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Xie X, Huang B, Su L, Cai M, Chen Y, Wu X, Xu L. Prenatal diagnosis and genetic etiology analysis of talipes equinovarus by chromosomal microarray analysis. BMC Med Genomics 2023; 16:298. [PMID: 37986075 PMCID: PMC10658977 DOI: 10.1186/s12920-023-01733-2] [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: 04/06/2023] [Accepted: 11/09/2023] [Indexed: 11/22/2023] Open
Abstract
BACKGROUND With the advancement of molecular technology, fetal talipes equinovarus (TE) is believed to be not only associated with chromosome aneuploidy, but also related to chromosomal microdeletion and microduplication. The study aimed to explore the molecular etiology of fetal TE and provide more information for the clinical screening and genetic counseling of TE by Chromosomal Microarray Analysis (CMA). METHODS This retrospectively study included 131 fetuses with TE identified by ultrasonography. Conventional karyotyping and SNP array analysis were performed for all the subjects. They were divided into isolated TE group (n = 55) and complex group (n = 76) according to structural anomalies. RESULTS Among the total of 131 fetuses, karyotype analysis found 12(9.2%) abnormal results, while SNP array found 27 (20.6%) cases. Trisomy 18 was detected most frequently among abnormal karyotypes. The detection rate of SNP array was significantly higher than that of traditional chromosome karyotype analysis (P < 0.05). SNP array detected 15 (11.5%) cases of submicroscopic abnormalities that karyotype analysis did not find. The most common CNV was the 22q11.2 microdeletion. For both analyses, the overall detection rates were significantly higher in the complex TE group than in the isolated TE group (karyotype: P < 0.05; SNP array: P < 0.05). The incremental yield of chromosomal abnormalities in fetuses with unilateral TE (22.0%) was higher than in fetuses with bilateral TE (19.8%), but this difference was not statistically significant (P > 0.05). Abnormal chromosomes were most frequently detected in fetuses with TE plus cardiovascular system abnormalities. CONCLUSION Fetal TE is related to chromosomal microdeletion or microduplication. Prenatal diagnosis is recommended for fetuses with TE, and CMA testing is preferred. CMA can improve the detection rate of chromosomal abnormalities associated with fetal TE, especially in pregnancies with complex TE.
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Affiliation(s)
- Xiaorui Xie
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Provincial Maternity and Children's Hospital, No. 18 Daoshan Road, Gulou District, Fuzhou, 350001, China
| | - Baojia Huang
- Prenatal Diagnosis Center, Quanzhou Maternity and Children's Hospital, Quanzhou, China
| | - Linjuan Su
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Provincial Maternity and Children's Hospital, No. 18 Daoshan Road, Gulou District, Fuzhou, 350001, China
| | - Meiying Cai
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Provincial Maternity and Children's Hospital, No. 18 Daoshan Road, Gulou District, Fuzhou, 350001, China
| | - Yuqin Chen
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Provincial Maternity and Children's Hospital, No. 18 Daoshan Road, Gulou District, Fuzhou, 350001, China
| | - Xiaoqing Wu
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Provincial Maternity and Children's Hospital, No. 18 Daoshan Road, Gulou District, Fuzhou, 350001, China.
| | - Liangpu Xu
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Provincial Maternity and Children's Hospital, No. 18 Daoshan Road, Gulou District, Fuzhou, 350001, China.
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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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Costa RL, Boroni M, Soares MA. Distinct co-expression networks using multi-omic data reveal novel interventional targets in HPV-positive and negative head-and-neck squamous cell cancer. Sci Rep 2018; 8:15254. [PMID: 30323202 PMCID: PMC6189122 DOI: 10.1038/s41598-018-33498-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 09/19/2018] [Indexed: 12/25/2022] Open
Abstract
The human papillomavirus (HPV) is present in a significant fraction of head-and-neck squamous cell cancer (HNSCC). The main goal of this study was to identify distinct co-expression patterns between HPV+ and HPV- HNSCC and to provide insights into potential regulatory mechanisms/effects within the analyzed networks. We selected cases deposited in The Cancer Genome Atlas database comprising data of gene expression, methylation profiles and mutational patterns, in addition to clinical information. The intersection among differentially expressed and differentially methylated genes showed the negative correlations between the levels of methylation and expression, suggesting that these genes have their expression levels regulated by methylation alteration patterns in their promoter. Weighted correlation network analysis was used to identify co-expression modules and a systematic approach was applied to refine them and identify key regulatory elements integrating results from the other omics. Three distinct co-expression modules were associated with HPV status and molecular signatures. Validation using independent studies reporting biological experimental data converged for the most significant genes in all modules. This study provides insights into complex genetic and epigenetic particularities in the development and progression of HNSCC according to HPV status, and contribute to unveiling specific genes/pathways as novel therapeutic targets in HNSCC.
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Affiliation(s)
- Raquel L Costa
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, Brazil.
- Bioinformatics and Computational Biology Lab, Instituto Nacional de Câncer, Rio de Janeiro, Brazil.
| | - Mariana Boroni
- Bioinformatics and Computational Biology Lab, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Marcelo A Soares
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
- Department of Genetics, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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Gene cloning and seamless site-directed mutagenesis using single-strand annealing (SSA). Appl Microbiol Biotechnol 2018; 102:10119-10126. [PMID: 30209551 DOI: 10.1007/s00253-018-9348-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 08/16/2018] [Accepted: 08/27/2018] [Indexed: 12/17/2022]
Abstract
The full length of interested genes can be usually cloned by assembling exons or RACE products through overlap PCR. However, the procedure requires multiple PCR steps, which are prone to random mutagenesis. Here, we present a novel SSA-based method for gene cloning and seamless site-directed mutagenesis. We firstly cloned the full-length coding sequence of Cashmere goat (Capra hircus) Hoxc13 gene by assembling exons amplified from genomic DNA. Secondly, we created a Hoxc13 loss-function mutant seamlessly and further illustrated that direct repeat length of 25 bp is enough to trigger the SSA repair in routine E. coli strains including DH5α, Trans1t1, JM109, and Top10. Moreover, we cloned another full-length mutant of Foxn1 gene from Cashmere goat cDNA using further shortened direct repeats of 19 bp. In summary, our study provided an alternative method to overcome the difficulties during overlap PCR in some particular cases for gene cloning.
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Deng J, Chen M, Liu Z, Song Y, Sui T, Lai L, Li Z. The disrupted balance between hair follicles and sebaceous glands in Hoxc13-ablated rabbits. FASEB J 2018; 33:1226-1234. [PMID: 30125135 DOI: 10.1096/fj.201800928rr] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Pure hair and nail ectodermal dysplasia 9 (ECTD-9) is an autosomal recessive genetic disease caused by mutation of HOXC13 and is characterized by hypotrichosis and nail dystrophy in humans. Unlike patients with ECTD-9, Hoxc13-mutated mice and pigs do not faithfully recapitulate the phenotype of hypotrichosis, so there is a limited understanding of the molecular mechanism of Hoxc13-mediated hypotrichosis in animal models and clinically. Here, the homozygous Hoxc13-/- rabbits showed complete loss of hair on the head and dorsum, whereas hypotrichosis in the limbs and tail were determined in the Hoxc13-/- rabbits. In addition, reduced hair follicles (HFs) while the enlarged and increased number of sebaceous glands (SGs) were also found in the Hoxc13-/- rabbits, showing that the disrupted balance between HFs and SGs may respond to hypotrichosis of ECTD-9 in an animal model and clinically. Therefore, our findings demonstrate that Hoxc13-/- rabbits can be used as a model for human ECTD-9, especially to understand the pathologic mechanism of hypotrichosis. Moreover, the disrupted balance between HFs and SGs, especially in the Hoxc13-/- rabbits, can be used as an ideal animal model for dermatology ailments, such as acne and hypotrichosis, in preclinical studies.-Deng, J., Chen, M., Liu, Z., Song, Y., Sui, T., Lai, L., Li, Z. The disrupted balance between hair follicles and sebaceous glands in Hoxc13-ablated rabbits.
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Affiliation(s)
- Jichao Deng
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Institute of Zoonosis, Jilin University, Changchun, China
| | - Mao Chen
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Institute of Zoonosis, Jilin University, Changchun, China
| | - Zhiquan Liu
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Institute of Zoonosis, Jilin University, Changchun, China
| | - Yuning Song
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Institute of Zoonosis, Jilin University, Changchun, China
| | - Tingting Sui
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Institute of Zoonosis, Jilin University, Changchun, China
| | - Liangxue Lai
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Institute of Zoonosis, Jilin University, Changchun, China.,Key Laboratory of Regenerative Biology, Chinese Academy of Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Zhanjun Li
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Institute of Zoonosis, Jilin University, Changchun, China
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