1
|
Bilal M, Haack TB, Buchert R, Peralta S, Ahmad I, Faisal, Abbasi S, Ahmad W. Sequence Variants in the WNT10B Underlying Non-Syndromic Split-Hand/Foot Malformation. Mol Syndromol 2023; 14:469-476. [PMID: 38058757 PMCID: PMC10697732 DOI: 10.1159/000531069] [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: 04/20/2023] [Accepted: 05/10/2023] [Indexed: 12/08/2023] Open
Abstract
Introduction Split hand and foot malformation (SHFM) or ectrodactyly is a rare limb deformity characterized by median cleft of the hand and foot with impaired or missing central rays. It can occur as an isolated anomaly or in association with abnormalities of other body parts. Methods After delineating the clinical features of two families (A-B), with non-syndromic SHFM, exome and Sanger sequencing were employed to search for the disease-causing variants. Results Analysis of exome and Sanger sequencing data revealed two causative variants in the WNT10B gene in affected members of the two families. This included a novel missense change [c.338G>C; p.(Gly113Ala)] in family A and a previously reported frameshift variant [c.884-896delTCCAGCCCCGTCT; p.(Phe295Cysfs*87)] in family B. Conclusion Our findings add a novel variant in WNT10B gene as the underlying cause of SHFM. The finding adds to the growing body of knowledge about the genetic basis of developmental disorders and provides valuable insights into the molecular mechanisms that regulate limb development.
Collapse
Affiliation(s)
- Muhammad Bilal
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
- Institute for Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Tobias B. Haack
- Institute for Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Rebecca Buchert
- Institute for Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Susana Peralta
- Institute for Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Imtiaz Ahmad
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Faisal
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Sanaullah Abbasi
- Department of Biochemistry, Shah Abdul Latif, Khairpur, Pakistan
| | - Wasim Ahmad
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| |
Collapse
|
2
|
Da Silva JD, Gonzaga D, Barreta A, Correia H, Fortuna AM, Soares AR, Tkachenko N. Refining the Clinical Spectrum of the 17p13.3 Microduplication Syndrome: Case-Report of a Familial Small Microduplication. Biomedicines 2022; 10:biomedicines10123078. [PMID: 36551834 PMCID: PMC9775100 DOI: 10.3390/biomedicines10123078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 11/18/2022] [Accepted: 11/26/2022] [Indexed: 12/02/2022] Open
Abstract
The chromosomal region 17p13.3 contains extensive repetitive sequences and is a well-recognized region of genomic instability. The 17p13.3 microduplication syndrome has been associated with a clinical spectrum of moderately non-specific phenotypes, including global developmental delay/intellectual disability, behavioral disorders, autism spectrum disorder and variable dysmorphic features. Depending on the genes involved in the microduplication, it can be categorized in two subtypes with different phenotypes. Here, we report a case of a 7-year-old boy with global developmental delay, speech impairment, hypotonia, behavioral conditions (ADHD and ODD), non-specific dysmorphic features and overgrowth. Genetic testing revealed a small 17p13.3 chromosomal duplication, which included the BHLHA9, CRK and YWHAE genes. Additionally, we observed that this was maternally inherited, and that the mother presented with a milder phenotype including mild learning disabilities, speech impairment and non-specific dysmorphic features, which did not significantly affect her. In conclusion, we present a clinical case of a 17p13.3 duplication that further delineates the clinical spectrum of this syndrome, including its intrafamilial/intergenerational variability.
Collapse
Affiliation(s)
- Jorge Diogo Da Silva
- Centro de Genética Médica Doutor Jacinto Magalhães (CGM), Centro Hospitalar Universitário do Porto, 4050-106 Porto, Portugal
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057 Braga, Portugal
- ICVS/3B’s—PT Government Associate Laboratory, 4806-909 Braga, Portugal
- Correspondence:
| | - Diana Gonzaga
- Centro de Genética Médica Doutor Jacinto Magalhães (CGM), Centro Hospitalar Universitário do Porto, 4050-106 Porto, Portugal
- Centro Materno-Infantil do Norte, Centro Hospital Universitário do Porto, 4099-001 Porto, Portugal
| | - Ana Barreta
- Medical Genetics Service, Joaquim Chaves Saúde, 2685-145 Oeiras, Portugal
| | - Hildeberto Correia
- Medical Genetics Service, Joaquim Chaves Saúde, 2685-145 Oeiras, Portugal
| | - Ana Maria Fortuna
- Centro de Genética Médica Doutor Jacinto Magalhães (CGM), Centro Hospitalar Universitário do Porto, 4050-106 Porto, Portugal
- Unit for Multidisciplinary Research in Biomedicine, Abel Salazar Biomedical Sciences Institute, Porto University, 4050-345 Porto, Portugal
| | - Ana Rita Soares
- Centro de Genética Médica Doutor Jacinto Magalhães (CGM), Centro Hospitalar Universitário do Porto, 4050-106 Porto, Portugal
- Unit for Multidisciplinary Research in Biomedicine, Abel Salazar Biomedical Sciences Institute, Porto University, 4050-345 Porto, Portugal
| | - Nataliya Tkachenko
- Centro de Genética Médica Doutor Jacinto Magalhães (CGM), Centro Hospitalar Universitário do Porto, 4050-106 Porto, Portugal
- Unit for Multidisciplinary Research in Biomedicine, Abel Salazar Biomedical Sciences Institute, Porto University, 4050-345 Porto, Portugal
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Bukowska-Olech E, Sowińska-Seidler A, Wierzba J, Jamsheer A. SHFLD3 phenotypes caused by 17p13.3 triplication/ duplication encompassing Fingerin (BHLHA9) invariably. Orphanet J Rare Dis 2022; 17:325. [PMID: 36028842 PMCID: PMC9419377 DOI: 10.1186/s13023-022-02480-w] [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: 03/23/2022] [Accepted: 08/13/2022] [Indexed: 11/21/2022] Open
Abstract
Background Split-hand/ foot malformation with long bone deficiency 3 (SHFLD3) is an extremely rare condition associated with duplications located on 17p13.3, which invariably encompasses the BHLHA9 gene. The disease inherits with variable expressivity and significant incomplete penetrance as high as 50%. Results We have detected 17p13.3 locus one-allele triplication in a male proband from family 1 (F1.1), and duplication in a male proband from family 2 (F2.1) applying array comparative genomic hybridization (array CGH). The rearrangements mapped to the following chromosomal regions–arr[GRCh38] 17p13.3(960254–1291856)×4 in F1.1 and arr[GRCh38] 17p13.3(1227482–1302716)×3 in F2.1. The targeted quantitative PCR revealed that the 17p13.3 locus was also duplicated in the second affected member from family 2 (F2.2; brother of F2.1). In the next step, we performed segregation studies using quantitative PCR and revealed that F1.1 inherited the triplication from his healthy father—F1.2, whereas the locus was unremarkable in the mother of F2.1 & F2.2 and the healthy son of F2.1. However, the duplication was present in a healthy daughter of F2.2, an asymptomatic carrier. The breakpoint analysis allowed to define the exact size and span of the duplicated region in Family 2, i.e., 78,948 bp chr17:1225063–1304010 (HG38). Interestingly, all symptomatic carriers from both families presented with variable SHFLD3 phenotype. The involvement of secondary modifying locus could not be excluded, however, the Sanger sequencing screening of BHLHA9 entire coding sequence was unremarkable for both families. Conclusions We have shed light on the one-allele CNV triplication occurrence that should be considered when a higher probe (over duplication range) signal is noted. Second, all SHFLD3 patients were accurately described regarding infrequent limb phenotypes, which were highly variable even when familial. Of note, all symptomatic individuals were males. SHFLD3 still remains a mysterious ultra-rare disease and our findings do not answer crucial questions regarding the disease low penetrance, variable expression and heterogeneity. However, we have presented some clinical and molecular aspects that may be helpful in daily diagnostic routine, both dysmorphological and molecular assessment, of patients affected with SHFLD3. Supplementary Information The online version contains supplementary material available at 10.1186/s13023-022-02480-w.
Collapse
Affiliation(s)
| | - Anna Sowińska-Seidler
- Department of Medical Genetics, Poznan University of Medical Sciences, Poznan, Poland
| | - Jolanta Wierzba
- Department of Pediatrics and Internal Medicine Nursing, Department of Rare Disorders, Medical University of Gdansk, Gdansk, Poland
| | - Aleksander Jamsheer
- Department of Medical Genetics, Poznan University of Medical Sciences, Poznan, Poland. .,Centers for Medical Genetics GENESIS, Poznan, Poland.
| |
Collapse
|
5
|
Inoue Y, Machida O, Kita Y, Yamamoto T. Need for revision of the ACMG/AMP guidelines for interpretation of X-linked variants. Intractable Rare Dis Res 2022; 11:120-124. [PMID: 36200025 PMCID: PMC9437996 DOI: 10.5582/irdr.2022.01067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/27/2022] [Accepted: 08/04/2022] [Indexed: 11/05/2022] Open
Abstract
The guidelines provided by American College of Medical Genetics and Genomics (ACMG) and the Association of Molecular Pathology (AMP) (ACMG/AMP guidelines) suggest a framework for the classification of clinical variants. However, the interpretations can be inconsistent, with each definition sometimes proving to be ambiguous. In particular, there can be difficulty with interpretation of variants related to the X-linked recessive trait. To confirm whether there are biases in the interpretation of inherited traits, we reanalyzed variants reported prior to the release of the ACMG/AMP guidelines. As expected, the interpretation ratio as pathogenic or likely pathogenic was significantly lower for variants related to the X-linked recessive trait. Evaluation of variants related to the X-linked recessive trait, hence, need to consider whether the variant is identified only in males in accordance with the X-linked recessive trait. The ACMG/AMP guidelines should be revised to eliminate the bias revealed in this study.
Collapse
Affiliation(s)
- Yoko Inoue
- Division of Gene Medicine, Graduate School of Medical Science, Tokyo Women's Medical University, Tokyo, Japan
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan
| | - Osamu Machida
- Division of Gene Medicine, Graduate School of Medical Science, Tokyo Women's Medical University, Tokyo, Japan
- Department of Pediatrics, Tokyo Women's Medical University, Tokyo, Japan
| | - Yosuke Kita
- Department of Psychology, Faculty of Letters, Keio University, Tokyo, Japan
| | - Toshiyuki Yamamoto
- Division of Gene Medicine, Graduate School of Medical Science, Tokyo Women's Medical University, Tokyo, Japan
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan
| |
Collapse
|
6
|
Homodimeric and Heterodimeric Interactions among Vertebrate Basic Helix-Loop-Helix Transcription Factors. Int J Mol Sci 2021; 22:ijms222312855. [PMID: 34884664 PMCID: PMC8657788 DOI: 10.3390/ijms222312855] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/11/2021] [Accepted: 11/17/2021] [Indexed: 01/01/2023] Open
Abstract
The basic helix–loop–helix transcription factor (bHLH TF) family is involved in tissue development, cell differentiation, and disease. These factors have transcriptionally positive, negative, and inactive functions by combining dimeric interactions among family members. The best known bHLH TFs are the E-protein homodimers and heterodimers with the tissue-specific TFs or ID proteins. These cooperative and dynamic interactions result in a complex transcriptional network that helps define the cell’s fate. Here, the reported dimeric interactions of 67 vertebrate bHLH TFs with other family members are summarized in tables, including specifications of the experimental techniques that defined the dimers. The compilation of these extensive data underscores homodimers of tissue-specific bHLH TFs as a central part of the bHLH regulatory network, with relevant positive and negative transcriptional regulatory roles. Furthermore, some sequence-specific TFs can also form transcriptionally inactive heterodimers with each other. The function, classification, and developmental role for all vertebrate bHLH TFs in four major classes are detailed.
Collapse
|
7
|
Sedighzadeh SS, Sedaghat A, Zamani M, Seifi T, Shariati G, Zeighami J, Mazaheri N, Galehdari H. Whole exome sequencing identified a novel frameshift variant in the BHLHA9 in an Iranian family with mesoaxial synostotic syndactyly. Congenit Anom (Kyoto) 2021; 61:220-225. [PMID: 34272776 DOI: 10.1111/cga.12439] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 06/04/2021] [Accepted: 06/29/2021] [Indexed: 12/01/2022]
Abstract
Mesoaxial synostotic syndactyly with phalangeal reduction (MSSD) represents a rare non-syndromic defect with an autosomal recessive pattern of inheritance. Sequence variants in the BHLHA9 gene cause MSSD and to date only a few mutations in this gene have been reported. In the present report, we have described a consanguineous Iranian family segregating MSSD in an autosomal recessive manner. The family had two affected siblings showing evidence of camptodactyly in some fingers, complete syndactyly of the 3rd and 4th fingers with synostoses of the corresponding metacarpals, and associated single phalanx in both right and left hand. Whole exome sequencing (WES) followed by segregation analysis using Sanger sequencing identified a novel homozygous frameshift variation [c.74_74delG p.(G25Afs*55)] in the BHLHA9 gene. This has expanded the spectrum of mutations in the BHLHA9 and will facilitate genetic counseling in Iranian families segregating MSSD-related phenotypes.
Collapse
Affiliation(s)
- Sahar Sadat Sedighzadeh
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran.,Narges Medical Genetics and Prenatal Diagnosis Laboratory, Ahvaz, Khuzestan, Iran
| | - Alireza Sedaghat
- Narges Medical Genetics and Prenatal Diagnosis Laboratory, Ahvaz, Khuzestan, Iran.,Health Research Institute, Diabetes Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mina Zamani
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran.,Narges Medical Genetics and Prenatal Diagnosis Laboratory, Ahvaz, Khuzestan, Iran
| | - Tahere Seifi
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran.,Narges Medical Genetics and Prenatal Diagnosis Laboratory, Ahvaz, Khuzestan, Iran
| | - Gholamreza Shariati
- Narges Medical Genetics and Prenatal Diagnosis Laboratory, Ahvaz, Khuzestan, Iran.,Ahvaz Jundishapur University of Medical Sciences, Department of Medical Genetics, Faculty of Medicine, Ahvaz, Iran
| | - Jawaher Zeighami
- Narges Medical Genetics and Prenatal Diagnosis Laboratory, Ahvaz, Khuzestan, Iran
| | - Neda Mazaheri
- Narges Medical Genetics and Prenatal Diagnosis Laboratory, Ahvaz, Khuzestan, Iran
| | - Hamid Galehdari
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran.,Narges Medical Genetics and Prenatal Diagnosis Laboratory, Ahvaz, Khuzestan, Iran
| |
Collapse
|
8
|
A Novel Missense Variant of TP63 Heterozygously Present in Split-Hand/Foot Malformation. BIOMED RESEARCH INTERNATIONAL 2020; 2020:4215632. [PMID: 33294441 PMCID: PMC7714569 DOI: 10.1155/2020/4215632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 10/29/2020] [Accepted: 11/11/2020] [Indexed: 11/18/2022]
Abstract
Background Split-hand/foot malformation (SHFM) is a severe congenital disability mainly characterized by the absence or hypoplasia of the central ray of the hand/foot. To date, several candidate genes associated with SHFM have been identified, including TP63, DLX5, DLX6, FGFR1, and WNT10B. Herein, we report a novel variant of TP63 heterozygously present in affected members of a family with SHFM. Methods This study investigated a Chinese family, in which the proband and his son suffered from SHFM. The peripheral blood sample of the proband was used to perform whole-exome sequencing (WES) to explore the possible genetic causes of this disease. Postsequencing bioinformatic analyses and Sanger sequencing were conducted to verify the identified variants and parental origins on all family members in the pedigree. Results By postsequencing bioinformatic analyses and Sanger sequencing, we identified a novel missense variant (NM_003722.4:c.948G>A; p.Met316Ile) of TP63 in this family that results in a substitution of methionine with isoleucine, which is probably associated with the occurrence of SHFM. Conclusion A novel missense variant (NM_003722.4:c.948G>A; p.Met316Ile) of TP63 in SHFM was thus identified, which may enlarge the spectrum of known TP63 variants and also provide new approaches for genetic counselling of families with SHFM.
Collapse
|
9
|
Bilal M, Hayat A, Umair M, Ullah A, Khawaja S, Malik E, Burmeister M, Bibi N, Umm-E-Kalsoom, Memon MI, Basit S, Ahmad W, Khan B. Sequence Variants in the WNT10B and TP63 Genes Underlying Isolated Split-Hand/Split-Foot Malformation. Genet Test Mol Biomarkers 2020; 24:600-607. [PMID: 32762550 DOI: 10.1089/gtmb.2020.0024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Aims: Split-hand/split-foot malformation (SHFM) is a developmental and congenital limb malformation characterized by variable degrees of medial clefting or absence of one or more digits in hands and/or feet. The aim of this study was to identify the underlying cause of three consanguineous Pakistani families showing various types of SHFM-related features. Materials and Methods: Standard molecular methods, including whole-genome sequencing (WGS), whole-exome sequencing (WES), microsatellite markers-based genotyping, and Sanger sequencing were performed to search for the likely causative variants. Results: In family A, WES revealed a novel homozygous missense variant [c.338G>A, p.(Gly113Asp)] in the WNT10B gene. In family B, microsatellite-based genotyping followed by Sanger sequencing revealed a novel homozygous 13 base pairs deletion [c.884-896delTCCAGCCCCGTCT, p.(Phe295Cysfs*87)] in the same gene. In family C, WGS divulged a previously reported heterozygous missense variant [c.956G>A, p.(Arg319His)] in the TP63 gene. Conclusions: Mapping and sequencing genes and variants for severe skeletal disorders, such as SHRM, will facilitate establishing specific genotype-phenotype correlations and providing genetic counseling for the families suffering from such conditions.
Collapse
Affiliation(s)
- Muhammad Bilal
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Amir Hayat
- Department of Biochemistry, Abdul Wali Khan University, Mardan, Pakistan
| | - Muhammad Umair
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Asmat Ullah
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan.,Department of Molecular Biology, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad, Pakistan.,Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, USA
| | - Sundus Khawaja
- Department of Biotechnology, University of Azad Jammu & Kashmir, Muzaffarabad, Pakistan
| | - Erum Malik
- Department of Biochemistry, Shah Abdul Latif University, Khairpur, Pakistan
| | - Margit Burmeister
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, USA
| | - Nousheen Bibi
- Department of Bioinformatics, Shaheed Benazir Bhutto Women University, Peshawar, Pakistan
| | - Umm-E-Kalsoom
- Department of Biochemistry, Hazara University Mansehra, Mansehra, Pakistan
| | - Muhammad Iqbal Memon
- Department of Anesthesia and Critical Care, PIMS, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad, Pakistan
| | - Sulman Basit
- Center for Genetics and Inherited Diseases, Taibah University, Medina, Saudi Arabia
| | - Wasim Ahmad
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Bushra Khan
- Department of Biochemistry, Abdul Wali Khan University, Mardan, Pakistan
| |
Collapse
|
10
|
Díaz-González F, Parrón-Pajares M, Barcia-Ramirez A, Heath KE. First case of compound heterozygous BHLHA9 variants in mesoaxial synostotic syndactyly with phalangeal reduction. Am J Med Genet A 2020; 182:628-631. [PMID: 31912643 DOI: 10.1002/ajmg.a.61480] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 12/22/2019] [Indexed: 12/23/2022]
Abstract
Mesoaxial synostotic syndactyly with phalangeal reduction (MSSD) is an extremely rare autosomal recessive limb abnormality characterized by the fusion of third and fourth fingers. To date, only homozygous missense and frameshift mutations have been reported in BHLHA9 associated to MSSD. In this study, we report a patient who presented with clinical and radiological features of MSSD. A customized skeletal dysplasia NGS panel revealed the presence of two novel compounds heterozygous variants in BHLHA9: NM_001164405.1: c.[226A>T][269G>C]; p.[(Lys76*)][(Arg90Pro)]. Thus, this is the first case of MSSD in a nonconsanguineous family.
Collapse
Affiliation(s)
- Francisca Díaz-González
- Institute of Medical & Molecular Genetics (INGEMM), Hospital Universitario La Paz, Universidad Autónoma de Madrid, IdiPAZ, Madrid, Spain
- Skeletal dysplasia Multidisciplinary Unit (UMDE), Hospital Universitario La Paz, Madrid, Spain
| | - Manuel Parrón-Pajares
- Skeletal dysplasia Multidisciplinary Unit (UMDE), Hospital Universitario La Paz, Madrid, Spain
- Department of Radiology, Hospital Universitario la Paz, Madrid, Spain
| | - Ana Barcia-Ramirez
- Department of Pediatrics, Hospital Universitario Virgen de Valme, Sevilla, Spain
| | - Karen E Heath
- Institute of Medical & Molecular Genetics (INGEMM), Hospital Universitario La Paz, Universidad Autónoma de Madrid, IdiPAZ, Madrid, Spain
- Skeletal dysplasia Multidisciplinary Unit (UMDE), Hospital Universitario La Paz, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER, U753), Instituto Carlos III, Madrid, Spain
| |
Collapse
|
11
|
Khan F, Arshad A, Majeed AI, Ullah A, Ahmad W. A novel frameshift variant in BHLHA9 underlies mesoaxial synostotic syndactyly associated with postaxial polydactyly. Eur J Med Genet 2019; 62:103688. [DOI: 10.1016/j.ejmg.2019.103688] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 05/26/2019] [Accepted: 05/28/2019] [Indexed: 10/26/2022]
|
12
|
Paththinige CS, Sirisena ND, Escande F, Manouvrier S, Petit F, Dissanayake VHW. Split hand/foot malformation with long bone deficiency associated with BHLHA9 gene duplication: a case report and review of literature. BMC MEDICAL GENETICS 2019; 20:108. [PMID: 31200655 PMCID: PMC6570964 DOI: 10.1186/s12881-019-0839-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 06/03/2019] [Indexed: 12/11/2022]
Abstract
Background Split hand/foot malformation (SHFM) is a group of congenital skeletal disorders which may occur either as an isolated abnormality or in syndromic forms with extra-limb manifestations. Chromosomal micro-duplication or micro-triplication involving 17p13.3 region has been described as the most common cause of split hand/foot malformation with long bone deficiency (SHFLD) in several different Caucasian and Asian populations. Gene dosage effect of the extra copies of BHLHA9 gene at this locus has been implicated in the pathogenesis of SHFLD. Case presentation The proband was a female child born to non-consanguineous parents. She was referred for genetic evaluation of bilateral asymmetric ectrodactyly involving both hands and right foot along with right tibial hemimelia. The right foot had fixed clubfoot deformity with only 2 toes. The mother had bilateral ectrodactyly involving both hands, but the rest of the upper limbs and both lower limbs were normal. Neither of them had any other congenital malformations or neurodevelopmental abnormalities. Genetic testing for rearrangement of BHLHA9 gene by quantitative polymerase chain reaction confirmed the duplication of the BHLHA9 gene in both the proband and the mother. Conclusions We report the first Sri Lankan family with genetic diagnosis of BHLHA9 duplication causing SHFLD. This report along with the previously reported cases corroborate the possible etiopathogenic role of BHLHA9 gene dosage imbalances in SHFM and SHFLD across different populations.
Collapse
Affiliation(s)
- Chamara Sampath Paththinige
- Human Genetics Unit, Faculty of Medicine, University of Colombo, Kynsey Road, Colombo, 00800, Sri Lanka. .,Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka, Saliyapura, Anuradhapura, 50008, Sri Lanka.
| | | | - Fabienne Escande
- Laboratoire de Biochimie et Oncologie Moléculaire, CHU Lille, F-59000, Lille, France
| | - Sylvie Manouvrier
- Clinique de Génétique Guy Fontaine, CHU Lille, F-59000, Lille, France
| | - Florence Petit
- Clinique de Génétique Guy Fontaine, CHU Lille, F-59000, Lille, France
| | | |
Collapse
|
13
|
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
|
14
|
Ullah A, Ali RH, Majeed AI, Liaqat K, Shah PW, Khan B, Bilal M, Umair M, Ahmad W. A novel insertion and deletion mutation in the BHLHA9 underlies polydactyly and mesoaxial synostotic syndactyly with phalangeal reduction. Eur J Med Genet 2019; 62:278-281. [DOI: 10.1016/j.ejmg.2018.08.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 07/23/2018] [Accepted: 08/09/2018] [Indexed: 10/28/2022]
|
15
|
Kantaputra PN, Carlson BM. Genetic regulatory pathways of split-hand/foot malformation. Clin Genet 2018; 95:132-139. [PMID: 30101460 DOI: 10.1111/cge.13434] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Accepted: 08/07/2018] [Indexed: 12/13/2022]
Abstract
Split-hand/foot malformation (SHFM) is caused by mutations in TP63, DLX5, DLX6, FGF8, FGFR1, WNT10B, and BHLHA9. The clinical features of SHFM caused by mutations of these genes are not distinguishable. This implies that in normal situations these SHFM-associated genes share an underlying regulatory pathway that is involved in the development of the central parts of the hands and feet. The mutations in SHFM-related genes lead to dysregulation of Fgf8 in the central portion of the apical ectodermal ridge (AER) and subsequently lead to misexpression of a number of downstream target genes, failure of stratification of the AER, and thus SHFM. Syndactyly of the remaining digits is most likely the effects of dysregulation of Fgf-Bmp-Msx signaling on apoptotic cell death. Loss of digit identity in SHFM is hypothesized to be the effects of misexpression of HOX genes, abnormal SHH gradient, or the loss of balance between GLI3A and GLI3R. Disruption of canonical and non-canonical Wnt signaling is involved in the pathogenesis of SHFM. Whatever the causative genes of SHFM are, the mutations seem to lead to dysregulation of Fgf8 in AER cells of the central parts of the hands and feet and disruption of Wnt-Bmp-Fgf signaling pathways in AER.
Collapse
Affiliation(s)
- Piranit N Kantaputra
- Center of Excellence in Medical Genetics Research, Chiang Mai University, Chiang Mai, Thailand.,Division of Pediatric Dentistry, Department of Orthodontics and Pediatric Dentistry, Faculty of Dentistry, Chiang Mai University, Chiang Mai, Thailand.,Dentaland Clinic, Chiang Mai, Thailand
| | - Bruce M Carlson
- Department of Anatomy and Cell Biology, University of Michigan, Ann Arbor, Michigan
| |
Collapse
|
16
|
Shen Y, Si N, Liu Z, Liu F, Meng X, Zhang Y, Zhang X. 17p13.3 genomic rearrangement in a Chinese family with split-hand/foot malformation with long bone deficiency: report of a complicated duplication with marked variation in phenotype. Orphanet J Rare Dis 2018; 13:106. [PMID: 29970136 PMCID: PMC6029155 DOI: 10.1186/s13023-018-0838-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Accepted: 06/05/2018] [Indexed: 11/29/2022] Open
Abstract
Background Split hand/foot malformation (SHFM) is a genetically heterogeneous limb malformation with variable expressivity. SHFM with tibia or femur aplasia is called SHFM with long bone deficiency (SHFLD). 17p13.3 duplications containing BHLHA9 are associated with SHFLD. Cases with variable SHFLD phenotype and different 17p13.3 duplicated regions are reported. The severity of long bone defect could not be simply explained by BHLHA9 overdosage or 17p13.3 duplication. Methods A four-generation Chinese SHFM family was recruited. Three family members have long bone defects, one male was severely affected with hypoplasia or aplasia in three of four limbs. Linkage analysis and direct sequencing of candidate genes were used to exclude six responsible genes/loci for isolated SHFM. Array comparative genomic hybridization (CGH) was performed to detect copy number variations on a genome-wide scale, and quantitative real-time polymerase chain reaction (qPCR) assays were designed to validate the identified copy number variation in the index and other family members. Results No mutations were found in genes or loci linked to isolated SHFM. A ~ 966 kb duplication was identified in 17p13.3 by array CGH, in which BHLHA9 surrounding region presented as triplication. The qPCR assays confirmed the indicated 17p13.3 duplication as well as BHLHA9 triplication in all available affected family members and other two asymptomatic carriers. Given the incomplete penetrance in SHFLD, those two carriers were regarded as non-penetrant, which suggested that the genomic rearrangement was co-segregated with malformation in this family. Conclusions The present study reports an additional SHFLD family case with 17p13.3 genomic rearrangement. To our knowledge, the 966 kb genomic rearrangement is larger in size than any previously reported SHFLD-associated 17p13.3 duplication, and the present family shows marked phenotypic variability with two asymptomatic carriers and one patient with an extremely severe phenotype. This rare case provides the opportunity to identify underlying genotype-phenotype correlations between SHFLD and 17p13.3 genomic rearrangement. Electronic supplementary material The online version of this article (10.1186/s13023-018-0838-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Yuqi Shen
- McKusick-Zhang Center for Genetic Medicine, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, No.5 Dong Dan San Tiao, Dongcheng District, Beijing, 100005, China
| | - Nuo Si
- McKusick-Zhang Center for Genetic Medicine, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, No.5 Dong Dan San Tiao, Dongcheng District, Beijing, 100005, China
| | - Zhe Liu
- Laboratory of Clinical Genetics, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1 Shuaifuyuan, Wangfujing, Dongcheng District, Beijing, 100073, China
| | - Fang Liu
- McKusick-Zhang Center for Genetic Medicine, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, No.5 Dong Dan San Tiao, Dongcheng District, Beijing, 100005, China
| | - Xiaolu Meng
- McKusick-Zhang Center for Genetic Medicine, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, No.5 Dong Dan San Tiao, Dongcheng District, Beijing, 100005, China
| | - Ying Zhang
- Department of Obstetrics and Gynecology, Tianjin Medical University General Hospital, No.154, Anshan Road, Heping District, Tianjin, 300052, China.
| | - Xue Zhang
- McKusick-Zhang Center for Genetic Medicine, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, No.5 Dong Dan San Tiao, Dongcheng District, Beijing, 100005, China. .,Laboratory of Clinical Genetics, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1 Shuaifuyuan, Wangfujing, Dongcheng District, Beijing, 100073, China.
| |
Collapse
|
17
|
Malik S. Mesoaxial synostotic syndactyly with phalangeal reduction (MSSD): syndactyly type IX. Skeletal Radiol 2018; 47:149. [PMID: 29230504 DOI: 10.1007/s00256-017-2842-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 11/28/2017] [Indexed: 02/02/2023]
Affiliation(s)
- Sajid Malik
- Human Genetics Program, Department of Animal Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan.
| |
Collapse
|
18
|
Zhu XJ, Fang Y, Xiong Y, Wang M, Yang X, Li Y, Zhang X, Dai ZM, Qiu M, Zhang Z, Zhang Z. Disruption of Wnt production in Shh
lineage causes bone malformation in mice, mimicking human Malik-Percin-type syndactyly. FEBS Lett 2018; 592:356-368. [DOI: 10.1002/1873-3468.12963] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 12/08/2017] [Accepted: 12/22/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Xiao-Jing Zhu
- Institute of Life Sciences; College of Life and Environmental Science; Key Laboratory of Mammalian Organogenesis and Regeneration; Hangzhou Normal University; Zhejiang China
| | - Yukun Fang
- Institute of Life Sciences; College of Life and Environmental Science; Key Laboratory of Mammalian Organogenesis and Regeneration; Hangzhou Normal University; Zhejiang China
| | - Yanan Xiong
- Institute of Life Sciences; College of Life and Environmental Science; Key Laboratory of Mammalian Organogenesis and Regeneration; Hangzhou Normal University; Zhejiang China
| | - Min Wang
- Institute of Life Sciences; College of Life and Environmental Science; Key Laboratory of Mammalian Organogenesis and Regeneration; Hangzhou Normal University; Zhejiang China
| | - Xueqin Yang
- Institute of Life Sciences; College of Life and Environmental Science; Key Laboratory of Mammalian Organogenesis and Regeneration; Hangzhou Normal University; Zhejiang China
| | - Yan Li
- Institute of Life Sciences; College of Life and Environmental Science; Key Laboratory of Mammalian Organogenesis and Regeneration; Hangzhou Normal University; Zhejiang China
| | - Xiaoyun Zhang
- Institute of Life Sciences; College of Life and Environmental Science; Key Laboratory of Mammalian Organogenesis and Regeneration; Hangzhou Normal University; Zhejiang China
| | - Zhong-Min Dai
- Institute of Life Sciences; College of Life and Environmental Science; Key Laboratory of Mammalian Organogenesis and Regeneration; Hangzhou Normal University; Zhejiang China
| | - Mengsheng Qiu
- Institute of Life Sciences; College of Life and Environmental Science; Key Laboratory of Mammalian Organogenesis and Regeneration; Hangzhou Normal University; Zhejiang China
| | - Ze Zhang
- Department of Ophthalmology; Tulane Medical Center; Tulane University; New Orleans LA USA
| | - Zunyi Zhang
- Institute of Life Sciences; College of Life and Environmental Science; Key Laboratory of Mammalian Organogenesis and Regeneration; Hangzhou Normal University; Zhejiang China
| |
Collapse
|
19
|
Kataoka K, Matsushima T, Ito Y, Sato T, Yokoyama S, Asahara H. Bhlha9 regulates apical ectodermal ridge formation during limb development. J Bone Miner Metab 2018; 36:64-72. [PMID: 28324176 PMCID: PMC6324935 DOI: 10.1007/s00774-017-0820-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 01/25/2017] [Indexed: 10/19/2022]
Abstract
Split hand/foot malformation (SHFM) and SHFM combined with long-bone deficiency (SHFLD) are congenital dysgeneses of the limb. Although six different loci/mutations (SHFM1-SHFM6) have been found from studies on families with SHFM, the causes and associated pathogenic mechanisms for a large number of patients remain unidentified. On the basis of the identification of a duplicated gene region involving BHLHA9 in some affected families, BHLHA9 was identified as a novel SHFM/SHFLD-related gene. Although Bhlha9 is predicted to participate in limb development as a transcription factor, its precise function is unclear. Therefore, to study its physiological function, we generated a Bhlha9-knockout mouse and investigated gene expression and the associated phenotype in the limb bud. Bhlha9-knockout mice showed syndactyly and poliosis in the limb. Moreover, some apical ectodermal ridge (AER) formation related genes, including Trp63, exhibited an aberrant expression pattern in the limb bud of Bhlha9-knockout mice; TP63 (Trp63) was regulated by Bhlha9 on the basis of in vitro analysis. These observations suggest that Bhlha9 regulates AER formation during limb/finger development by regulating the expression of some AER-formation-related genes and abnormal expression of Bhlha9 leads to SHFM and SHFLD via dysregulation of AER formation and associated gene expression.
Collapse
Affiliation(s)
- Kensuke Kataoka
- Department of Systems BioMedicine, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Takahide Matsushima
- Department of Systems BioMedicine, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Yoshiaki Ito
- Department of Systems BioMedicine, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Tempei Sato
- Department of Systems BioMedicine, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Shigetoshi Yokoyama
- Department of Systems Biomedicine, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo, 157-0074, Japan
| | - Hiroshi Asahara
- Department of Systems BioMedicine, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan.
- Department of Systems Biomedicine, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo, 157-0074, Japan.
| |
Collapse
|
20
|
Khan A, Wang R, Han S, Ahmad W, Zhang X. A novel homozygous missense mutation in BHLHA9 causes mesoaxial synostotic syndactyly with phalangeal reduction in a Pakistani family. Hum Genome Var 2017; 4:17054. [PMID: 29263794 PMCID: PMC5729216 DOI: 10.1038/hgv.2017.54] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 10/10/2017] [Accepted: 10/22/2017] [Indexed: 11/10/2022] Open
Abstract
Mesoaxial synostotic syndactyly with phalangeal reduction (MSSD) is a rare non-syndromic limb malformation with autosomal recessive inheritance. To date, only a few affected families with MSSD who had BHLHA9 mutations have been reported. The present report describes a consanguineous Pakistani family with five affected individuals with MSSD who exhibited an autosomal recessive pattern. Genotyping followed by Sanger sequencing was performed, and we identified a novel homozygous missense mutation (c.311T>C, p.Ile104Thr) in the BHLHA9 gene. This finding expands the spectrum of known mutations in the BHLHA9 gene that cause MSSD.
Collapse
Affiliation(s)
- Amjad Khan
- The Research Center for Medical Genomics, China Medical University, Shenyang, China.,McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China.,Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Rongrong Wang
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Shirui Han
- The Research Center for Medical Genomics, China Medical University, Shenyang, China.,McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Wasim Ahmad
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Xue Zhang
- The Research Center for Medical Genomics, China Medical University, Shenyang, China.,McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| |
Collapse
|
21
|
Noncoding copy-number variations are associated with congenital limb malformation. Genet Med 2017; 20:599-607. [PMID: 29236091 DOI: 10.1038/gim.2017.154] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 07/11/2017] [Indexed: 01/17/2023] Open
Abstract
PurposeCopy-number variants (CNVs) are generally interpreted by linking the effects of gene dosage with phenotypes. The clinical interpretation of noncoding CNVs remains challenging. We investigated the percentage of disease-associated CNVs in patients with congenital limb malformations that affect noncoding cis-regulatory sequences versus genes sensitive to gene dosage effects.MethodsWe applied high-resolution copy-number analysis to 340 unrelated individuals with isolated limb malformation. To investigate novel candidate CNVs, we re-engineered human CNVs in mice using clustered regularly interspaced short palindromic repeats (CRISPR)-based genome editing.ResultsOf the individuals studied, 10% harbored CNVs segregating with the phenotype in the affected families. We identified 31 CNVs previously associated with congenital limb malformations and four novel candidate CNVs. Most of the disease-associated CNVs (57%) affected the noncoding cis-regulatory genome, while only 43% included a known disease gene and were likely to result from gene dosage effects. In transgenic mice harboring four novel candidate CNVs, we observed altered gene expression in all cases, indicating that the CNVs had a regulatory effect either by changing the enhancer dosage or altering the topological associating domain architecture of the genome.ConclusionOur findings suggest that CNVs affecting noncoding regulatory elements are a major cause of congenital limb malformations.
Collapse
|
22
|
Carter TC, Sicko RJ, Kay DM, Browne ML, Romitti PA, Edmunds ZL, Liu A, Fan R, Druschel CM, Caggana M, Brody LC, Mills JL. Copy-number variants and candidate gene mutations in isolated split hand/foot malformation. J Hum Genet 2017; 62:877-884. [PMID: 28539665 PMCID: PMC5612852 DOI: 10.1038/jhg.2017.56] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 04/19/2017] [Accepted: 04/25/2017] [Indexed: 12/27/2022]
Abstract
Split hand/foot malformation (SHFM) is a congenital limb deficiency with missing or shortened central digits. Some SHFM genes have been identified but the cause of many SHFM cases is unknown. We used single-nucleotide polymorphism (SNP) microarray analysis to detect copy-number variants (CNVs) in 25 SHFM cases without other birth defects from New York State (NYS), prioritized CNVs absent from population CNV databases, and validated these CNVs using quantitative real-time polymerase chain reaction (qPCR). We tested for the validated CNVs in seven cases from Iowa using qPCR, and also sequenced 36 SHFM candidate genes in all the subjects. Seven NYS cases had a potentially deleterious variant: two had a p.R225H or p.R225L mutation in TP63, one had a 17q25 microdeletion, one had a 10q24 microduplication and three had a 17p13.3 microduplication. In addition, one Iowa case had a de novo 10q24 microduplication. The 17q25 microdeletion has not been reported previously in SHFM and included two SHFM candidate genes (SUMO2 and GRB2), while the 10q24 and 17p13.3 CNVs had breakpoints within genomic regions that contained putative regulatory elements and a limb development gene. In SHFM pathogenesis, the microdeletion may cause haploinsufficiency of SHFM genes and/or deletion of their regulatory regions, and the microduplications could disrupt regulatory elements that control transcription of limb development genes.
Collapse
Affiliation(s)
- Tonia C. Carter
- Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 6710B Building, Room 3117, Bethesda, MD 20892, USA
| | - Robert J. Sicko
- Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, Albany, NY 12201-2002, USA
| | - Denise M. Kay
- Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, Albany, NY 12201-2002, USA
| | - Marilyn L. Browne
- Congenital Malformations Registry, New York State Department of Health, Empire State Plaza-Corning Tower, Albany, NY 12237, USA
- University at Albany School of Public Health, One University Place, Rensselaer, NY 12144, USA
| | - Paul A. Romitti
- Department of Epidemiology, College of Public Health, The University of Iowa, 145 N. Riverside Drive, Iowa City, IA 52242, USA
| | - Zoë L. Edmunds
- Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, Albany, NY 12201-2002, USA
| | - Aiyi Liu
- Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 6710B Building, Room 3117, Bethesda, MD 20892, USA
| | - Ruzong Fan
- Department of Biostatistics, Bioinformatics, and Biomathematics, 4000 Reservoir Road NW, Building D-180, Georgetown University Medical Center, Washington DC 20057, USA
| | - Charlotte M. Druschel
- Congenital Malformations Registry, New York State Department of Health, Empire State Plaza-Corning Tower, Albany, NY 12237, USA
| | - Michele Caggana
- Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, Albany, NY 12201-2002, USA
| | - Lawrence C. Brody
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Building 50, 50 South Drive, MSC 8004, Bethesda, MD 20892, USA
| | - James L. Mills
- Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 6710B Building, Room 3117, Bethesda, MD 20892, USA
| |
Collapse
|
23
|
Baas M, Stubbs AP, van Zessen DB, Galjaard RJH, van der Spek PJ, Hovius SER, van Nieuwenhoven CA. Identification of Associated Genes and Diseases in Patients With Congenital Upper-Limb Anomalies: A Novel Application of the OMT Classification. J Hand Surg Am 2017; 42:533-545.e4. [PMID: 28669419 DOI: 10.1016/j.jhsa.2017.03.043] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 01/09/2017] [Accepted: 03/30/2017] [Indexed: 02/02/2023]
Abstract
PURPOSE Congenital upper-limb anomalies (CULA) can present as a part of a syndrome or association. There is a wide spectrum of CULA, each of which might be related to different diseases. The structure provided by the Oberg, Manske, and Tonkin (OMT) classification could aid in differential diagnosis formulation in patients with CULA. The aims of this study were to review the Human Phenotype Ontology (HPO) project database for diseases and causative genes related to the CULA described in the OMT classification and to develop a methodology for differential diagnosis formulation based on the observed congenital anomalies, CulaPhen. METHODS We reviewed the HPO database for all diseases, including causative genes related to CULA. All CULA were classified according to the OMT classification; associated non-hand phenotypes were classified into 12 anatomical groups. We analyzed the contribution of each anatomical group to a given disease and developed a tool for differential diagnosis formulation based on these contributions. We compared our results with cases from the literature and with a current HPO tool, Phenomizer. RESULTS In total, 514 hand phenotypes were obtained, 384 of which could be classified in the OMT classification. A total of 1,403 diseases could be related to those CULA. A comparison with 10 recently published cases with CULA revealed that the presented phenotype matched the descriptions in our dataset. The differential diagnosis produced using our methodology was more accurate than Phenomizer in 4 of 5 examples. CONCLUSIONS The OMT classification can be used to describe hand anomalies that may present in over 1,400 diseases. CulaPhen was developed to provide a (hand) phenotype-based differential diagnosis. Differential diagnosis formulation based on the proposed system outperforms the system in current use. CLINICAL RELEVANCE This study illustrates that the OMT diagnoses, either individually or combined, can be cross-referenced with different diseases and syndromes. Therefore, use of the OMT classification can aid differential diagnosis formulation for CULA patients.
Collapse
Affiliation(s)
- Martijn Baas
- Department of Plastic and Reconstructive Surgery and Hand Surgery, Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Andrew P Stubbs
- Department of Clinical Genetics, Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - David B van Zessen
- Department of Clinical Genetics, Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Robert-Jan H Galjaard
- Department of Bioinformatics, Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Peter J van der Spek
- Department of Clinical Genetics, Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Steven E R Hovius
- Department of Plastic and Reconstructive Surgery and Hand Surgery, Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Christianne A van Nieuwenhoven
- Department of Plastic and Reconstructive Surgery and Hand Surgery, Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands.
| |
Collapse
|
24
|
Martorana D, Bonatti F, Mozzoni P, Vaglio A, Percesepe A. Monogenic Autoinflammatory Diseases with Mendelian Inheritance: Genes, Mutations, and Genotype/Phenotype Correlations. Front Immunol 2017; 8:344. [PMID: 28421071 PMCID: PMC5376573 DOI: 10.3389/fimmu.2017.00344] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 03/10/2017] [Indexed: 12/28/2022] Open
Abstract
Autoinflammatory diseases (AIDs) are a genetically heterogeneous group of diseases caused by mutations of genes encoding proteins, which play a pivotal role in the regulation of the inflammatory response. In the pathogenesis of AIDs, the role of the genetic background is triggered by environmental factors through the modulation of the innate immune system. Monogenic AIDs are characterized by Mendelian inheritance and are caused by highly penetrant genetic variants in single genes. During the last years, remarkable progress has been made in the identification of disease-associated genes by using new technologies, such as next-generation sequencing, which has allowed the genetic characterization in undiagnosed patients and in sporadic cases by means of targeted resequencing of a gene panel and whole exome sequencing. In this review, we delineate the genetics of the monogenic AIDs, report the role of the most common gene mutations, and describe the evidences of the most sound genotype/phenotype correlations in AID.
Collapse
Affiliation(s)
- Davide Martorana
- Unit of Medical Genetics, University Hospital of Parma, Parma, Italy
| | - Francesco Bonatti
- Department of Medicine and Surgery, University Hospital of Parma, Parma, Italy
| | - Paola Mozzoni
- Department of Medicine and Surgery, University Hospital of Parma, Parma, Italy
| | - Augusto Vaglio
- Unit of Nephrology, University Hospital of Parma, Parma, Italy
| | - Antonio Percesepe
- Department of Medicine and Surgery, University Hospital of Parma, Parma, Italy
| |
Collapse
|
25
|
Abstract
The limb is a commonly used model system for developmental biology. Given the need for precise control of complex signalling pathways to achieve proper patterning, the limb is also becoming a model system for gene regulation studies. Recent developments in genomic technologies have enabled the genome-wide identification of regulatory elements that control limb development, yielding insights into the determination of limb morphology and forelimb versus hindlimb identity. The modulation of regulatory interactions - for example, through the modification of regulatory sequences or chromatin architecture - can lead to morphological evolution, acquired regeneration capacity or limb malformations in diverse species, including humans.
Collapse
Affiliation(s)
- Florence Petit
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, California 94158, USA.,University of Lille, CHU Lille, EA 7364-RADEME, F-59000 Lille, France
| | - Karen E Sears
- School of Integrative Biology, Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801, USA
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, California 94158, USA.,Institute for Human Genetics, University of California San Francisco, California 94158, USA
| |
Collapse
|
26
|
Fusco C, Nittis PD, Alfaiz AA, Pellico MT, Augello B, Malerba N, Zelante L, Reymond A, Merla G. A New Split Hand/Foot Malformation with Long Bone Deficiency Familial Case. J Pediatr Genet 2016; 6:98-102. [PMID: 28496997 DOI: 10.1055/s-0036-1588029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 07/19/2016] [Indexed: 12/16/2022]
Abstract
Split hand/foot malformation with long bone deficiency (SHFLD) is a congenital limb anomaly where hands and/or feet cleft and syndactyly are associated with long bone defects, usually involving the tibia. Previously published data reported that 17p13.3 chromosomal duplication, including the BHLHA9 gene, has been associated with the distinct entity, termed SHFLD3 (OMIM 612576), inherited as an autosomal dominant trait. Here, we present a family with three members affected by SHFLD harboring BHLHA9 duplication. We exploited in vitro differentiation system to promote proband's skin fibroblasts toward osteoblastic lineage, and we observed a slight but consistent delay in the mineralization pattern. This result possibly suggests an impairment of the osteogenic process in the affected members.
Collapse
Affiliation(s)
- Carmela Fusco
- Medical Genetics Unit, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy
| | - Pasquelena De Nittis
- Medical Genetics Unit, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy.,Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Ali Abdullah Alfaiz
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.,Bioinformatics Core Facility, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Maria Teresa Pellico
- Medical Genetics Unit, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy
| | - Bartolomeo Augello
- Medical Genetics Unit, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy
| | - Natascia Malerba
- Medical Genetics Unit, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy
| | - Leopoldo Zelante
- Medical Genetics Unit, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Giuseppe Merla
- Medical Genetics Unit, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy
| |
Collapse
|
27
|
Phadke SR, Kar A, Bhowmik AD, Dalal A. Complex Camptosynpolydactyly and Mesoaxial synostotic syndactyly with phalangeal reduction are allelic disorders. Am J Med Genet A 2016; 170:1622-5. [PMID: 27041388 DOI: 10.1002/ajmg.a.37643] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 03/20/2016] [Indexed: 11/06/2022]
Abstract
Complex Camptosynpolydactyly is an autosomal recessive disorder characterized by complex hand deformities described earlier by us in a consanguineous family. We report on identification of mutations in BHLHA9 gene in this condition. Our results indicate that Complex Camptosynpolydactyly and Mesoaxial synostotic syndactyly with phalangeal reduction (MSSD) are likely to be allelic disorders. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Shubha R Phadke
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Anjana Kar
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India.,Graduate Studies, Manipal University, Manipal, India
| | - Aneek Das Bhowmik
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Ashwin Dalal
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| |
Collapse
|