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Brady L, Ballantyne M, Duck J, Fisker T, Kleefman R, Li C, Nfonsam L, Schultz LA, Tarnopolsky M, McCready E. Further characterization of the 9q31 microdeletion phenotype; delineation of a common region of overlap containing ZNF462. Mol Genet Genomic Med 2023; 11:e2116. [PMID: 36461789 PMCID: PMC10009906 DOI: 10.1002/mgg3.2116] [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: 06/10/2022] [Accepted: 11/03/2022] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Loss of function variants and whole gene deletions of ZNF462 has been associated with a novel phenotype of developmental delay/intellectual disability and distinctive facial features. Over two dozen cases have been reported to date and the condition is now known as Weiss-Kruszka syndrome (OMIM# 618619). There are several older reports in the literature and DECIPER detailing individuals with interstitial deletions of 9q31 involving the ZNF462 gene. Many of the characteristic facial features described in these microdeletion cases are similar to those who have been diagnosed with Weiss-Kruszka syndrome. METHODS We describe three additional patients with overlapping 9q31 deletions and compare the phenotypes of the microdeletion cases reported in the literature to Weiss-Kruszka syndrome. RESULTS Phenotypic overlap was observed between patients with 9q31 deletions and Weiss-Kruszka syndrome. Several additional features were noted in 9q31 deletion patients, including hearing loss, small head circumference, palate abnormalities and short stature. CONCLUSIONS The common region of overlap of microdeletion cases implicates ZNF462 as the main driver of the recognizable 9q31 microdeletion phenotype. The observation of additional features in patients with 9q31 microdeletions that are not reported in Weiss-Kruszka syndrome further suggests that other genes from the 9q31 region likely act synergistically with ZNF462 to affect phenotypic expression.
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Affiliation(s)
- Lauren Brady
- Hamilton Health Sciences Centre, Hamilton, Ontario, Canada.,Division of Neuromuscular & Neurometabolic Disorders, Department of Paediatrics, McMaster University, Hamilton, Ontario, Canada
| | - Mark Ballantyne
- Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences Centre, Hamilton, Ontario, Canada
| | - John Duck
- Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences Centre, Hamilton, Ontario, Canada
| | - Thomas Fisker
- Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences Centre, Hamilton, Ontario, Canada
| | - Ryan Kleefman
- Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences Centre, Hamilton, Ontario, Canada
| | - Chumei Li
- Hamilton Health Sciences Centre, Hamilton, Ontario, Canada.,Division of Genetics, Department of Paediatrics, McMaster University, Hamilton, Ontario, Canada
| | - Landry Nfonsam
- Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences Centre, Hamilton, Ontario, Canada.,Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Lee-Anne Schultz
- Hamilton Health Sciences Centre, Hamilton, Ontario, Canada.,Division of Genetics, Department of Paediatrics, McMaster University, Hamilton, Ontario, Canada
| | - Mark Tarnopolsky
- Hamilton Health Sciences Centre, Hamilton, Ontario, Canada.,Division of Neuromuscular & Neurometabolic Disorders, Department of Paediatrics, McMaster University, Hamilton, Ontario, Canada
| | - Elizabeth McCready
- Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences Centre, Hamilton, Ontario, Canada.,Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
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Ramineni AK, Burgess T, Cruickshanks P, Coman D. A novel familial 9q31.2q32 microdeletion: Muscle cramping, somnolence, fatigue, sensorineural hearing loss, pubertal delay, and short stature. Clin Case Rep 2019; 7:304-310. [PMID: 30847195 PMCID: PMC6389485 DOI: 10.1002/ccr3.1970] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 11/04/2018] [Accepted: 11/22/2018] [Indexed: 02/01/2023] Open
Abstract
We report a novel 9q31.2q32 (chr9: 109195179-113974353, hg 18) microdeletion characterized by fatigue, muscle cramps, short stature, delayed puberty, sensorineural hearing loss, and mild developmental delay. Overlapping microdeletions reported in this region also demonstrate facial dysmorphism, skeletal anomalies, cleft palate, and cardiac valvular abnormalities. In comparing these cases, we suggest critical region of chr9: 109711873-113407621 (hg 18).
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Affiliation(s)
- Anand K. Ramineni
- Department of PaediatricsThe Wesley HospitalBrisbaneQueenslandAustralia
- Discipline of PaediatricsUnitingCare Clinical SchoolBrisbaneQueenslandAustralia
- Department of NeurosciencesLady Cilento Children's HospitalBrisbaneQueenslandAustralia
- School of MedicineThe University of QueenslandBrisbaneQueenslandAustralia
| | - Trent Burgess
- Victorian Clinical Genetics ServicesParkvilleVictoriaAustralia
- Murdoch Children's Research InstituteParkvilleVictoriaAustralia
- Department of PaediatricsUniversity of MelbourneParkvilleVictoriaAustralia
| | - Penny Cruickshanks
- Department of PaediatricsSunshine Coast University HospitalSunshine CoastQueenslandAustralia
| | - David Coman
- Department of PaediatricsThe Wesley HospitalBrisbaneQueenslandAustralia
- Discipline of PaediatricsUnitingCare Clinical SchoolBrisbaneQueenslandAustralia
- Department of NeurosciencesLady Cilento Children's HospitalBrisbaneQueenslandAustralia
- School of MedicineThe University of QueenslandBrisbaneQueenslandAustralia
- School of MedicineGriffith UniversityGold CoastQueenslandAustralia
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Dugan SL, Panza E, Openshaw A, Botto LD, Camacho JA, Toydemir RM. Delineation of the 9q31 deletion syndrome: Genomic microarray characterization of two patients with overlapping deletions. Am J Med Genet A 2018; 176:2901-2906. [PMID: 30346094 DOI: 10.1002/ajmg.a.40664] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 09/04/2018] [Accepted: 09/28/2018] [Indexed: 11/08/2022]
Abstract
Interstitial deletions of chromosome 9q31 are very rare. The deletions in most reported patients have been detected by conventional cytogenetics, with reported breakpoints ranging between 9q21 and 9q34. Therefore, an accurate description of a "9q31 deletion syndrome" could not be established. However, based on microarray studies, a small region of overlap has recently been proposed. We report clinical features of two unrelated individuals with overlapping 9q deletions identified by SNP microarray analysis. Patient 1 has a 9 Mb deletion, while Patient 2's deletion was 21.6 Mb. The clinical features common to our patients and those in the literature include developmental delay and short stature. Patient 2 shows additional features not reported in other 9q31 deletions, such as hearing loss, ventriculomegaly, cleft lip and palate, and small kidneys, which could be due to the larger size of the deletion, hence the influence of the genes in the region beyond the smallest region of overlap. Based on the comparison of these patients with the previously reported patients, we redefine the smallest region of overlap and characterize the clinical features of the 9q31 deletion syndrome.
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Affiliation(s)
- Sarah L Dugan
- Department of Pediatrics, University of Utah, Salt Lake City, Utah
| | - Emanuele Panza
- Department of Human Genetics, University of Utah, Salt Lake City, Utah.,Department of Medical and Surgical Sciences, University of Bologna, Italy
| | | | - Lorenzo D Botto
- Department of Pediatrics, University of Utah, Salt Lake City, Utah
| | - Jose A Camacho
- Department of Pediatrics, Miller Children's and Women's Hospital, Long Beach, California
| | - Reha M Toydemir
- Department of Pediatrics, University of Utah, Salt Lake City, Utah.,ARUP Laboratories, Salt Lake City, Utah.,Department of Pathology, University of Utah, Salt Lake City, Utah
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Krüppel-like factor 4 expression in oral carcinoma cells and hypermethylation at the gene promoter. BMC Oral Health 2016; 16:13. [PMID: 26847634 PMCID: PMC4743192 DOI: 10.1186/s12903-016-0172-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 01/25/2016] [Indexed: 11/30/2022] Open
Abstract
Background Krüppel-like factor 4 (KLF4) is a transcription factor regulating proliferation-differentiation balance of epithelium, and down-regulated in less-differentiated and advanced oral carcinomas. Although the expression is inactivated by the promoter hypermethylation in malignant tumor cells, it remains unknown in oral carcinoma cells. Methods Genomic DNA isolated from nine different oral carcinoma cell lines and a normal keratinocyte line was treated with sodium bisulfite, and methylation at KLF4 gene promoter was determined by PCR direct-sequence analysis. KLF4 expression in cells cultured with or without demethylation reagent was monitored by quantitative real-time PCR and immunoblot. Results A 237-bp promoter region spanning − 718 and − 482 of KLF4 gene was hypermethylated in oral carcinoma cells that express KLF4 at a low level, but the methylation was infrequent in cells expressing KLF4 high amount. The downstream region from − 481 to +192 was not methylated in any cell lines. Demethylation treatment of cells up-regulated the expression at mRNA and protein levels. Conclusion This study demonstrated that hypermethylation at a narrow range of the promoter region down-regulates KLF4 expression, and suggests that the loss of expression by the hypermethylation contributes to oral carcinoma progression. Electronic supplementary material The online version of this article (doi:10.1186/s12903-016-0172-5) contains supplementary material, which is available to authorized users.
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Mucciolo M, Magini P, Marozza A, Mongelli P, Mencarelli MA, Hayek G, Tavalazzi F, Mari F, Seri M, Renieri A, Graziano C. 9q31.1q31.3 deletion in two patients with similar clinical features: a newly recognized microdeletion syndrome? Am J Med Genet A 2013; 164A:685-90. [PMID: 24376033 DOI: 10.1002/ajmg.a.36361] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Accepted: 10/12/2013] [Indexed: 11/07/2022]
Abstract
Interstitial deletions of the long arm of chromosome 9 are rare and most patients have been detected by conventional cytogenetic techniques. Disparities in size and localization are large and no consistent region of overlap has been delineated. We report two similar de novo deletions of 6.3 Mb involving the 9q31.1q31.3 region, identified in two monozygotic twins and one unrelated patient through array-CGH analysis. By cloning the deletion breakpoints, we could show that these deletions are not mediated by segmental duplications. The patients displayed a distinct clinical phenotype characterized by mild intellectual disability, short stature with high body mass index, thick hair, arched eyebrows, flat profile with broad chin and mild prognathism, broad, and slightly overhanging tip of the nose, short neck with cervical gibbus. The twin patients developed a metabolic syndrome (type 2 diabetes, hypercholesterolemia, vascular hypertension) during the third decade of life. Although long-term follow-up and collection of additional patients will be needed to obtain a better definition of the phenotype, our findings characterize a previously undescribed syndromic disorder associated with haploinsufficiency of the chromosome 9q31.1q31.3 region.
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Affiliation(s)
- M Mucciolo
- U.O.C. Genetica Medica, Policlinico S. Maria alle Scotte, Siena, Italy
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Xu M, Zhou H, Yong J, Cong P, Li C, Yu Y, Qi M. A Chinese patient with KBG syndrome and a 9q31.2-33.1 microdeletion. Eur J Med Genet 2013; 56:245-50. [PMID: 23369839 DOI: 10.1016/j.ejmg.2013.01.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Accepted: 01/17/2013] [Indexed: 10/27/2022]
Abstract
KBG syndrome is characterized by postnatal short stature, macrodontia, facial and hand anomalies, delayed bone age and intellectual disability. KBG syndrome is an infrequently reported autosomal dominant condition caused by a mutation or haploinsufficiency of ANKRD11 at 16q24.3. We report on a patient, who showed many manifestations of KBG syndrome and was found to harbor a de novo ANKRD11 mutation, c.362T > A (p.Met121Lys). As the patient showed additional characteristics not occurring in KBG syndrome, a CGH array was performed which showed a de novo microdeletion of 9q31.2-q33.1. The majority of findings in our patient can be explained by the combined ANKRD11 mutation and 9q31.2-33.1 deletion. The case demonstrates well the need for comparing an abnormal genotype with a detailed phenotype analysis and the need for further studies in case the phenotype is unusual for the genotype.
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Affiliation(s)
- Mingzhi Xu
- Department of Endocrinology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China
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Chien SC, Li YC, Li LH, Wu JY, Hsu PC, Shi SL, Tsai FJ, Lin CC. A new familial insertion, ins(18;9)(q12.2;q33.1q31.1) with a 9q31.1-9q33.1 deletion in a girl with a cleft lip and palate. Am J Med Genet A 2010; 152A:1862-7. [PMID: 20583161 DOI: 10.1002/ajmg.a.33452] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Shu-Chin Chien
- Department of Obstetrics and Gynecology, China Medical University Hospital, Taichung, Taiwan
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Castanet M, Mallya U, Agostini M, Schoenmakers E, Mitchell C, Demuth S, Raymond FL, Schwabe J, Gurnell M, Chatterjee VK. Maternal isodisomy for chromosome 9 causing homozygosity for a novel FOXE1 mutation in syndromic congenital hypothyroidism. J Clin Endocrinol Metab 2010; 95:4031-6. [PMID: 20484477 DOI: 10.1210/jc.2010-0275] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
CONTEXT Homozygous loss-of-function mutations in forkhead box E1/thyroid transcription factor 2 (FOXE1/TTF-2) cause syndromic congenital hypothyroidism, with thyroid dysgenesis, cleft palate, spiky hair, and variable choanal atresia and bifid epiglottis in three cases reported hitherto. We have elucidated the molecular basis of the disorder in a female with a similar clinical phenotype, born to nonconsanguineous parents. OBJECTIVE AND DESIGN The FOXE1 gene, located on chromosome 9q22, was sequenced in the proband and family members. Microsatellite marker and multiplex ligation probe amplification analyses determined chromosomal inheritance patterns and FOXE1 copy number. Mutant FOXE1 function was predicted by structural modeling and tested in transfection assays. RESULTS The proband was homozygous for a novel missense (c.412T-->C; F137S) FOXE1 mutation, but her mother showed heterozygous and father wild-type alleles for this gene sequence. However, the proband was also homozygous for 10 microsatellite markers spanning chromosome 9 with exclusively maternal inheritance. Multiplex ligation probe amplification assays showed two copies of FOXE1 in the proband, indicating maternal isodisomy for chromosome 9. Consistent with structural modeling, the F137S mutant FOXE1 protein failed to bind DNA and showed negligible transcriptional activity. CONCLUSION We have described the first case of uniparental disomy causing homozygosity for a novel, loss-of-function FOXE1/TTF-2 mutation in dysgenetic congenital hypothyroidism.
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Affiliation(s)
- Mireille Castanet
- University of Cambridge, Metabolic Research Laboratories, Institute of Metabolic Science, Department of Medicine, Level 4, Box 289, Addenbrooke's Hospital, Cambridge CB2 0QQ, United Kingdom
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