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Li Y, Ran D, Basnet S, Zhang B, Pei H, Dan C, Zhang Z, Zhang L, Lu T, Peng Y, Du C. The expression and clinical significance of CFAP65 in colon cancer. BMC Gastroenterol 2024; 24:222. [PMID: 38992586 PMCID: PMC11238475 DOI: 10.1186/s12876-024-03317-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 07/04/2024] [Indexed: 07/13/2024] Open
Abstract
BACKGROUND CFAP65 (cilia and flagella associated protein 65) is a fundamental protein in the development and formation of ciliated flagella, but few studies have focused on its role in cancer. This study aimed to investigate the prognostic significance of CFAP65 in colon cancer. METHODS The functionally enriched genes related to CFAP65 were analyzed through the Gene Ontology (GO) database. Subsequently, CFAP65 expression levels in colon cancer were evaluated by reverse transcription and quantitative polymerase chain reaction (RT-qPCR) and immunoblotting in 20 pairs of frozen samples, including tumors and their matched paratumor tissue. Furthermore, protein expression of CFAP65 in 189 colon cancer patients were assessed via immunohistochemical staining. The correlations between CFAP65 expression and clinical features as well as long-term survival were statistically analyzed. RESULTS CFAP65-related genes are significantly enriched on cellular processes of cell motility, ion channels, and GTPase-associated signaling. The expression of CFAP65 was significantly higher in colon cancer tissue compared to paratumor tissue. The proportion of high expression and low expression of CFAP65 in the clinical samples of colon cancer were 61.9% and 38.1%, respectively, and its expression level was not associated with the clinical parameters including gender, age, tumor location, histological differentiation, tumor stage, vascular invasion and mismatch repair deficiency. The five-year disease-free survival rate of the patients with CFAP65 low expression tumors was significantly lower than that those with high expression tumors (56.9% vs. 72.6%, P = 0.03), but the overall survival rate has no significant difference (69% vs. 78.6%, P = 0.171). The cox hazard regression analysis model showed that CFAP65 expression, tumor stage and tumor location were independent prognostic factors. CONCLUSIONS In conclusion, we demonstrate CFAP65 is a potential predictive marker for tumor progression in colon cancer.
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Affiliation(s)
- Yunze Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Unit III & Ostomy Service, Gastrointestinal Cancer Center, Peking University Cancer Hospital & Institute, 52 Fucheng Road, Beijing, 100142, P.R. China
| | - Dongmei Ran
- Department of Pathology, Southern University of Science and Technology Hospital, Shenzhen, 518055, Guangdong, China
- Digestive Tumor Center, Southern University of Science and Technology Hospital, Shenzhen, 518055, Guangdong, China
| | - Shiva Basnet
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Unit III & Ostomy Service, Gastrointestinal Cancer Center, Peking University Cancer Hospital & Institute, 52 Fucheng Road, Beijing, 100142, P.R. China
| | - Buzhe Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Unit III & Ostomy Service, Gastrointestinal Cancer Center, Peking University Cancer Hospital & Institute, 52 Fucheng Road, Beijing, 100142, P.R. China
| | - Hongjing Pei
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Unit III & Ostomy Service, Gastrointestinal Cancer Center, Peking University Cancer Hospital & Institute, 52 Fucheng Road, Beijing, 100142, P.R. China
| | - Chenchen Dan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Unit III & Ostomy Service, Gastrointestinal Cancer Center, Peking University Cancer Hospital & Institute, 52 Fucheng Road, Beijing, 100142, P.R. China
| | - Zixuan Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Unit III & Ostomy Service, Gastrointestinal Cancer Center, Peking University Cancer Hospital & Institute, 52 Fucheng Road, Beijing, 100142, P.R. China
| | - Liang Zhang
- Department of Gastroenterology, Southern University of Science and Technology Hospital, Shenzhen, 518055, Guangdong, China
| | - Tianyu Lu
- Department of Gastroenterology, Southern University of Science and Technology Hospital, Shenzhen, 518055, Guangdong, China
| | - Yifan Peng
- Department of Unit III & Ostomy Service, Gastrointestinal Cancer Center, Peking University Cancer Hospital & Institute, Beijing, 100142, P.R. China.
| | - Changzheng Du
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Unit III & Ostomy Service, Gastrointestinal Cancer Center, Peking University Cancer Hospital & Institute, 52 Fucheng Road, Beijing, 100142, P.R. China.
- Digestive Tumor Center, Southern University of Science and Technology Hospital, Shenzhen, 518055, Guangdong, China.
- Beijing Tsinghua Changgung Hospital & Tsinghua University School of Medicine, 168 Litang Road, Changping District, Beijing, 102218, P.R. China.
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Brockmann K, Kaulfuß S. Moebius syndrome and gastroschisis-The second case of a rare association. Am J Med Genet A 2024; 194:111-114. [PMID: 37743766 DOI: 10.1002/ajmg.a.63411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/31/2023] [Accepted: 09/09/2023] [Indexed: 09/26/2023]
Affiliation(s)
- Knut Brockmann
- Interdisciplinary Pediatric Center for Children with Developmental Disabilities and Severe Chronic Disorders, Department of Pediatrics and Adolescent Medicine, University Medical Center, Göttingen, Germany
| | - Silke Kaulfuß
- Institute of Human Genetics, University Medical Center, Göttingen, Germany
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Diniz AMB, Gualberto IJN, Lima LA, Cirino MLDA, Murakami RK, Ishikiriama BLC, Ruano R, da Silva LFF, Tirapelli D, Sbragia L. miRNA-143 expression is associated with inflammation and time of exposure to amniotic fluid in experimental gastroschisis. Clinics (Sao Paulo) 2023; 78:100311. [PMID: 38008037 PMCID: PMC10757286 DOI: 10.1016/j.clinsp.2023.100311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/27/2023] [Accepted: 10/02/2023] [Indexed: 11/28/2023] Open
Abstract
OBJECTIVE Gastroschisis (GS) is a congenital anomaly in the abdominal wall with the intestinal loops exiting laterally to the umbilicus. The contact of the loops with Amniotic Fluid (AF) causes an inflammatory process in the exposed part, leading to an extended hospital stay and an increased risk of morbidity due to alterations related to intestinal motility. The authors aimed to evaluate the time of exposure to the AF in the experimental GS and to search for potential biomarkers of intestinal inflammation by measuring microRNAs. METHODS Rat fetuses were divided into three groups: a) CONTROL, b) GS reared on day 18 (GS = 18), and c) GS reared on day 19.5 (GS = 19) (term = 22 days). On day 21.5, the fetuses were removed for biometric parameters and biochemical analyses: 1) Biometrics: Body and Intestinal Weight (BW, IW), and intestinal-body weight ratio (IW/BW); 2) Descriptive histopathology and 3) miR-143 quantification by real-time Polymerase Chain Reaction (PCR). RESULTS BW was higher in CONTROL than GS 18 and G19 (p < 0.05). IW, IW/BW, intestinal water, and mRNA-143 were higher in GS 18 and GS 19 than in CONTROL, and GS 18 was higher than GS 19 (p < 0.05). The average of the inflammation score from the intestinal wall with mucosal inflammation and intra-epithelial lymphocytes shows worst in GS 18 and GS 19 vs. CONTROL (p < 0.05). CONCLUSIONS The tissue expression of mRNA-143 and the morphological changes in the intestine of GS worsened according to the time of exposure to AF, which could be a possible marker of fetal intestinal damage.
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Affiliation(s)
- Ana Maria Bicudo Diniz
- Division of Pediatric Surgery and Anatomy, Department of Surgery and Anatomy, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo (USP), Ribeirao Preto, SP, Brazil
| | - Igor José Nogueira Gualberto
- Faculdade de Medicina de Bauru, Department of Pediatric Dentistry, Orthodontics and Public Health, Faculdade de Odontologia de Bauru, Universidade de São Paulo (USP), Bauru, SP, Brazil
| | - Luiza Almeida Lima
- Division of Maternal Fetal Medicine, Jackson Fetal Care, Department Obstetrics, Gynecology and Reproductive Sciences, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Mucio Luiz de Assis Cirino
- Division of Pediatric Surgery and Anatomy, Department of Surgery and Anatomy, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo (USP), Ribeirao Preto, SP, Brazil
| | - Rodrigo Kendi Murakami
- Faculdade de Medicina de Bauru, Department of Pediatric Dentistry, Orthodontics and Public Health, Faculdade de Odontologia de Bauru, Universidade de São Paulo (USP), Bauru, SP, Brazil
| | - Bella Luna Colombini Ishikiriama
- Faculdade de Medicina de Bauru, Department of Pediatric Dentistry, Orthodontics and Public Health, Faculdade de Odontologia de Bauru, Universidade de São Paulo (USP), Bauru, SP, Brazil
| | - Rodrigo Ruano
- Division of Maternal Fetal Medicine, Jackson Fetal Care, Department Obstetrics, Gynecology and Reproductive Sciences, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Luiz Fernando Ferraz da Silva
- Department of Pathology, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo Death Verification Service (SVO), São Paulo, SP, Brazil
| | - Daniela Tirapelli
- Division of Pediatric Surgery and Anatomy, Department of Surgery and Anatomy, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo (USP), Ribeirao Preto, SP, Brazil
| | - Lourenço Sbragia
- Division of Pediatric Surgery and Anatomy, Department of Surgery and Anatomy, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo (USP), Ribeirao Preto, SP, Brazil.
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de Freitas AB, Francisco RPV, Hoshida MS, De Oliveira YG, Kulikowski LD, de Lourdes Brizot M. The complex search for the cause of gastroschisis. Birth Defects Res 2022; 114:1291-1297. [PMID: 35574732 DOI: 10.1002/bdr2.2047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/18/2022] [Accepted: 04/26/2022] [Indexed: 11/10/2022]
Abstract
BACKGROUND To reveal the complex etiology of gastroschisis through two independent cases. CASES Case 1 involves gastroschisis recurrence in a consanguineous marriage, and Case 2 concerns a fetus with gastroschisis whose mother had undergone gastroplasty. Methylation array was carried out in both cases (two fetuses with gastroschisis, their two mothers, one father from the consanguineous marriage), and in 16 controls (fetuses and their respective mothers). CONCLUSION The two cases presented different noninherited methylation profiles.
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Affiliation(s)
- Amanda Brasil de Freitas
- Department of Obstetrics and Gynecology, Faculdade de Medicina da Universidade de Sao Paulo (FMUSP), Sao Paulo, Brazil.,Cytogenomic Laboratory, Department of Pathology, Faculdade de Medicina da Universidade de Sao Paulo (FMUSP), Sao Paulo, Brazil
| | | | - Mara Sandra Hoshida
- Laboratory of Obstetric Physiology LIM57, Hospital das Clinicas, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Yanca Gasparini De Oliveira
- Cytogenomic Laboratory, Department of Pathology, Faculdade de Medicina da Universidade de Sao Paulo (FMUSP), Sao Paulo, Brazil
| | - Leslie Domenici Kulikowski
- Cytogenomic Laboratory, Department of Pathology, Faculdade de Medicina da Universidade de Sao Paulo (FMUSP), Sao Paulo, Brazil
| | - Maria de Lourdes Brizot
- Department of Obstetrics and Gynecology, Faculdade de Medicina da Universidade de Sao Paulo (FMUSP), Sao Paulo, Brazil
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Aprajita, Sharma R. Comprehending fibroblast growth factor receptor like 1: Oncogene or tumor suppressor? Cancer Treat Res Commun 2021; 29:100472. [PMID: 34689016 DOI: 10.1016/j.ctarc.2021.100472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 09/27/2021] [Accepted: 09/29/2021] [Indexed: 12/16/2022]
Abstract
Fibroblast Growth Factor Receptor Like 1 (FGFRL1) signaling has crucial role in a multitude of processes during genetic diseases, embryonic development and various types of cancer. Due to its partial structural similarity with its classical Fibroblast Growth Factor Receptor [FGFR] counterparts and lack of tyrosine kinase domain, FGFRL1 was thought to work as a decoy receptor in FGF/FGFR signaling. Later on, growing number evidences showed that expression of FGFRL1 affects major pathways like ERK1/2, Akt and others, which are dysfunctional in a wide range of human cancers. In this review, we provide an overview of the current understanding of FGFRL1 and its roles in cell differentiation, adhesion and proliferation pathways . Overexpression of FGFRL1 might lead to tumor progression and invasion. In this context, inhibitors for FGFRL1 might have therapeutic benefits in human cancer prognosis.
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Affiliation(s)
- Aprajita
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Dwarka, New Delhi, India
| | - Rinu Sharma
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Dwarka, New Delhi, India.
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Freitas ABD, Francisco RPV, Centofanti SF, Damasceno JG, Chehimi SN, Osmundo-Junior GDS, Kulikowski LD, Brizot MDL. Fetal gastroschisis: Maternal and fetal methylation profile. Prenat Diagn 2021; 41:449-456. [PMID: 33332636 DOI: 10.1002/pd.5881] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 12/01/2020] [Accepted: 12/08/2020] [Indexed: 01/04/2023]
Abstract
OBJECTIVE The purpose of this study was to describe the genomic deoxyribonucleic acid (DNA) methylation profile in fetuses with gastroschisis, determine whether the profile was inherited, and investigate any possible correlations with maternal risk factors. METHOD Genome-wide DNA methylation analysis of 96 blood samples was performed using the Illumina Human Methylation 850K BeadChip. The blood samples were collected as follows: 32 from the umbilical cord of fetuses with gastroschisis, 32 from their respective mothers, 16 from the umbilical cord of fetuses without malformation, and 16 from their respective mothers. RESULTS The differential DNA methylation analysis showed a significant difference between the groups. The enrichment analysis resulted in 12 sites related to T-cell activation (p = 0.0128). The sites with different methylation status contained 10 genes, three of which were related to the beta-2-microglobulin gene. The methylation profile observed in the fetuses with gastroschisis was not inherited from the mothers. In addition, there was no association between maternal urinary tract infection, smoking, and alcohol use and different methylated sites. CONCLUSION We established the methylation profile of gastroschisis fetuses, which differs from that of normal fetuses. The profile was not inherited and did not correlate with maternal risk factors.
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Affiliation(s)
- Amanda Brasil de Freitas
- Department of Obstetrics and Gynecology, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Sao Paulo, Brazil.,Cytogenomic Laboratory, Department of Pathology, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Sao Paulo, Brazil
| | | | - Sandra Frankfurt Centofanti
- Department of Obstetrics and Gynecology, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Sao Paulo, Brazil
| | - Jullian Gabriel Damasceno
- Cytogenomic Laboratory, Department of Pathology, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Sao Paulo, Brazil
| | - Samar Nasser Chehimi
- Cytogenomic Laboratory, Department of Pathology, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Sao Paulo, Brazil
| | - Gilmar de Souza Osmundo-Junior
- Department of Obstetrics and Gynecology, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Sao Paulo, Brazil
| | - Leslie Domenici Kulikowski
- Cytogenomic Laboratory, Department of Pathology, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Sao Paulo, Brazil
| | - Maria de Lourdes Brizot
- Department of Obstetrics and Gynecology, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Sao Paulo, Brazil
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Shao F, Wang Z, Wang S. Identification of MYCN-Related Gene as a Potential Biomarker for Neuroblastoma Prognostic Model by Integrated Analysis and Quantitative Real-Time PCR. DNA Cell Biol 2020; 40:332-347. [PMID: 33393844 DOI: 10.1089/dna.2020.6193] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Neuroblastoma (NB) has the highest incidence of all extracranial solid tumors in children and is highly lethal. This study aims to establish a prognostic model of NB with MYCN-related genes. We determined the gene expression profiles of 900 NB samples from the UCSC database and four Gene Expression Omnibus (GEO) data sets, and performed a comprehensive bioinformatics analysis and clinical sample verification. After univariate Cox regression, least absolute shrinkage and selection operator (Lasso), and multivariate Cox regression analyses, four (AKR1C1, CHD5, PDE4DIP, and PRKACB) genes were finally selected and used to construct a risk score prognostic model. In the UCSC data set, the high-risk group exhibited a significantly worse prognosis than the low-risk group. In addition, the nomogram, which includes prognostic markers and clinical factors, demonstrates high prognostic value. Finally, the differential expression of the four genes in the model was verified by quantitative real-time PCR in clinical tissues. These findings of MYCN-related genes provide a new and reliable prognostic model for NB related to MYCN.
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Affiliation(s)
- FengLing Shao
- Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Department of Pediatric Surgical Oncology, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, P.R. China
| | - Zhenni Wang
- Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Department of Pediatric Surgical Oncology, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, P.R. China
| | - Shan Wang
- Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Department of Pediatric Surgical Oncology, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, P.R. China
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Wojcik MH, Agrawal PB. Deciphering congenital anomalies for the next generation. Cold Spring Harb Mol Case Stud 2020; 6:mcs.a005504. [PMID: 32826208 PMCID: PMC7552931 DOI: 10.1101/mcs.a005504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Congenital anomalies are common, with 2%-3% of infants estimated to have at least one major congenital malformation and countless others with minor malformations of lesser cosmetic or medical importance. As congenital malformations are major drivers of morbidity and mortality, representing the leading cause of infant mortality in the United States, there is substantial interest in understanding the underlying etiologies-particularly if modifiable causes may be identified or pre- or postnatal treatments can be offered. Recent research has begun to reveal the spectrum of monogenic disorders that commonly result in birth defects, and newer approaches have revealed non-Mendelian genetic contributions including gene-environment interactions. Our experience suggests that increased efforts to sequence and analyze cases of perinatal death, as well as continued global collaboration, will be essential in understanding the genomic landscape of structural anomalies.
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Affiliation(s)
- Monica H Wojcik
- Divisions of Newborn Medicine and Genetics and Genomics, Department of Pediatrics, The Manton Center for Orphan Disease Research, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Pankaj B Agrawal
- Divisions of Newborn Medicine and Genetics and Genomics, Department of Pediatrics, The Manton Center for Orphan Disease Research, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
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Chang Q, Chen HL. Maternal occupational exposure to solvents and gastroschisis in offspring: are gene-environment interactions playing a role? Occup Environ Med 2020; 77:735. [PMID: 32513830 DOI: 10.1136/oemed-2020-106627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 05/13/2020] [Accepted: 05/18/2020] [Indexed: 11/03/2022]
Affiliation(s)
- Qing Chang
- Wuxi No.8 People's Hospital and Wuxi Occupational Disease Hospital, Wuxi, Jiangsu Province, China
| | - Hong-Lin Chen
- School of Public Health, Nantong University, Nantong, Jiangsu Province, China
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Salinas-Torres VM, Gallardo-Blanco HL, Salinas-Torres RA, Cerda-Flores RM, Lugo-Trampe JJ, Villarreal-Martínez DZ, Ibarra-Ramírez M, Martínez de Villarreal LE. Whole exome sequencing identifies multiple novel candidate genes in familial gastroschisis. Mol Genet Genomic Med 2020; 8:e1176. [PMID: 32163230 PMCID: PMC7216806 DOI: 10.1002/mgg3.1176] [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: 06/04/2019] [Revised: 01/18/2020] [Accepted: 01/30/2020] [Indexed: 12/20/2022] Open
Abstract
Background Genetic association studies for gastroschisis have highlighted several candidate variants. However, genetic basis in gastroschisis from noninvestigated heritable factors could provide new insights into the human biology for this birth defect. We aim to identify novel gastroschisis susceptibility variants by employing whole exome sequencing (WES) in a Mexican family with recurrence of gastroschisis. Methods We employed WES in two affected half‐sisters with gastroschisis, mother, and father of the proband. Additionally, functional bioinformatics analysis was based on SVS–PhoRank and Ensembl–Variant Effect Predictor. The latter assessed the potentially deleterious effects (high, moderate, low, or modifier impact) from exome variants based on SIFT, PolyPhen, dbNSFP, Condel, LoFtool, MaxEntScan, and BLOSUM62 algorithms. The analysis was based on the Human Genome annotation, GRCh37/hg19. Candidate genes were prioritized and manually curated based on significant phenotypic relevance (SVS–PhoRank) and functional properties (Ensembl–Variant Effect Predictor). Functional enrichment analysis was performed using ToppGene Suite, including a manual curation of significant Gene Ontology (GO) biological processes from functional similarity analysis of candidate genes. Results No single gene‐disrupting variant was identified. Instead, 428 heterozygous variations were identified for which SPATA17, PDE4DIP, CFAP65, ALPP, ZNF717, OR4C3, MAP2K3, TLR8, and UBE2NL were predicted as high impact in both cases, mother, and father of the proband. PLOD1, COL6A3, FGFRL1, HHIP, SGCD, RAPGEF1, PKD1, ZFHX3, BCAS3, EVPL, CEACAM5, and KLK14 were segregated among both cases and mother. Multiple interacting background modifiers may regulate gastroschisis susceptibility. These candidate genes highlight a role for development of blood vessel, circulatory system, muscle structure, epithelium, and epidermis, regulation of cell junction assembly, biological/cell adhesion, detection/response to endogenous stimulus, regulation of cytokine biosynthetic process, response to growth factor, postreplication repair/protein K63‐linked ubiquitination, protein‐containing complex assembly, and regulation of transcription DNA‐templated. Conclusion Considering the likely gene‐disrupting prediction results and similar biological pattern of mechanisms, we propose a joint “multifactorial model” in gastroschisis pathogenesis.
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Affiliation(s)
- Víctor M Salinas-Torres
- Department of Genetics, School of Medicine and University Hospital Dr. José Eleuterio González, Universidad Autónoma de Nuevo León, Monterrey, México
| | - Hugo L Gallardo-Blanco
- Department of Genetics, School of Medicine and University Hospital Dr. José Eleuterio González, Universidad Autónoma de Nuevo León, Monterrey, México
| | | | | | - José J Lugo-Trampe
- Department of Genetics, School of Medicine and University Hospital Dr. José Eleuterio González, Universidad Autónoma de Nuevo León, Monterrey, México
| | - Daniel Z Villarreal-Martínez
- Department of Genetics, School of Medicine and University Hospital Dr. José Eleuterio González, Universidad Autónoma de Nuevo León, Monterrey, México
| | - Marisol Ibarra-Ramírez
- Department of Genetics, School of Medicine and University Hospital Dr. José Eleuterio González, Universidad Autónoma de Nuevo León, Monterrey, México
| | - Laura E Martínez de Villarreal
- Department of Genetics, School of Medicine and University Hospital Dr. José Eleuterio González, Universidad Autónoma de Nuevo León, Monterrey, México
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