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Cai Y, Zhao Z, Huang J, Yu Z, Jiang M, Kang S, Yuan X, Liu Y, Wu X, Ouyang J, Li W, Qian L. Morphological changes in flatfoot: a 3D analysis using weight-bearing CT scans. BMC Med Imaging 2024; 24:219. [PMID: 39160476 PMCID: PMC11331803 DOI: 10.1186/s12880-024-01396-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 08/07/2024] [Indexed: 08/21/2024] Open
Abstract
BACKGROUND Flatfoot is a condition resulting from complex three-dimensional (3D) morphological changes. Most Previous studies have been constrained by using two-dimensional radiographs and non-weight-bearing conditions. The deformity in flatfoot is associated with the 3D morphology of the bone. These morphological changes affect the force line conduction of the hindfoot/midfoot/forefoot, leading to further morphological alterations. Given that a two-dimensional plane axis overlooks the 3D structural information, it is essential to measure the 3D model of the entire foot in conjunction with the definition under the standing position. This study aims to analyze the morphological changes in flatfoot using 3D measurements from weight-bearing CT (WBCT). METHOD In this retrospective comparative our CT database was searched between 4-2021 and 3-2022. Following inclusion criteria were used: Patients were required to exhibit clinical symptoms suggestive of flatfoot, including painful swelling of the medial plantar area or abnormal gait, corroborated by clinical examination and confirmatory radiological findings on CT or MRI. Healthy participants were required to be free of any foot diseases or conditions affecting lower limb movement. After applying the exclusion criteria (Flatfoot with other foot diseases), CT scans (mean age = 20.9375, SD = 16.1) confirmed eligible for further analysis. The distance, angle in sagittal/transverse/coronal planes, and volume of the two groups were compared on reconstructed 3D models using the t-test. Logistic regression was used to identify flatfoot risk factors, which were then analyzed using receiver operating characteristic curves and nomogram. RESULT The flatfoot group exhibited significantly lower values for calcaneofibular distance (p = 0.001), sagittal and transverse calcaneal inclination angle (p < 0.001), medial column height (p < 0.001), sagittal talonavicular coverage angle (p < 0.001), and sagittal (p < 0.001) and transverse (p = 0.015) Hibb angle. In contrast, the sagittal lateral talocalcaneal angle (p = 0.013), sagittal (p < 0.001) and transverse (p = 0.004) talocalcaneal angle, transverse talonavicular coverage angle (p < 0.001), coronal Hibb angle (p < 0.001), and sagittal (p < 0.001) and transverse (p = 0.001) Meary's angle were significantly higher in the flatfoot group. The sagittal Hibb angle (B = - 0.379, OR = 0.684) and medial column height (B = - 0.990, OR = 0.372) were identified as significant risk factors for acquiring a flatfoot. CONCLUSION The findings validate the 3D spatial position alterations in flatfoot. These include the abduction of the forefoot and prolapse of the first metatarsal proximal, the arch collapsed, subluxation of the talonavicular joint in the midfoot, adduction and valgus of the calcaneus, adduction and plantar ward movement of the talus in the hindfoot, along with the first metatarsal's abduction and dorsiflexion in the forefoot.
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Affiliation(s)
- Yuchun Cai
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Zhe Zhao
- Hand and Foot Surgery Department, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, Guangdong, 518035, People's Republic of China
| | - Jianzhang Huang
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Zhendong Yu
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Manqi Jiang
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Shengjie Kang
- School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
| | - Xinghong Yuan
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Yingying Liu
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Xiaoliu Wu
- Radiologic Department, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, Guangdong, 518035, People's Republic of China
| | - Jun Ouyang
- Guangdong Provincial Key Laboratory of Digital Medicine and Biomechanics and Guangdong Engineering Research Center for Translation of Medical 3D Printing Application and National Virtual and Reality Experimental Education Center for Medical Morphology (Southern Medical University) and National Experimental Education Demonstration Center for Basic Medical Sciences (Southern Medical University) and National Key Discipline of Human Anatomy, Department of Spine Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China.
| | - Wencui Li
- Hand and Foot Surgery Department, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, Guangdong, 518035, People's Republic of China.
| | - Lei Qian
- Guangdong Provincial Key Laboratory of Digital Medicine and Biomechanics and Guangdong Engineering Research Center for Translation of Medical 3D Printing Application and National Virtual & Reality Experimental Education Center for Medical Morphology (Southern Medical University) and National Experimental Education Demonstration Center for Basic Medical Sciences (Southern Medical University) and National Key Discipline of Human Anatomy., School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China.
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Muhammad H, Haryana SM, Magetsari R, Karsten S, Saraswati PA. Genes on syndromic and idiopathic CTEV: A systematic review. INTERNATIONAL JOURNAL OF SURGERY OPEN 2022. [DOI: 10.1016/j.ijso.2022.100547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Sherer DM, Hsieh V, Granderson F, Yusuf H, Dalloul M. Mid-trimester isolated bilateral rocker bottom feet leading to prenatal diagnosis of 7q11.23 microdeletion: Williams syndrome. J Ultrasound 2022; 25:645-647. [PMID: 35001324 PMCID: PMC9402838 DOI: 10.1007/s40477-021-00638-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 11/17/2021] [Indexed: 11/28/2022] Open
Abstract
Prenatal sonographic depiction of congenital vertical talus (rocker bottom feet), describing a prominent calcaneus and rounded convex appearance of the ventral aspect of the foot, has been reported with fetal Trisomies 18, 13, 9 HOXD10 mutations and recently 2q13 microdeletion. We present a 24 year old in whom mid-trimester sonographic finding of isolated bilateral rocker bottom feet led to diagnosis of 7q11.23 microdeletion-Williams syndrome. This association has not been reported previously. This case emphasizes the critical assessment of detail microarray upon prenatal sonographic notation of abnormal structural fetal features.
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Affiliation(s)
- David M Sherer
- The Division of Maternal-Fetal Medicine, The Department of Obstetrics and Gynecology, State University of New York (SUNY), Downstate Health Sciences University, 450 Clarkson Avenue, Box 24, Brooklyn, NY, USA.
| | - Vicky Hsieh
- The Division of Maternal-Fetal Medicine, The Department of Obstetrics and Gynecology, State University of New York (SUNY), Downstate Health Sciences University, 450 Clarkson Avenue, Box 24, Brooklyn, NY, USA
| | - Freeda Granderson
- The Division of Maternal-Fetal Medicine, The Department of Obstetrics and Gynecology, State University of New York (SUNY), Downstate Health Sciences University, 450 Clarkson Avenue, Box 24, Brooklyn, NY, USA
| | - Hakeem Yusuf
- The Division of Maternal-Fetal Medicine, The Department of Obstetrics and Gynecology, State University of New York (SUNY), Downstate Health Sciences University, 450 Clarkson Avenue, Box 24, Brooklyn, NY, USA
| | - Mudar Dalloul
- The Division of Maternal-Fetal Medicine, The Department of Obstetrics and Gynecology, State University of New York (SUNY), Downstate Health Sciences University, 450 Clarkson Avenue, Box 24, Brooklyn, NY, USA
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Tayebi N, Charng WL, Dickson PI, Dobbs MB, Gurnett CA. Diagnostic yield of exome sequencing in congenital vertical talus. Eur J Med Genet 2022; 65:104514. [PMID: 35487415 PMCID: PMC10039454 DOI: 10.1016/j.ejmg.2022.104514] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 04/23/2022] [Indexed: 11/23/2022]
Abstract
BACKGROUND Congenital vertical talus (CVT), also known as "rocker-bottom foot", is a rare foot deformity associated with a dislocation of the talonavicular joint. Although genetic causes of CVT have been described in single isolated and syndromic families, whole-exome sequencing (WES) of large cohorts have not yet been reported. METHODS In this study, 62 probands with CVT were evaluated for likely causative single nucleotide variants (SNVs) and copy number variants (CNVs) using WES. Segregation of variants within families was determined by Sanger sequencing. RESULTS In this cohort, CVT occurred as an isolated anomaly in 75.8% (47/62) and was familial in 19.3% (12/62) of cases. Analysis of WES data led to the identification of likely causative variants in known disease genes in 30.6% (19/62) of all CVT probands. More than one proband had likely causative SNVs in TSHZ1, GDF5, and LMX1B. Only two probands had likely causative CNVs: a chromosome 12q13.13 deletion of the 5' HOXC gene cluster, and a chromosome 18q22.3q23 deletion involving TSHZ1. Familial CVT was strongly predictive of identifying a molecular diagnosis [75% (9/12) of familial cases compared to 20% (10/50) of non-familial cases (Chi-square test, P-value = 0.0002)]. There was no difference in the solved rate based on isolated or syndromic presentation, unilateral or bilateral affectation, or sex. CONCLUSIONS CVT is genetically heterogeneous and more often caused by SNVs than CNVs. There is a high yield of WES in familial CVT cases (∼75%). Additional research is needed to identify the causes of sporadic CVT, which had much lower solved rates.
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Affiliation(s)
- Naeimeh Tayebi
- Department of Neurology, Washington University in St Louis, St Louis, MO, USA
| | - Wu-Lin Charng
- Department of Neurology, Washington University in St Louis, St Louis, MO, USA
| | - Patricia I Dickson
- Department of Pediatrics, Washington University in St Louis, St Louis, MO, USA
| | - Matthew B Dobbs
- Department of Paley Orthopedic and Spine Institute, West Palm Beach, FL, 33401, USA
| | - Christina A Gurnett
- Department of Neurology, Washington University in St Louis, St Louis, MO, USA.
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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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Quiggle A, Charng WL, Antunes L, Nikolov M, Bledsoe X, Hecht JT, Dobbs MB, Gurnett CA. Whole Exome Sequencing in Individuals with Idiopathic Clubfoot Reveals a Recurrent Filamin B (FLNB) Deletion. Clin Orthop Relat Res 2022; 480:421-430. [PMID: 34491919 PMCID: PMC8747482 DOI: 10.1097/corr.0000000000001957] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 08/11/2021] [Indexed: 02/03/2023]
Abstract
BACKGROUND Clubfoot, a congenital deformity that presents as a rigid, inward turning of the foot, affects approximately 1 in 1000 infants and occurs as an isolated birth defect in 80% of patients. Despite its high level of heritability, few causative genes have been identified, and mutations in known genes are only responsible for a small portion of clubfoot heritability. QUESTIONS/PURPOSES (1) Are any rare gene variants enriched (that is, shared) in unrelated patients with isolated clubfoot? (2) Are there other rare variants in the identified gene (Filamin B) in these patients with clubfoot? METHODS Whole-exome sequence data were generated from a discovery cohort of 183 unrelated probands with clubfoot and 2492 controls. Variants were filtered with minor allele frequency < 0.02 to identify rare variants as well as small insertions and deletions (indels) resulting in missense variants, nonsense or premature truncation, or in-frame deletions. A candidate deletion was then genotyped in another cohort of 974 unrelated patients with clubfoot (a replication cohort). Other rare variants in the candidate gene were also investigated. A segregation analysis was performed in multigenerational families of individuals with clubfoot to see if the genotypes segregate with phenotypes. Single-variant association analysis was performed using the Fisher two-tailed exact test (exact p values are presented to give an indication of the magnitude of the association). RESULTS There were no recurrent variants in the known genes causing clubfoot in this study. A three-base pair in-frame codon deletion of Filamin B (FLNB) (p.E1792del, rs1470699812) was identified in 1.6% (3 of 183) of probands with clubfoot in the discovery cohort compared with 0% of controls (0 of 2492) (odds ratio infinity (inf) [95% CI 5.64 to inf]; p = 3.18 x 10-5) and 0.0016% of gnomAD controls (2 of 125,709) (OR 1.01 x 103 [95% CI 117.42 to 1.64 x 104]; p = 3.13 x 10-8). By screening a replication cohort (n = 974 patients), we found two probands with the identical FLNB deletion. In total, the deletion was identified in 0.43% (5 of 1157) of probands with clubfoot compared with 0% of controls and 0.0016% of gnomAD controls (OR 268.5 [95% CI 43.68 to 2.88 x 103]; p = 1.43 x 10-9). The recurrent FLNB p.E1792del variant segregated with clubfoot, with incomplete penetrance in two families. Affected individuals were more likely to be male and have bilateral clubfoot. Although most patients had isolated clubfoot, features consistent with Larsen syndrome, including upper extremity abnormalities such as elbow and thumb hypermobility and wide, flat thumbs, were noted in affected members of one family. We identified 19 additional rare FLNB missense variants located throughout the gene in patients with clubfoot. One of these missense variants, FLNB p.G2397D, exhibited incomplete penetrance in one family. CONCLUSION A recurrent FLNB E1792 deletion was identified in 0.43% of 1157 isolated patients with clubfoot. Given the absence of any recurrent variants in our discovery phase (n = 183) for any of the known genes causing clubfoot, our findings support that novel and rare missense variants in FLNB in patients with clubfoot, although rare, may be among the most commonly known genetic causes of clubfoot. Patients with FLNB variants often have isolated clubfoot, but they and their family members may be at an increased risk of having additional clinical features consistent with Larsen syndrome. CLINICAL RELEVANCE Identification of FLNB variants may be useful for determining clubfoot recurrence risk and comorbidities.
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Affiliation(s)
- Ashley Quiggle
- Department of Orthopaedic Surgery, Washington University in St. Louis, St. Louis, MO, USA
| | - Wu-Lin Charng
- Department of Neurology, Washington University in St. Louis, St. Louis, MO, USA
| | - Lilian Antunes
- Department of Orthopaedic Surgery, Washington University in St. Louis, St. Louis, MO, USA
| | - Momchil Nikolov
- Department of Neurology, Washington University in St. Louis, St. Louis, MO, USA
| | - Xavier Bledsoe
- Department of Neurology, Washington University in St. Louis, St. Louis, MO, USA
| | - Jacqueline T. Hecht
- Department of Pediatrics, McGovern Medical School and School of Dentistry, the University of Texas Health Science Center at Houston, Houston, TX, USA
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Hordyjewska-Kowalczyk E, Nowosad K, Jamsheer A, Tylzanowski P. Genotype-phenotype correlation in clubfoot (talipes equinovarus). J Med Genet 2021; 59:209-219. [PMID: 34782442 DOI: 10.1136/jmedgenet-2021-108040] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 10/21/2021] [Indexed: 12/21/2022]
Abstract
Clubfoot (talipes equinovarus) is a congenital malformation affecting muscles, bones, connective tissue and vascular or neurological structures in limbs. It has a complex aetiology, both genetic and environmental. To date, the most important findings in clubfoot genetics involve PITX1 variants, which were linked to clubfoot phenotype in mice and humans. Additionally, copy number variations encompassing TBX4 or single nucleotide variants in HOXC11, the molecular targets of the PITX1 transcription factor, were linked to the clubfoot phenotype. In general, genes of cytoskeleton and muscle contractile apparatus, as well as components of the extracellular matrix and connective tissue, are frequently linked with clubfoot aetiology. Last but not least, an equally important element, that brings us closer to a better understanding of the clubfoot genotype/phenotype correlation, are studies on the two known animal models of clubfoot-the pma or EphA4 mice. This review will summarise the current state of knowledge of the molecular basis of this congenital malformation.
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Affiliation(s)
- Ewa Hordyjewska-Kowalczyk
- Department of Biomedical Sciences, Laboratory of Molecular Genetics, Medical University of Lublin, Lublin, Lubelskie, Poland
| | - Karol Nowosad
- Department of Biomedical Sciences, Laboratory of Molecular Genetics, Medical University of Lublin, Lublin, Lubelskie, Poland.,The Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland.,Department of Cell Biology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Aleksander Jamsheer
- Department of Medical Genetics, Poznan University of Medical Sciences, Poznan, Wielkopolskie, Poland
| | - Przemko Tylzanowski
- Department of Biomedical Sciences, Laboratory of Molecular Genetics, Medical University of Lublin, Lublin, Lubelskie, Poland .,Department of Development and Regeneration, Skeletal Biology and Engineering Research Centre, KU Leuven, Leuven, Flanders, Belgium
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Ding J, Liang Z, Feng W, Cai Q, Zhang Z. Integrated Bioinformatics Analysis Reveals Potential Pathway Biomarkers and Their Interactions for Clubfoot. Med Sci Monit 2020; 26:e925249. [PMID: 32829375 PMCID: PMC7462570 DOI: 10.12659/msm.925249] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Background Congenital talipes equinovarus (clubfoot), one of the most regular pediatric congenital skeletal anomalies, seriously affects the normal growth and development of about 1 in 1000 newborns. Although it has been investigated widely, the etiology and pathogenesis of clubfoot are still controversial. Material/Methods g: Profiler, NetworkAnalyst and WebGestalt were used to probe the enriched signaling pathways by using the Gene Ontology (GO), Human Phenotype Ontology (HP), Kyoto Encyclopedia of Genes and Genomes (KEGG), Reactome (REAC), and WikiPathways (WP) databases. Large numbers of enriched signaling pathways were identified using the integrated bioinformatics enrichment analyses. Results Apoptosis or programmed cell death (PCD), disease, muscle contraction, metabolism, and immune system were the top functions. Embryo or organ morphogenesis and development, cell or muscle contraction, and apoptosis were the top biological processes, and cell/muscle contraction and apoptosis were the top molecular functions using enriched GO terms analysis. There were a large number of complex interactions in the genes, enriched pathways, and transcription factor (TF)-miRNA co-regulatory networks. Transcription factors such as FOXN3, GLI3, HOX, and NCOR2 family regulated the gene expression of APAF1, BCL2, BID, CASP, MTHFR, and TPM family. Conclusions The results of bioinformatics enrichment analysis not only supported the previously proposed hypotheses, e.g., extracellular matrix (ECM) abnormality, fetal movement reducing, genetic abnormality, muscle abnormality, neurological abnormality, skeletal abnormality and vascular abnormality, but also indicated that cellular or immune responses to external stimulus, molecular transport and metabolism may be new etiological mechanisms in clubfoot.
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Affiliation(s)
- Jing Ding
- Department of Pediatric Orthopaedics, Xin Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China (mainland)
| | - Zhenpeng Liang
- Department of Pediatric Orthopaedics, Xin Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China (mainland)
| | - Weijia Feng
- Department of Pediatric Orthopaedics, Xin Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China (mainland)
| | - Qixun Cai
- Department of Pediatric Orthopaedics, Xin Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China (mainland)
| | - Ziming Zhang
- Department of Pediatric Orthopaedics, Xin Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China (mainland)
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Brotto DB, Siena ÁDD, de Barros II, Carvalho SDCES, Muys BR, Goedert L, Cardoso C, Plaça JR, Ramão A, Squire JA, Araujo LF, Silva WAD. Contributions of HOX genes to cancer hallmarks: Enrichment pathway analysis and review. Tumour Biol 2020; 42:1010428320918050. [PMID: 32456563 DOI: 10.1177/1010428320918050] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Homeobox genes function as master regulatory transcription factors during development, and their expression is often altered in cancer. The HOX gene family was initially studied intensively to understand how the expression of each gene was involved in forming axial patterns and shaping the body plan during embryogenesis. More recent investigations have discovered that HOX genes can also play an important role in cancer. The literature has shown that the expression of HOX genes may be increased or decreased in different tumors and that these alterations may differ depending on the specific HOX gene involved and the type of cancer being investigated. New studies are also emerging, showing the critical role of some members of the HOX gene family in tumor progression and variation in clinical response. However, there has been limited systematic evaluation of the various contributions of each member of the HOX gene family in the pathways that drive the common phenotypic changes (or "hallmarks") and that underlie the transformation of normal cells to cancer cells. In this review, we investigate the context of the engagement of HOX gene targets and their downstream pathways in the acquisition of competence of tumor cells to undergo malignant transformation and tumor progression. We also summarize published findings on the involvement of HOX genes in carcinogenesis and use bioinformatics methods to examine how their downstream targets and pathways are involved in each hallmark of the cancer phenotype.
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Affiliation(s)
- Danielle Barbosa Brotto
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.,National Institute of Science and Technology in Stem Cell and Cell Therapy (INCT/CNPq) and Center for Cell-Based Therapy, CEPID/FAPESP, Ribeirão Preto, Brazil
| | - Ádamo Davi Diógenes Siena
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.,National Institute of Science and Technology in Stem Cell and Cell Therapy (INCT/CNPq) and Center for Cell-Based Therapy, CEPID/FAPESP, Ribeirão Preto, Brazil
| | - Isabela Ichihara de Barros
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.,National Institute of Science and Technology in Stem Cell and Cell Therapy (INCT/CNPq) and Center for Cell-Based Therapy, CEPID/FAPESP, Ribeirão Preto, Brazil
| | - Simone da Costa E Silva Carvalho
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.,National Institute of Science and Technology in Stem Cell and Cell Therapy (INCT/CNPq) and Center for Cell-Based Therapy, CEPID/FAPESP, Ribeirão Preto, Brazil
| | - Bruna Rodrigues Muys
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.,National Institute of Science and Technology in Stem Cell and Cell Therapy (INCT/CNPq) and Center for Cell-Based Therapy, CEPID/FAPESP, Ribeirão Preto, Brazil
| | - Lucas Goedert
- National Institute of Science and Technology in Stem Cell and Cell Therapy (INCT/CNPq) and Center for Cell-Based Therapy, CEPID/FAPESP, Ribeirão Preto, Brazil.,Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Cibele Cardoso
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.,National Institute of Science and Technology in Stem Cell and Cell Therapy (INCT/CNPq) and Center for Cell-Based Therapy, CEPID/FAPESP, Ribeirão Preto, Brazil
| | - Jessica Rodrigues Plaça
- National Institute of Science and Technology in Stem Cell and Cell Therapy (INCT/CNPq) and Center for Cell-Based Therapy, CEPID/FAPESP, Ribeirão Preto, Brazil
| | - Anelisa Ramão
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.,National Institute of Science and Technology in Stem Cell and Cell Therapy (INCT/CNPq) and Center for Cell-Based Therapy, CEPID/FAPESP, Ribeirão Preto, Brazil
| | - Jeremy Andrew Squire
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.,Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON, Canada
| | - Luiza Ferreira Araujo
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.,National Institute of Science and Technology in Stem Cell and Cell Therapy (INCT/CNPq) and Center for Cell-Based Therapy, CEPID/FAPESP, Ribeirão Preto, Brazil
| | - Wilson Araújo da Silva
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.,National Institute of Science and Technology in Stem Cell and Cell Therapy (INCT/CNPq) and Center for Cell-Based Therapy, CEPID/FAPESP, Ribeirão Preto, Brazil.,Center for Integrative System Biology (CISBi), NAP/USP, University of São Paulo, Ribeirão Preto, Brazil.,Center for Medical Genomics, Clinics Hospital, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
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Habic A, Mattick JS, Calin GA, Krese R, Konc J, Kunej T. Genetic Variations of Ultraconserved Elements in the Human Genome. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2020; 23:549-559. [PMID: 31689173 DOI: 10.1089/omi.2019.0156] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Ultraconserved elements (UCEs) are among the most popular DNA markers for phylogenomic analysis. In at least three of five placental mammalian genomes (human, dog, cow, mouse, and rat), 2189 UCEs of at least 200 bp in length that are identical have been identified. Most of these regions have not yet been functionally annotated, and their associations with diseases remain largely unknown. This is an important knowledge gap in human genomics with regard to UCE roles in physiologically critical functions, and by extension, their relevance for shared susceptibilities to common complex diseases across several mammalian organisms in the event of their polymorphic variations. In the present study, we remapped the genomic locations of these UCEs to the latest human genome assembly, and examined them for documented polymorphisms in sequenced human genomes. We identified 29,983 polymorphisms within analyzed UCEs, but revealed that a vast majority exhibits very low minor allele frequencies. Notably, only 112 of the identified polymorphisms are associated with a phenotype in the Ensembl genome browser. Through literature analyses, we confirmed associations of 37 (i.e., out of the 112) polymorphisms within 23 UCEs with 25 diseases and phenotypic traits, including, muscular dystrophies, eye diseases, and cancers (e.g., familial adenomatous polyposis). Most reports of UCE polymorphism-disease associations appeared to be not cognizant that their candidate polymorphisms were actually within UCEs. The present study offers strategic directions and knowledge gaps for future computational and experimental work so as to better understand the thus far intriguing and puzzling role(s) of UCEs in mammalian genomes.
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Affiliation(s)
- Anamarija Habic
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domzale, Slovenia
| | - John S Mattick
- School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, Australia.,Green Templeton College, University of Oxford, Oxford, United Kingdom
| | - George Adrian Calin
- Department of Experimental Therapeutics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas.,The Center for RNA Interference and Noncoding RNAs, The University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Rok Krese
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domzale, Slovenia
| | - Janez Konc
- National Institute of Chemistry, Ljubljana, Slovenia
| | - Tanja Kunej
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domzale, Slovenia
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Sherer DM, Hsieh V, Muppala R, Granderson F, Dalloul M. Isolated Bilateral Rocker Bottom Feet Associated With 2q13 Microdeletion. JOURNAL OF ULTRASOUND IN MEDICINE : OFFICIAL JOURNAL OF THE AMERICAN INSTITUTE OF ULTRASOUND IN MEDICINE 2020; 39:637-638. [PMID: 31520474 DOI: 10.1002/jum.15132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 08/09/2019] [Indexed: 06/10/2023]
Affiliation(s)
- David M Sherer
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, State University of New York, Downstate Health Sciences University, Brooklyn, New York, USA
| | - Vicky Hsieh
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, State University of New York, Downstate Health Sciences University, Brooklyn, New York, USA
| | - Reshma Muppala
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, State University of New York, Downstate Health Sciences University, Brooklyn, New York, USA
| | - Freda Granderson
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, State University of New York, Downstate Health Sciences University, Brooklyn, New York, USA
| | - Mudar Dalloul
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, State University of New York, Downstate Health Sciences University, Brooklyn, New York, USA
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Zhang L, Xu X, Chen Y, Li L, Zhang L, Li Q. Mapping of developmental dysplasia of the hip to two novel regions at 8q23-q24 and 12p12. Exp Ther Med 2020; 19:2799-2803. [PMID: 32256763 DOI: 10.3892/etm.2020.8513] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Accepted: 01/01/2020] [Indexed: 12/24/2022] Open
Abstract
Developmental dysplasia of the hip (DDH), previously known as congenital hip dislocation, is a frequently disabling condition characterized by premature arthritis later in life. Genetic factors play a key role in the aetiology of DDH. In the present study, a genome-wide linkage scan with the Affymetrix 10K GeneChip was performed on a four-generation Chinese family, which included 19 healthy members and 5 patients. Parametric and non-parametric multipoint linkage analyses were carried out with Genespring GT v.2.0 software, and the logarithm of odds (LOD) score and nonparametric linkage (NPL) score were calculated. Parametric linkage analysis was performed, assuming an autosomal recessive trait with full penetrance and Affymetrix 'Asian' allele frequencies. The strongest evidence for linkage was found on chromosome 8q23-24, with a peak LOD score of 2.658 (θ=0), covering 2.377 Mb from single nucleotide polymorphisms (SNPs) rs724717 to rs720132. This interval included nine additional successive SNPs: rs1566071, rs1902121, rs756404, rs702768, rs777813, rs2033995, rs147959, rs2884367 and rs1898287. The same region also yielded the highest NPL score of 2.883 (P=0.0156) from the non-parametric multipoint linkage analysis. Additionally, the second highest NPL score of 2.727 (P=0.0156) and LOD score of 2.528 (θ=0) were obtained on chromosome 12p12 for three consecutive markers (rs1919980, rs763853 and rs725124). This region overlapped a narrow distance of 0.642 Mb. Notably, in addition to these two regions; no significant linkage was identified for other chromosomal regions (with LOD and NPL scores >2.0). For the first time, at least for this pedigree, the evidence in the present study showed that DDH is mapped to two novel regions at 8q23-q24 and 12p12.
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Affiliation(s)
- Lixin Zhang
- Department of Pediatric Orthopaedics, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Xiaowen Xu
- Department of Pediatric Orthopaedics, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Yufan Chen
- Department of Pediatric Orthopaedics, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Lianyong Li
- Department of Pediatric Orthopaedics, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Lijun Zhang
- Department of Pediatric Orthopaedics, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Qiwei Li
- Department of Pediatric Orthopaedics, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
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Cai G, Yang X, Chen T, Jin F, Ding J, Wu Z. Integrated bioinformatics analysis of potential pathway biomarkers using abnormal proteins in clubfoot. PeerJ 2020; 8:e8422. [PMID: 31998564 PMCID: PMC6977474 DOI: 10.7717/peerj.8422] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 12/17/2019] [Indexed: 12/28/2022] Open
Abstract
Background As one of the most common major congenital distal skeletal abnormalities, congenital talipes equinovarus (clubfoot) affects approximately one in one thousandth newborns. Although several etiologies of clubfoot have been proposed and several genes have been identified as susceptible genes, previous studies did not further explore signaling pathways and potential upstream and downstream regulatory networks. Therefore, the aim of the present investigation is to explore abnormal pathways and their interactions in clubfoot using integrated bioinformatics analyses. Methods KEGG, gene ontology (GO), Reactome (REAC), WikiPathways (WP) or human phenotype ontology (HP) enrichment analysis were performed using WebGestalt, g:Profiler and NetworkAnalyst. Results A large number of signaling pathways were enriched e.g. signal transduction, disease, metabolism, gene expression (transcription), immune system, developmental biology, cell cycle, and ECM. Protein-protein interactions (PPIs) and gene regulatory networks (GRNs) analysis results indicated that extensive and complex interactions occur in these proteins, enrichment pathways, and TF-miRNA coregulatory networks. Transcription factors such as SOX9, CTNNB1, GLI3, FHL2, TGFBI and HOXD13, regulated these candidate proteins. Conclusion The results of the present study supported previously proposed hypotheses, such as ECM, genetic, muscle, neurological, skeletal, and vascular abnormalities. More importantly, the enrichment results also indicated cellular or immune responses to external stimuli, and abnormal molecular transport or metabolism may be new potential etiological mechanisms of clubfoot.
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Affiliation(s)
- Guiquan Cai
- Department of Orthopaedics, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xuan Yang
- Department of Pediatric Orthopaedics, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ting Chen
- Department of Pediatric Orthopaedics, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Fangchun Jin
- Department of Pediatric Orthopaedics, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jing Ding
- Department of Pediatric Orthopaedics, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Zhenkai Wu
- Department of Pediatric Orthopaedics, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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Li J, Wu J, Liu Y, Li Y, Xiao Z, Jiang X, Tang Y, Xu H. HOXA9 rs3801776 G>A polymorphism increases congenital talipes equinovarus risk in a Chinese population. J Gene Med 2019; 21:e3119. [PMID: 31424148 DOI: 10.1002/jgm.3119] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 07/11/2019] [Accepted: 08/08/2019] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Congenital talipes equinovarus (CTEV) is the most common congenital deformity in children, and muscular dysplasia plays a potential role in the etiology of CTEV. Notably, previous studies have found that HOXA9 rs3801776 and TPM2 rs2025126 genetic polymorphisms play important roles in regulating muscle development in Caucasian children; however, there is a lack of investigations conducted in Chinese children. METHODS We conducted a hospital-based, case-control study of 189 children with CTEV and 457 CTEV-free children aiming to examine the associations between these two polymorphisms and CTEV susceptibility. The rs3801776 (G>A) and rs2025126 (G>A) polymorphisms were genotyped using TaqMan. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated to measure the associations between the selected polymorphisms and CTEV susceptibility. RESULTS We found that rs3801776A was associated with increased CTEV risk (GA versus GG: adjusted OR = 1.81, 95% CI = 1.22-2.69, p = 0.0031; AA versus GG: adjusted OR = 2.19, 95% CI = 1.28-3.73, p = 0.0041; GA/AA versus GG: adjusted OR = 1.89, 95% CI = 1.29-2.76, p = 0.0010). In a stratified analysis, the risk effect of rs3801776 GA/AA was observed in both unilateral and bilateral patients. CONCLUSIONS The present study suggests that the rs3801776 G>A polymorphism is associated with CTEV risk in Chinese children; however, this conclusion should be validated in larger studies.
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Affiliation(s)
- Jingchun Li
- Department of Paediatric Orthopaedics, Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jianping Wu
- Department of Paediatric Orthopaedics, Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Yanhan Liu
- Department of Paediatric Orthopaedics, Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Yiqiang Li
- Department of Paediatric Orthopaedics, Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Zhilan Xiao
- Department of Paediatric Surgery, Guangzhou Institute of Paediatrics, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Xiaoling Jiang
- Department of Paediatric Surgery, Guangzhou Institute of Paediatrics, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Yaping Tang
- Department of Paediatric Surgery, Guangzhou Institute of Paediatrics, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Hongwen Xu
- Department of Paediatric Orthopaedics, Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, Guangzhou, Guangdong, China
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Abstract
PURPOSE Congenital clubfoot is a serious birth defect that affects nearly 0.1% of all births. Though there is strong evidence for a genetic basis of isolated clubfoot, aside from a handful of associations, much of the heritability remains unexplained. METHODS By systematically examining the genes involved in syndromic clubfoot, we may find new candidate genes and pathways to investigate in isolated clubfoot. RESULTS In addition to the expected enrichment of extracellular matrix and transforming growth factor beta (TGF-β) signalling genes, we find many genes involved in syndromic clubfoot encode peroxisomal matrix proteins, as well as enzymes necessary for sulfation of proteoglycans, an important part of connective tissue. Further, the association of Filamin B with isolated clubfoot as well as syndromic clubfoot is an encouraging finding. CONCLUSION We should examine these categories for enrichment in isolated clubfoot patients to increase our understanding of the underlying biology and pathophysiology of this deformity. Understanding the spectrum of syndromes that have clubfoot as a feature enables a better understanding of the underlying pathophysiology of the disorder and directs future genetic screening efforts toward certain genes and genetic pathways. LEVEL OF EVIDENCE V.
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Affiliation(s)
- B. Sadler
- Department of Neurology, Washington University in St. Louis, St Louis, Missouri, USA
| | - C. A. Gurnett
- Department of Neurology, Washington University in St. Louis, St Louis, Missouri, USA
| | - M. B. Dobbs
- Department of Orthopaedic Surgery, Washington University in St. Louis, St. Louis, Missouri, USA,Correspondence should be sent to Matthew B. Dobbs, MD, 1 Children’s Place, Suite 4S-60, Department of Orthopedic Surgery, 660 S Euclid Ave, Campus Box 8233, Washington University in St Louis, St Louis, Missouri 63110, USA. E-mail:
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16
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Pavone V, Chisari E, Vescio A, Lucenti L, Sessa G, Testa G. The etiology of idiopathic congenital talipes equinovarus: a systematic review. J Orthop Surg Res 2018; 13:206. [PMID: 30134936 PMCID: PMC6104023 DOI: 10.1186/s13018-018-0913-z] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 08/15/2018] [Indexed: 12/19/2022] Open
Abstract
Background Also known as clubfoot, idiopathic congenital talipes equinovarus (ICTEV) is the most common pediatric deformity and occurs in 1 in every 1000 live births. Even though it has been widely researched, the etiology of ICTEV remains poorly understood and is often described as being based on a multifactorial genesis. Genetic and environmental factors seem to have a major role in the development of this disease. Thus, the aim of this review is to analyze the available literature to document the current evidence on ICTEV etiology. Methods The literature on ICTEV etiology was systematically reviewed using the following inclusion criteria: studies of any level of evidence, reporting clinical or preclinical results, published in the last 20 years (1998–2018), and dealing with the etiology of ICTEV. Results A total of 48 articles were included. ICTEV etiology is still controversial. Several hypotheses have been researched, but none of them are decisive. Emerging evidence suggests a role of several pathways and gene families associated with limb development (HOX family; PITX1-TBX4), the apoptotic pathway (caspases), and muscle contractile protein (troponin and tropomyosin), but a major candidate gene has still not been identified. Strong recent evidence emerging from twin studies confirmed major roles of genetics and the environment in the disease pathogenesis. Conclusions The available literature on the etiology of ICTEV presents major limitations in terms of great heterogeneity and a lack of high-profile studies. Although many studies focus on the genetic background of the disease, there is lack of consensus on one or multiple targets. Genetics and smoking seem to be strongly associated with ICTEV etiology, but more studies are needed to understand the complex and multifactorial genesis of this common congenital lower-limb disease.
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Affiliation(s)
- Vito Pavone
- Department of General Surgery and Medical Surgical Specialties, Section of Orthopaedics and Traumatology, University Hospital Policlinico-Vittorio Emanuele, University of Catania, Via Plebiscito, 628, 95124, Catania, Italy
| | - Emanuele Chisari
- Department of General Surgery and Medical Surgical Specialties, Section of Orthopaedics and Traumatology, University Hospital Policlinico-Vittorio Emanuele, University of Catania, Via Plebiscito, 628, 95124, Catania, Italy
| | - Andrea Vescio
- Department of General Surgery and Medical Surgical Specialties, Section of Orthopaedics and Traumatology, University Hospital Policlinico-Vittorio Emanuele, University of Catania, Via Plebiscito, 628, 95124, Catania, Italy
| | - Ludovico Lucenti
- Department of General Surgery and Medical Surgical Specialties, Section of Orthopaedics and Traumatology, University Hospital Policlinico-Vittorio Emanuele, University of Catania, Via Plebiscito, 628, 95124, Catania, Italy
| | - Giuseppe Sessa
- Department of General Surgery and Medical Surgical Specialties, Section of Orthopaedics and Traumatology, University Hospital Policlinico-Vittorio Emanuele, University of Catania, Via Plebiscito, 628, 95124, Catania, Italy
| | - Gianluca Testa
- Department of General Surgery and Medical Surgical Specialties, Section of Orthopaedics and Traumatology, University Hospital Policlinico-Vittorio Emanuele, University of Catania, Via Plebiscito, 628, 95124, Catania, Italy.
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Rubio EI, Mehta N, Blask AR, Bulas DI. Prenatal congenital vertical talus (rocker bottom foot): a marker for multisystem anomalies. Pediatr Radiol 2017; 47:1793-1799. [PMID: 28879597 DOI: 10.1007/s00247-017-3957-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 06/18/2017] [Accepted: 07/26/2017] [Indexed: 11/30/2022]
Abstract
BACKGROUND Congenital vertical talus is a rare foot anomaly characterized by a prominent calcaneus and rigid forefoot dorsiflexion. While congenital vertical talus has been associated with anomalies such as trisomy 18, myelomeningocele and arthrogryposis, postnatal series have reported cases of isolated congenital vertical talus. OBJECTIVE The purpose of our study was to determine the incidence of isolated congenital vertical talus prenatally and identify the most common anomalies associated with this finding. MATERIALS AND METHODS A retrospective review was performed of congenital vertical talus cases identified in our fetal center from 2006 to 2015. The prenatal US and MR imaging appearance of congenital vertical talus was evaluated and differentiation from congenital talipes equinovarus was assessed. Studies were evaluated for additional abnormalities affecting the central nervous system, face, limbs, viscera, growth and amniotic fluid. Imaging findings were recorded and correlated with outcomes when available. RESULTS Twenty-four cases of congenital vertical talus were identified prenatally (gestational age: 19-36 weeks). All 24 had prenatal US and 21 also underwent fetal MRI on the same day. There were no isolated cases of congenital vertical talus in this series; all 24 had additional anomalies identified prenatally. Sixteen cases had bilateral congenital vertical talus (67%). Additional anomalies were identified in the brain (15), spine (11), face (6), abdominal wall (3), heart (8) and other limbs (12). Chromosomal abnormalities were identified in 6 of 20 patients who underwent genetic testing. Overall, US held some advantage in detecting the abnormality: in 10 cases, US depicted congenital vertical talus more clearly than MRI; in 8 cases, US and MRI were equal in detection and in 3 cases, MRI was superior. In 9/15 cases with intracranial abnormalities, MRI was superior to US in demonstrating structural anomalies. Outcomes included termination (11), intrauterine fetal demise (1), stillbirth or immediate neonatal demise (5), lost to follow-up (1), and 6 survivors with postnatal follow-up. CONCLUSION In our series, there were no cases of isolated congenital vertical talus, with additional anomalies variably affecting multiple systems including the brain, spine, face, viscera and limbs. When congenital vertical talus is identified prenatally, a thorough search for additional anomalies is indicated. Fetal MRI can be a useful adjunct in confirming the diagnosis and further delineating additional anomalies, particularly in the brain and spine.
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Affiliation(s)
- Eva I Rubio
- Division of Diagnostic Imaging and Radiology, Children's National Health System, 111 Michigan Ave., NW, Washington, DC, 20010, USA.
| | - Nimisha Mehta
- George Washington University School of Medicine, Washington, DC, USA
| | - Anna R Blask
- Division of Diagnostic Imaging and Radiology, Children's National Health System, 111 Michigan Ave., NW, Washington, DC, 20010, USA
| | - Dorothy I Bulas
- Division of Diagnostic Imaging and Radiology, Children's National Health System, 111 Michigan Ave., NW, Washington, DC, 20010, USA
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Basit S, Khoshhal KI. Genetics of clubfoot; recent progress and future perspectives. Eur J Med Genet 2017; 61:107-113. [PMID: 28919208 DOI: 10.1016/j.ejmg.2017.09.006] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 09/05/2017] [Accepted: 09/10/2017] [Indexed: 12/20/2022]
Abstract
Clubfoot or talipes equinovarus (TEV) is an inborn three-dimensional deformity of leg, ankle and foot. It results from structural defects of several tissues of foot and lower leg leading to abnormal positioning of foot and ankle joints. TEV can lead to long-lasting functional disability, malformation and discomfort if left untreated. Substantial progress has been achieved in the management and diagnosis of limb defects; however, not much is known about the molecular players and signalling pathways underlying TEV disorder. The homeostasis and development of the limb depends on the complex interactions between the lateral plate mesoderm cells and outer ectoderm. These complex interactions include HOX signalling and PITX1-TBX4 pathways. The susceptibility to develop TEV is determined by a number of environmental and genetic factors, although the nature and level of interplay between them remains unclear. Familial occurrence and inter and intra phenotypic variability of TEV is well documented. Variants in genes that code for contractile proteins of skeletal myofibers might play a role in the aetiology of TEV but, to date, no strong candidate genes conferring increased risk have emerged, although variants in TBX4, PITX1, HOXA, HOXC and HOXD clusters genes, NAT2 and others have been shown to be associated with TEV. The mechanisms by which variants in these genes confer risk and the nature of the physical and genetic interaction between them remains to be determined. Elucidation of genetic players and cellular pathways underlying TEV will certainly increase our understanding of the pathophysiology of this deformity.
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Affiliation(s)
- Sulman Basit
- Centre for Genetics and Inherited Diseases, Taibah University Almadinah Almunawwarah, Saudi Arabia.
| | - Khalid I Khoshhal
- College of Medicine, Taibah University Almadinah Almunawwarah, Saudi Arabia
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Dobbs MB, Gurnett CA. The 2017 ABJS Nicolas Andry Award: Advancing Personalized Medicine for Clubfoot Through Translational Research. Clin Orthop Relat Res 2017; 475:1716-1725. [PMID: 28236079 PMCID: PMC5406347 DOI: 10.1007/s11999-017-5290-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 02/16/2017] [Indexed: 01/31/2023]
Abstract
BACKGROUND Clubfoot is one of the most common pediatric orthopaedic disorders. While the Ponseti method has revolutionized clubfoot treatment, it is not effective for all patients. When the Ponseti method does not correct the foot, patients are at risk for lifelong disability and may require more-extensive surgery. QUESTIONS/PURPOSES (1) What genetic and morphologic abnormalities contribute to the development of clubfoot? (2) How can this information be used to devise personalized treatment paradigms for patients with clubfoot? METHODS Human gene sequencing, molecular genetic engineering of mouse models of clubfoot, MRI of clubfoot, and development of new treatment methods all have been used by our group to understand the biological basis and improve therapy for this group of disorders. RESULTS We gained new insight into clubfoot pathogenesis from our discovery that mutations in the PITX1-TBX4-HOXC transcriptional pathway cause familial clubfoot and vertical talus in a small number of families, with the unique lower limb expression of these genes providing an explanation for the lack of upper extremity involvement in these disorders. MRI studies revealed corresponding morphologic abnormalities, including hypomorphic muscle, bone, and vasculature, that are not only associated with these gene mutations, but also are biomarkers for treatment-resistant clubfoot. CONCLUSIONS Based on an understanding of the underlying biology, we improved treatment methods for neglected and syndromic clubfoot, developed new treatment for congenital vertical talus based on the principles of the Ponseti method, and designed a new dynamic clubfoot brace to improve strength and compliance.
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Affiliation(s)
- Matthew B. Dobbs
- 0000 0000 9953 7617grid.416775.6Department of Orthopaedics, St. Louis Children’s Hospital, 1 Children’s Place, Suite 4S-60, St. Louis, MO 63110 USA
| | - Christina A. Gurnett
- 0000 0001 2355 7002grid.4367.6Department of Neurology, Washington University School of Medicine in St Louis, St. Louis, MO USA
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Sinha N, A. Seeley M, S. Horwitz D, Maniar H, H. Seeley A. Pediatric Orthogenomics: The Latest Trends and Controversies. AIMS MEDICAL SCIENCE 2017. [DOI: 10.3934/medsci.2017.2.192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Jin K, Sukumar S. HOX genes: Major actors in resistance to selective endocrine response modifiers. Biochim Biophys Acta Rev Cancer 2016; 1865:105-10. [PMID: 26803986 DOI: 10.1016/j.bbcan.2016.01.003] [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: 12/14/2015] [Revised: 01/19/2016] [Accepted: 01/20/2016] [Indexed: 12/29/2022]
Abstract
Long term treatment with therapies aimed at blocking the estrogen- (ER) or androgen receptor (AR) action often leads to the development of resistance to selective modulators of the estrogen receptor (SERMs) in ERα-positive breast cancer, or of the androgen receptor (SARMs) in AR-positive prostate cancer. Many underlying molecular events that confer resistance are known, but a unifying theme is yet to be revealed. Receptor tyrosine kinases (RTKs) such EGFR, ERBB2 and IGF1R are major mediators that can directly alter cellular response to the SERM, tamoxifen, but the mechanisms underlying increased expression of RTKs are not clear. A number of HOX genes and microRNAs and non-coding RNAs residing in the HOX cluster, have been identified as important independent predictors of endocrine resistant breast cancer. Recently, convincing evidence has accumulated that several members belonging to the four different HOX clusters contribute to endocrine therapy resistant breast cancer, but the mechanisms remain obscure. In this article, we have reviewed recent progress in understanding of the functioning of HOX genes and regulation of their expression by hormones. We also discuss, in particular, the contributions of several members of the HOX gene family to endocrine resistant breast cancer.
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Affiliation(s)
- Kideok Jin
- Breast Cancer Program, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States; Department of Biomedical Engineering at Johns Hopkins, 720 Rutland Avenue, 617 Traylor Bldg., Baltimore, MD 21205, United States.
| | - Saraswati Sukumar
- Breast Cancer Program, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States.
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Alvarado DM, McCall K, Hecht JT, Dobbs MB, Gurnett CA. Deletions of 5' HOXC genes are associated with lower extremity malformations, including clubfoot and vertical talus. J Med Genet 2016; 53:250-5. [PMID: 26729820 DOI: 10.1136/jmedgenet-2015-103505] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 11/29/2015] [Indexed: 01/07/2023]
Abstract
BACKGROUND Deletions of the HOXC gene cluster result in variable phenotypes in mice, but have been rarely described in humans. OBJECTIVE To report chromosome 12q13.13 microdeletions ranging from 13 to 175 kb and involving the 5' HOXC genes in four families, segregating congenital lower limb malformations, including clubfoot, vertical talus and hip dysplasia. METHODS Probands (N=253) with clubfoot or vertical talus were screened for point mutations and copy number variants using multiplexed direct genomic selection, a pooled BAC targeted capture approach. SNP genotyping included 1178 probands with clubfoot or vertical talus and 1775 controls. RESULTS The microdeletions share a minimal non-coding region overlap upstream of HOXC13, with variable phenotypes depending upon HOXC13, HOXC12 or the HOTAIR lncRNA inclusion. SNP analysis revealed HOXC11 p.Ser191Phe segregating with clubfoot in a small family and enrichment of HOXC12 p.Asn176Lys in patients with clubfoot or vertical talus (rs189468720, p=0.0057, OR=3.8). Defects in limb morphogenesis include shortened and overlapping toes, as well as peroneus muscle hypoplasia. Finally, HOXC and HOXD gene expression is reduced in fibroblasts from a patient with a 5' HOXC deletion, consistent with previous studies demonstrating that dosage of lncRNAs alters expression of HOXD genes in trans. CONCLUSIONS Because HOXD10 has been implicated in the aetiology of congenital vertical talus, variation in its expression may contribute to the lower limb phenotypes occurring with 5' HOXC microdeletions. Identification of 5' HOXC microdeletions highlights the importance of transcriptional regulators in the aetiology of severe lower limb malformations and will improve their diagnosis and management.
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Affiliation(s)
- David M Alvarado
- Department of Orthopedic Surgery, Washington University, St. Louis, Missouri, USA
| | - Kevin McCall
- Department of Orthopedic Surgery, Washington University, St. Louis, Missouri, USA
| | - Jacqueline T Hecht
- Department of Pediatrics, University of Texas Medical School, Houston, Texas, USA
| | - Matthew B Dobbs
- Department of Orthopedic Surgery, Washington University, St. Louis, Missouri, USA Shriners Hospital for Children, St Louis, Missouri, USA
| | - Christina A Gurnett
- Department of Orthopedic Surgery, Washington University, St. Louis, Missouri, USA Department of Neurology, Washington University, St. Louis, Missouri, USA Department of Pediatrics, Washington University, St. Louis, Missouri, USA
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Kember RL, Georgi B, Bailey-Wilson JE, Stambolian D, Paul SM, Bućan M. Copy number variants encompassing Mendelian disease genes in a large multigenerational family segregating bipolar disorder. BMC Genet 2015; 16:27. [PMID: 25887117 PMCID: PMC4382929 DOI: 10.1186/s12863-015-0184-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 02/19/2015] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Bipolar affective disorder (BP) is a common, highly heritable psychiatric disorder characterized by periods of depression and mania. Using dense SNP genotype data, we characterized CNVs in 388 members of an Old Order Amish Pedigree with bipolar disorder. We identified CNV regions arising from common ancestral mutations by utilizing the pedigree information. By combining this analysis with whole genome sequence data in the same individuals, we also explored the role of compound heterozygosity. RESULTS Here we describe 541 inherited CNV regions, of which 268 are rare in a control population of European origin but present in a large number of Amish individuals. In addition, we highlight a set of CNVs found at higher frequencies in BP individuals, and within genes known to play a role in human development and disease. As in prior reports, we find no evidence for an increased burden of CNVs in BP individuals, but we report a trend towards a higher burden of CNVs in known Mendelian disease loci in bipolar individuals (BPI and BPII, p = 0.06). CONCLUSIONS We conclude that CNVs may be contributing factors in the phenotypic presentation of mood disorders and co-morbid medical conditions in this family. These results reinforce the hypothesis of a complex genetic architecture underlying BP disorder, and suggest that the role of CNVs should continue to be investigated in BP data sets.
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Affiliation(s)
- Rachel L Kember
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA.
| | - Benjamin Georgi
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA.
| | - Joan E Bailey-Wilson
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, MD, USA.
| | - Dwight Stambolian
- Department of Ophthalmology, University of Pennsylvania, Philadelphia, PA, USA.
| | - Steven M Paul
- Appel Alzheimer's Disease Research Institute, Mind and Brain Institute, Weill Cornell Medical College, New York, NY, USA.
| | - Maja Bućan
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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24
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Ritelli M, Chiarelli N, Zoppi N, Dordoni C, Quinzani S, Traversa M, Venturini M, Calzavara-Pinton P, Colombi M. Insights in the etiopathology of galactosyltransferase II (GalT-II) deficiency from transcriptome-wide expression profiling of skin fibroblasts of two sisters with compound heterozygosity for two novel B3GALT6 mutations. Mol Genet Metab Rep 2014. [PMID: 28649518 PMCID: PMC5471164 DOI: 10.1016/j.ymgmr.2014.11.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Mutations in B3GALT6, encoding the galactosyltransferase II (GalT-II) involved in the synthesis of the glycosaminoglycan (GAG) linkage region of proteoglycans (PGs), have recently been associated with a spectrum of connective tissue disorders, including spondyloepimetaphyseal dysplasia with joint laxity type 1 (SEMDJL1) and Ehlers–Danlos-like syndrome. Here, we report on two sisters compound heterozygous for two novel B3GALT6 mutations that presented with severe short stature and progressive kyphoscoliosis, joint hypermobility and laxity, hyperextensible skin, platyspondyly, short ilia, and elbow malalignment. Microarray-based transcriptome analysis revealed the differential expression of several genes encoding extracellular matrix (ECM) structural components, including COMP, SPP1, COL5A1, and COL15A1, enzymes involved in GAG synthesis and in ECM remodeling, such as CSGALNACT1, CHPF, LOXL3, and STEAP4, signaling transduction molecules of the TGFβ/BMP pathway, i.e., GDF6, GDF15, and BMPER, and transcription factors of the HOX and LIM families implicated in skeletal and limb development. Immunofluorescence analyses confirmed the down-regulated expression of some of these genes, in particular of the cartilage oligomeric matrix protein and osteopontin, encoded by COMP and SPP1, respectively, and showed the predominant reduction and disassembly of the heparan sulfate specific GAGs, as well as of the PG perlecan and type III and V collagens. The key role of GalT-II in GAG synthesis and the crucial biological functions of PGs are consistent with the perturbation of many physiological functions that are critical for the correct architecture and homeostasis of various connective tissues, including skin, bone, cartilage, tendons, and ligaments, and generates the wide phenotypic spectrum of GalT-II-deficient patients. Clinical features/molecular characterization of two patients with spondyloepimetaphyseal dysplasia with joint laxity type 1 Identification of two novel B3GALT6 mutations First report of transcriptome-wide gene expression profiling on GalT-II-deficient fibroblasts Immunofluorescence studies of several ECM structural components in GalT-II-deficient cells Enlargement of the knowledge on the GalT-II deficiency’s molecular pathogenesis
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Key Words
- ATCS, adducted-thumb club foot syndrome
- Abs, antibodies
- B3GALT6
- BMP, bone morphogenetic proteins
- C4ST, chondroitin 4-sulfotransferase
- C6ST, chondroitin 6-sulfotransferase
- COLLI, type I collagen
- COLLIII, type III collagen
- COLLV, type V collagen
- COLLs, collagens
- COMP, cartilage oligomeric matrix protein
- CS, chondroitin sulfate
- CSGALNACT1, chondroitin sulfate N-acetylgalactosaminyltransferase 1
- CTDs, connective tissue disorders
- Cartilage oligomeric matrix protein
- ChPF, chondroitin polymerizing factor
- ChSy, chondroitin synthase
- D4ST, dermatan 4 sulfotransferase 1
- DCN, decorin
- DEGs, differentially expressed genes
- DS, dermatan sulfate
- ECM, extracellular matrix
- EDS, Ehlers–Danlos syndrome
- Ehlers–Danlos syndrome
- FN, fibronectin
- GAGs, glycosaminoglycans
- GO, gene ontology
- Gal, galactose
- GalNAc, N-acetylgalactosamine
- GalNAc4S-6ST, GalNAc 4-sulfate 6-O-sulfotransferase
- GalNAcT, β1,4-N-acetylgalactosaminyltransferase
- GalNAcT-16, N-acetylgalactosaminyltransferase 16
- GalT-I/II, galactosyltransferase I and II
- GalT-II deficiency
- GlcA, glucuronic acid
- GlcAT, glucuronosyltransferase
- GlcNAc, N-acetylglucosamine
- GlcNAcT, α1,4-N-acetylglucosaminyltransferase
- HA, hyaluronic acid
- HAS2, hyaluronan synthase 2
- HOX, homeobox gene family
- HPO, human phenotype ontology
- HS, heparan sulfate
- Hep, heparin
- IF, immunofluorescence microscopy studies
- IdoA, iduronic acid
- OPN, osteopontin
- Osteopontin
- PGs, proteoglycans
- PTC, premature termination codon of translation
- SEMDJL1, spondyloepimetaphyseal dysplasia with joint laxity type 1
- Spondyloepimetaphyseal dysplasia with joint laxity type 1
- TNs, tenascins
- Xyl, xylose
- XylT, xylosyltransferase
- qPCR, quantitative polymerase chain reaction
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Affiliation(s)
- Marco Ritelli
- Division of Biology and Genetics, Department of Molecular and Translational Medicine, School of Medicine, University of Brescia, Brescia, Italy
| | - Nicola Chiarelli
- Division of Biology and Genetics, Department of Molecular and Translational Medicine, School of Medicine, University of Brescia, Brescia, Italy
| | - Nicoletta Zoppi
- Division of Biology and Genetics, Department of Molecular and Translational Medicine, School of Medicine, University of Brescia, Brescia, Italy
| | - Chiara Dordoni
- Division of Biology and Genetics, Department of Molecular and Translational Medicine, School of Medicine, University of Brescia, Brescia, Italy
| | - Stefano Quinzani
- Division of Biology and Genetics, Department of Molecular and Translational Medicine, School of Medicine, University of Brescia, Brescia, Italy
| | - Michele Traversa
- Division of Biology and Genetics, Department of Molecular and Translational Medicine, School of Medicine, University of Brescia, Brescia, Italy
| | - Marina Venturini
- Division of Dermatology, Department of Clinical and Experimental Sciences, Spedali Civili University Hospital, Brescia, Italy
| | - Piergiacomo Calzavara-Pinton
- Division of Dermatology, Department of Clinical and Experimental Sciences, Spedali Civili University Hospital, Brescia, Italy
| | - Marina Colombi
- Division of Biology and Genetics, Department of Molecular and Translational Medicine, School of Medicine, University of Brescia, Brescia, Italy
- Corresponding author at: Division of Biology and Genetics, Department of Molecular and Translational Medicine, School of Medicine, University of Brescia, Viale Europa 11, 25123 Brescia, Italy.
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25
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Bacino CA, Hecht JT. Etiopathogenesis of equinovarus foot malformations. Eur J Med Genet 2014; 57:473-9. [PMID: 24932901 DOI: 10.1016/j.ejmg.2014.06.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 06/03/2014] [Indexed: 01/28/2023]
Abstract
Congenital talipes equinovarus (CTEV) is the most common musculoskeletal birth defect affecting approximately 1/700-1/1000 of liveborns. Even though extensive epidemiological and genetic studies have been carried out to address its causes, the precise mechanisms leading to this common birth defect remain elusive. CTEV is a multifactorial disorder, hence the combination of genetic and environmental factors are known contributors to this developmental abnormality. So far a handful of genes involved in limb patterning like PITX1, HOXA, HOXD, TBX4, and RBM10, as well as genes involved in muscle contraction, have been identified as possible players. Among many environmental factors investigated, maternal smoking seems to hold the strongest consistent association with this disorder. This article will review and discuss some of the most common genetic and environmental factors associated with the etiopathogenesis of CTEV.
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Affiliation(s)
- Carlos A Bacino
- Baylor College of Medicine, Department of Molecular and Human Genetics, Houston, TX, USA.
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26
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Zhang TX, Haller G, Lin P, Alvarado DM, Hecht JT, Blanton SH, Stephens Richards B, Rice JP, Dobbs MB, Gurnett CA. Genome-wide association study identifies new disease loci for isolated clubfoot. J Med Genet 2014; 51:334-9. [DOI: 10.1136/jmedgenet-2014-102303] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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27
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Abstract
The Hox genes are an evolutionarily conserved family of genes, which encode a class of important transcription factors that function in numerous developmental processes. Following their initial discovery, a substantial amount of information has been gained regarding the roles Hox genes play in various physiologic and pathologic processes. These processes range from a central role in anterior-posterior patterning of the developing embryo to roles in oncogenesis that are yet to be fully elucidated. In vertebrates there are a total of 39 Hox genes divided into 4 separate clusters. Of these, mutations in 10 Hox genes have been found to cause human disorders with significant variation in their inheritance patterns, penetrance, expressivity and mechanism of pathogenesis. This review aims to describe the various phenotypes caused by germline mutation in these 10 Hox genes that cause a human phenotype, with specific emphasis paid to the genotypic and phenotypic differences between allelic disorders. As clinical whole exome and genome sequencing is increasingly utilized in the future, we predict that additional Hox gene mutations will likely be identified to cause distinct human phenotypes. As the known human phenotypes closely resemble gene-specific murine models, we also review the homozygous loss-of-function mouse phenotypes for the 29 Hox genes without a known human disease. This review will aid clinicians in identifying and caring for patients affected with a known Hox gene disorder and help recognize the potential for novel mutations in patients with phenotypes informed by mouse knockout studies.
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Affiliation(s)
- Shane C Quinonez
- University of Michigan, Department of Pediatrics, Division of Pediatric Genetics, 1500 East Medical Center Drive, D5240 MPB/Box 5718, Ann Arbor, MI 48109-5718, USA.
| | - Jeffrey W Innis
- University of Michigan, Department of Pediatrics, Division of Pediatric Genetics, 1500 East Medical Center Drive, D5240 MPB/Box 5718, Ann Arbor, MI 48109-5718, USA; University of Michigan, Department of Human Genetics, 1241 E. Catherine, 4909 Buhl Building, Ann Arbor, MI 48109-5618, USA.
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28
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Nishida N, Tokunaga K, Mizokami M. Genome-Wide Association Study Reveals Host Genetic Factors for Liver Diseases. J Clin Transl Hepatol 2013; 1:45-50. [PMID: 26357606 PMCID: PMC4521269 DOI: 10.14218/jcth.2013.010xx] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Revised: 05/13/2013] [Accepted: 05/22/2013] [Indexed: 12/11/2022] Open
Abstract
A number of disease-associated genetic markers for common liver diseases have been identified using genome-wide association studies (GWASs). The GWAS strategy is based on genome-wide single-nucleotide polymorphism typing technologies, which are now commercially available, accompanied by statistical methods to identify host genetic factors that are associated with target diseases or complex genetic traits. One of the most striking features of the GWAS strategy is the ability to identify unexpected disease-associated genetic markers across the entire human genome. Here, we describe the technological aspects of the GWAS strategy with examples from actual GWAS reports related to hepatitis research, including drug response for patients with chronic hepatitis C, susceptibility to primary biliary cirrhosis, and hepatitis-B-related hepatocellular carcinoma.
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Affiliation(s)
- Nao Nishida
- The Research Center for Hepatitis & Immunology, National Center for Global Health and Medicine, Ichikawa, Chiba, Japan
- Department of Human Genetics, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Katsushi Tokunaga
- Department of Human Genetics, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Masashi Mizokami
- The Research Center for Hepatitis & Immunology, National Center for Global Health and Medicine, Ichikawa, Chiba, Japan
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29
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Mark PR, Radlinski BC, Core N, Fryer A, Kirk EP, Haldeman-Englert CR. Narrowing the critical region for congenital vertical talus in patients with interstitial 18q deletions. Am J Med Genet A 2013; 161A:1117-21. [PMID: 23495172 DOI: 10.1002/ajmg.a.35791] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2012] [Accepted: 10/31/2012] [Indexed: 11/11/2022]
Abstract
Interstitial deletions of 18q lead to a number of phenotypic features, including multiple types of foot deformities. Many of these associated phenotypes have had their critical regions narrowly defined. Here we report on three patients with small overlapping deletions of chromosome 18q determined by microarray analysis (chr18:72493281-73512553 hg19 coordinates). All of the patients have congenital vertical talus (CVT). Based on these findings and previous reports in the literature and databases, we narrow the critical region for CVT to a minimum of five genes (ZNF407, ZADH2, TSHZ1, C18orf62, and ZNF516), and propose that TSHZ1 is the likely causative gene for CVT in 18q deletion syndrome.
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Affiliation(s)
- Paul R Mark
- Department of Medical Genetics, Spectrum Health, Grand Rapids, MI 49503, USA.
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30
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Okamoto N, Tamura D, Nishimura G, Shimojima K, Yamamoto T. Submicroscopic deletion of 12q13 including HOXC gene cluster with skeletal anomalies and global developmental delay. Am J Med Genet A 2011; 155A:2997-3001. [PMID: 22069146 DOI: 10.1002/ajmg.a.34324] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2011] [Accepted: 09/04/2011] [Indexed: 11/11/2022]
Abstract
We report on a patient with a submicroscopic deletion of 12q13 detected by array-CGH and confirmed by FISH. He was haploinsufficient for the HOXC gene cluster and some other neighboring genes. HOX genes have an important role in the initial formation of the body. The patient showed characteristic features including severe kyphoscoliosis, digital abnormalities, cardiac anomaly, expressive language, and global developmental delay. Radiologic features of the fingers had some similarities with those for multiple synostosis syndrome. No human genetic disorders due to HOXC abnormalities are yet known. We tentatively assume that his skeletal anomalies are associated with haploinsufficiency of the HOXC gene cluster. Further studies are necessary to determine the clinical importance of haploinsufficiency of the HOXC gene cluster.
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Affiliation(s)
- Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Medical Center and Research Institute for Maternal and Child Health, Osaka, Japan.
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31
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Samuels ME. Saturation of the human phenome. Curr Genomics 2011; 11:482-99. [PMID: 21532833 PMCID: PMC3048311 DOI: 10.2174/138920210793175886] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2010] [Revised: 06/22/2010] [Accepted: 06/22/2010] [Indexed: 12/26/2022] Open
Abstract
The phenome is the complete set of phenotypes resulting from genetic variation in populations of an organism. Saturation of a phenome implies the identification and phenotypic description of mutations in all genes in an organism, potentially constrained to those encoding proteins. The human genome is believed to contain 20-25,000 protein coding genes, but only a small fraction of these have documented mutant phenotypes, thus the human phenome is far from complete. In model organisms, genetic saturation entails the identification of multiple mutant alleles of a gene or locus, allowing a consistent description of mutational phenotypes for that gene. Saturation of several model organisms has been attempted, usually by targeting annotated coding genes with insertional transposons (Drosophila melanogaster, Mus musculus) or by sequence directed deletion (Saccharomyces cerevisiae) or using libraries of antisense oligonucleotide probes injected directly into animals (Caenorhabditis elegans, Danio rerio). This paper reviews the general state of the human phenome, and discusses theoretical and practical considerations toward a saturation analysis in humans. Throughout, emphasis is placed on high penetrance genetic variation, of the kind typically asociated with monogenic versus complex traits.
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Affiliation(s)
- Mark E Samuels
- Centre de Recherche de Ste-Justine, 3175, Côte Ste-Catherine, Montréal QC H3T 1C5, Canada
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32
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Merrill LJ, Gurnett CA, Connolly AM, Pestronk A, Dobbs MB. Skeletal muscle abnormalities and genetic factors related to vertical talus. Clin Orthop Relat Res 2011; 469:1167-74. [PMID: 20645034 PMCID: PMC3048242 DOI: 10.1007/s11999-010-1475-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2010] [Accepted: 07/06/2010] [Indexed: 02/07/2023]
Abstract
BACKGROUND/RATIONALE Congenital vertical talus is a fixed dorsal dislocation of the talonavicular joint and fixed equinus contracture of the hindfoot, causing a rigid deformity recognizable at birth. The etiology and epidemiology of this condition are largely unknown, but some evidence suggests it relates to aberrations of skeletal muscle. Identifying the tissue abnormalities and genetic causes responsible for vertical talus has the potential to lead to improved treatment and preventive strategies. QUESTIONS/PURPOSES We therefore (1) determined whether skeletal muscle abnormalities are present in patients with vertical talus and (2) identified associated congenital anomalies and genetic abnormalities in these patients. METHODS We identified associated congenital anomalies and genetic abnormalities present in 61 patients affected with vertical talus. We obtained abductor hallucis muscle biopsy specimens from the affected limbs of 11 of the 61 patients and compared the histopathologic characteristics with those of age-matched control subjects. RESULTS All muscle biopsy specimens (n = 11) had abnormalities compared with those from control subjects including combinations of abnormal variation in muscle fiber size (n = 7), type I muscle fiber smallness (n = 6), and abnormal fiber type predominance (n = 5). Isolated vertical talus occurred in 23 of the 61 patients (38%), whereas the remaining 38 patients had associated nervous system, musculoskeletal system, and/or genetic and genomic abnormalities. Ten of the 61 patients (16%) had vertical talus in one foot and clubfoot in the other. Chromosomal abnormalities, all complete or partial trisomies, were identified in three patients with vertical talus who had additional congenital abnormalities. CONCLUSIONS Vertical talus is a heterogeneous birth defect resulting from many diverse etiologies. Abnormal skeletal muscle biopsies are common in patients with vertical talus although it is unclear whether this is primary or secondary to the joint deformity. Associated anomalies are present in 62% of all cases.
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Affiliation(s)
- Laura J. Merrill
- Departments of Orthopaedic Surgery, Washington University School of Medicine, 1 Children’s Place, Suite 4S-60, St. Louis, MO 63110
USA
| | - Christina A. Gurnett
- Departments of Orthopaedic Surgery, Washington University School of Medicine, 1 Children’s Place, Suite 4S-60, St. Louis, MO 63110
USA ,Department of Neurology, Washington University School of Medicine, St. Louis
, MO
USA ,Department of Pediatrics, Washington University School of Medicine, St. Louis
, MO
USA
| | - Anne M. Connolly
- Department of Neurology, Washington University School of Medicine, St. Louis
, MO
USA
| | - Alan Pestronk
- Department of Neurology, Washington University School of Medicine, St. Louis
, MO
USA
| | - Matthew B. Dobbs
- Departments of Orthopaedic Surgery, Washington University School of Medicine, 1 Children’s Place, Suite 4S-60, St. Louis, MO 63110
USA ,St. Louis Shriners Hospital for Children, Frontenac, MI
USA
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33
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Ester AR, Weymouth KS, Burt A, Wise C, Scott A, Gurnett CA, Dobbs MB, Blanton SH, Hecht JT. Altered transmission of HOX and apoptotic SNPs identify a potential common pathway for clubfoot. Am J Med Genet A 2009; 149A:2745-52. [PMID: 19938081 PMCID: PMC2795347 DOI: 10.1002/ajmg.a.33130] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Clubfoot is a common birth defect that affects 135,000 newborns each year worldwide. It is characterized by equinus deformity of one or both feet and hypoplastic calf muscles. Despite numerous study approaches, the cause(s) remains poorly understood although a multifactorial etiology is generally accepted. We considered the HOXA and HOXD gene clusters and insulin-like growth factor binding protein 3 (IGFBP3) as candidate genes because of their important roles in limb and muscle morphogenesis. Twenty SNPs from the HOXA and HOXD gene clusters and 12 SNPs in IGFBP3 were genotyped in a sample composed of non-Hispanic white and Hispanic multiplex and simplex families (discovery samples) and a second sample of non-Hispanic white simplex trios (validation sample). Four SNPs (rs6668, rs2428431, rs3801776, and rs3779456) in the HOXA cluster demonstrated altered transmission in the discovery sample, but only rs3801776, located in the HOXA basal promoter region, showed altered transmission in both the discovery and validation samples (P = 0.004 and 0.028). Interestingly, HOXA9 is expressed in muscle during development. An SNP in IGFBP3, rs13223993, also showed altered transmission (P = 0.003) in the discovery sample. Gene-gene interactions were identified between variants in HOXA, HOXD, and IGFBP3 and with previously associated SNPs in mitochondrial-mediated apoptotic genes. The most significant interactions were found between CASP3 SNPS and variants in HOXA, HOXD, and IGFBP3. These results suggest a biologic model for clubfoot in which perturbation of HOX and apoptotic genes together affect muscle and limb development, which may cause the downstream failure of limb rotation into a plantar grade position.
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Affiliation(s)
- Audrey R. Ester
- Department of Pediatrics, University of Texas Medical School at Houston, Houston, TX 77030, USA
| | - Katelyn S. Weymouth
- Department of Pediatrics, University of Texas Medical School at Houston, Houston, TX 77030, USA
| | - Amber Burt
- Miami Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Carol Wise
- Charles E. Seay Center for Musculoskeletal Research, Texas Scottish Rite Hospital for Children, Dallas, TX 75219, USA
| | - Allison Scott
- Shriners Hospital for Children, Houston 77030, TX, USA
| | - Christina A Gurnett
- Department of Neurology, Washington School of Medicine, St. Louis, MO, 63110, USA
| | - Matthew B. Dobbs
- Department of Neurology, Washington School of Medicine, St. Louis, MO, 63110, USA
- Department of Orthopaedic Surgery, Washington University School of Medicine and Shriners Hospital for Children, St. Louis, MO 63110, USA
| | - Susan H. Blanton
- Miami Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Jacqueline T. Hecht
- Department of Pediatrics, University of Texas Medical School at Houston, Houston, TX 77030, USA
- Shriners Hospital for Children, Houston 77030, TX, USA
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Lalwani S, Wu HH, Reindollar RH, Gray MR. HOXA10 mutations in congenital absence of uterus and vagina. Fertil Steril 2008; 89:325-30. [PMID: 17482600 DOI: 10.1016/j.fertnstert.2007.03.033] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2006] [Revised: 03/06/2007] [Accepted: 03/07/2007] [Indexed: 10/23/2022]
Abstract
OBJECTIVE To analyze the HOXA10 genes in CAUV patients for mutations. Congenital absence of the uterus and vagina (CAUV) is the most extreme female reproductive tract developmental defect known. The HOXA10 gene is expressed in the developing and adult uterus. Female mice with loss-of-function Hoxa10 gene mutations have anteriorly directed homeotic transformations of the uterus. Because the HOXA10 gene is expressed in the embryonic paramesonephric (Müllerian) ducts, abnormally low expression by mutant HOXA10 genes might cause CAUV. This hypothesis was tested by analyzing the HOXA10 genes in CAUV patients for mutations. DESIGN Case-control study. SETTING Academic reproductive endocrinology and infertility practice. PATIENT(S) Blood samples were obtained from 26 patients with CAUV and 30 normal controls. INTERVENTION(S) DNA samples prepared from blood leukocytes were used as templates for polymerase chain reaction (PCR) amplification of DNA fragments from the HOXA10 gene. The gene fragments were tested for DNA sequence differences using denaturing gradient gel electrophoresis (DGGE). MAIN OUTCOME MEASURE(S) To detect DNA sequence differences between patients with CAUV and normal controls. RESULT(S) No DNA sequence differences were found in either patients with CAUV or normal controls in either of the two protein-coding exons of the HOXA10 gene. CONCLUSION(S) Because no HOXA10 gene mutations were found in 26 patients from 25 unrelated families, germ- line mutations in the HOXA10 gene are not a common cause of CAUV.
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Affiliation(s)
- Sasmira Lalwani
- Department of Obstetrics and Gynecology, Division of Reproductive Endocrinology and Infertility, Tufts-New England Medical Center, Boston, Massachusetts 02111, USA.
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Gurnett CA, Keppel C, Bick J, Bowcock AM, Dobbs MB. Absence of HOXD10 mutations in idiopathic clubfoot and sporadic vertical talus. Clin Orthop Relat Res 2007; 462:27-31. [PMID: 17417092 DOI: 10.1097/blo.0b013e31805d8649] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The genetic etiology of idiopathic clubfoot is unknown. There have been cases reported in which both clubfoot and vertical talus appears in the same family; therefore, the genes responsible for vertical talus are reasonable candidates for idiopathic clubfoot. A mutation in HOXD10 was previously identified in a family with isolated congenital vertical talus. To determine whether HOXD10 is involved in the etiology of idiopathic clubfoot, HOXD10 coding and 5' and 3' untranslated regions were resequenced in 190 patients (177 with clubfoot, 10 with sporadic vertical talus, and 3 with both clubfoot and vertical talus), and 160 ethnically matched control subjects. Rare nonsynonymous HOXD10 amino acid substitutions (Leu154Val, Asn202Lys, and Thr175Ala), likely benign variants, were all detected once in patients and control subjects. Nucleotide substitutions were also identified in HOXD10 intronic and 3' untranslated regions, but were not more frequent in cases compared to controls. To investigate the possibility that unsequenced regulatory regions play a role in this disorder, we performed linkage analysis with markers on chromosome 2q near HOXD10 in one large family. We found no evidence of linkage near the HOXD gene cluster on chromosome 2q, suggesting genes other than HOXD10 are responsible for idiopathic clubfoot.
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Affiliation(s)
- Christina A Gurnett
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA
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36
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Alaee F, Boehm S, Dobbs MB. A new approach to the treatment of congenital vertical talus. J Child Orthop 2007; 1:165-74. [PMID: 19308490 PMCID: PMC2656724 DOI: 10.1007/s11832-007-0037-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2007] [Accepted: 07/03/2007] [Indexed: 02/03/2023] Open
Abstract
Congenital vertical talus is an uncommon foot deformity that is present at birth and results in a rigid flatfoot deformity. Left untreated the deformity can result in pain and disability. Though the exact etiology of vertical talus is unknown, an increasing number of cases have been shown to have a genetic cause. Approximately 50% of all cases of vertical talus are associated with other neuromuscular abnormalities or known genetic syndromes. The remaining 50% of cases were once thought to be idiopathic in nature. However, there is increasing evidence that many of these cases are related to single gene defects. Most patients with vertical talus have been treated with major reconstructive surgeries that are fraught with complications such as wound necrosis, talar necrosis, undercorrection of the deformity, stiffness of the ankle and subtalar joint, and the eventual need for multiple operative procedures. Recently, a new approach to vertical talus that consists of serial casting and minimal surgery has resulted in excellent correction in the short-term. Longer follow-up will be necessary to ensure maintenance of correction with this new technique. A less invasive approach to the correction of vertical talus may provide more favorable long-term outcomes than more extensive surgery as has been shown to be true for clubfoot outcomes.
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Affiliation(s)
- Farhang Alaee
- Department of Orthopaedic Surgery, Washington University School of Medicine, One Children´s Place, Suite 4S20, St. Louis, MO 63110 USA
| | - Stephanie Boehm
- Department of Orthopaedic Surgery, Washington University School of Medicine, One Children´s Place, Suite 4S20, St. Louis, MO 63110 USA
| | - Matthew B. Dobbs
- Department of Orthopaedic Surgery, Washington University School of Medicine, One Children´s Place, Suite 4S20, St. Louis, MO 63110 USA ,Saint Louis Shriners Hospital for Children, Saint Louis, MO 63110 USA
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37
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Yue Y, Farcas R, Thiel G, Bommer C, Grossmann B, Galetzka D, Kelbova C, Küpferling P, Daser A, Zechner U, Haaf T. De novo t(12;17)(p13.3;q21.3) translocation with a breakpoint near the 5′ end of the HOXB gene cluster in a patient with developmental delay and skeletal malformations. Eur J Hum Genet 2007; 15:570-7. [PMID: 17327879 DOI: 10.1038/sj.ejhg.5201795] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
A boy with severe mental retardation, funnel chest, bell-shaped thorax, and hexadactyly of both feet was found to have a balanced de novo t(12;17)(p13.3;q21.3) translocation. FISH with BAC clones and long-range PCR products assessed in the human genome sequence localized the breakpoint on chromosome 17q21.3 to a 21-kb segment that lies <30 kb upstream of the HOXB gene cluster and immediately adjacent to the 3' end of the TTLL6 gene. The breakpoint on chromosome 12 occurred within telomeric hexamer repeats and, therefore, is not likely to affect gene function directly. We propose that juxtaposition of the HOXB cluster to a repetitive DNA domain and/or separation from required cis-regulatory elements gave rise to a position effect.
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Affiliation(s)
- Ying Yue
- Institute for Human Genetics, Johannes Gutenberg University Mainz, Mainz, Germany
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38
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Garcia-Barceló MM, Miao X, Lui VCH, So MT, Ngan ESW, Leon TYY, Lau DKC, Liu TT, Lao X, Guo W, Holden WT, Moore J, Tam PKH. Correlation between genetic variations in Hox clusters and Hirschsprung's disease. Ann Hum Genet 2007; 71:526-36. [PMID: 17274802 DOI: 10.1111/j.1469-1809.2007.00347.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Interactions between migrating neural crest cells and the environment of the gut are crucial for the development of the enteric nervous system (ENS). A key signalling mediator is the RET-receptor-tyrosine-kinase which, when defective, causes Hirschprung's disease (HSCR, colon aganglionosis). RET mutations alone cannot account for the variable HSCR phenotype, invoking interactions with as yet unknown, and probably inter-related, loci involved in ENS development. Homeobox (HOX) genes have a major role in gut development as depicted by the enteric Hox code. We investigated whether DNA alterations in HOX genes, either alone or in combination with RET, are implicated in HSCR. Genotyping effort was minimized by applying the HapMap data on Han Chinese from Beijing (CHB). 194 HSCR patients and 168 controls were genotyped using Sequenom technology for 72 tag, single nucleotide polymorphisms (SNPs) distributed along the HOX clusters. The HapMap frequencies were compared to those in our population and standard statistics were used for frequency comparisons. The multifactor-dimensionality-reduction method was used for multilocus analysis, in which RET promoter SNP genotypes were included. Genetic interactions were found between two HOX loci (5'-HOXA13 and 3'UTR-HOXB7) and the RET loci tested. Minor allele frequencies (MAF) of the SNPs tested in our sample were not significantly different from those reported by HapMap when the sample sizes of the populations compared were considered. This is the first evaluation of the HOX genes in HSCR and the first application of HapMap data in a Chinese population. The interacting HOX loci may affect the penetrance of the RET risk allele. HapMap data for the CHB population correlated well with the general Chinese population.
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Affiliation(s)
- M M Garcia-Barceló
- Division of Paediatric Surgery, Department of Surgery, Li Ka Shing Faculty of Medicine of the University of Hong Kong, Hong Kong SAR, China
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39
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Melin M, Entesarian M, Carlsson G, Garwicz D, Klein C, Fadeel B, Nordenskjöld M, Palmblad J, Henter JI, Dahl N. Assignment of the gene locus for severe congenital neutropenia to chromosome 1q22 in the original Kostmann family from Northern Sweden. Biochem Biophys Res Commun 2006; 353:571-5. [PMID: 17188649 PMCID: PMC2721957 DOI: 10.1016/j.bbrc.2006.12.086] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2006] [Accepted: 12/06/2006] [Indexed: 11/25/2022]
Abstract
Autosomal recessive severe congenital neutropenia (SCN) or Kostmann syndrome is characterised by reduced neutrophil counts and subsequent recurrent bacterial infections. The disease was originally described in a large consanguineous pedigree from Northern Sweden. A genome-wide autozygosity scan was initiated on samples from four individuals in the original pedigree using high density single nucleotide polymorphism (SNP) genotyping arrays in order to map the disease locus. Thirty candidate regions were identified and the ascertainment of samples from two additional patients confirmed a single haplotype with significant association to the disorder (p<0.01) on chromosome 1q22. One affected individual from the original Kostmann pedigree was confirmed as a phenocopy. The minimal haplotype shared by affected individuals spans a candidate region of 1.2 Mb, containing several potential candidate genes.
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Affiliation(s)
- M Melin
- Department of Genetics and Pathology, The Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - M Entesarian
- Department of Genetics and Pathology, The Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - G Carlsson
- Department of Woman and Child Health, Karolinska Hospital, Stockholm, Sweden
| | - D Garwicz
- Department of Molecular Medicine, Karolinska University Hospital Solna, Stockholm, Sweden
| | - C Klein
- Department of Pediatric Haematology/Oncology, Hannover Medical School, Hannover, Germany
| | - B Fadeel
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - M Nordenskjöld
- Department of Molecular Medicine, Karolinska University Hospital Solna, Stockholm, Sweden
| | - J Palmblad
- Department of Medicine, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - JI Henter
- Department of Woman and Child Health, Karolinska Hospital, Stockholm, Sweden
| | - N Dahl
- Department of Genetics and Pathology, The Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
- Corresponding author. Fax: +46-18-554025. E-mail address: (N. Dahl)
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40
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Abstract
The scope of single nucleotide polymorphism genotyping for genetic association studies has expanded recently from the use of relatively small numbers of candidate genes and markers, to include hypothesis-free, whole-genome approaches using hundreds of thousands of polymorphisms. The ability to perform such large-scale association studies has been dependant on the development of highly parallel and cost-effective genotyping platforms, of which those based on oligonucleotide arrays have proved to be the most scalable and widely adopted. It is to be expected that the new array-based genotyping methods will not only greatly expand the scope of genetic studies, but, as further content is added to arrays, will also form part of an integrated set of DNA, RNA and proteomic analyses enabling the detailed, multilayered study of complex disease-linked phenotypes.
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Affiliation(s)
- Neil J Gibson
- AstraZeneca Pharmaceuticals, 19G9, Mereside, Alderley Park, Macclesfield, SK10 4TG, UK.
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41
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Ragoussis J, Elvidge G. Affymetrix GeneChip system: moving from research to the clinic. Expert Rev Mol Diagn 2006; 6:145-52. [PMID: 16512775 DOI: 10.1586/14737159.6.2.145] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Affymetrix Inc.'s GeneChip technology has become the industry standard in microarray-based research. Due to the high density of content per array that can be achieved today (an industry leading 6.5 million features) the GeneChips can be used for high-throughput mutation detection, single nucleotide polymorphism genotyping, expression profiling and detection of chromosomal aberrations. This in turn opens the way for clinical applications in genetics, cytogenetics, pharmacogenetics, oncology and pathogen recognition. Establishing standards is a central issue in improving data quality and, in combination with automatic, easy-to-interpret reports, will form the basis of the clinical applicability. Future pricing policies and the resolving of ethical considerations will also dictate the technology's full translation from research into clinical laboratories.
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Affiliation(s)
- Jiannis Ragoussis
- Genomics Laboratory, Wellcome Trust Centre for Human Genetics, Oxford University, Oxford, OX3 7BN, UK.
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42
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Abstract
Identifying genes involved in the development of cancer is crucial to fully understanding cancer biology, for developing novel therapeutics for cancer treatment and for providing methods for cancer prevention and early diagnosis. The use of polymorphic markers, in particular single nucleotide polymorphisms (SNPs), promises to provide a comprehensive tool for analysing the human genome and identifying those genes and genomic regions contributing to the cancer phenotype. This review summarizes the various analytical methodologies in which SNPs are used and presents examples of how each of these methodologies have been used to locate genes and genomic regions of interest for various cancer types. Additionally many of the current SNP-analysing technologies will be reviewed with particular attention paid to the advantages and disadvantages of each and how each technology can be applied to the analysis of the genome for identifying cancer-related genes.
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Affiliation(s)
- L J Engle
- Cetek Corporation, Marlborough, MA, USA
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43
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Dobbs MB, Gurnett CA, Pierce B, Exner GU, Robarge J, Morcuende JA, Cole WG, Templeton PA, Foster B, Bowcock AM. HOXD10 M319K mutation in a family with isolated congenital vertical talus. J Orthop Res 2006; 24:448-53. [PMID: 16450407 DOI: 10.1002/jor.20052] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Congenital vertical talus (CVT) is a primary dislocation of the talonavicular joint that often occurs in neuromusculoskeletal syndromes, but may also be seen as an isolated abnormality. Six families with isolated CVT were ascertained. DNA was isolated from 21 affected individuals and 17 unaffected individuals from these families, as well as from five sporadic patients with CVT. Variable expressivity was noted in three families, manifesting as clubfoot in three individuals. Genome-wide linkage analysis generated a maximum two-point logarithm of odds score on chromosome 2q with D2S1353 (Zmax = 1.43 at theta(max) = 0.1), 17 Mb from the HOXD gene cluster. DNA from one affected individual of each family was subjected to mutational analysis of the HOXD10 gene. A single missense mutation was identified (M319K, 956T > A) in the homeodomain recognition helix of the HOXD10 gene that segregated with disease in one large British family. This mutation was recently described in a family of Italian descent with CVT and Charcot-Marie-Tooth deformity HOXD10 gene mutations were not identified in any of the other families or sporadic patients with CVT, suggesting that genetic heterogeneity underlies this disorder.
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Affiliation(s)
- Matthew B Dobbs
- Department of Orthopedic Surgery, Washington University School of Medicine, One Child Place, Suite 45 Saint Louis, Missouri 63110, USA.
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44
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Dobbs MB, Gurnett CA, Robarge J, Gordon JE, Morcuende JA, Bowcock AM. Variable hand and foot abnormalities in family with congenital vertical talus and CDMP-1 gene mutation. J Orthop Res 2005; 23:1490-4. [PMID: 16005596 DOI: 10.1016/j.orthres.2005.04.011.1100230636] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2004] [Revised: 03/07/2005] [Accepted: 04/25/2005] [Indexed: 02/04/2023]
Abstract
Isolated foot anomalies, including congenital vertical talus, were shown recently to occur in heterozygous carriers of CDMP-1 (cartilage-derived morphogenetic protein-1) gene mutations. Six families with isolated congenital vertical talus with apparent autosomal dominant inheritance were ascertained. DNA was isolated from 17 affected individuals and 24 unaffected individuals from these families and subjected to mutational analysis of the CDMP-1 gene. A missense mutation was identified (1312C>T) that results in an R438C substitution in the CDMP-1 active domain. This segregated with disease in one Northeren American family. Phenotypic variability in this family includes brachydactyly type C, clinodactyly, calcaneo valgus deformity, and congenital vertical talus. Metacarpophalangeal profiles (MCPPs) confirm incomplete penetrance in one family member. Hence, CDMP-1 mutations may be found in individuals with apparently isolated CVT, although careful examination of family members may reveal additional, subtle hand and foot abnormalities. However, mutations in CDMP-1 do not appear to be a frequent cause of isolated congenital vertical talus.
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Affiliation(s)
- Matthew B Dobbs
- Department of Orthopedic Surgery, Washington University School of Medicine, One Children's Place, Suite 4S20, St. Louis, MO 63110, USA.
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45
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Tischfield MA, Bosley TM, Salih MAM, Alorainy IA, Sener EC, Nester MJ, Oystreck DT, Chan WM, Andrews C, Erickson RP, Engle EC. Homozygous HOXA1 mutations disrupt human brainstem, inner ear, cardiovascular and cognitive development. Nat Genet 2005; 37:1035-7. [PMID: 16155570 DOI: 10.1038/ng1636] [Citation(s) in RCA: 201] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2005] [Accepted: 07/11/2005] [Indexed: 02/08/2023]
Abstract
We identified homozygous truncating mutations in HOXA1 in three genetically isolated human populations. The resulting phenotype includes horizontal gaze abnormalities, deafness, facial weakness, hypoventilation, vascular malformations of the internal carotid arteries and cardiac outflow tract, mental retardation and autism spectrum disorder. This is the first report to our knowledge of viable homozygous truncating mutations in any human HOX gene and of a mendelian disorder resulting from mutations in a human HOX gene critical for development of the central nervous system.
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Affiliation(s)
- Max A Tischfield
- Department of Medicine, Program in Genomics, Children's Hospital Boston, Boston, Massachusetts 02115, USA
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46
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Zhai J, Lin H, Canete-Soler R, Schlaepfer WW. HoxB2 binds mutant SOD1 and is altered in transgenic model of ALS. Hum Mol Genet 2005; 14:2629-40. [PMID: 16079151 DOI: 10.1093/hmg/ddi297] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Mutations in Cu/Zn superoxide dismutase (SOD1) cause approximately 20% of familial amyotrophic lateral sclerosis by a toxic gain of function; however, the precise mechanisms remain unclear. Here, we report the identification of HoxB2, a homeodomain-containing transcription factor, as a G93A mutant SOD1 interactive protein in a yeast two-hybrid screen. We show that HoxB2 co-precipitates and co-localizes with mutant SOD1 in neuronal cell lines, as well as in brain and spinal cord of G93A mutant SOD1 transgenic mice. Mutagenesis further shows that this interaction is mediated by the central homeodomain of HoxB2. In motor neuron-like NSC-34 cells, overexpression of HoxB2 or its homeodomain decreases the insolubility of mutant SOD1 and inhibits G93A or G86R mutant SOD1-induced neuronal cell death. In human and mouse tissues, we show that expression of HoxB2 persists in adult spinal cord and is primarily localized in nuclei of motor neurons. In G93A transgenic mice, HoxB2 co-localizes with mutant SOD1 and is redistributed to perikarya and proximal neurites of motor neurons. In addition, there is progressive accumulation of HoxB2 and mutant SOD1 as punctate inclusions in the neuropil surrounding motor neurons. Taken together, our findings demonstrate that interaction of HoxB2 with mutant SOD1 occurs in motor neurons of G93A mutant SOD1 transgenic mice and suggest that this interaction may modulate the neurotoxicity of mutant SOD1.
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Affiliation(s)
- Jinbin Zhai
- Division of Neuropathology, Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA.
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47
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Abstract
The technology to simultaneously genotype hundreds of thousands of single nucleotide polymorphisms in a single assay has only recently been developed. These advances have the potential to revolutionize our ability to identify disease-associated proteins and their corresponding pathways as drugable targets. Several strategies that can take advantage of extremely high-density, genome-wide single nucleotide polymorphism genotyping to hone in on pathogenic genetic variants will be discussed. In familial linkage studies, high-density single nucleotide polymorphism genotyping has already been proven to speed up mutation identification of Mendelian traits several fold. Many studies now report examining loss of heterozygosity and genomic amplifications on a whole-genome level. Genotyping hundreds of thousands of single nucleotide polymorphisms in a single set of assays now also allows for whole-genome association studies in complex, multigenic diseases. The technology of high-density single nucleotide polymorphism genotyping has emerged rapidly, leaving data analysis and bioinformatic challenges only partially met. In this review, the immediate applications and implications of the rapidly changing high-density, whole-genome single nucleotide polymorphism genotyping field on translational research will be described.
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Affiliation(s)
- David W Craig
- The Translational Genomics Research Institute, Neurogenomics Division, 445 North Fifth Street, Phoenix, AZ 85004, USA.
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48
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Dlugaszewska B, Silahtaroglu A, Menzel C, Kübart S, Cohen M, Mundlos S, Tümer Z, Kjaer K, Friedrich U, Ropers HH, Tommerup N, Neitzel H, Kalscheuer VM. Breakpoints around the HOXD cluster result in various limb malformations. J Med Genet 2005; 43:111-8. [PMID: 15980115 PMCID: PMC2564623 DOI: 10.1136/jmg.2005.033555] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
BACKGROUND Characterisation of disease associated balanced chromosome rearrangements is a promising starting point in the search for candidate genes and regulatory elements. METHODS We have identified and investigated three patients with limb abnormalities and breakpoints involving chromosome 2q31. Patient 1 with severe brachydactyly and syndactyly, mental retardation, hypoplasia of the cerebellum, scoliosis, and ectopic anus, carries a balanced t(2;10)(q31.1;q26.3) translocation. Patient 2, with translocation t(2;10)(q31.1;q23.33), has aplasia of the ulna, shortening of the radius, finger anomalies, and scoliosis. Patient 3 carries a pericentric inversion of chromosome 2, inv(2)(p15q31). Her phenotype is characterised by bilateral aplasia of the fibula and the radius, bilateral hypoplasia of the ulna, unossified carpal bones, and hypoplasia and dislocation of both tibiae. RESULTS By fluorescence in situ hybridisation, we have mapped the breakpoints to intervals of approximately 170 kb or less. None of the three 2q31 breakpoints, which all mapped close to the HOXD cluster, disrupted any known genes. CONCLUSIONS Hoxd gene expression in the mouse is regulated by cis-acting DNA elements acting over distances of several hundred kilobases. Moreover, Hoxd genes play an established role in bone development. It is therefore very likely that the three rearrangements disturb normal HOXD gene regulation by position effects.
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Affiliation(s)
- B Dlugaszewska
- Max Planck Institute for Molecular Genetics, Ihnestrasse 73, D-14195 Berlin, Germany
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49
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Grier DG, Thompson A, Kwasniewska A, McGonigle GJ, Halliday HL, Lappin TR. The pathophysiology of HOX genes and their role in cancer. J Pathol 2005; 205:154-71. [PMID: 15643670 DOI: 10.1002/path.1710] [Citation(s) in RCA: 232] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The HOM-C clustered prototype homeobox genes of Drosophila, and their counterparts, the HOX genes in humans, are highly conserved at the genomic level. These master regulators of development continue to be expressed throughout adulthood in various tissues and organs. The physiological and patho-physiological functions of this network of genes are being avidly pursued within the scientific community, but defined roles for them remain elusive. The order of expression of HOX genes within a cluster is co-ordinated during development, so that the 3' genes are expressed more anteriorly and earlier than the 5' genes. Mutations in HOXA13 and HOXD13 are associated with disorders of limb formation such as hand-foot-genital syndrome (HFGS), synpolydactyly (SPD), and brachydactyly. Haematopoietic progenitors express HOX genes in a pattern characteristic of the lineage and stage of differentiation of the cells. In leukaemia, dysregulated HOX gene expression can occur due to chromosomal translocations involving upstream regulators such as the MLL gene, or the fusion of a HOX gene to another gene such as the nucleoporin, NUP98. Recent investigations of HOX gene expression in leukaemia are providing important insights into disease classification and prediction of clinical outcome. Whereas the oncogenic potential of certain HOX genes in leukaemia has already been defined, their role in other neoplasms is currently being studied. Progress has been hampered by the experimental approach used in many studies in which the expression of small subsets of HOX genes was analysed, and complicated by the functional redundancy implicit in the HOX gene system. Attempts to elucidate the function of HOX genes in malignant transformation will be enhanced by a better understanding of their upstream regulators and downstream target genes.
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Affiliation(s)
- D G Grier
- Department of Child Health, Queen's University, Belfast, Grosvenor Road, Belfast BT12 6BA, UK
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50
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Di X, Matsuzaki H, Webster TA, Hubbell E, Liu G, Dong S, Bartell D, Huang J, Chiles R, Yang G, Shen MM, Kulp D, Kennedy GC, Mei R, Jones KW, Cawley S. Dynamic model based algorithms for screening and genotyping over 100K SNPs on oligonucleotide microarrays. Bioinformatics 2005; 21:1958-63. [PMID: 15657097 DOI: 10.1093/bioinformatics/bti275] [Citation(s) in RCA: 155] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION A high density of single nucleotide polymorphism (SNP) coverage on the genome is desirable and often an essential requirement for population genetics studies. Region-specific or chromosome-specific linkage studies also benefit from the availability of as many high quality SNPs as possible. The availability of millions of SNPs from both Perlegen and the public domain and the development of an efficient microarray-based assay for genotyping SNPs has brought up some interesting analytical challenges. Effective methods for the selection of optimal subsets of SNPs spanning the genome and methods for accurately calling genotypes from probe hybridization patterns have enabled the development of a new microarray-based system for robustly genotyping over 100,000 SNPs per sample. RESULTS We introduce a new dynamic model-based algorithm (DM) for screening over 3 million SNPs and genotyping over 100,000 SNPs. The model is based on four possible underlying states: Null, A, AB and B for each probe quartet. We calculate a probe-level log likelihood for each model and then select between the four competing models with an SNP-level statistical aggregation across multiple probe quartets to provide a high-quality genotype call along with a quality measure of the call. We assess performance with HapMap reference genotypes, informative Mendelian inheritance relationship in families, and consistency between DM and another genotype classification method. At a call rate of 95.91% the concordance with reference genotypes from the HapMap Project is 99.81% based on over 1.5 million genotypes, the Mendelian error rate is 0.018% based on 10 trios, and the consistency between DM and MPAM is 99.90% at a comparable rate of 97.18%. We also develop methods for SNP selection and optimal probe selection. AVAILABILITY The DM algorithm is available in Affymetrix's Genotyping Tools software package and in Affymetrix's GDAS software package. See http://www.affymetrix.com for further information. 10 K and 100 K mapping array data are available on the Affymetrix website.
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Affiliation(s)
- Xiaojun Di
- Affymetrix, Inc., Santa Clara, CA 95051, USA.
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