciences, University of Sassari, 07100 Sassari, Italy
| | - Katia Bencardino
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, 20162 Milano, Italy;
| | - Domenico Coviello
- UOC Laboratorio di Genetica Umana, IRCCS G. Gaslini, 16147 Genova, Italy; (M.M.); (M.M.); (D.C.)
| | - Giovanni Albani
- Department of Neurology and Neurorehabilitation for Severe Brain Injures Acquired Ospedale Moriggia Pelascini, 22015 Gravedona, Italy;
| | | | | | - Andrea Guala
- Scientific Committee of A.B.C. Associazione Bambini Cri du Chat, 50026 Firenze, Italy; (A.C.); (A.G.)
- UOC Pediatria, Ospedale Castelli, 28921 Verbania, Italy
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van der Laan L, Rooney K, Trooster TM, Mannens MM, Sadikovic B, Henneman P. DNA methylation episignatures: insight into copy number variation. Epigenomics 2022; 14:1373-1388. [PMID: 36537268 DOI: 10.2217/epi-2022-0287] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
In this review we discuss epigenetic disorders that result from aberrations in genes linked to epigenetic regulation. We describe current testing methods for the detection of copy number variants (CNVs) in Mendelian disorders, dosage sensitivity, reciprocal phenotypes and the challenges of test selection and overlapping clinical features in genetic diagnosis. We discuss aberrations of DNA methylation and propose a role for episignatures as a novel clinical testing method in CNV disorders. Finally, we postulate that episignature mapping in CNV disorders may provide novel insights into the molecular mechanisms of disease and unlock key findings of the genome-wide impact on disease gene networks.
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Affiliation(s)
- Liselot van der Laan
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, Amsterdam, 1105 AZ, The Netherlands
| | - Kathleen Rooney
- Department of Pathology & Laboratory Medicine, Western University, London, Ontario, N5A 3K7, Canada.,Verspeeten Clinical Genome Centre, London Health Science Centre, London, Ontario, N6A 5W9, Canada
| | - Tessa Ma Trooster
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, Amsterdam, 1105 AZ, The Netherlands
| | - Marcel Mam Mannens
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, Amsterdam, 1105 AZ, The Netherlands
| | - Bekim Sadikovic
- Department of Pathology & Laboratory Medicine, Western University, London, Ontario, N5A 3K7, Canada.,Verspeeten Clinical Genome Centre, London Health Science Centre, London, Ontario, N6A 5W9, Canada
| | - Peter Henneman
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, Amsterdam, 1105 AZ, The Netherlands
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