1
|
Rafeeq MM, Murad HAS, Najumuddin, Ullah S, Ahmed Z, Alam Q, Bilal M, Habib AH, Sain ZM, Khan MJ, Umair M. Case report: A novel de novo loss of function variant in the DNA-binding domain of TBX2 causes severe osteochondrodysplasia. Front Genet 2023; 13:1117500. [PMID: 36733940 PMCID: PMC9888409 DOI: 10.3389/fgene.2022.1117500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 12/29/2022] [Indexed: 01/19/2023] Open
Abstract
Background: T-box family members are transcription factors characterized by highly conserved residues corresponding to the DNA-binding domain known as the T-box. TBX2 has been implicated in several developmental processes, such as coordinating cell fate, patterning, and morphogenesis of a wide range of tissues and organs, including lungs, limbs, heart, kidneys, craniofacial structures, and mammary glands. Methods: In the present study, we have clinically and genetically characterized a proband showing a severe form of chondrodysplasia with developmental delay. Whole-exome sequencing (WES), Sanger sequencing, and 3D protein modeling were performed in the present investigation. Results: Whole-exome sequencing revealed a novel nonsense variant (c.529A>T; p.Lys177*; NM_005994.4) in TBX2. 3D-TBX2 protein modeling revealed a substantial reduction of the mutated protein, which might lead to a loss of function (LOF) or nonsense-mediated decay (NMD). Conclusion: This study has not only expanded the mutation spectrum in the gene TBX2 but also facilitated the diagnosis and genetic counseling of related features in affected families.
Collapse
Affiliation(s)
- Misbahuddin M. Rafeeq
- Department of Pharmacology, Faculty of Medicine, Rabigh, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hussam Aly Sayed Murad
- Department of Pharmacology, Faculty of Medicine, Rabigh, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Najumuddin
- National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad, Pakistan
| | - Samee Ullah
- National Center for Bioinformatics (NCB), Islamabad, Pakistan
| | - Zaheer Ahmed
- Department of Biosciences, COMSATS University, Islamabad, Pakistan
| | - Qamre Alam
- Molecular Genomics and Precision Medicine, ExpressMed Laboratories, Zinj, Bahrain
| | - Muhammad Bilal
- Department of Biochemistry, Quaid-i-Azam University, Islamabad, Pakistan
| | - Alaa Hamed Habib
- Department of Physiology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ziaullah M. Sain
- Department of Microbiology, Faculty of Medicine, Rabigh, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Muhammad Umair
- Department of Life Sciences, School of Science, University of Management and Technology (UMT), Lahore, Pakistan,Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGH), Riyadh, Saudi Arabia,*Correspondence: Muhammad Umair, ,
| |
Collapse
|
2
|
Wang C, Han J, Liu M, Huang Y, Zhou T, Jiang N, Hui H, Xu K. RNA-sequencing of human aortic valves identifies that miR-629-3p and TAGLN miRNA-mRNA pair involving in calcified aortic valve disease. J Physiol Biochem 2022; 78:819-831. [PMID: 35776288 DOI: 10.1007/s13105-022-00905-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 06/11/2022] [Indexed: 12/20/2022]
Abstract
This study aimed to uncover the microRNA and messenger RNA (miRNA/mRNA) interactions in the pathophysiological process of calcified aortic valve disease (CAVD) of the human aortic valve. RNA sequencing of six selected samples (3 healthy control samples vs. 3 CAVD samples) was performed to obtain mRNA and miRNA sequences, and differential expression (DE) analysis of miRNA and mRNAs was performed. To build a CAVD-specific miRNA-mRNA interactome, the upregulated mRNAs and downregulated miRNAs were selected, followed by the establishment of inverse DE of mRNA-miRNA co-expression network based on Pearson's correlation coefficient using miRanda in the R language software. Subsequently, pathway enrichment analysis was performed to elucidate CAVD-related pathways that were likely mediated by miRNA regulatory mechanisms. In addition, miRNAs with an mRNA correlation greater than 0.9 in the co-expression network were selected for anti-calcification verification in a CAVD cellular model. We identified 216 mRNAs (99 downregulated and 117 upregulated) and 602 miRNAs (371 downregulated and 231 upregulated) that were differentially expressed between CAVD and healthy aortic valves. After applying Pearson's correlation toward miRNA-mRNA targets, a regulatory network of 67 miRNAs targeting 76 mRNAs was created. The subsequent pathway enrichment analysis of these targeted mRNAs elucidated that genes within the focal adhesion pathway are likely mediated by miRNA regulatory mechanisms. The selected hsa-miR-629-3p and TAGLN pair exhibited anti-calcification effects on osteogenic differentiation-induced human aortic valve interstitial cells (hVICs). On integrating the miRNA and mRNA sequencing data for healthy aortic valves and those with CAVD, the CAVD-associated miRNA-mRNA interactome and related pathways were elucidated. Additional cell function data demonstrated anti-calcification effects of the selected hsa-miR-629-3p targeting TAGLN, validating that it is a potential therapeutic target for inhibiting CAVD.
Collapse
Affiliation(s)
- Chunli Wang
- Hubei Engineering Technology Research Center of Chinese Materia Medica Processing, College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065, China
| | - Juanjuan Han
- Hubei Engineering Technology Research Center of Chinese Materia Medica Processing, College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065, China
| | - Ming Liu
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Yuming Huang
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Tingwen Zhou
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Nan Jiang
- Hubei Engineering Technology Research Center of Chinese Materia Medica Processing, College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065, China
| | - Haipeng Hui
- Department of Cardiology, the Second Medical Center & National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, No. 28 Fuxing Road, Beijing, 100853, China.
| | - Kang Xu
- Hubei Engineering Technology Research Center of Chinese Materia Medica Processing, College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065, China.
| |
Collapse
|
3
|
Almonaem ERA, Soliman DR, El Sayed MAM, Ahmed IA, Abdelrahman EG. Association between SNP rs59382073 in TBX2 3′ UTR and susceptibility to congenital heart diseases. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2022.101609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
4
|
Mäkitie RE, Toiviainen-Salo S, Kaitila I, Mäkitie O. A Novel Osteochondrodysplasia With Empty Sella Associates With a TBX2 Variant. Front Endocrinol (Lausanne) 2022; 13:845889. [PMID: 35311234 PMCID: PMC8927981 DOI: 10.3389/fendo.2022.845889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 02/09/2022] [Indexed: 11/13/2022] Open
Abstract
Skeletal dysplasias comprise a heterogenous group of developmental disorders of skeletal and cartilaginous tissues. Several different forms have been described and the full spectrum of their clinical manifestations and underlying genetic causes are still incompletely understood. We report a three-generation Finnish family with an unusual, autosomal dominant form of osteochondrodysplasia and an empty sella. Affected individuals (age range 24-44 years) exhibit unusual codfish-shaped vertebrae, severe early-onset and debilitating osteoarthritis and an empty sella without endocrine abnormalities. Clinical characteristics also include mild dysmorphic features, reduced sitting height ratio, and obesity. Whole-exome sequencing excluded known skeletal dysplasias and identified a novel heterozygous missense mutation c.899C>T (p.Thr300Met) in TBX2, confirmed by Sanger sequencing. TBX2 is important for development of the skeleton and the brain and three prior reports have described variations in TBX2 in patients portraying a complex phenotype with vertebral anomalies, craniofacial dysmorphism and endocrine dysfunctions. Our mutation lies near a previously reported disease-causing variant and is predicted pathogenic with deleterious effects on protein function. Our findings expand the current spectrum of skeletal dysplasias, support the association of TBX2 mutations with skeletal dysplasia and suggest a role for TBX2 in development of the spinal and craniofacial structures and the pituitary gland.
Collapse
Affiliation(s)
- Riikka E. Mäkitie
- Folkhälsan Institute of Genetics, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Otorhinolaryngology–Head and Neck Surgery, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
- *Correspondence: Riikka E. Mäkitie,
| | - Sanna Toiviainen-Salo
- Children’s Hospital, Pediatric Research Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Medical Imaging Center, Pediatric Radiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Ilkka Kaitila
- Department of Medical Genetics, University of Helsinki, Helsinki, Finland
- Department of Clinical Genetics, Helsinki University Hospital, Helsinki, Finland
| | - Outi Mäkitie
- Folkhälsan Institute of Genetics, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Children’s Hospital, Pediatric Research Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| |
Collapse
|
5
|
Katraki-Pavlou S, Kastana P, Bousis D, Ntenekou D, Varela A, Davos CH, Nikou S, Papadaki E, Tsigkas G, Athanasiadis E, Herradon G, Mikelis CM, Beis D, Papadimitriou E. Protein tyrosine phosphatase receptor zeta 1 deletion triggers defective heart morphogenesis in mice and zebrafish. Am J Physiol Heart Circ Physiol 2021; 322:H8-H24. [PMID: 34767486 PMCID: PMC8754060 DOI: 10.1152/ajpheart.00400.2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Protein tyrosine phosphatase receptor-ζ1 (PTPRZ1) is a transmembrane
tyrosine phosphatase receptor highly expressed in embryonic stem cells. In the
present work, gene expression analyses of Ptprz1−/− and Ptprz1+/+ mice endothelial cells and hearts pointed to
an unidentified role of PTPRZ1 in heart development through the regulation of
heart-specific transcription factor genes. Echocardiography analysis in mice
identified that both systolic and diastolic functions are affected in Ptprz1−/− compared with Ptprz1+/+ hearts, based on a dilated left
ventricular (LV) cavity, decreased ejection fraction and fraction shortening,
and increased angiogenesis in Ptprz1−/−
hearts, with no signs of cardiac hypertrophy. A zebrafish ptprz1−/− knockout was also generated and exhibited
misregulated expression of developmental cardiac markers, bradycardia, and
defective heart morphogenesis characterized by enlarged ventricles and defected
contractility. A selective PTPRZ1 tyrosine phosphatase inhibitor affected
zebrafish heart development and function in a way like what is observed in the
ptprz1−/− zebrafish. The same
inhibitor had no effect in the function of the adult zebrafish heart, suggesting
that PTPRZ1 is not important for the adult heart function, in line with data
from the human cell atlas showing very low to negligible PTPRZ1 expression in
the adult human heart. However, in line with the animal models, Ptprz1 was expressed in many different cell types in
the human fetal heart, such as valvar, fibroblast-like, cardiomyocytes, and
endothelial cells. Collectively, these data suggest that PTPRZ1 regulates
cardiac morphogenesis in a way that subsequently affects heart function and
warrant further studies for the involvement of PTPRZ1 in idiopathic congenital
cardiac pathologies. NEW & NOTEWORTHY Protein tyrosine phosphatase receptor
ζ1 (PTPRZ1) is expressed in fetal but not adult heart and seems
to affect heart development. In both mouse and zebrafish animal models, loss of
PTPRZ1 results in dilated left ventricle cavity, decreased ejection fraction,
and fraction shortening, with no signs of cardiac hypertrophy. PTPRZ1 also seems
to be involved in atrioventricular canal specification, outflow tract
morphogenesis, and heart angiogenesis. These results suggest that PTPRZ1 plays a
role in heart development and support the hypothesis that it may be involved in
congenital cardiac pathologies.
Collapse
Affiliation(s)
- Stamatiki Katraki-Pavlou
- Zebrafish Disease Models Lab, Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation Academy of Athens, Greece.,Laboratory of Molecular Pharmacology, Department of Pharmacy, School of Health Sciences, University of Patras, Greece
| | - Pinelopi Kastana
- Laboratory of Molecular Pharmacology, Department of Pharmacy, School of Health Sciences, University of Patras, Greece
| | - Dimitris Bousis
- Laboratory of Molecular Pharmacology, Department of Pharmacy, School of Health Sciences, University of Patras, Greece
| | - Despoina Ntenekou
- Laboratory of Molecular Pharmacology, Department of Pharmacy, School of Health Sciences, University of Patras, Greece
| | - Aimilia Varela
- Cardiovascular Research Laboratory, Biomedical Research Foundation, Academy of Athens, Greece
| | - Constantinos H Davos
- Cardiovascular Research Laboratory, Biomedical Research Foundation, Academy of Athens, Greece
| | - Sophia Nikou
- Department of Anatomy-Histology-Embryology, Medical School, University of Patras, Greece
| | - Eleni Papadaki
- Department of Anatomy-Histology-Embryology, Medical School, University of Patras, Greece
| | - Grigorios Tsigkas
- Department of Cardiology, Patras University Hospital, Rio, Patras, Greece
| | | | - Gonzalo Herradon
- Department of Pharmaceutical and Health Sciences, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Madrid, Spain
| | - Constantinos M Mikelis
- Department of Pharmaceutical Sciences, School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, TX, United States
| | - Dimitris Beis
- Zebrafish Disease Models Lab, Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation Academy of Athens, Greece
| | - Evangelia Papadimitriou
- Laboratory of Molecular Pharmacology, Department of Pharmacy, School of Health Sciences, University of Patras, Greece
| |
Collapse
|
6
|
Abstract
PURPOSE OF REVIEW The goal of the review is to provide a comprehensive overview of the current understanding of the mechanisms underlying variation in human stature. RECENT FINDINGS Human height is an anthropometric trait that varies considerably within human populations as well as across the globe. Historically, much research focus was placed on understanding the biology of growth plate chondrocytes and how modifications to core chondrocyte proliferation and differentiation pathways potentially shaped height attainment in normal as well as pathological contexts. Recently, much progress has been made to improve our understanding regarding the mechanisms underlying the normal and pathological range of height variation within as well as between human populations, and today, it is understood to reflect complex interactions among a myriad of genetic, environmental, and evolutionary factors. Indeed, recent improvements in genetics (e.g., GWAS) and breakthroughs in functional genomics (e.g., whole exome sequencing, DNA methylation analysis, ATAC-sequencing, and CRISPR) have shed light on previously unknown pathways/mechanisms governing pathological and common height variation. Additionally, the use of an evolutionary perspective has also revealed important mechanisms that have shaped height variation across the planet. This review provides an overview of the current knowledge of the biological mechanisms underlying height variation by highlighting new research findings on skeletal growth control with an emphasis on previously unknown pathways/mechanisms influencing pathological and common height variation. In this context, this review also discusses how evolutionary forces likely shaped the genomic architecture of height across the globe.
Collapse
Affiliation(s)
| | - Terence D Capellini
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| |
Collapse
|
7
|
Wu D, Chen Y, Chen Q, Wang G, Xu X, Peng A, Hao J, He J, Huang L, Dai J. Clinical presentation and genetic profiles of Chinese patients with velocardiofacial syndrome in a large referral centre. J Genet 2019. [DOI: 10.1007/s12041-019-1090-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
8
|
Susceptibility to congenital heart defects associated with a polymorphism in TBX2 3' untranslated region in the Han Chinese population. Pediatr Res 2019; 85:378-383. [PMID: 30262811 DOI: 10.1038/s41390-018-0181-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 06/15/2018] [Accepted: 06/19/2018] [Indexed: 12/13/2022]
Abstract
BACKGROUND Tbx2 plays a critical role in determining fates of cardiomyocytes. Little is known about the contribution of TBX2 3' untranslated region (UTR) variants to the risk of congenital heart defect (CHD). Thus, we aimed to determine the association of single-nucleotide polymorphisms (SNPs) in TBX2 3' UTR with CHD susceptibility. METHODS We recruited 1285 controls and 1241 CHD children from China. SNPs identification and genotyping were detected using Sanger Sequencing and SNaPshot. Stratified analysis was conducted to explore the association between rs59382073 polymorphism and CHD subtypes. Functional analyses were performed by luciferase assays in HEK-293T and H9c2 cells. RESULTS Among five TBX2 3'UTR variants identified, rs59382073 minor allele T carriers had a 1.89-fold increased CHD risk compared to GG genotype (95% CI = 1.48-2.46, P = 4.48 × 10-7). The most probable subtypes were right ventricular outflow tract obstruction, conotruncal, and septal defect. G to T variation decreased luciferase activity in cells. This discrepancy was exaggerated by miR-3940 and miR-708, while their corresponding inhibitors eliminated it. CONCLUSION T allele of rs59382073 in TBX2 3'UTR contributed to greater CHD risk in the Han Chinese population. G to T variation created binding sites for miR-3940 and miR-708 to inhibit gene expression.
Collapse
|
9
|
Zhang RR, Cai K, Liu L, Yang Q, Zhang P, Gui YH, Wang F. A regulatory variant in TBX2 promoter is related to the decreased susceptibility of congenital heart disease in the Han Chinese population. Mol Genet Genomic Med 2018; 7:e00530. [PMID: 30525309 PMCID: PMC6393683 DOI: 10.1002/mgg3.530] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 09/30/2018] [Accepted: 11/15/2018] [Indexed: 12/26/2022] Open
Abstract
Background Tbx2 plays a vital role in the cardiac cushion development. In this study, we aimed to determine the relationship between common genetic variants in the promoter region of TBX2 gene and the risk of congenital heart disease (CHD). Methods Blood samples of 516 CHD patients and 587 control subjects were enrolled. Sanger sequencing and SNaPshot analysis were performed for genotyping in our case–control cohort. Luciferase and electrophoretic mobility shift assay (EMSA) were conducted to uncover the potential modulatory mechanism of the related variants. Results Variant rs4455026(c.‐1028G>C) in TBX2 promoter region was found to be associated with significantly lower CHD susceptibility. The risk of CHD in C allele carriers (GC and CC genotypes) decreased by 30% compared to the wild‐type GG genotype subjects (OR = 0.70, 95% CI = 0.55–0.89, p = 0.0038). It was revealed that G to C variation resulted in a decrease in the transcriptional activity of luciferase gene, and a potential change in binding affinity with certain nucleoproteins in EMSA data. Conclusion The minor C allele of rs4455026 in TBX2 promoter region was related with lower CHD susceptibility in the Han Chinese population via repressing its transcriptional activity.
Collapse
Affiliation(s)
- Ran-Ran Zhang
- Department of Cardiology, Children's Hospital of Fudan University, Shanghai, China.,Department of Pediatrics, the Affiliated Hospital of Qingdao University, Qingdao, China
| | - Ke Cai
- Department of Cardiology, Children's Hospital of Fudan University, Shanghai, China
| | - Lian Liu
- Department of Cardiology, Children's Hospital of Fudan University, Shanghai, China
| | - Qian Yang
- Department of Cardiology, Children's Hospital of Fudan University, Shanghai, China
| | - Ping Zhang
- Department of Cardiology, Children's Hospital of Fudan University, Shanghai, China
| | - Yong-Hao Gui
- Department of Cardiology, Children's Hospital of Fudan University, Shanghai, China
| | - Feng Wang
- Department of Cardiology, Children's Hospital of Fudan University, Shanghai, China
| |
Collapse
|
10
|
Liu N, Schoch K, Luo X, Pena LDM, Bhavana VH, Kukolich MK, Stringer S, Powis Z, Radtke K, Mroske C, Deak KL, McDonald MT, McConkie-Rosell A, Markert ML, Kranz PG, Stong N, Need AC, Bick D, Amaral MD, Worthey EA, Levy S, Wangler MF, Bellen HJ, Shashi V, Yamamoto S. Functional variants in TBX2 are associated with a syndromic cardiovascular and skeletal developmental disorder. Hum Mol Genet 2018; 27:2454-2465. [PMID: 29726930 PMCID: PMC6030957 DOI: 10.1093/hmg/ddy146] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 04/07/2018] [Accepted: 04/16/2018] [Indexed: 12/15/2022] Open
Abstract
The 17 genes of the T-box family are transcriptional regulators that are involved in all stages of embryonic development, including craniofacial, brain, heart, skeleton and immune system. Malformation syndromes have been linked to many of the T-box genes. For example, haploinsufficiency of TBX1 is responsible for many structural malformations in DiGeorge syndrome caused by a chromosome 22q11.2 deletion. We report four individuals with an overlapping spectrum of craniofacial dysmorphisms, cardiac anomalies, skeletal malformations, immune deficiency, endocrine abnormalities and developmental impairments, reminiscent of DiGeorge syndrome, who are heterozygotes for TBX2 variants. The p.R20Q variant is shared by three affected family members in an autosomal dominant manner; the fourth unrelated individual has a de novo p.R305H mutation. Bioinformatics analyses indicate that these variants are rare and predict them to be damaging. In vitro transcriptional assays in cultured cells show that both variants result in reduced transcriptional repressor activity of TBX2. We also show that the variants result in reduced protein levels of TBX2. Heterologous over-expression studies in Drosophila demonstrate that both p.R20Q and p.R305H function as partial loss-of-function alleles. Hence, these and other data suggest that TBX2 is a novel candidate gene for a new multisystem malformation disorder.
Collapse
Affiliation(s)
- Ning Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Kelly Schoch
- Division of Medical Genetics, Department of Pediatrics, Duke Health, Durham, NC, USA
| | - Xi Luo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Loren D M Pena
- Division of Medical Genetics, Department of Pediatrics, Duke Health, Durham, NC, USA
| | | | - Mary K Kukolich
- Department of Genetics, Cook Children’s Hospital, Fort Worth, TX, USA
| | - Sarah Stringer
- Department of Genetics, Cook Children’s Hospital, Fort Worth, TX, USA
| | - Zöe Powis
- Clinical Genomics, Ambry Genetics, Aliso Viejo, CA, USA
| | - Kelly Radtke
- Clinical Genomics, Ambry Genetics, Aliso Viejo, CA, USA
| | | | - Kristen L Deak
- Department of Pathology, Duke University, Durham, NC, USA
| | - Marie T McDonald
- Division of Medical Genetics, Department of Pediatrics, Duke Health, Durham, NC, USA
| | - Allyn McConkie-Rosell
- Division of Medical Genetics, Department of Pediatrics, Duke Health, Durham, NC, USA
| | - M Louise Markert
- Division of Allergy and Immunology, Department of Pediatrics, Duke Health, Durham, NC, USA
| | - Peter G Kranz
- Division of Neuroradiology, Department of Radiology, Duke Health, Durham, NC, USA
| | - Nicholas Stong
- Institute for Genomic Medicine, Columbia University, New York, NY, USA
| | - Anna C Need
- Division of Brain Sciences, Department of Medicine, Imperial College London, London, UK
| | - David Bick
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | | | | | - Shawn Levy
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | | | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, USA
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX, USA
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, USA
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
- Howard Hughes Medical Institute, Houston, TX, USA
| | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke Health, Durham, NC, USA
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, USA
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| |
Collapse
|
11
|
Genome-wide Analysis of Body Proportion Classifies Height-Associated Variants by Mechanism of Action and Implicates Genes Important for Skeletal Development. Am J Hum Genet 2015; 96:695-708. [PMID: 25865494 DOI: 10.1016/j.ajhg.2015.02.018] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 02/27/2015] [Indexed: 01/20/2023] Open
Abstract
Human height is a composite measurement, reflecting the sum of leg, spine, and head lengths. Many common variants influence total height, but the effects of these or other variants on the components of height (body proportion) remain largely unknown. We studied sitting height ratio (SHR), the ratio of sitting height to total height, to identify such effects in 3,545 African Americans and 21,590 individuals of European ancestry. We found that SHR is heritable: 26% and 39% of the total variance of SHR can be explained by common variants in European and African Americans, respectively, and global European admixture is negatively correlated with SHR in African Americans (r(2) ≈ 0.03). Six regions reached genome-wide significance (p < 5 × 10(-8)) for association with SHR and overlapped biological candidate genes, including TBX2 and IGFBP3. We found that 130 of 670 height-associated variants are nominally associated (p < 0.05) with SHR, more than expected by chance (p = 5 × 10(-40)). At these 130 loci, the height-increasing alleles are associated with either a decrease (71 loci) or increase (59 loci) in SHR, suggesting that different height loci disproportionally affect either leg length or spine/head length. Pathway analyses via DEPICT revealed that height loci affecting SHR, and especially those affecting leg length, show enrichment of different biological pathways (e.g., bone/cartilage/growth plate pathways) than do loci with no effect on SHR (e.g., embryonic development). These results highlight the value of using a pair of related but orthogonal phenotypes, in this case SHR with height, as a prism to dissect the biology underlying genetic associations in polygenic traits and diseases.
Collapse
|
12
|
Zhang Y, Han Q, Fan H, Li W, Xing Q, Yan B. Genetic analysis of the TBX2 gene promoter in indirect inguinal hernia. Hernia 2013; 18:513-7. [PMID: 24309999 DOI: 10.1007/s10029-013-1199-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2013] [Accepted: 11/24/2013] [Indexed: 12/13/2022]
Abstract
PURPOSE Inguinal hernia is a common disease, majority of which are indirect inguinal hernia (IIH). A positive family history indicates that genetic factors play important roles in the IIH development. To date, genetic causes for IIH remain unknown. T-box transcription factor 2 (TBX2) is a major regulator in the morphogenesis and organogenesis. The human TBX2 gene is widely expressed in fetal and adult tissues, including muscle and connective tissues. Therefore, we speculated that altered TBX2 gene expression may be involved in the IIH formation. METHODS IIH patients (n = 129) and ethnic-matched healthy subjects (n = 198) were recruited for this study. The human TBX2 gene promoters were generated with PCR and directly sequenced to identify DNA sequence variants (DSVs). Furthermore, biological functions of the DSVs were examined with reporter gene constructs in cultured cells. RESULTS Total six DSVs within the TBX2 gene promoter were identified. A heterozygous DSV (g.59476307G>C) was identified in an IIH patient, but in none of controls, which significantly decreased the TBX2 gene promoter activities. Another heterozygous DSV (g.59476704G>C) was only found in one control, which did not affect TBX2 gene promoter activities. Four DSVs, g.59476316C>A (rs73991913), g.59476415T>C (rs1476781), g.59476510G>C (rs4455026) and g.59476892C>T (rs2286524), all of which were single nucleotide polymorphisms, were found in both IIH patients and controls with similar frequencies. CONCLUSIONS Our data suggested that the DSV within the TBX2 gene promoter was implicated in the IIH development as a rare cause.
Collapse
Affiliation(s)
- Y Zhang
- Division of Hand and Foot Surgery, Jining Medical University Affiliated Hospital, Jining Medical University, Jining, 272029, Shandong, China
| | | | | | | | | | | |
Collapse
|
13
|
Peterson JF, Ghaloul-Gonzalez L, Madan-Khetarpal S, Hartman J, Surti U, Rajkovic A, Yatsenko SA. Familial microduplication of 17q23.1-q23.2 involving TBX4 is associated with congenital clubfoot and reduced penetrance in females. Am J Med Genet A 2013; 164A:364-9. [DOI: 10.1002/ajmg.a.36238] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Jess F. Peterson
- Pittsburgh Cytogenetics Laboratory; Center for Medical Genetics and Genomics, Magee-Womens Hospital of UPMC; Pittsburgh Pennsylvania
- Department of Human Genetics; Graduate School of Public Health, University of Pittsburgh; Pittsburgh Pennsylvania
| | - Lina Ghaloul-Gonzalez
- Department of Medical Genetics; Children's Hospital of Pittsburgh of UPMC; Pittsburgh Pennsylvania
| | - Suneeta Madan-Khetarpal
- Department of Medical Genetics; Children's Hospital of Pittsburgh of UPMC; Pittsburgh Pennsylvania
| | - Jessica Hartman
- Department of Medical Genetics; Children's Hospital of Pittsburgh of UPMC; Pittsburgh Pennsylvania
| | - Urvashi Surti
- Pittsburgh Cytogenetics Laboratory; Center for Medical Genetics and Genomics, Magee-Womens Hospital of UPMC; Pittsburgh Pennsylvania
- Department of Human Genetics; Graduate School of Public Health, University of Pittsburgh; Pittsburgh Pennsylvania
- Department of Obstetrics, Gynecology and Reproductive Sciences; University of Pittsburgh School of Medicine; Pittsburgh Pennsylvania
- Department of Pathology; University of Pittsburgh School of Medicine; Pittsburgh Pennsylvania
| | - Aleksandar Rajkovic
- Pittsburgh Cytogenetics Laboratory; Center for Medical Genetics and Genomics, Magee-Womens Hospital of UPMC; Pittsburgh Pennsylvania
- Department of Human Genetics; Graduate School of Public Health, University of Pittsburgh; Pittsburgh Pennsylvania
- Department of Obstetrics, Gynecology and Reproductive Sciences; University of Pittsburgh School of Medicine; Pittsburgh Pennsylvania
- Department of Pathology; University of Pittsburgh School of Medicine; Pittsburgh Pennsylvania
| | - Svetlana A. Yatsenko
- Pittsburgh Cytogenetics Laboratory; Center for Medical Genetics and Genomics, Magee-Womens Hospital of UPMC; Pittsburgh Pennsylvania
- Department of Obstetrics, Gynecology and Reproductive Sciences; University of Pittsburgh School of Medicine; Pittsburgh Pennsylvania
- Department of Pathology; University of Pittsburgh School of Medicine; Pittsburgh Pennsylvania
| |
Collapse
|
14
|
Thi Thu HN, Haw Tien SF, Loh SL, Bok Yan JS, Korzh V. Tbx2a is required for specification of endodermal pouches during development of the pharyngeal arches. PLoS One 2013; 8:e77171. [PMID: 24130849 PMCID: PMC3795029 DOI: 10.1371/journal.pone.0077171] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2013] [Accepted: 09/01/2013] [Indexed: 11/21/2022] Open
Abstract
Tbx2 is a member of the T-box family of transcription factors essential for embryo- and organogenesis. A deficiency in the zebrafish paralogue tbx2a causes abnormalities of the pharyngeal arches in a p53-independent manner. The pharyngeal arches are formed by derivatives of all three embryonic germ layers: endodermal pouches, mesenchymal condensations and neural crest cells. While tbx2a expression is restricted to the endodermal pouches, its function is required for the normal morphogenesis of the entire pharyngeal arches. Given the similar function of Tbx1 in craniofacial development, we explored the possibility of an interaction between Tbx1 and Tbx2a. The use of bimolecular fluorescence complementation revealed the interaction between Tbx2a and Tbx1, thus providing support for the idea that functional interaction between different, co-expressed Tbx proteins could be a common theme across developmental processes in cell lineages and tissues. Together, this work provides mechanistic insight into the role of TBX2 in human disorders affecting the face and neck.
Collapse
Affiliation(s)
- Hang Nguyen Thi Thu
- Institute of Molecular and Cell Biology, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | | | - Siau Lin Loh
- Institute of Molecular and Cell Biology, Singapore, Singapore
| | - Jimmy So Bok Yan
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Vladimir Korzh
- Institute of Molecular and Cell Biology, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- * E-mail:
| |
Collapse
|
15
|
Pang S, Liu Y, Zhao Z, Huang W, Chen D, Yan B. Novel and functional sequence variants within the TBX2 gene promoter in ventricular septal defects. Biochimie 2013; 95:1807-9. [PMID: 23727221 DOI: 10.1016/j.biochi.2013.05.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 05/17/2013] [Indexed: 12/13/2022]
Abstract
Congenital heart disease (CHD) is the most common birth defects in humans. To date, genetic causes for CHD remain largely unknown. T-box transcription factor 2 (TBX2) gene is expressed in the myocardium of atrioventricular canal, outflow tract and inflow tract and plays a critical role in heart chamber formation. Genomic deletion and duplication of TBX2 gene have been associated with cardiac defects. As TBX2 acts in a dose-dependent manner, we hypothesized that DNA sequence variants (DSVs) within TBX2 gene promoter may mediate CHD development by changing TBX2 levels. In this study, TBX2 gene promoter was genetically analyzed in large cohorts of patients with ventricular septal defect (VSD) (n = 324) and ethnic-matched healthy controls (n = 328). Four novel and heterozygous DSVs, g.59477201C > T, g.59477347G > A, g.59477353delG and g.59477371G > A were identified in VSD patients, but in none of controls. Functional analyses revealed that all of the four DSVs significantly decreased transcriptional activities of TBX2 gene promoter. Therefore, our data suggested that the DSVs within TBX2 gene promoter identified in VSD patients may contribute to VSD etiology.
Collapse
Affiliation(s)
- Shuchao Pang
- Shandong Provincial Key Laboratory of Cardiac Disease Diagnosis and Treatment, Jining Medical University Affiliated Hospital, Jining Medical University, 79 Guhuai Road, Jining, Shandong 272029, China
| | | | | | | | | | | |
Collapse
|
16
|
Davis SW, Ellsworth BS, Peréz Millan MI, Gergics P, Schade V, Foyouzi N, Brinkmeier ML, Mortensen AH, Camper SA. Pituitary gland development and disease: from stem cell to hormone production. Curr Top Dev Biol 2013; 106:1-47. [PMID: 24290346 DOI: 10.1016/b978-0-12-416021-7.00001-8] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Many aspects of pituitary development have become better understood in the past two decades. The signaling pathways regulating pituitary growth and shape have emerged, and the balancing interactions between the pathways are now appreciated. Markers for multipotent progenitor cells are being identified, and signature transcription factors have been discovered for most hormone-producing cell types. We now realize that pulsatile hormone secretion involves a 3D integration of cellular networks. About a dozen genes are known to cause pituitary hypoplasia when mutated due to their essential roles in pituitary development. Similarly, a few genes are known that predispose to familial endocrine neoplasia, and several genes mutated in sporadic pituitary adenomas are documented. In the next decade, we anticipate gleaning a deeper appreciation of these processes at the molecular level, insight into the development of the hypophyseal portal blood system, and evolution of better therapeutics for congenital and acquired hormone deficiencies and for common craniopharyngiomas and pituitary adenomas.
Collapse
Affiliation(s)
- Shannon W Davis
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
17
|
Chen CP, Chen YY, Chern SR, Wu PS, Su JW, Chen YT, Chen LF, Wang W. Prenatal diagnosis and molecular cytogenetic characterization of de novo partial trisomy 12q (12q24.21→qter) and partial monosomy 6q (6q27→qter) associated with coarctation of the aorta, ventriculomegaly and thickened nuchal fold. Gene 2012; 516:138-42. [PMID: 23266815 DOI: 10.1016/j.gene.2012.12.051] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Accepted: 12/03/2012] [Indexed: 11/19/2022]
Abstract
We present rapid aneuploidy diagnosis of de novo partial trisomy 12q (12q24.21→qter) and partial monosomy 6q (6q27→qter) by aCGH using uncultured amniocytes in a fetus with coarctation of the aorta, ventriculomegaly and thickened nuchal fold. We discuss the association of TBX3, TBX5 and MED13L gene duplication with coarctation of the aorta, and the association of RNASET2 gene haploinsufficiency with ventriculomegaly in this case.
Collapse
Affiliation(s)
- Chih-Ping Chen
- Department of Obstetrics and Gynecology, Mackay Memorial Hospital, Taipei, Taiwan.
| | | | | | | | | | | | | | | |
Collapse
|
18
|
Börnigen D, Tranchevent LC, Bonachela-Capdevila F, Devriendt K, De Moor B, De Causmaecker P, Moreau Y. An unbiased evaluation of gene prioritization tools. Bioinformatics 2012; 28:3081-8. [PMID: 23047555 DOI: 10.1093/bioinformatics/bts581] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
MOTIVATION Gene prioritization aims at identifying the most promising candidate genes among a large pool of candidates-so as to maximize the yield and biological relevance of further downstream validation experiments and functional studies. During the past few years, several gene prioritization tools have been defined, and some of them have been implemented and made available through freely available web tools. In this study, we aim at comparing the predictive performance of eight publicly available prioritization tools on novel data. We have performed an analysis in which 42 recently reported disease-gene associations from literature are used to benchmark these tools before the underlying databases are updated. RESULTS Cross-validation on retrospective data provides performance estimate likely to be overoptimistic because some of the data sources are contaminated with knowledge from disease-gene association. Our approach mimics a novel discovery more closely and thus provides more realistic performance estimates. There are, however, marked differences, and tools that rely on more advanced data integration schemes appear more powerful. CONTACT yves.moreau@esat.kuleuven.be SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Daniela Börnigen
- Department of Electrical Engineering, ESAT-SCD, Katholieke Universiteit Leuven, Leuven, Belgium
| | | | | | | | | | | | | |
Collapse
|
19
|
Prontera P, Bernardini L, Stangoni G, Capalbo A, Rogaia D, Romani R, Ardisia C, Dallapiccola B, Donti E. Deletion 2p15-16.1 syndrome: case report and review. Am J Med Genet A 2011; 155A:2473-8. [PMID: 21910216 DOI: 10.1002/ajmg.a.33875] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2010] [Accepted: 11/22/2010] [Indexed: 01/19/2023]
Abstract
We report on a 9-year-old female patient with facial anomalies and developmental delay, heterozygous for three de novo rearrangements: a paracentric inversion of chromosome 7, an apparently balanced translocation between chromosome 1 and 7, involving the same inverted chromosome 7, detected by standard cytogenetic analysis [46,XX, der(7) inv(7)(q21.1q32.1)t(1;7)(q23q32.1)]; and a 2p16.1 deletion, spanning about 3.5 Mb of genomic DNA, shown by SNP-array analysis [arr 2p16.1 (56,706,666-60,234,485)x1 dn]. Clinical features and cytogenetic imbalance in our patient were similar to those reported in five published cases, suggesting that this genomic region is prone to recombination and its hemizygosity results in a distinct although variable spectrum of clinical manifestations.
Collapse
Affiliation(s)
- Paolo Prontera
- Sezione di Genetica Medica, Università e Azienda Ospedaliera di Perugia, Italy
| | | | | | | | | | | | | | | | | |
Collapse
|