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Yogi A, Iemura R, Nakatani H, Takasawa K, Gau M, Yamauchi T, Yoshida M, Moriyama K, Ishii T, Hosokawa S, Yamada M, Suzuki H, Kosaki K, Kashimada K, Morio T. BMP2 is a potential causative gene for isolated dextrocardia situs solitus. Eur J Med Genet 2023; 66:104820. [PMID: 37572998 DOI: 10.1016/j.ejmg.2023.104820] [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: 07/20/2022] [Revised: 07/27/2023] [Accepted: 08/10/2023] [Indexed: 08/14/2023]
Abstract
BMP2 (bone morphogenic protein-2) is a member of the TGF-β superfamily and has essential roles in the development of multiple organs, including osteogenesis. Because of its crucial role in organ and skeletal development, Bmp2 null mice is fetal lethal. The recent report has characterized multiple patients with BMP2 haploinsufficiency, describing individuals with BMP2 sequence variants and deletions associated with short stature without endocrinological abnormalities, a recognizable craniofacial gestalt, skeletal anomalies, and congenital heart disease. However, due to a small number of reported patients with BMP2 haploinsufficiency, the genotype and phenotype correlations are not fully understood. We experienced a family of BMP2 haploinsufficiency with a novel frameshift variant NM_001200.4: c.231dup (p.Tyr78Leufs*38) which was predicted to be "pathogenic" by the American College of Genetics and Genomics (ACGM) criteria. In addition to short stature, impaired hearing ability and minor skeletal deformities, the proband exhibited isolated dextrocardia situs solitus without cardiac anomalies and abnormal locations of other visceral organs. Our study would shed light on the crucial role of BMP2 in determining the cardiac axis, and further studies are needed to assemble more cases to elucidate BMP2 role in human heart development.
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Affiliation(s)
- Analia Yogi
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Ryosei Iemura
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Hisae Nakatani
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Kei Takasawa
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Maki Gau
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Takeru Yamauchi
- Neonatal Intensive Care Unit, Tsuchiura General Hospital, Ibaraki, Japan
| | - Masayuki Yoshida
- Department of Medical Genetics, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Keiji Moriyama
- Department of Maxillofacial Orthognathics, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Taku Ishii
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Susumu Hosokawa
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Mamiko Yamada
- Center for Medical Genetics, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Hisato Suzuki
- Center for Medical Genetics, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Kenjiro Kosaki
- Center for Medical Genetics, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Kenichi Kashimada
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan.
| | - Tomohiro Morio
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
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Hernández-García A, Pendleton KE, Kim S, Li Y, Kim BJ, Zaveri HP, Jordan VK, Berry AM, Ljungberg MC, Chen R, Lanz RB, Scott DA. SOX7 deficiency causes ventricular septal defects through its effects on endocardial-to-mesenchymal transition and the expression of Wnt4 and Bmp2. Hum Mol Genet 2023; 32:2152-2161. [PMID: 37000005 PMCID: PMC10281751 DOI: 10.1093/hmg/ddad050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 03/09/2023] [Accepted: 03/27/2023] [Indexed: 04/01/2023] Open
Abstract
SOX7 is a transcription factor-encoding gene located in a region on chromosome 8p23.1 that is recurrently deleted in individuals with ventricular septal defects (VSDs). We have previously shown that Sox7-/- embryos die of heart failure around E11.5. Here, we demonstrate that these embryos have hypocellular endocardial cushions with severely reduced numbers of mesenchymal cells. Ablation of Sox7 in the endocardium also resulted in hypocellular endocardial cushions, and we observed VSDs in rare E15.5 Sox7flox/-;Tie2-Cre and Sox7flox/flox;Tie2-Cre embryos that survived to E15.5. In atrioventricular explant studies, we showed that SOX7 deficiency leads to a severe reduction in endocardial-to-mesenchymal transition (EndMT). RNA-seq studies performed on E9.5 Sox7-/- heart tubes revealed severely reduced Wnt4 transcript levels. Wnt4 is expressed in the endocardium and promotes EndMT by acting in a paracrine manner to increase the expression of Bmp2 in the myocardium. Both WNT4 and BMP2 have been previously implicated in the development of VSDs in individuals with 46,XX sex reversal with dysgenesis of kidney, adrenals and lungs (SERKAL) syndrome and in individuals with short stature, facial dysmorphism and skeletal anomalies with or without cardiac anomalies 1 (SSFSC1) syndrome, respectively. We now show that Sox7 and Wnt4 interact genetically in the development of VSDs through their additive effects on endocardial cushion development with Sox7+/-;Wnt4+/- double heterozygous embryos having hypocellular endocardial cushions and perimembranous and muscular VSDs not seen in their Sox7+/- and Wnt4+/- littermates. These results provide additional evidence that SOX7, WNT4 and BMP2 function in the same pathway during mammalian septal development and that their deficiency can contribute to the development of VSDs in humans.
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Affiliation(s)
- Andrés Hernández-García
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Katherine E Pendleton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sangbae Kim
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yumei Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Bum J Kim
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hitisha P Zaveri
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Valerie K Jordan
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Aliska M Berry
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - M Cecilia Ljungberg
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX 77030, USA
| | - Rui Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Rainer B Lanz
- Department of Molecular & Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA
| | - Daryl A Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
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Spedicati B, Morgan A, Pianigiani G, Musante L, Rubinato E, Santin A, Nardone GG, Faletra F, Girotto G. Challenging Occam’s Razor: Dual Molecular Diagnoses Explain Entangled Clinical Pictures. Genes (Basel) 2022; 13:genes13112023. [PMID: 36360260 PMCID: PMC9690221 DOI: 10.3390/genes13112023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 10/31/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022] Open
Abstract
Dual molecular diagnoses are defined as the presence of pathogenic variants at two distinct and independently segregating loci that cause two different Mendelian conditions. In this study, we report the identification of double genetic disorders in a series of patients with complex clinical features. In the last 24 months, 342 syndromic patients have been recruited and clinically characterised. Whole Exome Sequencing analysis has been performed on the proband and on both parents and identified seven patients affected by a dual molecular diagnosis. Upon a detailed evaluation of both their clinical and molecular features, subjects are able to be divided into two groups: (A) five patients who present distinct phenotypes, due to each of the two different underlying genetic diseases; (B) two patients with overlapping clinical features that may be underpinned by both the identified genetic variations. Notably, only in one case a multilocus genomic variation was already suspected during the clinical evaluation. Overall, our findings highlight how dual molecular diagnoses represent a challenging model of complex inheritance that should always be considered whenever a patient shows atypical clinical features. Indeed, an accurate genetic characterisation is of the utmost importance to provide patients with a personalised and safe clinical management.
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Affiliation(s)
- Beatrice Spedicati
- Department of Medicine, Surgery and Health Sciences, University of Trieste, 34149 Trieste, Italy
| | - Anna Morgan
- Institute for Maternal and Child Health-I.R.C.C.S. “Burlo Garofolo”, 34137 Trieste, Italy
| | - Giulia Pianigiani
- Institute for Maternal and Child Health-I.R.C.C.S. “Burlo Garofolo”, 34137 Trieste, Italy
- Correspondence: ; Tel.: +39-040-3785539
| | - Luciana Musante
- Institute for Maternal and Child Health-I.R.C.C.S. “Burlo Garofolo”, 34137 Trieste, Italy
| | - Elisa Rubinato
- Institute for Maternal and Child Health-I.R.C.C.S. “Burlo Garofolo”, 34137 Trieste, Italy
| | - Aurora Santin
- Department of Medicine, Surgery and Health Sciences, University of Trieste, 34149 Trieste, Italy
| | | | - Flavio Faletra
- Institute for Maternal and Child Health-I.R.C.C.S. “Burlo Garofolo”, 34137 Trieste, Italy
| | - Giorgia Girotto
- Department of Medicine, Surgery and Health Sciences, University of Trieste, 34149 Trieste, Italy
- Institute for Maternal and Child Health-I.R.C.C.S. “Burlo Garofolo”, 34137 Trieste, Italy
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Huang RT, Guo YH, Yang CX, Gu JN, Qiu XB, Shi HY, Xu YJ, Xue S, Yang YQ. SOX7 loss-of-function variation as a cause of familial congenital heart disease. Am J Transl Res 2022; 14:1672-1684. [PMID: 35422912 PMCID: PMC8991148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 02/08/2022] [Indexed: 06/14/2023]
Abstract
INTRODUCTION As the most frequent type of birth defect in humans, congenital heart disease (CHD) leads to a large amount of morbidity and mortality as well as a tremendous socioeconomic burden. Accumulating studies have convincingly substantiated the pivotal roles of genetic defects in the occurrence of familial CHD, and deleterious variations in a great number of genes have been reported to cause various types of CHD. However, owing to pronounced genetic heterogeneity, the hereditary components underpinning CHD remain obscure in most cases. This investigation aimed to identify novel genetic determinants underlying CHD. METHODS AND RESULTS A four-generation pedigree with high incidence of autosomal-dominant CHD was enrolled from the Chinese Han race population. Using whole-exome sequencing and Sanger sequencing assays of the family members available, a novel SOX7 variation in heterozygous status, NM_031439.4: c.310C>T; p.(Gln104*), was discovered to be in co-segregation with the CHD phenotype in the whole family. The truncating variant was absent in 500 unrelated healthy subjects utilized as control individuals. Functional measurements by dual-luciferase reporter analysis revealed that Gln104*-mutant SOX7 failed to transactivate its two important target genes, GATA4 and BMP2, which are both responsible for CHD. In addition, the nonsense variation invalidated the cooperative transactivation between SOX7 and NKX2.5, which is another recognized CHD-causative gene. CONCLUSION The present study demonstrates for the first time that genetically defective SOX7 predisposes to CHD, which sheds light on the novel molecular mechanism underpinning CHD, and implies significance for precise prevention and personalized treatment in a subset of CHD patients.
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Affiliation(s)
- Ri-Tai Huang
- Department of Cardiovascular Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong UniversityShanghai 200127, China
| | - Yu-Han Guo
- Department of Cardiology, Shanghai Fifth People’s Hospital, Fudan UniversityShanghai 200240, China
| | - Chen-Xi Yang
- Department of Cardiology, Shanghai Fifth People’s Hospital, Fudan UniversityShanghai 200240, China
| | - Jia-Ning Gu
- Department of Cardiology, Shanghai Fifth People’s Hospital, Fudan UniversityShanghai 200240, China
| | - Xing-Biao Qiu
- Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiao Tong UniversityShanghai 200030, China
| | - Hong-Yu Shi
- Department of Cardiology, Zhongshan Hospital Wusong Branch, Fudan UniversityShanghai 200940, China
| | - Ying-Jia Xu
- Department of Cardiology, Shanghai Fifth People’s Hospital, Fudan UniversityShanghai 200240, China
| | - Song Xue
- Department of Cardiovascular Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong UniversityShanghai 200127, China
| | - Yi-Qing Yang
- Department of Cardiology, Shanghai Fifth People’s Hospital, Fudan UniversityShanghai 200240, China
- Department of Cardiovascular Research Laboratory, Shanghai Fifth People’s Hospital, Fudan UniversityShanghai 200240, China
- Department of Central Laboratory, Shanghai Fifth People’s Hospital, Fudan UniversityShanghai 200240, China
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A genotype-first analysis in a cohort of Mullerian anomaly. J Hum Genet 2022; 67:347-352. [PMID: 35022528 DOI: 10.1038/s10038-021-00996-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 11/15/2021] [Accepted: 11/16/2021] [Indexed: 11/08/2022]
Abstract
Müllerian anomaly (M.A.) is a group of congenital anatomic abnormalities caused by aberrations of the development process of the Müllerian duct. M.A. can either be isolated or be involved in Mendelian syndromes, such as Dandy-Walker syndrome, Holt-Oram syndrome and Bardet-Biedl syndrome, which are often associated with both uterus and kidney malformations. In this study, we applied a genotype-first approach to analyze the whole-exome sequencing data of 492 patients with M.A. Six potential pathogenic variants were found in five genes previously related to female urogenital deformities (PKD1, SON, SALL1, BMPR1B, ITGA8), which are partially overlapping with our patients' phenotypes. We further identified eight incidental findings in seven genes related to Mendelian syndromes without known association with reproductive anomalies (TEK, COL11A1, ANKRD11, LEMD3, DLG5, SPTB, BMP2), which represent potential phenotype expansions of these genes.
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Mensah NE, Sabir AH, Bond A, Roworth W, Irving M, Davies AC, Ahn JW. Automated reanalysis application to assist in detecting novel gene–disease associations after genome sequencing. Genet Med 2021; 24:811-820. [DOI: 10.1016/j.gim.2021.11.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 08/31/2021] [Accepted: 11/24/2021] [Indexed: 02/02/2023] Open
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Zhang H, Zhuang Z, Yang M, Ding R, Quan J, Zhou S, Gu T, Xu Z, Zheng E, Cai G, Yang J, Wu Z. Genome-Wide Detection of Genetic Loci and Candidate Genes for Body Conformation Traits in Duroc × Landrace × Yorkshire Crossbred Pigs. Front Genet 2021; 12:664343. [PMID: 34707635 PMCID: PMC8542986 DOI: 10.3389/fgene.2021.664343] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 09/16/2021] [Indexed: 11/30/2022] Open
Abstract
The Duroc × (Landrace × Yorkshire) hybrid pigs (DLY) are the most popular commercial pigs, providing consumers with the largest source of pork. In order to gain more insights into the genetic architecture of economically important traits in pigs, we performed a genome-wide association study (GWAS) using the GeneSeek Porcine 50 K SNP Chip to map the genetic markers and genes associated with body conformation traits (BCT) in 311 DLY pigs. The quantitative traits analyzed included body weight (BW), carcass length (CL), body length (BL), body height (BH), and body mass index (BMI). BMI was defined as BMICL, BMIBL, and BMIBH, respectively, based on CL, BL, and BH phenotypic data. We identified 82 SNPs for the seven traits by GEMMA-based and FarmCPU-based GWASs. Both methods detected two quantitative trait loci (QTL) on SSC8 and SSC17 for body conformation traits. Several candidate genes (such as TNFAIP3, KDM4C, HSPG2, BMP2, PLCB4, and GRM5) were found to be associated with body weight and body conformation traits in pigs. Notably, the BMP2 gene had pleiotropic effects on CL, BL, BH, BMICL, and BMIBL and is proposed as a strong candidate gene for body size due to its involvement in growth and bone development. Furthermore, gene set enrichment analysis indicated that most of the pathway terms are associated with regulation of cell growth, negative regulation of cell population proliferation, and chondrocyte differentiation. We anticipate that these results further advance our understanding of the genetic architecture of body conformation traits in the popular commercial DLY pigs and provide new insights into the genetic architecture of BMI in pigs.
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Affiliation(s)
- Hui Zhang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, China
| | - Zhanwei Zhuang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, China
| | - Ming Yang
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangdong, China
| | - Rongrong Ding
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, China
| | - Jianping Quan
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, China
| | - Shenping Zhou
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, China
| | - Ting Gu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, China
| | - Zheng Xu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, China
| | - Enqin Zheng
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, China
| | - Gengyuan Cai
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, China
| | - Jie Yang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, China
| | - Zhenfang Wu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, China
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Zhu Z, Zhang X, Jiang Y, Ruan S, Huang F, Zeng H, Liu M, Xia W, Zeng F, Chen J, Cui Y, Chen H. NEAT1 functions as a key mediator of BMP2 to promote osteogenic differentiation of renal interstitial fibroblasts. Epigenomics 2021; 13:1171-1186. [PMID: 34325517 DOI: 10.2217/epi-2021-0212] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Aim: To clarify the mechanism of NEAT1, an aberrantly upregulated lncRNA in Randall's plaques (RP) similar to biomineralization, in mediating osteogenic differentiation of human renal interstitial fibroblasts. Materials & methods: A comprehensive strategy of bioinformatic analysis and experimental verification was performed. Results: BMP2 silence abolished the osteogenic differentiation of human renal interstitial fibroblasts promoted by NEAT1. Mechanically, NEAT1 not only induced the nucleolar translocation of EGR1 binding to BMP2 promotor, but also functioned as a sponge of miR-129-5p in the cytoplasm to promote BMP2 expression. Moreover, there was a positive correlation between NEAT1 and BMP2 expression in RP instead of normal renal papilla. Conclusion: NEAT1 acted as a key mediator of BMP2 to promote human renal interstitial fibroblast osteogenic differentiation, through which NEAT1 might be involved in RP formation.
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Affiliation(s)
- Zewu Zhu
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Xiaoqiong Zhang
- Transplantation Center, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Yingcheng Jiang
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Shuhao Ruan
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Fang Huang
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Huimin Zeng
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Minghui Liu
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Weiping Xia
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Feng Zeng
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Jinbo Chen
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Yu Cui
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Hequn Chen
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
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9
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Audain E, Wilsdon A, Breckpot J, Izarzugaza JMG, Fitzgerald TW, Kahlert AK, Sifrim A, Wünnemann F, Perez-Riverol Y, Abdul-Khaliq H, Bak M, Bassett AS, Benson WD, Berger F, Daehnert I, Devriendt K, Dittrich S, Daubeney PEF, Garg V, Hackmann K, Hoff K, Hofmann P, Dombrowsky G, Pickardt T, Bauer U, Keavney BD, Klaassen S, Kramer HH, Marshall CR, Milewicz DM, Lemaire S, Coselli JS, Mitchell ME, Tomita-Mitchell A, Prakash SK, Stamm K, Stewart AFR, Silversides CK, Siebert R, Stiller B, Rosenfeld JA, Vater I, Postma AV, Caliebe A, Brook JD, Andelfinger G, Hurles ME, Thienpont B, Larsen LA, Hitz MP. Integrative analysis of genomic variants reveals new associations of candidate haploinsufficient genes with congenital heart disease. PLoS Genet 2021; 17:e1009679. [PMID: 34324492 PMCID: PMC8354477 DOI: 10.1371/journal.pgen.1009679] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 08/10/2021] [Accepted: 06/23/2021] [Indexed: 11/18/2022] Open
Abstract
Numerous genetic studies have established a role for rare genomic variants in Congenital Heart Disease (CHD) at the copy number variation (CNV) and de novo variant (DNV) level. To identify novel haploinsufficient CHD disease genes, we performed an integrative analysis of CNVs and DNVs identified in probands with CHD including cases with sporadic thoracic aortic aneurysm. We assembled CNV data from 7,958 cases and 14,082 controls and performed a gene-wise analysis of the burden of rare genomic deletions in cases versus controls. In addition, we performed variation rate testing for DNVs identified in 2,489 parent-offspring trios. Our analysis revealed 21 genes which were significantly affected by rare CNVs and/or DNVs in probands. Fourteen of these genes have previously been associated with CHD while the remaining genes (FEZ1, MYO16, ARID1B, NALCN, WAC, KDM5B and WHSC1) have only been associated in small cases series or show new associations with CHD. In addition, a systems level analysis revealed affected protein-protein interaction networks involved in Notch signaling pathway, heart morphogenesis, DNA repair and cilia/centrosome function. Taken together, this approach highlights the importance of re-analyzing existing datasets to strengthen disease association and identify novel disease genes and pathways.
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Affiliation(s)
- Enrique Audain
- Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital of Schleswig-Holstein, Kiel, Germany
- German Center for Cardiovascular Research (DZHK), Kiel, Germany
| | - Anna Wilsdon
- School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Jeroen Breckpot
- Centre for Human Genetics, Katholieke Universiteit Leuven, Leuven, Belgium
| | | | - Tomas W. Fitzgerald
- European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, United Kingdom
| | - Anne-Karin Kahlert
- Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital of Schleswig-Holstein, Kiel, Germany
- German Center for Cardiovascular Research (DZHK), Kiel, Germany
- Institute for Clinical Genetics, Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Alejandro Sifrim
- Department of Human Genetics, University of Leuven, KU Leuven, Leuven, Belgium
- Sanger Institute-EBI Single-Cell Genomics Centre, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | | | - Yasset Perez-Riverol
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Hashim Abdul-Khaliq
- Clinic for Pediatric Cardiology—University Hospital of Saarland, Homburg (Saar), Germany
| | - Mads Bak
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Anne S. Bassett
- Toronto Congenital Cardiac Centre for Adults, and Division of Cardiology, Department of Medicine, University Health Network, Toronto, Canada
- Department of Psychiatry, University of Toronto, Toronto, Canada
| | - Woodrow D. Benson
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Felix Berger
- Department of Congenital Heart Disease—Pediatric Cardiology, German Heart Center Berlin, Berlin, Germany
| | - Ingo Daehnert
- Department of Pediatric Cardiology and Congenital Heart Disease, Heart Center, University of Leipzig, Leipzig, Germany
| | - Koenraad Devriendt
- Centre for Human Genetics, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Sven Dittrich
- Department of Pediatric Cardiology, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Piers EF Daubeney
- Division of Paediatric Cardiology, Royal Brompton Hospital, London, United Kingdom
| | - Vidu Garg
- The Heart Center, Nationwide Children’s Hospital, Columbus, Ohio, United States of America
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, United States of America
- Center for Cardiovascular Research, Nationwide Children’s Hospital, Columbus, Ohio, United States of America
- Department of Pediatrics, The Ohio State University, Columbus, Ohio, United States of America
| | - Karl Hackmann
- Institute for Clinical Genetics, Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Kirstin Hoff
- Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital of Schleswig-Holstein, Kiel, Germany
- German Center for Cardiovascular Research (DZHK), Kiel, Germany
| | - Philipp Hofmann
- Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital of Schleswig-Holstein, Kiel, Germany
- German Center for Cardiovascular Research (DZHK), Kiel, Germany
| | - Gregor Dombrowsky
- Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital of Schleswig-Holstein, Kiel, Germany
- German Center for Cardiovascular Research (DZHK), Kiel, Germany
| | - Thomas Pickardt
- Competence Network for Congenital Heart Defects, Berlin, Germany
| | - Ulrike Bauer
- Competence Network for Congenital Heart Defects, Berlin, Germany
| | - Bernard D. Keavney
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
- Division of Evolution & Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Sabine Klaassen
- Experimental and Clinical Research Center (ECRC), a joint cooperation between the Charité Medical Faculty and the Max-Delbrück-Center for Molecular Medicine (MDC), Berlin, Germany
- Charité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Pediatric Cardiology, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Berlin, Germany
| | - Hans-Heiner Kramer
- Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital of Schleswig-Holstein, Kiel, Germany
- German Center for Cardiovascular Research (DZHK), Kiel, Germany
| | - Christian R. Marshall
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Canada
- Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Canada
| | - Dianna M. Milewicz
- Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Scott Lemaire
- Michael E. DeBakey Department of Surgery, Baylor College of Medicine, Houston, Texas, United States of America
| | - Joseph S. Coselli
- Department of Surgery, Division of Cardiothoracic Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Michael E. Mitchell
- Department of Surgery, Division of Cardiothoracic Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Aoy Tomita-Mitchell
- Department of Surgery, Division of Cardiothoracic Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Siddharth K. Prakash
- Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Karl Stamm
- Department of Surgery, Division of Cardiothoracic Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Alexandre F. R. Stewart
- Ruddy Canadian Cardiovascular Genetics Centre, University of Ottawa Heart Institute, Ottawa, Canada
| | - Candice K. Silversides
- Toronto Congenital Cardiac Centre for Adults, and Division of Cardiology, Department of Medicine, University Health Network, Toronto, Canada
| | - Reiner Siebert
- Institute of Human Genetics, University Hospital Ulm, Ulm, Germany
- Department of Human Genetics, University Medical Center Schleswig-Holstein (UKSH), Kiel, Germany
| | - Brigitte Stiller
- Department of Congenital Heart Disease and Pediatric Cardiology, University Heart Center Freiburg—Bad Krozingen, Freiburg, Germany
| | - Jill A. Rosenfeld
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Inga Vater
- Department of Human Genetics, University Medical Center Schleswig-Holstein (UKSH), Kiel, Germany
| | - Alex V. Postma
- Department of Medical Biology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Almuth Caliebe
- Department of Human Genetics, University Medical Center Schleswig-Holstein (UKSH), Kiel, Germany
| | - J. David Brook
- School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Gregor Andelfinger
- Cardiovascular Genetics, Department of Pediatrics, Centre Hospitalier Universitaire Saint-Justine Research Centre, Université de Montréal, Montreal, Canada
| | - Matthew E. Hurles
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Bernard Thienpont
- Centre for Human Genetics, Katholieke Universiteit Leuven, Leuven, Belgium
- Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Lars Allan Larsen
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Marc-Phillip Hitz
- Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital of Schleswig-Holstein, Kiel, Germany
- German Center for Cardiovascular Research (DZHK), Kiel, Germany
- Department of Human Genetics, University Medical Center Schleswig-Holstein (UKSH), Kiel, Germany
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
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10
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Whole-Genome Sequencing Identifies Two Novel Rare Mutations in BMP5 and BMP2 in Monozygotic Twins With Microtia. J Craniofac Surg 2021; 33:e212-e217. [PMID: 34183628 DOI: 10.1097/scs.0000000000007689] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
ABSTRACT Microtia is a rare congenital anomaly of the ear; it is regulated by both genetic and environmental factors. However, the mechanisms underlying its pathogenesis are unknown. In this study, the genomes of 2-year-old twin sisters with right microtia were sequenced using human genome-wide sequencing, an approach useful for identifying mutations in genes responsible for congenital microtia. The phenotypes of the twin sisters included congenital microtia on the right side, abnormal auricle shape in the right external ear, a peanut shape for the residual ear, and complete atresia of the right external auditory canal. In the twin sisters, we identified a previously unknown mutation in BMP5(exon4:c.833- 4C>G), as well as a new mutation (exon2:c.G332T:p.S111I) in BMP2, both of which were confirmed using polymerase chain reaction-based amplification of the corresponding genome regions, followed by first-generation sequencing. The exon4:c.833-4C>G mutation in human BMP5 may be the main cause of microtia in the twin sisters. A pathogenic mutation in human BMP2 (exon2:c.G332T:p.S111I) may be responsible for the facial deformity in the twin sisters. Thus, our study demonstrates the potential of genome-wide sequencing for identifying novel mutations associated with microtia on the whole-genome scale and extends the mutation spectrum of BMP5. Additionally, our data suggest that BMP2 is another pathogenic gene associated with microtia.
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11
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Gumus E, Temiz E, Sarikaya B, Yuksekdag O, Sipahioglu S, Gonel A. The Association Between BMP- 2, UQCC1 and CX3CR1 Polymorphisms and the Risk of Developmental Dysplasia of the Hip. Indian J Orthop 2021; 55:169-175. [PMID: 33569111 PMCID: PMC7851229 DOI: 10.1007/s43465-020-00235-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 08/13/2020] [Indexed: 02/07/2023]
Abstract
OBJECTIVE Developmental dysplasia of the hip (DDH) is a complicated skeletal disease ranging from subluxation to complete dislocation of the hip as a result of insufficient development of the acetabulum and femur. To date, numerous genes such as C-X3-C motif chemokine receptor 1 (CX3CR1), ubiquinol-cytochrome c reductase complex assembly factor 1 (UQCC1) and growth/differentiation factor 5 (GDF5), have been investigated to elucidate the underlying genetic etiology. Turkish population is one of the communities where DDH patients frequently observed, but almost no study has been conducted to elucidate the genetic etiology. In our study, we aimed to investigate the polymorphism of CX3CR1 rs3732378 and UQCC1 rs6060373, which have been shown to be associated with DDH in different populations. In addition, we aimed to investigate the BMP-2 rs235768 polymorphism which has not been investigated in the etiology of DDH. METHODS Overall, 168 subjects (68 participants in the patient group, 100 participants in the control group) were investigated. The participants with following evidence and symptoms were excluded from the two groups: any systemic syndrome, another congenital anomaly, hereditary diseases, breech presentation, history of oligohydramnios, swaddling and high birth weight (> 4000 g). 3 single-nucleotide polymorphisms (SNP) were examined by qRT-PCR method. RESULTS For CX3CR1 rs3732378 polymorphism, significant differences were observed in genotypes and allele frequencies (p < 0.0001). This condition was associated with a 12-fold increased risk in recessive modeling and 75-fold increased risk in dominant modeling. There was no significant relationship between DDH and the other two polymorphisms. CONCLUSIONS Our work is the first study to investigate DDH and genetic polymorphisms in Turkish population where DDH is observed quite frequently. It is also the first study to investigate the relationship between BMP-2 rs235768 polymorphism and DDH. Our study revealed a clear relationship between CX3CR1 rs3732378 polymorphism and DDH in Turkish population.
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Affiliation(s)
- Evren Gumus
- Department of Medical Genetics, Faculty of Medicine, University of Harran, Sanliurfa, Turkey
- Department of Medical Genetics, Faculty of Medicine, University of Mugla Sitki Kocman, Mugla, 48000 Turkey
| | - Ebru Temiz
- Department of Medical Biochemistry, Faculty of Medicine, University of Harran, Sanliurfa, Turkey
| | - Baran Sarikaya
- Department of Orthopedics and Traumatology, Faculty of Medicine, University of Harran, Sanliurfa, Turkey
| | - Ozgur Yuksekdag
- Department of Medical Biochemistry, Faculty of Medicine, University of Harran, Sanliurfa, Turkey
| | - Serkan Sipahioglu
- Department of Orthopedics and Traumatology, Faculty of Medicine, University of Harran, Sanliurfa, Turkey
| | - Ataman Gonel
- Department of Medical Biochemistry, Faculty of Medicine, University of Harran, Sanliurfa, Turkey
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12
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Lin YC, Niceta M, Muto V, Vona B, Pagnamenta AT, Maroofian R, Beetz C, van Duyvenvoorde H, Dentici ML, Lauffer P, Vallian S, Ciolfi A, Pizzi S, Bauer P, Grüning NM, Bellacchio E, Del Fattore A, Petrini S, Shaheen R, Tiosano D, Halloun R, Pode-Shakked B, Albayrak HM, Işık E, Wit JM, Dittrich M, Freire BL, Bertola DR, Jorge AAL, Barel O, Sabir AH, Al Tenaiji AMJ, Taji SM, Al-Sannaa N, Al-Abdulwahed H, Digilio MC, Irving M, Anikster Y, Bhavani GSL, Girisha KM, Haaf T, Taylor JC, Dallapiccola B, Alkuraya FS, Yang RB, Tartaglia M. SCUBE3 loss-of-function causes a recognizable recessive developmental disorder due to defective bone morphogenetic protein signaling. Am J Hum Genet 2021; 108:115-133. [PMID: 33308444 PMCID: PMC7820739 DOI: 10.1016/j.ajhg.2020.11.015] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 11/20/2020] [Indexed: 12/11/2022] Open
Abstract
Signal peptide-CUB-EGF domain-containing protein 3 (SCUBE3) is a member of a small family of multifunctional cell surface-anchored glycoproteins functioning as co-receptors for a variety of growth factors. Here we report that bi-allelic inactivating variants in SCUBE3 have pleiotropic consequences on development and cause a previously unrecognized syndromic disorder. Eighteen affected individuals from nine unrelated families showed a consistent phenotype characterized by reduced growth, skeletal features, distinctive craniofacial appearance, and dental anomalies. In vitro functional validation studies demonstrated a variable impact of disease-causing variants on transcript processing, protein secretion and function, and their dysregulating effect on bone morphogenetic protein (BMP) signaling. We show that SCUBE3 acts as a BMP2/BMP4 co-receptor, recruits the BMP receptor complexes into raft microdomains, and positively modulates signaling possibly by augmenting the specific interactions between BMPs and BMP type I receptors. Scube3-/- mice showed craniofacial and dental defects, reduced body size, and defective endochondral bone growth due to impaired BMP-mediated chondrogenesis and osteogenesis, recapitulating the human disorder. Our findings identify a human disease caused by defective function of a member of the SCUBE family, and link SCUBE3 to processes controlling growth, morphogenesis, and bone and teeth development through modulation of BMP signaling.
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Affiliation(s)
- Yuh-Charn Lin
- Department of Physiology, School of Medicine, Taipei Medical University, 110301 Taipei, Taiwan; Institute of Biomedical Sciences, Academia Sinica, 115201 Taipei, Taiwan
| | - Marcello Niceta
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Valentina Muto
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Barbara Vona
- Institute of Human Genetics, Julius Maximilians University, 97074 Würzburg, Germany; Department of Otolaryngology - Head and Neck Surgery, Eberhard Karls University, 72076 Tübingen, Germany
| | - Alistair T Pagnamenta
- NIHR Oxford Biomedical Research Centre, Wellcome Centre for Human Genetics, University of Oxford, OX3 7BN Oxford, UK
| | - Reza Maroofian
- Genetics and Molecular Cell Sciences Research Centre, St George's University of London, Cranmer Terrace, SW17 0RE London, UK
| | | | - Hermine van Duyvenvoorde
- Department of Clinical Genetics, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Maria Lisa Dentici
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Peter Lauffer
- Department of Paediatric Endocrinology, Emma Children's Hospital, Amsterdam University Medical Center, 1105 AZ Amsterdam, the Netherlands
| | - Sadeq Vallian
- Department of Cell and Molecular Biology & Microbiology, University of Isfahan, 8174673441 Isfahan, Iran
| | - Andrea Ciolfi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Simone Pizzi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | | | | | - Emanuele Bellacchio
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Andrea Del Fattore
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Stefania Petrini
- Confocal Microscopy Core Facility, Research Laboratories, IRCCS Ospedale Pediatrico Bambino Gesù, 00146 Rome, Italy
| | - Ranad Shaheen
- Department of Genetics, King Faisal Specialist Hospital and Research Center, 11211 Riyadh, Saudi Arabia; Qatar Biomedical Research Institute, Hamad Bin Khalifa University, 34110 Doha, Qatar
| | - Dov Tiosano
- Pediatric Endocrinology Unit, Ruth Rappaport Children's Hospital, Rambam Healthcare Campus, 352540 Haifa, Israel; Ruth and Bruce Rappaport Faculty of Medicine, Technion, Israel Institute of Technology, 352540 Haifa, Israel
| | - Rana Halloun
- Pediatric Endocrinology Unit, Ruth Rappaport Children's Hospital, Rambam Healthcare Campus, 352540 Haifa, Israel
| | - Ben Pode-Shakked
- Edmond and Lily Safra Children's Hospital, Sheba Medical Center, 52621 Tel-Hashomer, Israel; The Sackler Faculty of Medicine, Tel-Aviv University, 6997801 Tel-Aviv, Israel
| | - Hatice Mutlu Albayrak
- Department of Pediatric Endocrinology, Gaziantep Cengiz Gökcek Maternity & Children's Hospital, 27010 Gaziantep, Turkey
| | - Emregül Işık
- Department of Pediatric Endocrinology, Gaziantep Cengiz Gökcek Maternity & Children's Hospital, 27010 Gaziantep, Turkey
| | - Jan M Wit
- Department of Pediatrics, Leiden University Medical Center, 2333ZA Leiden, the Netherlands
| | - Marcus Dittrich
- Institute of Human Genetics, Julius Maximilians University, 97074 Würzburg, Germany; Institute of Bioinformatics, Julius Maximilians University, 97070 Würzburg, Germany
| | - Bruna L Freire
- Unidade de Endocrinologia Genética, Hospital das Clínicas da Faculdade de Medicina da Universidade de Sao Paulo, 01246903 Sao Paulo, Brazil
| | - Debora R Bertola
- Unidade de Genética do Instituto da Criança, Hospital das Clínicas da Faculdade de Medicina da Universidade de Sao Paulo, 05403000 Sao Paulo, Brazil
| | - Alexander A L Jorge
- Unidade de Endocrinologia Genética, Hospital das Clínicas da Faculdade de Medicina da Universidade de Sao Paulo, 01246903 Sao Paulo, Brazil
| | - Ortal Barel
- Sheba Cancer Research Center, Sheba Medical Center, 52621 Tel-Hashomer, Israel; Wohl Institute for Translational Medicine, Sheba Medical Center, 52621 Tel-Hashomer, Israel
| | - Ataf H Sabir
- Department of Clinical Genetics, Guy's and St Thomas' NHS Foundation Trust, SE1 9RT London, UK; Birmingham Women's and Children's NHS Foundation Trust, University of Birmingham, B4 6NH Birmingham, UK
| | - Amal M J Al Tenaiji
- Department of Paediatrics, Sheikh Khalifa Medical City, 51900 Abu Dhabi, United Arab Emirates
| | - Sulaima M Taji
- Department of Paediatrics, Sheikh Khalifa Medical City, 51900 Abu Dhabi, United Arab Emirates
| | | | | | - Maria Cristina Digilio
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Melita Irving
- Department of Clinical Genetics, Guy's and St Thomas' NHS Foundation Trust, SE1 9RT London, UK
| | - Yair Anikster
- Edmond and Lily Safra Children's Hospital, Sheba Medical Center, 52621 Tel-Hashomer, Israel; The Sackler Faculty of Medicine, Tel-Aviv University, 6997801 Tel-Aviv, Israel; Wohl Institute for Translational Medicine, Sheba Medical Center, 52621 Tel-Hashomer, Israel
| | - Gandham S L Bhavani
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal 576104, India
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal 576104, India
| | - Thomas Haaf
- Institute of Human Genetics, Julius Maximilians University, 97074 Würzburg, Germany
| | - Jenny C Taylor
- NIHR Oxford Biomedical Research Centre, Wellcome Centre for Human Genetics, University of Oxford, OX3 7BN Oxford, UK
| | - Bruno Dallapiccola
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, 11211 Riyadh, Saudi Arabia
| | - Ruey-Bing Yang
- Institute of Biomedical Sciences, Academia Sinica, 115201 Taipei, Taiwan; Ph.D. Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, 110301 Taipei, Taiwan; Institute of Pharmacology, School of Medicine, National Yang-Ming University, 112304, Taipei, Taiwan.
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy.
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13
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Donoghue SE, White SM, Tan TY, Kowalski R, Morava E, Yaplito‐Lee J. Galactose treatment of a PGM1 patient presenting with restrictive cardiomyopathy. JIMD Rep 2021; 57:29-37. [PMID: 33473337 PMCID: PMC7802629 DOI: 10.1002/jmd2.12177] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 10/11/2020] [Accepted: 10/13/2020] [Indexed: 12/04/2022] Open
Abstract
We report a patient diagnosed with PGM1-CDG at 11 years of age after two biallelic likely pathogenic variants in PGM1 were found on research genomic sequencing. To our knowledge, he is the first patient with PGM1-CDG to be reported with a restrictive cardiomyopathy. Other clinical manifestations included cleft palate, asymptomatic elevated transaminases, intellectual disability and myopathy resulting in exercise intolerance. He was trialed on oral galactose therapy in increasing doses for 18 weeks to assess if there was any biochemical and clinical benefit. His galactose was continued for a further 9 months beyond the initial galactose treatment period due to improvements in exercise tolerance and myopathy. Treatment with galactose demonstrated an improvement in liver function and myopathy with improved exercise tolerance. Treatment with galactose for 15 months did not change heart function and exercise stress test results were stable.
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Affiliation(s)
- Sarah E. Donoghue
- Department of Metabolic MedicineRoyal Children's HospitalMelbourneVictoriaAustralia
- Victorian Clinical Genetics ServicesMurdoch Children's Research InstituteMelbourneVictoriaAustralia
| | - Susan M. White
- Victorian Clinical Genetics ServicesMurdoch Children's Research InstituteMelbourneVictoriaAustralia
- Department of PaediatricsUniversity of MelbourneMelbourneVictoriaAustralia
| | - Tiong Yang Tan
- Victorian Clinical Genetics ServicesMurdoch Children's Research InstituteMelbourneVictoriaAustralia
- Department of PaediatricsUniversity of MelbourneMelbourneVictoriaAustralia
| | - Remi Kowalski
- Department of CardiologyRoyal Children's HospitalMelbourneVictoriaAustralia
| | - Eva Morava
- Department of Clinical GenomicsMayo ClinicRochesterMinnesotaUSA
- Department of PediatricsUniversity Hospitals LeuvenLeuvenBelgium
| | - Joy Yaplito‐Lee
- Department of Metabolic MedicineRoyal Children's HospitalMelbourneVictoriaAustralia
- Department of PaediatricsUniversity of MelbourneMelbourneVictoriaAustralia
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14
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Ahluwalia N, Gelb BD. A de novo pathogenic BMP2 variant-related phenotype with the novel finding of bicuspid aortic valve. Am J Med Genet A 2020; 185:575-578. [PMID: 33247540 DOI: 10.1002/ajmg.a.61992] [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: 10/01/2020] [Revised: 11/04/2020] [Accepted: 11/06/2020] [Indexed: 11/10/2022]
Abstract
A rare autosomal dominant syndrome with craniofacial dysmorphisms, skeletal abnormalities, short stature, and congenital heart defects has recently been described, associated with monoallelic truncating and frameshift bone morphogenetic protein 2 (BMP2) variants and deletions. We describe a patient harboring a novel de novo BMP2 nonsense variant, who exhibited craniofacial and skeletal features previously described for this trait and the novel findings of bicuspid aortic valve (BAV) and aortic root and ascending aortic aneurysm. This first instance of aortic valve involvement provides another potential cause of BAV and confirms the role of BMP2 in left ventricular outflow development.
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Affiliation(s)
- Neha Ahluwalia
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Bruce D Gelb
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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15
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Gariballa N, Ali BR. Endoplasmic Reticulum Associated Protein Degradation (ERAD) in the Pathology of Diseases Related to TGFβ Signaling Pathway: Future Therapeutic Perspectives. Front Mol Biosci 2020; 7:575608. [PMID: 33195419 PMCID: PMC7658374 DOI: 10.3389/fmolb.2020.575608] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 09/29/2020] [Indexed: 02/05/2023] Open
Abstract
The transforming growth factor signaling pathway (TGFβ) controls a wide range of cellular activities in adulthood as well as during embryogenesis including cell growth, differentiation, apoptosis, immunological responses and other cellular functions. Therefore, germline mutations in components of the pathway have given rise to a heterogeneous spectrum of hereditary diseases with variable phenotypes associated with malformations in the cardiovascular, muscular and skeletal systems. Our extensive literature and database searches revealed 47 monogenic diseases associated with germline mutations in 24 out of 41 gene variant encoding for TGFβ components. Most of the TGFβ components are membrane or secretory proteins and they are therefore expected to pass through the endoplasmic reticulum (ER), where fidelity of proteins folding is stringently monitored via the ER quality control machineries. Elucidation of the molecular mechanisms of mutant proteins’ folding and trafficking showed the implication of ER associated protein degradation (ERAD) in the pathogenesis of some of the diseases. For example, hereditary hemorrhagic telangiectasia types 1 and 2 (HHT1 and HHT2) and familial pulmonary arterial hypertension (FPAH) associated with mutations in Endoglin, ALK1 and BMPR2 components of the signaling pathway, respectively, have all exhibited loss of function phenotype as a result of ER retention of some of their disease-causing variants. In some cases, this has led to premature protein degradation through the proteasomal pathway. We anticipate that ERAD will be involved in the mechanisms of other TGFβ signaling components and therefore warrants further research. In this review, we highlight advances in ER quality control mechanisms and their modulation as a potential therapeutic target in general with particular focus on prospect of their implementation in the treatment of monogenic diseases associated with TGFβ components including HHT1, HHT2, and PAH. In particular, we emphasis the need to establish disease mechanisms and to implement such novel approaches in modulating the molecular pathway of mutant TGFβ components in the quest for restoring protein folding and trafficking as a therapeutic approach.
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Affiliation(s)
- Nesrin Gariballa
- Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates.,Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Bassam R Ali
- Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates.,Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates.,Zayed Bin Sultan Center for Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
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16
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Halloran D, Durbano HW, Nohe A. Bone Morphogenetic Protein-2 in Development and Bone Homeostasis. J Dev Biol 2020; 8:E19. [PMID: 32933207 PMCID: PMC7557435 DOI: 10.3390/jdb8030019] [Citation(s) in RCA: 124] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 09/01/2020] [Accepted: 09/11/2020] [Indexed: 12/11/2022] Open
Abstract
Bone morphogenetic proteins (BMPs) are multi-functional growth factors belonging to the Transforming Growth Factor-Beta (TGF-β) superfamily. These proteins are essential to many developmental processes, including cardiogenesis, neurogenesis, and osteogenesis. Specifically, within the BMP family, Bone Morphogenetic Protein-2 (BMP-2) was the first BMP to be characterized and has been well-studied. BMP-2 has important roles during embryonic development, as well as bone remodeling and homeostasis in adulthood. Some of its specific functions include digit formation and activating osteogenic genes, such as Runt-Related Transcription Factor 2 (RUNX2). Because of its diverse functions and osteogenic potential, the Food and Drug Administration (FDA) approved usage of recombinant human BMP-2 (rhBMP-2) during spinal fusion surgery, tibial shaft repair, and maxillary sinus reconstructive surgery. However, shortly after initial injections of rhBMP-2, several adverse complications were reported, and alternative therapeutics have been developed to limit these side-effects. As the clinical application of BMP-2 is largely implicated in bone, we focus primarily on its role in bone. However, we also describe briefly the role of BMP-2 in development. We then focus on the structure of BMP-2, its activation and regulation signaling pathways, BMP-2 clinical applications, and limitations of using BMP-2 as a therapeutic. Further, this review explores other potential treatments that may be useful in treating bone disorders.
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Affiliation(s)
| | | | - Anja Nohe
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA; (D.H.); (H.W.D.)
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17
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Asadollahpour Nanaei H, Esmailizadeh A, Ayatollahi Mehrgardi A, Han J, Wu DD, Li Y, Zhang YP. Comparative population genomic analysis uncovers novel genomic footprints and genes associated with small body size in Chinese pony. BMC Genomics 2020; 21:496. [PMID: 32689947 PMCID: PMC7370493 DOI: 10.1186/s12864-020-06887-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 07/06/2020] [Indexed: 12/15/2022] Open
Abstract
Background Body size is considered as one of the most fundamental properties of an organism. Due to intensive breeding and artificial selection throughout the domestication history, horses exhibit striking variations for heights at withers and body sizes. Debao pony (DBP), a famous Chinese horse, is known for its small body size and lives in Guangxi mountains of southern China. In this study, we employed comparative population genomics to study the genetic basis underlying the small body size of DBP breed based on the whole genome sequencing data. To detect genomic signatures of positive selection, we applied three methods based on population comparison, fixation index (FST), cross population composite likelihood ratio (XP-CLR) and nucleotide diversity (θπ), and further analyzed the results to find genomic regions under selection for body size-related traits. Results A number of protein-coding genes in windows with the top 1% values of FST (367 genes), XP-CLR (681 genes), and log2 (θπ ratio) (332 genes) were identified. The most significant signal of positive selection was mapped to the NELL1 gene, probably underlies the body size and development traits, and may also have been selected for short stature in the DBP population. In addition, some other loci on different chromosomes were identified to be potentially involved in the development of body size. Conclusions Results of our study identified some positively selected genes across the horse genome, which are possibly involved in body size traits. These novel candidate genes may be useful targets for clarifying our understanding of the molecular basis of body size and as such they should be of great interest for future research into the genetic architecture of relevant traits in horse breeding program.
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Affiliation(s)
- Hojjat Asadollahpour Nanaei
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, PB, 76169-133, Iran
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, PB, 76169-133, Iran. .,State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, No. 32 Jiaochang Donglu, Kunming, Yunnan, China.
| | - Ahmad Ayatollahi Mehrgardi
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, PB, 76169-133, Iran
| | - Jianlin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.,Livestock Genetics Program, International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, No. 32 Jiaochang Donglu, Kunming, Yunnan, China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan and Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, China
| | - Yan Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan and Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, China.
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, No. 32 Jiaochang Donglu, Kunming, Yunnan, China. .,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan and Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, China.
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18
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Gonzaga-Jauregui C, Yesil G, Nistala H, Gezdirici A, Bayram Y, Nannuru KC, Pehlivan D, Yuan B, Jimenez J, Sahin Y, Paine IS, Akdemir ZC, Rajamani S, Staples J, Dronzek J, Howell K, Fatih JM, Smaldone S, Schlesinger AE, Ramírez N, Cornier AS, Kelly MA, Haber R, Chim SM, Nieman K, Wu N, Walls J, Poueymirou W, Siao CJ, Sutton VR, Williams MS, Posey JE, Gibbs RA, Carlo S, Tegay DH, Economides AN, Lupski JR. Functional biology of the Steel syndrome founder allele and evidence for clan genomics derivation of COL27A1 pathogenic alleles worldwide. Eur J Hum Genet 2020; 28:1243-1264. [PMID: 32376988 PMCID: PMC7608441 DOI: 10.1038/s41431-020-0632-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 03/31/2020] [Accepted: 04/07/2020] [Indexed: 01/20/2023] Open
Abstract
Previously we reported the identification of a homozygous COL27A1 (c.2089G>C; p.Gly697Arg) missense variant and proposed it as a founder allele in Puerto Rico segregating with Steel syndrome (STLS, MIM #615155); a rare osteochondrodysplasia characterized by short stature, congenital bilateral hip dysplasia, carpal coalitions, and scoliosis. We now report segregation of this variant in five probands from the initial clinical report defining the syndrome and an additional family of Puerto Rican descent with multiple affected adult individuals. We modeled the orthologous variant in murine Col27a1 and found it recapitulates some of the major Steel syndrome associated skeletal features including reduced body length, scoliosis, and a more rounded skull shape. Characterization of the in vivo murine model shows abnormal collagen deposition in the extracellular matrix and disorganization of the proliferative zone of the growth plate. We report additional COL27A1 pathogenic variant alleles identified in unrelated consanguineous Turkish kindreds suggesting Clan Genomics and identity-by-descent homozygosity contributing to disease in this population. The hypothesis that carrier states for this autosomal recessive osteochondrodysplasia may contribute to common complex traits is further explored in a large clinical population cohort. Our findings augment our understanding of COL27A1 biology and its role in skeletal development; and expand the functional allelic architecture in this gene underlying both rare and common disease phenotypes.
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Affiliation(s)
| | - Gozde Yesil
- Istanbul Faculty of Medicine Department of Medical Genetics, Istanbul University, 34093, Istanbul, Turkey
| | - Harikiran Nistala
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY, 10591, USA
| | - Alper Gezdirici
- Department of Medical Genetics, Kanuni Sultan Suleyman Training and Research Hospital, 34303, Istanbul, Turkey
| | - Yavuz Bayram
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Pediatrics, Division of Pediatric Neurology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Bo Yuan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | | | - Yavuz Sahin
- Medical Genetics, Genoks Genetics Center, 06570, Ankara, Turkey
| | - Ingrid S Paine
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Zeynep Coban Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | | | - Jeffrey Staples
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY, 10591, USA
| | - John Dronzek
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY, 10591, USA
| | - Kristen Howell
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY, 10591, USA
| | - Jawid M Fatih
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | | | - Alan E Schlesinger
- Texas Children's Hospital, Houston, TX, 77030, USA.,Department of Radiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | | | - Alberto S Cornier
- Genetics Section, San Jorge Children's Hospital, San Juan, PR, 00912, USA.,Ponce Health Sciences University, Ponce, PR, 00716, USA.,Department of Pediatrics, Universidad Central del Caribe School of Medicine, Bayamon, PR, 00960, USA
| | | | - Robert Haber
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY, 10591, USA
| | - Shek Man Chim
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY, 10591, USA
| | - Kristy Nieman
- Regeneron Pharmaceuticals Inc., Tarrytown, NY, 10591, USA
| | - Nan Wu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Orthopedic Surgery, Beijing Key Laboratory for Genetic Research of Skeletal Deformity, and Medical Research Center of Orthopedics, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, 100730, Beijing, China
| | | | | | | | - Chia-Jen Siao
- Regeneron Pharmaceuticals Inc., Tarrytown, NY, 10591, USA
| | - V Reid Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Texas Children's Hospital, Houston, TX, 77030, USA
| | | | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Simon Carlo
- Mayagüez Medical Center, Mayagüez, PR, 00681, USA.,Ponce Health Sciences University, Ponce, PR, 00716, USA
| | - David H Tegay
- Department of Pediatrics, Division of Medical Genetics, Cohen Children's Medical Center of Northwell Health, New Hyde Park, NY, 11040, USA
| | - Aris N Economides
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY, 10591, USA.,Regeneron Pharmaceuticals Inc., Tarrytown, NY, 10591, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA. .,Texas Children's Hospital, Houston, TX, 77030, USA.
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19
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Olsson B, Calixto RD, da Silva Machado NC, Meger MN, Paula-Silva FWG, Rebellato NLB, da Costa DJ, Küchler EC, Scariot R. MSX1 is differentially expressed in the deepest impacted maxillary third molars. Br J Oral Maxillofac Surg 2020; 58:789-794. [PMID: 32381388 DOI: 10.1016/j.bjoms.2020.04.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 04/04/2020] [Indexed: 10/24/2022]
Abstract
An impacted third molar is one of the most common dental abnormalities. Among the reasons for impaction the most common are: insufficient space, time of eruption, improper position of the tooth bud, and genetic disruptions. To investigate if runt-related transcription factor 2 (RUNX2), bone morphogenetic protein 2 (BMP2), and msh homeobox 1 (MSX1) are differently expressed depending on the position of the molar, we studied 32 patients who had been referred for surgical removal. An orthopantomogram was used to separate them according to Winter's, and Pell & Gregory's, classifications. Bone samples were harvested during the operation for gene expression assay. The Kruskal-Wallis, Dunn's post hoc, and Spearman's correlation, tests were used to assess the significance of differences. No correlations were found in expression of the genes, and no differences between expression in maxillary and mandibular third molars, nor were they expressed differently according to Winter's or Pell and Gregory's classifications or in relation to impaction of the mandibular ramus. However, MSX1 was expressed differently when account was taken of the depth of impaction in maxillary third molars (p = 0.029), but there was no difference in expression of RUNX2, BMP2, and MSX1 for the Pell and Gregory classification of depth of impaction (p > 0.05). We conclude that MSX1 is expressed differently depending on the depth of maxillary impaction phenotypes.
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Affiliation(s)
- B Olsson
- Department of Stomatology, Department of Oral and Maxillofacial Surgery, Federal University of Paraná, Av. Prefeito Lothário Meissner, 632, Jardim Botânico, Curitiba, PR, 80210-170, Brazil.
| | - R D Calixto
- Department of Stomatology, Department of Oral and Maxillofacial Surgery, Federal University of Paraná, Av. Prefeito Lothário Meissner, 632, Jardim Botânico, Curitiba, PR, 80210-170, Brazil.
| | - N C da Silva Machado
- Department of Stomatology, Department of Oral and Maxillofacial Surgery, Federal University of Paraná, Av. Prefeito Lothário Meissner, 632, Jardim Botânico, Curitiba, PR, 80210-170, Brazil.
| | - M N Meger
- School of Health Sciences, Department of Oral and Maxillofacial Surgery, Positivo University, Professor Pedro Viriato Parigot de Souza, 5300, Campo Comprido, Curitiba, Paraná, 81280330, Brazil.
| | - F W G Paula-Silva
- Department of Pediatric Dentistry, University of São Paulo, Av. do Café, Subsetor Oeste-11 (N-11), Ribeirão Preto, SP, 14040-904, Brazil.
| | - N L B Rebellato
- Department of Stomatology, Department of Oral and Maxillofacial Surgery, Federal University of Paraná, Av. Prefeito Lothário Meissner, 632, Jardim Botânico, Curitiba, PR, 80210-170, Brazil.
| | - D J da Costa
- Department of Stomatology, Department of Oral and Maxillofacial Surgery, Federal University of Paraná, Av. Prefeito Lothário Meissner, 632, Jardim Botânico, Curitiba, PR, 80210-170, Brazil.
| | - E C Küchler
- Department of Pediatric Dentistry, University of São Paulo, Av. do Café, Subsetor Oeste-11 (N-11), Ribeirão Preto, SP, 14040-904, Brazil.
| | - R Scariot
- Department of Stomatology, Department of Oral and Maxillofacial Surgery, Federal University of Paraná, Av. Prefeito Lothário Meissner, 632, Jardim Botânico, Curitiba, PR, 80210-170, Brazil; School of Health Sciences, Department of Oral and Maxillofacial Surgery, Positivo University, Professor Pedro Viriato Parigot de Souza, 5300, Campo Comprido, Curitiba, Paraná, 81280330, Brazil.
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20
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Mishra R, Jain V, Gupta D, Saxena R, Kulshreshtha S, Ramprasad VL, Verma IC, Dua Puri R. Robinow Syndrome and Brachydactyly: An Interplay of High-Throughput Sequencing and Deep Phenotyping in a Kindred. Mol Syndromol 2020; 11:43-49. [PMID: 32256301 DOI: 10.1159/000505506] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/25/2019] [Indexed: 12/26/2022] Open
Abstract
We report a family with a spectrum of short stature, craniofacial dysmorphism, and digital anomalies in a father and 2 daughters, with the youngest (proband) displaying a severe phenotype. Clinically, autosomal dominant Robinow syndrome (ADRS) was diagnosed. Whole-exome sequencing identified a heterozygous pathogenic BMP2 variant in the father and his daughters. The phenotype of short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies related to BMP2 haploinsufficiency has some facial and digital resemblance to ADRS. Although this variant segregated in the affected members, it failed to explain the severe phenotype of the proband. A reanalysis of the girl's raw data confirmed 2 disorders: a de novo likely pathogenic DVL1 variant implicated in ADRS and the familial BMP2 variant. A close interplay of high-throughput sequencing and deep phenotyping unraveled the complexities of the blended phenotype in the proband.
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Affiliation(s)
- Ranjana Mishra
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Vibha Jain
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Deepti Gupta
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Renu Saxena
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Samarth Kulshreshtha
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | | | - Ishwar C Verma
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Ratna Dua Puri
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
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21
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Middelkamp S, Vlaar JM, Giltay J, Korzelius J, Besselink N, Boymans S, Janssen R, de la Fonteijne L, van Binsbergen E, van Roosmalen MJ, Hochstenbach R, Giachino D, Talkowski ME, Kloosterman WP, Cuppen E. Prioritization of genes driving congenital phenotypes of patients with de novo genomic structural variants. Genome Med 2019; 11:79. [PMID: 31801603 PMCID: PMC6894143 DOI: 10.1186/s13073-019-0692-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 11/14/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Genomic structural variants (SVs) can affect many genes and regulatory elements. Therefore, the molecular mechanisms driving the phenotypes of patients carrying de novo SVs are frequently unknown. METHODS We applied a combination of systematic experimental and bioinformatic methods to improve the molecular diagnosis of 39 patients with multiple congenital abnormalities and/or intellectual disability harboring apparent de novo SVs, most with an inconclusive diagnosis after regular genetic testing. RESULTS In 7 of these cases (18%), whole-genome sequencing analysis revealed disease-relevant complexities of the SVs missed in routine microarray-based analyses. We developed a computational tool to predict the effects on genes directly affected by SVs and on genes indirectly affected likely due to the changes in chromatin organization and impact on regulatory mechanisms. By combining these functional predictions with extensive phenotype information, candidate driver genes were identified in 16/39 (41%) patients. In 8 cases, evidence was found for the involvement of multiple candidate drivers contributing to different parts of the phenotypes. Subsequently, we applied this computational method to two cohorts containing a total of 379 patients with previously detected and classified de novo SVs and identified candidate driver genes in 189 cases (50%), including 40 cases whose SVs were previously not classified as pathogenic. Pathogenic position effects were predicted in 28% of all studied cases with balanced SVs and in 11% of the cases with copy number variants. CONCLUSIONS These results demonstrate an integrated computational and experimental approach to predict driver genes based on analyses of WGS data with phenotype association and chromatin organization datasets. These analyses nominate new pathogenic loci and have strong potential to improve the molecular diagnosis of patients with de novo SVs.
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Affiliation(s)
- Sjors Middelkamp
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, 3584 CX, Utrecht, the Netherlands
| | - Judith M Vlaar
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, 3584 CX, Utrecht, the Netherlands
| | - Jacques Giltay
- Department of Genetics, University Medical Center Utrecht, 3584 EA, Utrecht, the Netherlands
| | - Jerome Korzelius
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, 3584 CX, Utrecht, the Netherlands
- Max Planck Institute for Biology of Aging, Cologne, Germany
| | - Nicolle Besselink
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, 3584 CX, Utrecht, the Netherlands
| | - Sander Boymans
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, 3584 CX, Utrecht, the Netherlands
| | - Roel Janssen
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, 3584 CX, Utrecht, the Netherlands
| | - Lisanne de la Fonteijne
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, 3584 CX, Utrecht, the Netherlands
| | - Ellen van Binsbergen
- Department of Genetics, University Medical Center Utrecht, 3584 EA, Utrecht, the Netherlands
| | - Markus J van Roosmalen
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, 3584 CX, Utrecht, the Netherlands
| | - Ron Hochstenbach
- Department of Genetics, University Medical Center Utrecht, 3584 EA, Utrecht, the Netherlands
| | - Daniela Giachino
- Medical Genetics Unit, Department of Clinical and Biological Sciences, University of Torino, 10043, Orbassano, Italy
| | - Michael E Talkowski
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Wigard P Kloosterman
- Department of Genetics, University Medical Center Utrecht, 3584 EA, Utrecht, the Netherlands
| | - Edwin Cuppen
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, 3584 CX, Utrecht, the Netherlands.
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22
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Wang Z, Song HM, Wang F, Zhao CM, Huang RT, Xue S, Li RG, Qiu XB, Xu YJ, Liu XY, Yang YQ. A New ISL1 Loss-of-Function Mutation Predisposes to Congenital Double Outlet Right Ventricle. Int Heart J 2019; 60:1113-1122. [DOI: 10.1536/ihj.18-685] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Zhi Wang
- Department of Pediatrics, Tongji Hospital, Tongji University School of Medicine
| | - Hao-Ming Song
- Department of Cardiology, Tongji Hospital, Tongji University School of Medicine
| | - Fei Wang
- Department of Neurosurgery, Tongji Hospital, Tongji University School of Medicine
| | - Cui-Mei Zhao
- Department of Cardiology, Tongji Hospital, Tongji University School of Medicine
| | - Ri-Tai Huang
- Department of Cardiovascular Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University
| | - Song Xue
- Department of Cardiovascular Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University
| | - Ruo-Gu Li
- Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiao Tong University
| | - Xing-Biao Qiu
- Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiao Tong University
| | - Ying-Jia Xu
- Department of Cardiology, The Fifth People's Hospital of Shanghai, Fudan University
| | - Xing-Yuan Liu
- Department of Pediatrics, Tongji Hospital, Tongji University School of Medicine
| | - Yi-Qing Yang
- Department of Cardiology, The Fifth People's Hospital of Shanghai, Fudan University
- Department of Cardiovascular Research Laboratory, The Fifth People's Hospital of Shanghai, Fudan University
- Department of Central Laboratory, The Fifth People's Hospital of Shanghai, Fudan University
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23
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Simsek-Kiper PO, Taskiran E, Kosukcu C, Arslan UE, Cormier-Daire V, Gonc N, Ozon A, Alikasifoglu A, Kandemir N, Utine GE, Alanay Y, Alikasifoglu M, Boduroglu K. Further expanding the mutational spectrum and investigation of genotype-phenotype correlation in 3M syndrome. Am J Med Genet A 2019; 179:1157-1172. [PMID: 30980518 DOI: 10.1002/ajmg.a.61154] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 03/10/2019] [Accepted: 03/31/2019] [Indexed: 12/14/2022]
Abstract
3M syndrome is characterized by severe pre- and postnatal growth retardation, typical facial features, and normal intelligence. Homozygous or compound heterozygous mutations in either CUL7, OBSL1, or CCDC8 have been identified in the etiology so far. Clinical and molecular features of 24 patients (23 patients and a fetus) from 19 unrelated families with a clinical diagnosis of 3M syndrome were evaluated and genotype-phenotype correlations were investigated with the use of DNA sequencing, chromosomal microarray, and whole exome sequencing accordingly. A genetic etiology could be established in 20 patients (n = 20/24, 83%). Eleven distinct CUL7 or OBSL1 mutations, among which eight was novel, were identified in 18 patients (n = 18/24, 75%). Ten patients had CUL7 (n = 10/18, 56%) while eight had OBSL1 (n = 8/18, 44%) mutations. Birth weight and height standard deviation scores at admission were significantly (p < 0.05) lower in patients with CUL7 mutation compared to that of patients with OBSL1 mutation. Two patients with a similar phenotype had a de novo 20p13p deletion involving BMP2. No genetic etiology could be established in four patients (n = 4/28, 17%). This study yet represents the largest cohort of 3M syndrome patients from a single center in Turkey. Microdeletions involving BMP2 may cause a phenotype similar to 3M syndrome with some distinctive features. Larger cohort of patients are required to establish genotype-phenotype correlations in 3M syndrome.
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Affiliation(s)
| | - Ekim Taskiran
- Department of Medical Genetics, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Can Kosukcu
- Department of Medical Genetics, Hacettepe University Faculty of Medicine, Ankara, Turkey.,Department of Bioinformatics, Hacettepe University Institute of Health Sciences, Ankara, Turkey
| | - Umut Ece Arslan
- Department of Health Research, Institute of Public Health, Hacettepe University, Ankara, Turkey
| | - Valérie Cormier-Daire
- Department of Genetics, INSERM UMR 1163, Université Paris Descartes-Sorbonne Paris Cité, Institut Imagine, AP-HP, Hôpital Necker Enfants Malades, Paris, France
| | - Nazlı Gonc
- Department of Pediatric Endocrinology, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Alev Ozon
- Department of Pediatric Endocrinology, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Ayfer Alikasifoglu
- Department of Pediatric Endocrinology, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Nurgun Kandemir
- Department of Pediatric Endocrinology, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Gulen Eda Utine
- Department of Pediatric Genetics, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Yasemin Alanay
- Department of Pediatric Genetics, Hacettepe University Faculty of Medicine, Ankara, Turkey.,Department of Pediatric Genetics, Acibadem University Faculty of Medicine, Istanbul, Turkey
| | - Mehmet Alikasifoglu
- Department of Pediatric Genetics, Hacettepe University Faculty of Medicine, Ankara, Turkey.,Department of Medical Genetics, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Koray Boduroglu
- Department of Pediatric Genetics, Hacettepe University Faculty of Medicine, Ankara, Turkey.,Department of Medical Genetics, Hacettepe University Faculty of Medicine, Ankara, Turkey
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24
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王 皓, 刘 洋, 刘 浩, 韩 冬, 冯 海. [Detection and functional analysis of BMP2 gene mutation in patients with tooth agenesis]. BEIJING DA XUE XUE BAO. YI XUE BAN = JOURNAL OF PEKING UNIVERSITY. HEALTH SCIENCES 2019; 51:9-15. [PMID: 30773537 PMCID: PMC7433555 DOI: 10.19723/j.issn.1671-167x.2019.01.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Indexed: 11/20/2022]
Abstract
OBJECTIVE To screen for BMP2 mutation with functional impact in patients with congenital tooth agenesis and to make oral and skeletal phenotype record and functional analysis with in vitro experiments. METHODS We enrolled eighteen patients with congenital tooth agenesis. The medical and dental history was collected,and clinical and dental examinations including the X-ray examination of oral-facial and skeletal bone were performed for the phenotypic analysis. Blood samples were collected to extract DNA and whole exome sequencing was conducted. The genes involved in oral-facial development and congenital skeletal diseases were investigated for mutation screening. The mutations with functional impact were then investigated. In one patient, the BMP2 mutation with putative functional impact was selected for functional analysis. Wild type and mutant BMP2 plasmids with green fluorescent protein (GFP) tag were constructed and transfected into HEK293T cells. Subcellular protein distribution was observed under laser scanning confocal microscope. The activation of downstream SMAD1/5/9 phosphorylation by BMP2 was detected by Western blotting to investigate the functional impact and genetic pathogenicity. RESULTS BMP2 mutation NM_001200.3:c.393A>T (p.Arg131Ser), rs140417301 was detected in one patient with congenital tooth agenesis, while for other genes involved in oral-facial development and congenital skeletal diseases, no functionally significant mutation was found. The proband's parents didn't carry this mutation. The father had normal dentition, while the mother lacked one premolar, and both the parents showed normal palate and maxilla. The patient also had maxillary hypoplasia in both sagittal and coronal planes, palatal dysmorphology, and malocclusion, and was diagonsed with osteopenia after the X-ray examnination of his skeletal bone. Functional analysis showed this mutation had normal subcelluar localization but reduced phosphorylation of SMAD1/5/9 (reduction by 32%, 22%, and 27% in three independent replicates). Taken together with family co-segregation, this mutaion was considered as "likely pathogenic". CONCLUSION BMP2 mutation c.393A>T (p. Arg131Ser) affects bone morphogenetic protein signaling activity, and may affect the number of teeth, growth of maxilla and palate, and bone mineral density.
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Affiliation(s)
- 皓 王
- />北京大学口腔医学院·口腔医院,修复科 国家口腔疾病临床研究中心 口腔数字化医疗技术和材料国家工程实验室 口腔数字医学北京市重点实验室,北京 100081Department of Prosthodontics, Peking University School and Hospital of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Laboratory for Digital and Material Technology of Stomatology & Beijing Key Laboratory of Digital Stomatology, Beijing 100081, China
| | - 洋 刘
- />北京大学口腔医学院·口腔医院,修复科 国家口腔疾病临床研究中心 口腔数字化医疗技术和材料国家工程实验室 口腔数字医学北京市重点实验室,北京 100081Department of Prosthodontics, Peking University School and Hospital of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Laboratory for Digital and Material Technology of Stomatology & Beijing Key Laboratory of Digital Stomatology, Beijing 100081, China
| | - 浩辰 刘
- />北京大学口腔医学院·口腔医院,修复科 国家口腔疾病临床研究中心 口腔数字化医疗技术和材料国家工程实验室 口腔数字医学北京市重点实验室,北京 100081Department of Prosthodontics, Peking University School and Hospital of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Laboratory for Digital and Material Technology of Stomatology & Beijing Key Laboratory of Digital Stomatology, Beijing 100081, China
| | - 冬 韩
- />北京大学口腔医学院·口腔医院,修复科 国家口腔疾病临床研究中心 口腔数字化医疗技术和材料国家工程实验室 口腔数字医学北京市重点实验室,北京 100081Department of Prosthodontics, Peking University School and Hospital of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Laboratory for Digital and Material Technology of Stomatology & Beijing Key Laboratory of Digital Stomatology, Beijing 100081, China
| | - 海兰 冯
- />北京大学口腔医学院·口腔医院,修复科 国家口腔疾病临床研究中心 口腔数字化医疗技术和材料国家工程实验室 口腔数字医学北京市重点实验室,北京 100081Department of Prosthodontics, Peking University School and Hospital of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Laboratory for Digital and Material Technology of Stomatology & Beijing Key Laboratory of Digital Stomatology, Beijing 100081, China
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Salazar VS, Capelo LP, Cantù C, Zimmerli D, Gosalia N, Pregizer S, Cox K, Ohte S, Feigenson M, Gamer L, Nyman JS, Carey DJ, Economides A, Basler K, Rosen V. Reactivation of a developmental Bmp2 signaling center is required for therapeutic control of the murine periosteal niche. eLife 2019; 8:42386. [PMID: 30735122 PMCID: PMC6386520 DOI: 10.7554/elife.42386] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 02/06/2019] [Indexed: 12/21/2022] Open
Abstract
Two decades after signals controlling bone length were discovered, the endogenous ligands determining bone width remain unknown. We show that postnatal establishment of normal bone width in mice, as mediated by bone-forming activity of the periosteum, requires BMP signaling at the innermost layer of the periosteal niche. This developmental signaling center becomes quiescent during adult life. Its reactivation however, is necessary for periosteal growth, enhanced bone strength, and accelerated fracture repair in response to bone-anabolic therapies used in clinical orthopedic settings. Although many BMPs are expressed in bone, periosteal BMP signaling and bone formation require only Bmp2 in the Prx1-Cre lineage. Mechanistically, BMP2 functions downstream of Lrp5/6 pathway to activate a conserved regulatory element upstream of Sp7 via recruitment of Smad1 and Grhl3. Consistent with our findings, human variants of BMP2 and GRHL3 are associated with increased risk of fractures.
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Affiliation(s)
- Valerie S Salazar
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, United States.,Institute for Molecular Life Sciences, University of Zürich, Zürich, Switzerland
| | - Luciane P Capelo
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, United States.,Instituto de Ciência e Tecnologia, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Claudio Cantù
- Institute for Molecular Life Sciences, University of Zürich, Zürich, Switzerland.,Wallenberg Centre for Molecular Medicine, Department of Clinical and Experimental Medicine (IKE), Faculty of Health Sciences, Linköping University, Linköping, Sweden
| | - Dario Zimmerli
- Institute for Molecular Life Sciences, University of Zürich, Zürich, Switzerland
| | | | - Steven Pregizer
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, United States
| | - Karen Cox
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, United States
| | - Satoshi Ohte
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, United States.,Department of Microbial Chemistry, Graduate School of Pharmaceutical Sciences, Kitasato University, Tokyo, Japan
| | - Marina Feigenson
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, United States
| | - Laura Gamer
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, United States
| | - Jeffry S Nyman
- Department of Orthopaedic Surgery and Rehabilitation, Vanderbilt University Medical Center, Nashville, United States
| | | | | | | | - Vicki Rosen
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, United States
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26
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Xie H, Hong N, Zhang E, Li F, Sun K, Yu Y. Identification of Rare Copy Number Variants Associated With Pulmonary Atresia With Ventricular Septal Defect. Front Genet 2019; 10:15. [PMID: 30745907 PMCID: PMC6360179 DOI: 10.3389/fgene.2019.00015] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 01/14/2019] [Indexed: 11/13/2022] Open
Abstract
Copy number variants (CNVs) are major variations contributing to the gene heterogeneity of congenital heart diseases (CHD). pulmonary atresia with ventricular septal defect (PA-VSD) is a rare form of cyanotic CHD characterized by complex manifestations and the genetic determinants underlying PA-VSD are still largely unknown. We investigated rare CNVs in a recruited cohort of 100 unrelated patients with PA-VSD, PA-IVS, or TOF and a population-matched control cohort of 100 healthy children using whole-exome sequencing. Comparing rare CNVs in PA-VSD cases and that in PA-IVS or TOF positive controls, we observed twenty-two rare CNVs only in PA-VSD, five rare CNVs only in PA-VSD and TOF as well as thirteen rare CNVs only in PA-VSD and PA-IVS. Six of these CNVs were considered pathogenic or potentially pathogenic to PA-VSD: 16p11.2 del (PPP4C and TBX6), 5q35.3 del (FLT4), 5p13.1 del (RICTOR), 6p21.33 dup (TNXB), 7p15.2 del (HNRNPA2B1), and 19p13.3 dup (FGF22). The gene networks showed that four putative candidate genes for PA-VSD, PPP4C, FLT4, RICTOR, and FGF22 had strong interaction with well-known cardiac genes relevant to heart or blood vessel development. Meanwhile, the analysis of transcriptome array revealed that PPP4C and RICTOR were also significantly expressed in human embryonic heart. In conclusion, three rare novel CNVs were identified only in PA-VSD: 16p11.2 del (PPP4C), 5q35.3 del (FLT4) and 5p13.1 del (RICTOR), implicating novel candidate genes of interest for PA-VSD. Our study provided new insights into understanding for the pathogenesis of PA-VSD and helped elucidate critical genes for PA-VSD.
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Affiliation(s)
- Huilin Xie
- Department of Pediatric Cardiology, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Nanchao Hong
- Department of Pediatric Cardiology, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Erge Zhang
- Department of Pediatric Cardiology, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Fen Li
- Department of Pediatric Cardiology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Kun Sun
- Department of Pediatric Cardiology, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yu Yu
- Department of Pediatric Cardiology, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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27
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Ma L, Wang J, Li L, Qiao Q, Di RM, Li XM, Xu YJ, Zhang M, Li RG, Qiu XB, Li X, Yang YQ. ISL1 loss-of-function mutation contributes to congenital heart defects. Heart Vessels 2018; 34:658-668. [PMID: 30390123 DOI: 10.1007/s00380-018-1289-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Accepted: 10/26/2018] [Indexed: 02/08/2023]
Abstract
Congenital heart defect (CHD) is the most common form of birth deformity and is responsible for substantial morbidity and mortality in humans. Increasing evidence has convincingly demonstrated that genetic defects play a pivotal role in the pathogenesis of CHD. However, CHD is a genetically heterogeneous disorder and the genetic basis underpinning CHD in the vast majority of cases remains elusive. This study was sought to identify the pathogenic mutation in the ISL1 gene contributing to CHD. A cohort of 210 unrelated patients with CHD and a total of 256 unrelated healthy individuals used as controls were registered. The coding exons and splicing boundaries of ISL1 were sequenced in all study subjects. The functional effect of an identified ISL1 mutation was evaluated using a dual-luciferase reporter assay system. A novel heterozygous ISL1 mutation, c.409G > T or p.E137X, was identified in an index patient with congenital patent ductus arteriosus and ventricular septal defect. Analysis of the proband's pedigree revealed that the mutation co-segregated with CHD, which was transmitted in the family in an autosomal dominant pattern with complete penetrance. The nonsense mutation was absent in 512 control chromosomes. Functional analysis unveiled that the mutant ISL1 protein failed to transactivate the promoter of MEF2C, alone or in synergy with TBX20. This study firstly implicates ISL1 loss-of-function mutation with CHD in humans, which provides novel insight into the molecular mechanism of CHD, implying potential implications for genetic counseling and individually tailored treatment of CHD patients.
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Affiliation(s)
- Lan Ma
- Department of Cardiology, The First Affiliated Hospital of Soochow University, Suzhou, 215006, Jiangsu, China.,Department of Ultrasound, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Juan Wang
- Department of Cardiovascular Medicine, East Hospital, Tongji University School of Medicine, Shanghai, 200120, China
| | - Li Li
- Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital, Tongji University School of Medicine, Shanghai, 200120, China
| | - Qi Qiao
- Department of Cardiology, The Fifth People's Hospital of Shanghai, Fudan University, Shanghai, 200240, China
| | - Ruo-Min Di
- Department of Cardiology, The Fifth People's Hospital of Shanghai, Fudan University, Shanghai, 200240, China
| | - Xiu-Mei Li
- Department of Cardiology, The Fifth People's Hospital of Shanghai, Fudan University, Shanghai, 200240, China
| | - Ying-Jia Xu
- Department of Cardiology, The Fifth People's Hospital of Shanghai, Fudan University, Shanghai, 200240, China
| | - Min Zhang
- Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Ruo-Gu Li
- Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Xing-Biao Qiu
- Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Xun Li
- Department of Cardiology, The First Affiliated Hospital of Soochow University, Suzhou, 215006, Jiangsu, China.
| | - Yi-Qing Yang
- Department of Cardiology, The Fifth People's Hospital of Shanghai, Fudan University, Shanghai, 200240, China. .,Department of Cardiovascular Research Laboratory, The Fifth People's Hospital of Shanghai, Fudan University, Shanghai, 200240, China. .,Department of Central Laboratory, The Fifth People's Hospital of Shanghai, Fudan University, Shanghai, 200240, China.
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Abstract
PURPOSE OF REVIEW Genome-wide approaches including genome-wide association studies as well as exome and genome sequencing represent powerful new approaches that have improved our ability to identify genetic causes of human disorders. The purpose of this review is to describe recent advances in the genetic causes of short stature. RECENT FINDINGS In addition to SHOX deficiency which is one of the most common causes of isolated short stature, PAPPA2, ACAN, NPPC, NPR2, PTPN11 (and other rasopathies), FBN1, IHH and BMP2 have been identified in isolated growth disorders with or without other mild skeletal findings. In addition, novel genetic causes of syndromic short stature have been discovered, including pathogenic variants in BRCA1, DONSON, AMMECR1, NFIX, SLC25A24, and FN1. SUMMARY Isolated growth disorders are often monogenic. Specific genetic causes typically have specific biochemical and/or phenotype characteristics which are diagnostically helpful. Identification of additional subjects with a specific genetic cause of short stature often leads to a broadening of the known clinical spectrum for that condition. The identification of novel genetic causes of short stature has provided important insights into the underlying molecular mechanisms of growth failure.
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