1
|
Caraffi SG, van der Laan L, Rooney K, Trajkova S, Zuntini R, Relator R, Haghshenas S, Levy MA, Baldo C, Mandrile G, Lauzon C, Cordelli DM, Ivanovski I, Fetta A, Sukarova E, Brusco A, Pavinato L, Pullano V, Zollino M, McConkey H, Tartaglia M, Ferrero GB, Sadikovic B, Garavelli L. Identification of the DNA methylation signature of Mowat-Wilson syndrome. Eur J Hum Genet 2024; 32:619-629. [PMID: 38351292 PMCID: PMC11153515 DOI: 10.1038/s41431-024-01548-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 01/10/2024] [Accepted: 01/18/2024] [Indexed: 06/07/2024] Open
Abstract
Mowat-Wilson syndrome (MOWS) is a rare congenital disease caused by haploinsufficiency of ZEB2, encoding a transcription factor required for neurodevelopment. MOWS is characterized by intellectual disability, epilepsy, typical facial phenotype and other anomalies, such as short stature, Hirschsprung disease, brain and heart defects. Despite some recognizable features, MOWS rarity and phenotypic variability may complicate its diagnosis, particularly in the neonatal period. In order to define a novel diagnostic biomarker for MOWS, we determined the genome-wide DNA methylation profile of DNA samples from 29 individuals with confirmed clinical and molecular diagnosis. Through multidimensional scaling and hierarchical clustering analysis, we identified and validated a DNA methylation signature involving 296 differentially methylated probes as part of the broader MOWS DNA methylation profile. The prevalence of hypomethylated CpG sites agrees with the main role of ZEB2 as a transcriptional repressor, while differential methylation within the ZEB2 locus supports the previously proposed autoregulation ability. Correlation studies compared the MOWS cohort with 56 previously described DNA methylation profiles of other neurodevelopmental disorders, further validating the specificity of this biomarker. In conclusion, MOWS DNA methylation signature is highly sensitive and reproducible, providing a useful tool to facilitate diagnosis.
Collapse
Grants
- MNESYS (PE0000006) Ministero dell'Istruzione, dell'Università e della Ricerca (Ministry of Education, University and Research)
- 20203P8C3X Ministero dell'Istruzione, dell'Università e della Ricerca (Ministry of Education, University and Research)
- FOE 2020 Ministero dell'Istruzione, dell'Università e della Ricerca (Ministry of Education, University and Research)
- RCR-2022-23682289 Ministero della Salute (Ministry of Health, Italy)
- PNRR-MR1-2022-12376811 Ministero della Salute (Ministry of Health, Italy)
- OGI-188 Ontario Genomics Institute (OGI)
- Ministero dell'Istruzione, dell'Università e della Ricerca (Ministry of Education, University and Research)
Collapse
Affiliation(s)
| | - Liselot van der Laan
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Kathleen Rooney
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, Canada
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Slavica Trajkova
- Department of Medical Sciences, University of Torino, Torino, Italy
- Molecular Biotechnology Center "Guido Tarone", University of Torino, 10126, Torino, Italy
| | - Roberta Zuntini
- Medical Genetics Unit, Azienda USL-IRCCS di Reggio Emilia, 42122, Reggio Emilia, Italy
| | - Raissa Relator
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, Canada
| | - Sadegheh Haghshenas
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, Canada
| | - Michael A Levy
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, Canada
| | - Chiara Baldo
- Laboratory of Human Genetics, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Giorgia Mandrile
- Medical Genetics Unit and Thalassemia Center, San Luigi University Hospital, University of Torino, 10043, Orbassano (Torino), Italy
| | - Carolyn Lauzon
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, Canada
| | - Duccio Maria Cordelli
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Neuropsichiatria dell'Età Pediatrica, 40139, Bologna, Italy
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126, Bologna, Italy
| | - Ivan Ivanovski
- Institute of Medical Genetics, University of Zürich, Zürich, Switzerland
| | - Anna Fetta
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Neuropsichiatria dell'Età Pediatrica, 40139, Bologna, Italy
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126, Bologna, Italy
| | - Elena Sukarova
- Department of Endocrinology and Genetics, University Clinic for Pediatric Diseases, Faculty of Medicine, Ss. Cyril and Methodius University in Skopje, 1000, Skopje, Republic of North Macedonia
| | - Alfredo Brusco
- Department of Medical Sciences, University of Torino, Torino, Italy
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Torino, Italy
| | - Lisa Pavinato
- Department of Medical Sciences, University of Torino, Torino, Italy
- Molecular Biotechnology Center "Guido Tarone", University of Torino, 10126, Torino, Italy
| | - Verdiana Pullano
- Department of Medical Sciences, University of Torino, Torino, Italy
- Molecular Biotechnology Center "Guido Tarone", University of Torino, 10126, Torino, Italy
| | - Marcella Zollino
- Institute of Genomic Medicine, Department of Life Sciences and Public Health, 'Sacro Cuore' Catholic University of Rome, 00168, Rome, Italy
| | - Haley McConkey
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, Canada
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Marco Tartaglia
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | | | - Bekim Sadikovic
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands.
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, Canada.
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada.
| | - Livia Garavelli
- Medical Genetics Unit, Azienda USL-IRCCS di Reggio Emilia, 42122, Reggio Emilia, Italy.
| |
Collapse
|
2
|
van der Laan L, Karimi K, Rooney K, Lauffer P, McConkey H, Caro P, Relator R, Levy MA, Bhai P, Mignot C, Keren B, Briuglia S, Sobering AK, Li D, Vissers LELM, Dingemans AJM, Valenzuela I, Verberne EA, Misra-Isrie M, Zwijnenburg PJG, Waisfisz Q, Alders M, Sailer S, Schaaf CP, Mannens MMAM, Sadikovic B, van Haelst MM, Henneman P. DNA methylation episignature, extension of the clinical features, and comparative epigenomic profiling of Hao-Fountain syndrome caused by variants in USP7. Genet Med 2024; 26:101050. [PMID: 38126281 DOI: 10.1016/j.gim.2023.101050] [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: 07/04/2023] [Revised: 12/06/2023] [Accepted: 12/11/2023] [Indexed: 12/23/2023] Open
Abstract
PURPOSE Hao-Fountain syndrome (HAFOUS) is a neurodevelopmental disorder caused by pathogenic variants in USP7. HAFOUS is characterized by developmental delay, intellectual disability, speech delay, behavioral abnormalities, autism spectrum disorder, seizures, hypogonadism, and mild dysmorphic features. We investigated the phenotype of 18 participants with HAFOUS and performed DNA methylation (DNAm) analysis, aiming to generate a diagnostic biomarker. Furthermore, we performed comparative analysis with known episignatures to gain more insight into the molecular pathophysiology of HAFOUS. METHODS We assessed genomic DNAm profiles of 18 individuals with pathogenic variants and variants of uncertain significance (VUS) in USP7 to map and validate a specific episignature. The comparison between the USP7 cohort and 56 rare genetic disorders with earlier reported DNAm episignatures was performed with statistical and functional correlation. RESULTS We mapped a sensitive and specific DNAm episignature for pathogenic variants in USP7 and utilized this to reclassify the VUS. Comparative epigenomic analysis showed evidence of HAFOUS similarity to a number of other rare genetic episignature disorders. CONCLUSION We discovered a sensitive and specific DNAm episignature as a robust diagnostic biomarker for HAFOUS that enables VUS reclassification in USP7. We also expand the phenotypic spectrum of 9 new and 5 previously reported individuals with HAFOUS.
Collapse
Affiliation(s)
- Liselot van der Laan
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Karim Karimi
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, Ontario, Canada; Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | - Kathleen Rooney
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, Ontario, Canada; Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | - Peter Lauffer
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Haley McConkey
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, Ontario, Canada; Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | - Pilar Caro
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Raissa Relator
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, Ontario, Canada
| | - Michael A Levy
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, Ontario, Canada
| | - Pratibha Bhai
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, Ontario, Canada
| | - Cyril Mignot
- APHP Sorbonne Université, Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière, Paris, France; Hôpital Armand Trousseau, Paris, France AND Centre de Référence Déficiences Intellectuelles de Causes Rares, Paris, France
| | - Boris Keren
- APHP Sorbonne Université, Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
| | - Silvana Briuglia
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Messina, Italy
| | - Andrew K Sobering
- AU/UGA Medical Partnership Campus of the Medical College of Georgia, Athens, Georgia; Windward Islands Research and Education Foundation, True Blue, St. George's, Grenada; St. George's University School of Medicine, Department of Biochemistry, Grenada
| | - Dong Li
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA; Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA; Department of Pediatrics, University of Pennsylvania Perelman school of Medicine, Philadelphia, PA
| | - Lisenka E L M Vissers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Irene Valenzuela
- Àrea de Genètica Clínica i Malalties Minoritàries, Hospital Vall d'Hebron, Barcelona, Spain
| | - Eline A Verberne
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Mala Misra-Isrie
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Petra J G Zwijnenburg
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Quinten Waisfisz
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Mariëlle Alders
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Sebastian Sailer
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | | | - Marcel M A M Mannens
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Bekim Sadikovic
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, Ontario, Canada; Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada.
| | - Mieke M van Haelst
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Peter Henneman
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands.
| |
Collapse
|
3
|
Wu Q, Fang L, Wang Y, Yang P. Unraveling the role of ZNF506 as a human PBS-pro-targeting protein for ERVP repression. Nucleic Acids Res 2023; 51:10309-10325. [PMID: 37697430 PMCID: PMC10602909 DOI: 10.1093/nar/gkad731] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 08/09/2023] [Accepted: 08/21/2023] [Indexed: 09/13/2023] Open
Abstract
Krüppel-associated box zinc finger proteins (KZFPs) function as a defense mechanism to maintain the genome stability of higher vertebrates by regulating the transcriptional activities of transposable elements (TEs). While previous studies have characterized ZFP809 as responsible for binding and repressing ERVs containing a proline tRNA primer-binding site (PBS-Pro) in mice, comparable KZFPs have not been identified in humans yet. Here, we identified ZNF506 as a PBS-Pro-binding protein in humans, which functions as a transcriptional repressor of PBS-Pro-utilizing retroviruses by recruiting heterochromatic modifications. Although they have similar functions, the low protein similarities between ZNF506, ZFP809 and KZFPs of other species suggest their independent evolution against the invasion of PBS-Pro-utilizing retroviruses into their respective ancestor genomes after species divergence. We also explored the link between ZNF506 and leukemia. Our findings suggest that ZNF506 is a unique human KZFP that can bind to PBS-Pro, highlighting the diverse evolution of KZFPs in defending against retroviral invasions. Additionally, our study provides insights into the potential role of ZNF506 in leukemia, contributing to the expanding knowledge of KZFPs' crucial function in disease and genome stability.
Collapse
Affiliation(s)
- Qian Wu
- Shanghai Key Laboratory of Anesthesiology and Brain Functional Modulation, Clinical Research Center for Anesthesiology and Perioperative Medicine, Translational Research Institute of Brain and Brain-Like Intelligence, Shanghai Fourth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Lu Fang
- Shanghai Key Laboratory of Anesthesiology and Brain Functional Modulation, Clinical Research Center for Anesthesiology and Perioperative Medicine, Translational Research Institute of Brain and Brain-Like Intelligence, Shanghai Fourth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Yixuan Wang
- Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Peng Yang
- Shanghai Key Laboratory of Anesthesiology and Brain Functional Modulation, Clinical Research Center for Anesthesiology and Perioperative Medicine, Translational Research Institute of Brain and Brain-Like Intelligence, Shanghai Fourth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| |
Collapse
|
4
|
Yang Y, Wang W, Hu Q, Raman H, Liu J. Genome-wide association and RNA-seq analyses identify loci for pod orientation in rapeseed ( Brassica napus). FRONTIERS IN PLANT SCIENCE 2023; 13:1097534. [PMID: 36714779 PMCID: PMC9880488 DOI: 10.3389/fpls.2022.1097534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 12/21/2022] [Indexed: 06/18/2023]
Abstract
Spatial distribution and orientation of pods on the main raceme (stem) and branches could affect rapeseed yield. However, genomic regions underlying the pod orientation were not described in Brassica species. Here, we determined the extent of genetic variation in pod orientation, described as the angles of pedicel on raceme (APR) and angles of the pod on pedicel (APP) among 136 rapeseed accessions grown across three environments of the upper, middle and lower Yangtze River in China. The APR ranged from 59° to 109°, while the APP varied from 142° to 178°. Statistical analysis showed that phenotypic variation was due to genotypic (G) and environmental (E) effects. Using the genome-wide association analysis (GWAS) approach, two QTLs for APR (qBnAPR.A02 and qBnAPR.C02) and two for APP (qBnAPP.A05 and qBnAPP.C05), having minor to moderate allelic effects (4.30% to 19.47%) were identified. RNA-seq analysis revealed 606 differentially expressed genes (DEGs) in two rapeseed accessions representing the extreme phenotypes for pod orientation and different alleles at the QTLs of APR. Three DEGs (BnLAZY4.A02, BnSAUR32.A02, and BnSAUR32.C02) were identified as the most likely candidates responsible for variation in pod orientation (APR). This study elucidates the genomic regions and putative candidate genes underlying pod orientation in B. napus.
Collapse
Affiliation(s)
- Yuting Yang
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
- Shenzhen Graduate School, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Wenxiang Wang
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Qiong Hu
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Harsh Raman
- New South Wales (NSW) Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, Australia
| | - Jia Liu
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| |
Collapse
|