1
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Duan R, Hijazi H, Gulec EY, Eker HK, Costa SR, Sahin Y, Ocak Z, Isikay S, Ozalp O, Bozdogan S, Aslan H, Elcioglu N, Bertola DR, Gezdirici A, Du H, Fatih JM, Grochowski CM, Akay G, Jhangiani SN, Karaca E, Gu S, Coban-Akdemir Z, Posey JE, Bayram Y, Sutton VR, Carvalho CM, Pehlivan D, Gibbs RA, Lupski JR. Developmental genomics of limb malformations: Allelic series in association with gene dosage effects contribute to the clinical variability. HGG ADVANCES 2022; 3:100132. [PMID: 36035248 PMCID: PMC9403727 DOI: 10.1016/j.xhgg.2022.100132] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 07/19/2022] [Indexed: 11/26/2022] Open
Abstract
Genetic heterogeneity, reduced penetrance, and variable expressivity, the latter including asymmetric body axis plane presentations, have all been described in families with congenital limb malformations (CLMs). Interfamilial and intrafamilial heterogeneity highlight the complexity of the underlying genetic pathogenesis of these developmental anomalies. Family-based genomics by exome sequencing (ES) and rare variant analyses combined with whole-genome array-based comparative genomic hybridization were implemented to investigate 18 families with limb birth defects. Eleven of 18 (61%) families revealed explanatory variants, including 7 single-nucleotide variant alleles and 3 copy number variants (CNVs), at previously reported "disease trait associated loci": BHLHA9, GLI3, HOXD cluster, HOXD13, NPR2, and WNT10B. Breakpoint junction analyses for all three CNV alleles revealed mutational signatures consistent with microhomology-mediated break-induced replication, a mechanism facilitated by Alu/Alu-mediated rearrangement. Homozygous duplication of BHLHA9 was observed in one Turkish kindred and represents a novel contributory genetic mechanism to Gollop-Wolfgang Complex (MIM: 228250), where triplication of the locus has been reported in one family from Japan (i.e., 4n = 2n + 2n versus 4n = 3n + 1n allelic configurations). Genes acting on limb patterning are sensitive to a gene dosage effect and are often associated with an allelic series. We extend an allele-specific gene dosage model to potentially assist, in an adjuvant way, interpretations of interconnections among an allelic series, clinical severity, and reduced penetrance of the BHLHA9-related CLM spectrum.
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Affiliation(s)
- Ruizhi Duan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Hadia Hijazi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Elif Yilmaz Gulec
- Department of Medical Genetics, School of Medicine, Istanbul Medeniyet University, Istanbul, Turkey
| | | | - Silvia R. Costa
- Human Genome and Stem Cell Research Center, Institute of Bioscience, Universidade de São Paulo, São Paulo, Brazil
| | - Yavuz Sahin
- Medical Genetics, Genoks Genetics Center, Ankara, Turkey
| | - Zeynep Ocak
- Department of Medical Genetics, Faculty of Medicine, Istinye University, Istanbul, Turkey
| | - Sedat Isikay
- Department of Pediatric Neurology, Faculty of Medicine, Gaziantep University, Gaziantep, Turkey
| | - Ozge Ozalp
- Department of Medical Genetics, Adana City Training and Research Hospital, Adana, Turkey
| | - Sevcan Bozdogan
- Department of Medical Genetics, Faculty of Medicine, Cukurova University, Adana, Turkey
| | - Huseyin Aslan
- Department of Medical Genetics, Adana City Training and Research Hospital, Adana, Turkey
| | - Nursel Elcioglu
- Department of Pediatric Genetics, School of Medicine, Marmara University, Istanbul, Turkey
- Eastern Mediterranean University Medical School, Magosa, 10 Mersin, Turkey
| | - Débora R. Bertola
- Human Genome and Stem Cell Research Center, Institute of Bioscience, Universidade de São Paulo, São Paulo, Brazil
- Genetics Unit, Instituto da Criança do Hospital das Clínicas da Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Alper Gezdirici
- Department of Medical Genetics, Basaksehir Cam and Sakura City Hospital, Istanbul, Turkey
| | - Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jawid M. Fatih
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | - Gulsen Akay
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Baylor-Hopkins Center for Mendelian Genomics
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Medical Genetics, School of Medicine, Istanbul Medeniyet University, Istanbul, Turkey
- Department of Medical Genetics, Konya City Hospital, Konya, Turkey
- Human Genome and Stem Cell Research Center, Institute of Bioscience, Universidade de São Paulo, São Paulo, Brazil
- Medical Genetics, Genoks Genetics Center, Ankara, Turkey
- Department of Medical Genetics, Faculty of Medicine, Istinye University, Istanbul, Turkey
- Department of Pediatric Neurology, Faculty of Medicine, Gaziantep University, Gaziantep, Turkey
- Department of Medical Genetics, Adana City Training and Research Hospital, Adana, Turkey
- Department of Medical Genetics, Faculty of Medicine, Cukurova University, Adana, Turkey
- Department of Pediatric Genetics, School of Medicine, Marmara University, Istanbul, Turkey
- Eastern Mediterranean University Medical School, Magosa, 10 Mersin, Turkey
- Genetics Unit, Instituto da Criança do Hospital das Clínicas da Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
- Department of Medical Genetics, Basaksehir Cam and Sakura City Hospital, Istanbul, Turkey
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | | | - Ender Karaca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Shen Gu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jennifer E. Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Yavuz Bayram
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - V. Reid Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
| | - Claudia M.B. Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX, USA
| | - Richard A. Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - James R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
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2
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Zhu M, Wang Y, Guan L, Lu C, Sun R, Chen Y, Shi J, Zhu Y, Wang D. A novel chromosome 2q24.3-q32.1 microdeletion in a fetus with multiple malformations. J Clin Lab Anal 2022; 36:e24602. [PMID: 35819063 PMCID: PMC9396185 DOI: 10.1002/jcla.24602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 06/28/2022] [Accepted: 06/29/2022] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Terminal or interstitial deletion of chromosome 2q is rarely reported but clinically significant, which can result in developmental malformations and psychomotor retardation in humans. In the present study, we analyzed this deletion to comprehensively clarify the relationship between phenotype and microdeletion region. METHODS We collected clinical records of the fetus and summarized patient symptoms. Subsequently, genomic DNA was extracted from fetal tissue or peripheral blood collected from parents. In addition, whole-exome sequencing (WES) and copy number variation sequencing (CNV-seq) were performed. RESULTS The fetus presented a previously unreported interstitial deletion of 2q24.3-q32.1. WES and CNV-seq revealed a de novo 18.46 Mb deletion at 2q24.3-q32.1, a region involving 94 protein-coding genes, including HOXD13, MAP3K20, DLX1, DLX2, SCN2A, and SCN1A. The fetus had upper and lower limb malformations, including camptodactyly and syndactyly, along with congenital cardiac defects. CONCLUSION Herein, we report a fetus with a novel microdeletion of chromosome 2q24.3-q32.1, likely a heterozygous pathogenic variant. Haploinsufficiency of HOXD13 might be related to limb deformity in the fetus.
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Affiliation(s)
- Mianmian Zhu
- Department of Pediatrics, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yihong Wang
- Department of Pediatrics, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Lijie Guan
- Department of Ultrasound imaging, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Chaosheng Lu
- Department of Pediatrics, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Rongyue Sun
- Department of Pediatrics, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yuan Chen
- Department of Pediatrics, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Jiamin Shi
- Department of Pediatrics, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yanying Zhu
- Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Dan Wang
- Department of Pediatrics, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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3
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Zaib T, Rashid H, Khan H, Zhou X, Sun P. Recent Advances in Syndactyly: Basis, Current Status and Future Perspectives. Genes (Basel) 2022; 13:771. [PMID: 35627156 PMCID: PMC9141913 DOI: 10.3390/genes13050771] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/21/2022] [Accepted: 04/22/2022] [Indexed: 02/05/2023] Open
Abstract
A comprehensive summary of recent knowledge in syndactyly (SD) is important for understanding the genetic etiology of SD and disease management. Thus, this review article provides background information on SD, as well as insights into phenotypic and genetic heterogeneity, newly identified gene mutations in various SD types, the role of HOXD13 in limb deformities, and recently introduced modern surgical techniques for SD. This article also proposes a procedure for genetic analysis to obtain a clearer genotype-phenotype correlation for SD in the future. We briefly describe the classification of non-syndromic SD based on variable phenotypes to explain different phenotypic features and mutations in the various genes responsible for the pathogenesis of different types of SD. We describe how different types of mutation in HOXD13 cause various types of SD, and how a mutation in HOXD13 could affect its interaction with other genes, which may be one of the reasons behind the differential phenotypes and incomplete penetrance. Furthermore, we also discuss some recently introduced modern surgical techniques, such as free skin grafting, improved flap techniques, and dermal fat grafting in combination with the Z-method incision, which have been successfully practiced clinically with no post-operative complications.
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Affiliation(s)
- Tahir Zaib
- Stem Cell Research Center, Shantou University Medical College, Shantou 515041, China
- (T.Z.)
- (X.Z.)
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou 515041, China
| | - Hibba Rashid
- Department of Biotechnology and Microbiology, Abasyn University, Peshawar 25000, Pakistan
| | - Hanif Khan
- Department of Pharmacology, Shantou University Medical College, Shantou 515041, China
| | - Xiaoling Zhou
- Stem Cell Research Center, Shantou University Medical College, Shantou 515041, China
- (T.Z.)
- (X.Z.)
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou 515041, China
| | - Pingnan Sun
- Stem Cell Research Center, Shantou University Medical College, Shantou 515041, China
- (T.Z.)
- (X.Z.)
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou 515041, China
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4
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Starosta RT, Granadillo JL, Patel KR, Finegold MJ, Stoll J, Kulkarni S. Intrahepatic Cholestasis, Refractory Epilepsy, Skeletal Dysplasia, Endocrine Failure, and Dysmorphic Features in a Child With a Monoallelic 2q24-32.2 Deletion Encompassing ABCB11. Pediatr Dev Pathol 2022; 25:174-179. [PMID: 34428094 DOI: 10.1177/10935266211036084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
We report a newborn who presented with multiple limb and facial anomalies, endocrine disorders, and progressively worsening low-GGT cholestasis. A liver biopsy revealed hepatocellular cholestasis with giant cell transformation. Immunohistochemical staining revealed complete absence of BSEP protein compared to control liver. A large 2q24-32.2 deletion leading to loss of 78 OMIM genes. Multiple structural anomalies, epilepsy and endocrine anomalies have been described with hemizygous loss of these genes. This deletion also resulted in complete heterozygous deletion of ABCB11, which encodes the bile salt export pump (BSEP). Genetic analysis did not reveal any pathogenic variants, deletions, or duplications in the other ABCB11 allele. A heterozygous variant in NR1H4, which causes the autosomal recessive progressive familial intrahepatic cholestasis type 5, was also detected. The possible explanations for the PFIC type 2 phenotype in heterozygous loss of ABCB11 include genetic modifiers or di-genic disease with a compound ABCB11 deletion and an NR1H4 missense variant; or undetected pathogenic variants in the other ABCB11 or NR1H4 alleles.
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Affiliation(s)
- Rodrigo Tzovenos Starosta
- Division of Genetics and Genomic Medicine, Department of Pediatrics, 7548Washington University in Saint Louis, Saint Louis Children's Hospital, Washington University in Saint Louis, Saint Louis, Missouri.,Department of Pediatrics, 7548Washington University in Saint Louis, Washington University in Saint Louis, St. Louis Children's Hospital, Saint Louis, Missouri
| | - Jorge Luis Granadillo
- Division of Genetics and Genomic Medicine, Department of Pediatrics, 7548Washington University in Saint Louis, Saint Louis Children's Hospital, Washington University in Saint Louis, Saint Louis, Missouri
| | - Kalyani R Patel
- Department of Pathology and Immunology, Texas Children's Hospital, Houston, Texas
| | | | - Janis Stoll
- Department of Pediatrics, 7548Washington University in Saint Louis, Washington University in Saint Louis, St. Louis Children's Hospital, Saint Louis, Missouri
| | - Sakil Kulkarni
- Department of Pediatrics, 7548Washington University in Saint Louis, Washington University in Saint Louis, St. Louis Children's Hospital, Saint Louis, Missouri
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5
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Xie G, Peng Z, Liang J, Larabee SM, Drachenberg CB, Yfantis H, Raufman JP. Zinc finger protein 277 is an intestinal transit-amplifying cell marker and colon cancer oncogene. JCI Insight 2022; 7:150894. [PMID: 35015732 PMCID: PMC8876557 DOI: 10.1172/jci.insight.150894] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 01/05/2022] [Indexed: 01/10/2023] Open
Abstract
Sustained proliferative signaling and resisting cell death are hallmarks of cancer. Zinc finger protein 277 (ZNF277; murine Zfp277), a transcription factor regulating cellular senescence, is overexpressed in colon cancer, but its actions in intestinal homeostasis and neoplasia are unclear. Using human and murine intestine, human colon cancer cells, and ApcMin/+ mice with dysregulated β-catenin signaling and exuberant intestinal neoplasia, we explored the actions of ZNF277/Zfp277 and defined the underlying mechanisms. In normal human and murine intestine, ZNF277/Zfp277 was expressed uniquely in early stem cell progenitors, undifferentiated transit-amplifying cells (TACs). Zfp277 was overexpressed in the ApcMin/+ mouse colon, implicating ZNF277/Zfp277 as a transcriptional target of β-catenin signaling. We confirmed this by showing β-catenin knockdown reduced ZNF277 expression and, using chromatin IP, identified 2 β-catenin binding sites in the ZNF277 promoter. Zfp277 deficiency attenuated intestinal epithelial cell proliferation and tumor formation, and it strikingly prolonged ApcMin/+ mouse survival. RNA-Seq and PCR analyses revealed that Zfp277 modulates expression of genes in key cancer pathways, including β-catenin signaling, the HOXD family that regulates development, and p21WAF1, a cell cycle inhibitor and tumor suppressor. In both human colon cancer cells and the murine colon, ZNF277/Zfp277 deficiency induced p21WAF1 expression and promoted senescence. Our findings identify ZNF277/Zfp277 as both a TAC marker and colon cancer oncogene that regulates cellular proliferation and senescence, in part by repressing p21WAF1 expression.
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Affiliation(s)
- Guofeng Xie
- University of Maryland School of Medicine, Baltimore, United States of America
| | - Zhongsheng Peng
- Department of Medicine, University of Maryland School of Medicine, Baltimore, United States of America
| | - Jinqing Liang
- Department of Medicine, University of Maryland School of Medicine, Baltimore, United States of America
| | - Shannon M Larabee
- Department of Surgery, University of Maryland School of Medicine, Baltimore, United States of America
| | - Cinthia B Drachenberg
- Department of Pathology, University of Maryland School of Medicine, Baltimore, United States of America
| | - Harris Yfantis
- Department of Pathology and Laboratory Medicine, Baltimore Veterans Affairs Medical Center, Baltimore, United States of America
| | - Jean-Pierre Raufman
- Department of Medicine, University of Maryland School of Medicine, Baltimore, United States of America
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6
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Melas M, Kautto EA, Franklin SJ, Mori M, McBride KL, Mosher TM, Pfau RB, Hernandez-Gonzalez ME, McGrath SD, Magrini VJ, White P, Samora JB, Koboldt DC, Wilson RK. Long-read whole genome sequencing reveals HOXD13 alterations in synpolydactyly. Hum Mutat 2021; 43:189-199. [PMID: 34859533 DOI: 10.1002/humu.24304] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 09/24/2021] [Accepted: 11/20/2021] [Indexed: 12/11/2022]
Abstract
Synpolydactyly 1, also called syndactyly type II (SDTY2), is a genetic limb malformation characterized by polydactyly with syndactyly involving the webbing of the third and fourth fingers, and the fourth and fifth toes. It is caused by heterozygous alterations in HOXD13 with incomplete penetrance and phenotypic variability. In our study, a five-generation family with an SPD phenotype was enrolled in our Rare Disease Genomics Protocol. A comprehensive examination of three generations using Illumina short-read whole-genome sequencing (WGS) did not identify any causative variants. Subsequent WGS using Pacific Biosciences (PacBio) long-read HiFi Circular Consensus Sequencing (CCS) revealed a heterozygous 27-bp duplication in the polyalanine tract of HOXD13. Sanger sequencing of all available family members confirmed that the variant segregates with affected individuals. Reanalysis of an unrelated family with a similar SPD phenotype uncovered a 21-bp (7-alanine) duplication in the same region of HOXD13. Although ExpansionHunter identified these events in most individuals in a retrospective analysis, low sequence coverage due to high GC content in the HOXD13 polyalanine tract makes detection of these events challenging. Our findings highlight the value of long-read WGS in elucidating the molecular etiology of congenital limb malformation disorders.
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Affiliation(s)
- Marilena Melas
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Esko A Kautto
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Samuel J Franklin
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Mari Mori
- Division of Genetic and Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Kim L McBride
- Division of Genetic and Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA.,Center for Cardiovascular Research, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Theresa Mihalic Mosher
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA.,Division of Genetic and Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Ruthann B Pfau
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA.,Department of Pathology, The Ohio State University, Columbus, Ohio, USA
| | | | - Sean D McGrath
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Vincent J Magrini
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Peter White
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Julie Balch Samora
- Department of Orthopedic Surgery, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Daniel C Koboldt
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Richard K Wilson
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
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7
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Zu B, Wang Z, Xu Y, You G, Fu Q. Nonframeshifting indel variations in polyalanine repeat of
HOXD13
gene underlies hereditary limb malformation for two Chinese families. Dev Dyn 2021; 250:1220-1228. [DOI: 10.1002/dvdy.310] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 01/16/2021] [Accepted: 01/17/2021] [Indexed: 12/18/2022] Open
Affiliation(s)
- Bailing Zu
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center Shanghai Jiao Tong University School of Medicine Shanghai China
| | - Zhigang Wang
- Department of Pediatric Orthopedic Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine Shanghai China
| | - Yunlan Xu
- Department of Pediatric Orthopedic Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine Shanghai China
| | - Guoling You
- Department of Laboratory Medicine Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine Shanghai China
| | - Qihua Fu
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center Shanghai Jiao Tong University School of Medicine Shanghai China
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8
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Zhang M, Lu L, Wei B, Zhang Y, Li X, Shi Y, Ge W, Sun M. Brachydactyly type A3 is caused by a novel 13 bp HOXD13 frameshift deletion in a Chinese family. Am J Med Genet A 2020; 182:2432-2436. [PMID: 32789964 DOI: 10.1002/ajmg.a.61788] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 07/01/2020] [Accepted: 07/11/2020] [Indexed: 12/13/2022]
Abstract
Brachydactyly type A (BDA) is defined as short middle phalanges of the affected digits and is subdivided into four types (BDA1-4). To date, the molecular cause is unknown. However, there is some evidence that pathogenic variants of HOXD13 could be associated with BDA3 and BDA4. Here, we report a Chinese autosomal dominant BDA3 pedigree with a novel HOXD13 mutation. The affected individuals presented with an obviously shorter fifth middle phalanx. The radial side of the middle phalanx was shorter than the ulnar side, and the terminal phalanx of the fifth finger inclined radially and formed classical clinodactyly. Interestingly, the index finger was normal. The initial diagnosis was BDA3. However, the distal third and fourth middle phalanges were also slightly affected, resulting in mild radial clinodactyly. Both feet showed shortening of the middle phalanges, which were fused to the distal phalanges of the second to the fifth toes, as reported in BDA4. Therefore, this pedigree had combined BDA3 and atypical BDA4. By direct sequencing, a 13 bp deletion within exon 1 of HOXD13 (NM_000523.4: c.708_720del13; NP_000514.2: p.Gly237fs) was identified. The 13 bp deletion resulted in a frameshift and premature termination of HOXD13. This study provides further evidences that variants in HOXD13 cause BDA3-BDA4 phenotypes.
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Affiliation(s)
- Mengshu Zhang
- Institute for Fetology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Likui Lu
- Institute for Fetology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Bin Wei
- Institute for Fetology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Yingying Zhang
- Institute for Fetology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Xiang Li
- Institute for Fetology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Yajun Shi
- Institute for Fetology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Wei Ge
- Department of Neurology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Miao Sun
- Institute for Fetology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
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9
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A Review of the Phenotype of Synpolydactyly Type 1 in Homozygous Patients: Defining the Relatively Long and Medially Deviated Big Toe with/without Cupping of the Forefoot as a Pathognomonic Feature in the Phenotype. BIOMED RESEARCH INTERNATIONAL 2020; 2020:2067186. [PMID: 32509852 PMCID: PMC7246408 DOI: 10.1155/2020/2067186] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Accepted: 05/02/2020] [Indexed: 12/03/2022]
Abstract
Synpolydactyly type 1 (SPD1, OMIM 186000) is inherited as autosomal dominant and is caused by HOXD13 mutations. The condition is rare and is known for its phenotypic heterogeneity. In the homozygous state, the phenotype is generally more severe and is characterized by three main features: a more severe degree of syndactyly, a more severe degree of brachydactyly, and the frequent loss of the normal tubular shape of the metacarpals/metatarsals. Due to the phenotypic heterogeneity and the phenotypic overlap with other types of syndactyly, no pathognomonic feature has been described for the homozygous phenotype of SPD1. In the current communication, the author reviews the literature on the phenotypes of SPD1 in homozygous patients. The review documents that not all homozygous patients show a severe hand phenotype. The review also defines the “relatively long and medially deviated big toe with/without cupping of the forefoot” as a pathognomonic feature in the phenotype. Illustration of this feature is done through a demonstrative clinical report in a multigeneration family with SPD1 and HOXD13 polyalanine repeat expansion. Finally, the pathogenesis of the clinical features is reviewed.
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10
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A heterozygous duplication variant of the HOXD13 gene caused synpolydactyly type 1 with variable expressivity in a Chinese family. BMC MEDICAL GENETICS 2019; 20:203. [PMID: 31870337 PMCID: PMC6929446 DOI: 10.1186/s12881-019-0908-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 10/15/2019] [Indexed: 11/19/2022]
Abstract
Background Synpolydactyly type 1 (SPD1), also known as syndactyly type II, is an autosomal dominant limb deformity generally results in webbing of 3rd and 4th fingers, duplication of 4th or 5th toes. It is most commonly caused by mutation in HOXD13 gene. In this study, a five-generation Chinese family affected with SPD1 disease were collected. We tried to identify the pathogenic variations associated with SPD1 involved in the family. Methods We used the whole genome sequencing (WGS) to identify the pathogenic variant in this family which was later confirmed by PCR-Sanger sequencing. The genetic variation were evaluated with the frequencies in the 1000 Genome Project and Exome Aggregation Consortium (ExAC) dataset. The significance of variants were assessed using different mutation predictor softwares like Mutation Taster, PROVEAN and SIFT. The classification of variants was assessed according to American College of Medical Genetics and Genomics (ACMG) guidelines. Results Our results showed the mutation of 24-base pair duplication (c.183_206dupAGCGGCGGCTGCGGCGGCGGCGGC) in exon one of HOXD13 in heterozygous form which was predicted to result in eight extra alanine (A) residues in N-terminal domain of HOXD13 protein. The mutation was detected in all affected members of the family. Conclusion Based on our mutation analysis of variant c.183_206dupAGCGGCGGCTGCGGCGGCGGCGGC in HOXD13 and its cosegregation in all affected family members, we found this variant as likely pathogenic to this SPD1 family. Our study highlights variable expressivity of HOXD13 mutation. Our results also widen the spectrum of HOXD13 mutation responsible for SPD1.
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11
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A Comprehensive review of genetic skeletal disorders reported from Pakistan: A brief commentary. Meta Gene 2019. [DOI: 10.1016/j.mgene.2019.100559] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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12
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WITHDRAWN: A 24-base pair duplication in exon one of HOXD13 gene linked to synpolydactyly type 1 in a Chinese family. Meta Gene 2018. [DOI: 10.1016/j.mgene.2018.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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13
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Deng H, Tan T, He Q, Lin Q, Yang Z, Zhu A, Guan L, Xiao J, Song Z, Guo Y. Identification of a missense HOXD13 mutation in a Chinese family with syndactyly type I-c using exome sequencing. Mol Med Rep 2017; 16:473-477. [PMID: 28498426 DOI: 10.3892/mmr.2017.6576] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 02/02/2017] [Indexed: 11/05/2022] Open
Abstract
Syndactyly is one of the most common hereditary limb malformations, and is characterized by the fusion of specific fingers and/or toes. Syndactyly type I‑c is associated with bilateral cutaneous or bony webbing of the third and fourth fingers and occasionally of the third to fifth fingers, with normal feet. The aim of the present study was to identify the genetic basis of syndactyly type I‑c in four generations of a Chinese Han family by exome sequencing. Exome sequencing was conducted in the proband of the family, followed by direct sequencing of other family members of the same ancestry, as well as 100 ethnically‑matched, unrelated normal controls. A missense mutation, c.917G>A (p.R306Q), was identified in the homeobox D13 gene (HOXD13). Sanger sequencing verified the presence of this mutation in all of the affected family members. By contrast, this mutation was absent in the unaffected family members and the 100 ethnically‑matched normal controls. The results suggest that the c.917G>A (p.R306Q) mutation in the HOXD13 gene, may be responsible for syndactyly type I‑c in this family. Exome sequencing may therefore be a powerful tool for identifying mutations associated with syndactyly, which is a disorder with high genetic and clinical heterogeneity. The results provide novel insights into the etiology and diagnosis of syndactyly, and may influence genetic counseling and the clinical management of the disease.
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Affiliation(s)
- Hao Deng
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, P.R. China
| | - Ting Tan
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, P.R. China
| | - Quanyong He
- Department of Burn and Plastic Surgery, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, P.R. China
| | - Qiongfen Lin
- BGI‑Shenzhen, Shenzhen, Guangdong 518083, P.R. China
| | - Zhijian Yang
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, P.R. China
| | - Anding Zhu
- Department of Neurology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, P.R. China
| | - Liping Guan
- BGI‑Shenzhen, Shenzhen, Guangdong 518083, P.R. China
| | - Jingjing Xiao
- BGI‑Shenzhen, Shenzhen, Guangdong 518083, P.R. China
| | - Zhi Song
- Department of Neurology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, P.R. China
| | - Yi Guo
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, P.R. China
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14
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Wang B, Li N, Geng J, Wang Z, Fu Q, Wang J, Xu Y. Exome sequencing identifies a novel nonsense mutation of HOXD13 in a Chinese family with synpolydactyly. Congenit Anom (Kyoto) 2017; 57:4-7. [PMID: 27254532 DOI: 10.1111/cga.12173] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 05/24/2016] [Accepted: 05/30/2016] [Indexed: 12/30/2022]
Abstract
Synpolydactyly (SPD) is an autosomal dominant limb malformation with a distinctive combination of syndactyly and polydactyly. SPD is clinically heterogeneous and could be genetically classified into three types. The clinical phenotype of SPD is complicated by its variable expressivity. In the present study, whole exome sequencing (WES) was used to identify the affected gene(s) in a Chinese family with atypical SPD phenotype. Our results showed that a novel heterogenous nonsense mutation (c.556C > T, p.R186X) in HOXD13 was associated with this SPD case. Due to variable expressivity, the diagnosis of a clinical heterogenous disease such as SPD is usually difficult. Our results also suggested that WES is an efficient tool to assist with these diagnoses.
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Affiliation(s)
- Bo Wang
- Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Niu Li
- Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Juan Geng
- Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Zhigang Wang
- Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Qihua Fu
- Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Jian Wang
- Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yunlan Xu
- Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
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15
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Ibrahim DM, Tayebi N, Knaus A, Stiege AC, Sahebzamani A, Hecht J, Mundlos S, Spielmann M. A homozygous HOXD13 missense mutation causes a severe form of synpolydactyly with metacarpal to carpal transformation. Am J Med Genet A 2015; 170:615-21. [PMID: 26581570 DOI: 10.1002/ajmg.a.37464] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 10/22/2015] [Indexed: 11/06/2022]
Abstract
Synpolydactyly (SPD) is a rare congenital limb disorder characterized by syndactyly between the third and fourth fingers and an additional digit in the syndactylous web. In most cases SPD is caused by heterozygous mutations in HOXD13 resulting in the expansion of a N-terminal polyalanine tract. If homozygous, the mutation results in severe shortening of all metacarpals and phalanges with a morphological transformation of metacarpals to carpals. Here, we describe a novel homozygous missense mutation in a family with unaffected consanguineous parents and severe brachydactyly and metacarpal-to-carpal transformation in the affected child. We performed whole exome sequencing on the index patient, followed by Sanger sequencing of parents and patient to investigate cosegregation. The DNA-binding ability of the mutant protein was tested with electrophoretic mobility shift assays. We demonstrate that the c.938C>G (p.313T>R) mutation in the DNA-binding domain of HOXD13 prevents binding to DNA in vitro. Our results show to our knowledge for the first time that a missense mutation in HOXD13 underlies severe brachydactyly with metacarpal-to-carpal transformation. The mutation is non-penetrant in heterozygous carriers. In conjunction with the literature we propose the possibility that the metacarpal-to-carpal transformation results from a homozygous loss of functional HOXD13 protein in humans in combination with an accumulation of non-functional HOXD13 that might be able to interact with other transcription factors in the developing limb.
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Affiliation(s)
- Daniel M Ibrahim
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany.,Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Naeimeh Tayebi
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany.,Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Alexej Knaus
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Asita C Stiege
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | | | - Jochen Hecht
- Max Planck Institute for Molecular Genetics, Berlin, Germany.,Berlin Brandenburg Center for Regenerative Therapies, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Stefan Mundlos
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany.,Max Planck Institute for Molecular Genetics, Berlin, Germany.,Berlin-Brandenburg School for Regenerative Therapies (BSRT), Berlin, Germany.,Berlin Brandenburg Center for Regenerative Therapies, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Malte Spielmann
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany.,Max Planck Institute for Molecular Genetics, Berlin, Germany.,Berlin-Brandenburg School for Regenerative Therapies (BSRT), Berlin, Germany
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16
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Deng H, Tan T. Advances in the Molecular Genetics of Non-syndromic Syndactyly. Curr Genomics 2015; 16:183-93. [PMID: 26069458 PMCID: PMC4460222 DOI: 10.2174/1389202916666150317233103] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 02/18/2015] [Accepted: 03/16/2015] [Indexed: 12/16/2022] Open
Abstract
Syndactyly, webbing of adjacent digits with or without bony fusion, is one of the most common hereditary limb malformations. It occurs either as an isolated abnormality or as a component of more than 300 syndromic anomalies. There are currently nine types of phenotypically diverse nonsyndromic syndactyly. Non-syndromic syndactyly is usually inherited as an autosomal dominant trait, although the more severe presenting types and subtypes may show autosomal recessive or X-linked pattern of inheritance. The phenotype appears to be not only caused by a main gene, but also dependant on genetic background and subsequent signaling pathways involved in limb formation. So far, the principal genes identified to be involved in congenital syndactyly are mainly involved in the zone of polarizing activity and sonic hedgehog pathway. This review summarizes the recent progress made in the molecular genetics, including known genes and loci responsible for non-syndromic syndactyly, and the signaling pathways those genetic factors involved in, as well as clinical features and animal models. We hope our review will contribute to the understanding of underlying pathogenesis of this complicated disorder and have implication on genetic counseling.
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Affiliation(s)
- Hao Deng
- Center for Experimental Medicine ; Department of Neurology, the Third Xiangya Hospital, Central South University, Changsha, China
| | - Ting Tan
- Center for Experimental Medicine
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17
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Zhou J, Chen Y, Cao K, Zou Y, Zhou H, Hu F, Ni B, Chen Y. Functional classification and mutation analysis of a synpolydactyly kindred. Exp Ther Med 2014; 8:1569-1574. [PMID: 25289061 PMCID: PMC4186389 DOI: 10.3892/etm.2014.1957] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Accepted: 08/07/2014] [Indexed: 01/30/2023] Open
Abstract
The aim of the present study was to analyze a congenital syndactyly/polydactyly kindred and propose a new functional classification method of clinical significance. The modes of inheritance and mutational mechanisms were also determined using genetic analyses. Hand and foot anatomy and functions were measured using photographic images, X-ray imaging and grip ability tests. Genetic analysis comprised the genotyping of polymorphic microsatellite markers at known polydactyly-associated loci and the sequencing of the candidate gene. A functional classification system was devised to divide the clinical features into three types, which included mild, moderate or severe deformity. The family was concluded to have syndactyly type II with autosomal dominant inheritance. The microsatellites, D2S2310 and D2S2314, at the 2q31–32 chromosome, which have previously been associated with synpolydactyly type I, were found to be associated with the disorder in the current family. A 27-bp insertion mutation was identified in the affected individuals in the HOXD13 gene at this locus. The insertion added a further nine alanine residues to the polyalanine stretch within the encoded protein. In conclusion, the functional classification method described in the present study may be used to guide surgical approaches to treatment. A family was identified in whom expansion of the polyalanine tract in the HOXD13 gene causes autosomal dominant hereditary synpolydactyly.
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Affiliation(s)
- Jianda Zhou
- Department of Plastic Surgery, Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, P.R. China
| | - Yao Chen
- Department of Plastic Surgery, Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, P.R. China
| | - Ke Cao
- Department of Plastic Surgery, Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, P.R. China
| | - Yonghua Zou
- Key Laboratory of Genetics and Birth Health of Hunan Province, Family Planning Institute of Hunan Province, Changsha, Hunan 410078, P.R. China
| | - Haiyan Zhou
- Key Laboratory of Genetics and Birth Health of Hunan Province, Family Planning Institute of Hunan Province, Changsha, Hunan 410078, P.R. China
| | - Feng Hu
- Department of Plastic Surgery, Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, P.R. China
| | - Bin Ni
- Key Laboratory of Genetics and Birth Health of Hunan Province, Family Planning Institute of Hunan Province, Changsha, Hunan 410078, P.R. China
| | - Yong Chen
- Key Laboratory of Genetics and Birth Health of Hunan Province, Family Planning Institute of Hunan Province, Changsha, Hunan 410078, P.R. China
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18
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Dai L, Liu D, Song M, Xu X, Xiong G, Yang K, Zhang K, Meng H, Guo H, Bai Y. Mutations in the homeodomain of HOXD13 cause syndactyly type 1-c in two Chinese families. PLoS One 2014; 9:e96192. [PMID: 24789103 PMCID: PMC4006867 DOI: 10.1371/journal.pone.0096192] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 04/04/2014] [Indexed: 11/18/2022] Open
Abstract
Background Syndactyly type 1 (SD1) is an autosomal dominant limb malformation characterized in its classical form by complete or partial webbing between the third and fourth fingers and/or the second and third toes. Its four subtypes (a, b, c, and d) are defined based on variable phenotypes, but the responsible gene is yet to be identified. SD1-a has been mapped to chromosome 3p21.31 and SD1-b to 2q34–q36. SD1-c and SD1-d are very rare and, to our knowledge, no gene loci have been identified. Methods and Results In two Chinese families with SD1-c, linkage and haplotype analyses mapped the disease locus to 2q31-2q32. Copy number variation (CNV) analysis, using array-based comparative genomic hybridization (array CGH), excluded the possibility of microdeletion or microduplication. Sequence analyses of related syndactyly genes in this region identified c.917G>A (p.R306Q) in the homeodomain of HOXD13 in family A. Analysis on family B identified the mutation c.916C>G (p.R306G) and therefore confirmed the genetic homogeneity. Luciferase assays indicated that these two mutations affected the transcriptional activation ability of HOXD13. The spectrum of HOXD13 mutations suggested a close genotype-phenotype correlation between the different types of HOXD13-Syndactyly. Overlaps of the various phenotypes were found both among and within families carrying the HOXD13 mutation. Conclusions Mutations (p.R306Q and p.R306G) in the homeodomain of HOXD13 cause SD1-c. There are affinities between SD1-c and synpolydactyly. Different limb malformations due to distinct classes of HOXD13 mutations should be considered as a continuum of phenotypes and further classification of syndactyly should be done based on phenotype and genotype.
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Affiliation(s)
- Limeng Dai
- Department of Medical Genetics, College of Basic Medical Sciences, Third Military Medical University, Chongqing, China
| | - Dan Liu
- Department of Medical Genetics, College of Basic Medical Sciences, Third Military Medical University, Chongqing, China
| | - Min Song
- Department of Medical Genetics, College of Basic Medical Sciences, Third Military Medical University, Chongqing, China
| | - Xueqing Xu
- Department of Medical Genetics, College of Basic Medical Sciences, Third Military Medical University, Chongqing, China
| | - Gang Xiong
- Department of Thoracic and Cardiac Surgery, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Kang Yang
- Department of Thoracic and Cardiac Surgery, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Kun Zhang
- Department of Medical Genetics, College of Basic Medical Sciences, Third Military Medical University, Chongqing, China
| | - Hui Meng
- Department of Medical Genetics, College of Basic Medical Sciences, Third Military Medical University, Chongqing, China
| | - Hong Guo
- Department of Medical Genetics, College of Basic Medical Sciences, Third Military Medical University, Chongqing, China
- * E-mail: (YB); (HG)
| | - Yun Bai
- Department of Thoracic and Cardiac Surgery, Southwest Hospital, Third Military Medical University, Chongqing, China
- * E-mail: (YB); (HG)
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Shi X, Ji C, Cao L, Wu Y, Shang Y, Wang W, Luo Y. A splice donor site mutation in HOXD13 underlies synpolydactyly with cortical bone thinning. Gene 2013; 532:297-301. [PMID: 24055421 DOI: 10.1016/j.gene.2013.09.040] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2013] [Revised: 08/08/2013] [Accepted: 09/09/2013] [Indexed: 11/30/2022]
Abstract
Synpolydactyly 1(SPD1) is a dominantly inherited distal limb anomaly that is characterized by incomplete digit separation and increased number of digits. SPD1 is most commonly caused by polyalanine repeat expansions and mutations in the homeodomain of the HOXD13. We report a splice donor site mutation in HOXD13 associated in most cases with cortical bone thinning. In vitro study of transcripts and truncated protein analysis indicated that c.781+1G>A mutation results in truncated HOXD13 protein p.G190fsX4. Luciferase assay indicated that the truncated HOXD13 protein failed to bind to DNA. The mechanism for this phenotype was truncated protein loss of function.
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Affiliation(s)
- Xiuyan Shi
- The Research Center for Medical Genomics, Key Laboratory of Cell Biology, Ministry of Public Health and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang 110001, China
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20
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Brison N, Debeer P, Tylzanowski P. Joining the fingers: AHOXD13story. Dev Dyn 2013; 243:37-48. [DOI: 10.1002/dvdy.24037] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 06/27/2013] [Accepted: 07/01/2013] [Indexed: 12/21/2022] Open
Affiliation(s)
- Nathalie Brison
- Center for Human Genetics; University Hospitals Leuven, University of Leuven; Belgium
| | - Philippe Debeer
- Department of Development and Regeneration; University of Leuven; Belgium
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21
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Xin Q, Li L, Li J, Qiu R, Guo C, Gong Y, Liu Q. Eight-alanine duplication in homeobox D13 in a Chinese family with synpolydactyly. Gene 2012; 499:48-51. [PMID: 22406499 DOI: 10.1016/j.gene.2012.02.046] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Revised: 02/15/2012] [Accepted: 02/21/2012] [Indexed: 11/30/2022]
Abstract
Human synpolydactyly (SPD), belonging to syndactyly (SD) II, is an inherited autosomal-dominant limb malformation characterized by SD of finger 3 or 4 or toe 4 or 5, usually with digit duplication. Previous studies have demonstrated that homeobox protein D13 (HOXD13) is responsible for this Mendelian disorder. In this paper, we report on a family with SPD - 7 members show typical SPD malformations. We used PCR and Sanger sequencing of DNA from peripheral blood samples and found an 8-Ala expansion in exon 1 of HOXD13 by mutation detection; this variant was absent in unaffected members and in 50 unaffected non-related subjects. This study further confirmed the correlation between SPD and alanine expansion in HOXD13.
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Affiliation(s)
- Qian Xin
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Medical Genetics, Shandong University School of Medicine, Jinan 250012, PR China
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