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Hu Z, Xu Y, Li J, Zhu Z, Qiu Y, Liu Z. Bioinformatics Analysis and Experimental Verification Identify Downregulation of COL27A1 in Poor Segmental Congenital Scoliosis. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:2616827. [PMID: 35186112 PMCID: PMC8849967 DOI: 10.1155/2022/2616827] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/26/2021] [Accepted: 12/31/2021] [Indexed: 12/23/2022]
Abstract
BACKGROUND Congenital scoliosis (CS) represents the congenital defect disease, and poor segmental congenital scoliosis (PSCS) represents one of its types. Delayed intervention can result in disability and paralysis. In this study, we would identify the core biomarkers for PSCS progression through bioinformatics analysis combined with experimental verification. METHODS This work obtained the GSE11854 expression dataset associated with somite formation in the GEO database, which covers data of 13 samples. Thereafter, we utilized the edgeR of the R package to obtain DEGs in this dataset. Then, GO annotation, KEGG analyses, and DO annotation of DEGs were performed by "clusterProfiler" of the R package. This study performed LASSO regression for screening the optimal predicting factors for somite formation. Through RNA sequencing based on peripheral blood samples from healthy donors and PSCS cases, we obtained the RNA expression patterns and screen out DEGs using the R package DESeq2. The present work analyzed COL27A1 expression in PSCS patients by the RT-PCR assay. RESULTS A total of 443 genes from the GSE11854 dataset were identified as DEGs, which were involved in BP associated with DNA replication, CC associated with chromosomal region, and MF associated with ATPase activity. These DEGs were primarily enriched in the TGF-β signaling pathway and spinal deformity. Further, LASSO regression suggested that 9 DEGs acted as the signature markers for somite formation. We discovered altogether 162 DEGs in PSCS patients, which were involved in BP associated with cardiac myofibril assembly and MF associated with structural constituent of muscle. However, these 162 DEGs were not significantly correlated with any pathways. Finally, COL27A1 was identified as the only intersected gene between the best predictors for somite formation and PSCS-related DEGs, which was significantly downregulated in PSCS patients. CONCLUSION This work sheds novel lights on DEGs related to the PSCS pathogenic mechanism, and COL27A1 is the possible therapeutic target for PSCS. Findings in this work may contribute to developing therapeutic strategies for PSCS.
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Affiliation(s)
- Zongshan Hu
- Division of Spine Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing 210008, China
| | - Yanjie Xu
- Division of Spine Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing 210008, China
| | - Jie Li
- Division of Spine Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing 210008, China
| | - Zezhang Zhu
- Division of Spine Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing 210008, China
| | - Yong Qiu
- Division of Spine Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing 210008, China
| | - Zhen Liu
- Division of Spine Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing 210008, China
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Onesimo R, Versacci P, Delogu AB, De Rosa G, Pugnaloni F, Blandino R, Leoni C, Calcagni G, Digilio MC, Zollino M, Marino B, Zampino G. Smith-Magenis syndrome: Report of morphological and new functional cardiac findings with review of the literature. Am J Med Genet A 2021; 185:2003-2011. [PMID: 33811726 DOI: 10.1002/ajmg.a.62196] [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: 11/24/2020] [Revised: 03/12/2021] [Accepted: 03/18/2021] [Indexed: 11/05/2022]
Abstract
Smith-Magenis syndrome (SMS) is a genetic disorder characterized by multiple congenital anomalies, sleep disturbance, behavioral impairment, and intellectual disability. Its genetic cause has been defined as an alteration in the Retinoic Acid-Induced 1 gene. Cardiac anomalies have been reported since the first description of this condition in patients with 17p11.2 deletion. Variable cardiac defects, including ventricular septal defects, atrial septal defects, tricuspid stenosis, mitral stenosis, tricuspid and mitral regurgitation, aortic stenosis, pulmonary stenosis, mitral valve prolapse, tetralogy of Fallot, and total anomalous pulmonary venous connection, have been anecdotally reported and systematic case series are still lacking. Herein, we define the spectrum of the cardiac phenotype and describe for the first time the cardiac function in a large cohort of pediatric patients with SMS. Revision of the literature and correlations between genotype and cardiac phenotype was performed.
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Affiliation(s)
- Roberta Onesimo
- Rare Diseases Unit, Fondazione Policlinico Universitario Agostino Gemelli-IRCCS, Rome, Italy.,Pediatric Unit, Fondazione Policlinico Universitario Agostino Gemelli-IRCCS, Rome, Italy
| | - Paolo Versacci
- Department of Pediatrics, Obstetrics and Gynecology, "Sapienza" University of Rome, Policlinico Umberto I, Rome, Italy
| | | | - Gabriella De Rosa
- Pediatric Unit, Fondazione Policlinico Universitario Agostino Gemelli-IRCCS, Rome, Italy
| | - Flaminia Pugnaloni
- Department of Pediatrics, Obstetrics and Gynecology, "Sapienza" University of Rome, Policlinico Umberto I, Rome, Italy
| | - Rita Blandino
- Pediatric Unit, Fondazione Policlinico Universitario Agostino Gemelli-IRCCS, Rome, Italy
| | - Chiara Leoni
- Rare Diseases Unit, Fondazione Policlinico Universitario Agostino Gemelli-IRCCS, Rome, Italy.,Pediatric Unit, Fondazione Policlinico Universitario Agostino Gemelli-IRCCS, Rome, Italy
| | - Giulio Calcagni
- Department of Pediatric Cardiology and Cardiac Surgery, Bambino Gesù Children's Hospital and Research Institute, Rome, Italy
| | - Maria C Digilio
- Medical Genetics Unit, Bambino Gesù Children's Hospital and Research Institute, Rome, Italy
| | - Marcella Zollino
- Dipartimento Universitario Scienze della Vita e Sanità Pubblica, Sezione di Medicina Genomica, Università Cattolica Sacro Cuore, Rome, Italy.,Genetica Medica, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Bruno Marino
- Department of Pediatrics, Obstetrics and Gynecology, "Sapienza" University of Rome, Policlinico Umberto I, Rome, Italy
| | - Giuseppe Zampino
- Rare Diseases Unit, Fondazione Policlinico Universitario Agostino Gemelli-IRCCS, Rome, Italy.,Pediatric Unit, Fondazione Policlinico Universitario Agostino Gemelli-IRCCS, Rome, Italy.,Dipartimento Universitario Scienze della Vita e Sanità Pubblica, Sezione di Medicina Genomica, Università Cattolica Sacro Cuore, Rome, Italy
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Robertson J, Baines S, Emerson E, Hatton C. Postural care for people with intellectual disabilities and severely impaired motor function: A scoping review. JOURNAL OF APPLIED RESEARCH IN INTELLECTUAL DISABILITIES 2016; 31 Suppl 1:11-28. [DOI: 10.1111/jar.12325] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/22/2016] [Indexed: 11/29/2022]
Affiliation(s)
- Janet Robertson
- Centre for Disability Research; Division of Health Research; Faculty of Health and Medicine; Lancaster University; Lancaster UK
| | - Susannah Baines
- Centre for Disability Research; Division of Health Research; Faculty of Health and Medicine; Lancaster University; Lancaster UK
| | - Eric Emerson
- Centre for Disability Research; Division of Health Research; Faculty of Health and Medicine; Lancaster University; Lancaster UK
- Centre for Disability Research and Policy; University of Sydney; Lidcombe NSW Australia
| | - Chris Hatton
- Centre for Disability Research; Division of Health Research; Faculty of Health and Medicine; Lancaster University; Lancaster UK
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Dias AT, Zanardo ÉA, Dutra RL, Piazzon FB, Novo-Filho GM, Montenegro MM, Nascimento AM, Rocha M, Madia FAR, Costa TVMM, Milani C, Schultz R, Gonçalves FT, Fridman C, Yamamoto GL, Bertola DR, Kim CA, Kulikowski LD. Post-mortem cytogenomic investigations in patients with congenital malformations. Exp Mol Pathol 2016; 101:116-23. [PMID: 27450648 DOI: 10.1016/j.yexmp.2016.07.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 06/16/2016] [Accepted: 07/19/2016] [Indexed: 11/16/2022]
Abstract
Congenital anomalies are the second highest cause of infant deaths, and, in most cases, diagnosis is a challenge. In this study, we characterize patterns of DNA copy number aberrations in different samples of post-mortem tissues from patients with congenital malformations. Twenty-eight patients undergoing autopsy were cytogenomically evaluated using several methods, specifically, Multiplex Ligation-dependent Probe Amplification (MLPA), microsatellite marker analysis with a MiniFiler kit, FISH, a cytogenomic array technique and bidirectional Sanger sequencing, which were performed on samples of different tissues (brain, heart, liver, skin and diaphragm) preserved in RNAlater, in formaldehyde or by paraffin-embedding. The results identified 13 patients with pathogenic copy number variations (CNVs). Of these, eight presented aneuploidies involving chromosomes 13, 18, 21, X and Y (two presented inter- and intra-tissue mosaicism). In addition, other abnormalities were found, including duplication of the TYMS gene (18p11.32); deletion of the CHL1 gene (3p26.3); deletion of the HIC1 gene (17p13.3); and deletion of the TOM1L2 gene (17p11.2). One patient had a pathogenic missense mutation of g.8535C>G (c.746C>G) in exon 7 of the FGFR3 gene consistent with Thanatophoric Dysplasia type I. Cytogenomic techniques were reliable for the analysis of autopsy material and allowed the identification of inter- and intra-tissue mosaicism and a better understanding of the pathogenesis of congenital malformations.
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Affiliation(s)
- Alexandre Torchio Dias
- Department of Pathology, Cytogenomic Laboratory - LIM 03 - HC-FMUSP, Universidade de São Paulo, SP, Brazil.
| | - Évelin Aline Zanardo
- Department of Pathology, Cytogenomic Laboratory - LIM 03 - HC-FMUSP, Universidade de São Paulo, SP, Brazil
| | - Roberta Lelis Dutra
- Department of Pathology, Cytogenomic Laboratory - LIM 03 - HC-FMUSP, Universidade de São Paulo, SP, Brazil
| | - Flavia Balbo Piazzon
- Department of Pathology, Cytogenomic Laboratory - LIM 03 - HC-FMUSP, Universidade de São Paulo, SP, Brazil
| | - Gil Monteiro Novo-Filho
- Department of Pathology, Cytogenomic Laboratory - LIM 03 - HC-FMUSP, Universidade de São Paulo, SP, Brazil
| | - Marilia Moreira Montenegro
- Department of Pathology, Cytogenomic Laboratory - LIM 03 - HC-FMUSP, Universidade de São Paulo, SP, Brazil
| | - Amom Mendes Nascimento
- Department of Pathology, Cytogenomic Laboratory - LIM 03 - HC-FMUSP, Universidade de São Paulo, SP, Brazil
| | - Mariana Rocha
- Department of Pathology, Cytogenomic Laboratory - LIM 03 - HC-FMUSP, Universidade de São Paulo, SP, Brazil; Human Reproduction and Genetic Center, Department of Coletive Health - Faculdade de Medicina do ABC, Santo André, SP, Brazil
| | | | | | - Cintia Milani
- Department of Pathology, Cytogenomic Laboratory - LIM 03 - HC-FMUSP, Universidade de São Paulo, SP, Brazil
| | - Regina Schultz
- Division of Pathology - Clinical Hospital - HC -FMUSP, Universidade de São Paulo, SP, Brazil
| | | | - Cintia Fridman
- Department of Legal Medicine - HC-FMUSP, Universidade de São Paulo, SP, Brazil
| | | | - Débora Romeo Bertola
- Genetics Unit, Instituto da Criança HC-FMUSP - Universidade de São Paulo, SP, Brazil
| | - Chong Ae Kim
- Genetics Unit, Instituto da Criança HC-FMUSP - Universidade de São Paulo, SP, Brazil
| | - Leslie Domenici Kulikowski
- Department of Pathology, Cytogenomic Laboratory - LIM 03 - HC-FMUSP, Universidade de São Paulo, SP, Brazil; Human Reproduction and Genetic Center, Department of Coletive Health - Faculdade de Medicina do ABC, Santo André, SP, Brazil
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