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Abstract
PURPOSE OF REVIEW Given a general lack of emphasis on the molecular underpinnings of single ventricle (SV) congenital heart diseases (CHD), our review highlights and summarizes recent advances in uncovering the genetic and molecular mechanisms in SV CHD etiology. RECENT FINDINGS While common SV-associated genetic mutations were found in key cardiac transcription factors, other mutations were sporadic. With advances in genetic sequencing technologies and animal models, more disease-associated factors have been identified to act in critical cardiac signaling pathways such as NOTCH, Wnt, and TGF signaling. Recent studies have also revealed that different cardiac lineages play different roles in disease pathogenesis. SV defects are attributed to complex combinations of genetic mutations, indicating that sophisticated spatiotemporal regulation of gene transcription networks and functional cellular pathways govern disease progression. Future studies will warrant in-depth investigations into better understanding how different genetic factors converge to influence common downstream cellular pathways, resulting in SV abnormalities.
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Bremm JM, Boquett JA, Silva Michels M, Kowalski TW, Gomes FG, Vianna FSL, Vieira Sanseverino MT, Fraga LR. Investigating the role of EGF-CFC gene family in recurrent pregnancy loss through bioinformatics and molecular approaches. Syst Biol Reprod Med 2021; 67:450-462. [PMID: 34498535 DOI: 10.1080/19396368.2021.1965673] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Recurrent pregnancy loss (RPL) is the most common reproductive failure, reaching 1-5% of women throughout their lives, and having unknown etiology in 50% of the cases. In humans, EGF-CFC1 (Epidermal Growth Factors & Cripto/FRL-1/Cryptic) gene family is composed by TDGF1 and CFC1, two developmental genes. The aim of this study was to investigate the role of EGF-CFC on RPL. To this, multiple approaches were performed; we conducted an expression analysis of TDGF1 and CFC1 using publicly available data from Gene Omnibus Expression (GEO), systems biology analyses and functional prediction; and a molecular analysis carried out in a case-control study. Our GEO analysis showed a decrease in TDGF1 expression in the endometrium (p=0.049) and CFC1 expression in placenta (p=0.015) of women with RPL. Network analysis, gene ontology and literature pointed to a strong connection between EGF-CFC1 gene family to pathways that play key roles during pregnancy, including TGF-β, c-Src/MAPK/AKT, Notch, TNFα, IFNγ and IL-6. A pathogenicity score developed for this gene family showed that the c.-14+1429T>C (rs3806702) variant in the TDGF1 and the p.Arg47Gln (rs201431919) variant in CFC1 gene would be the ones with the highest deleterious effect for RPL. In the case-control study, which involved 149 women with RPL and 159 controls, no statistical difference was observed in the allele and genotype distributions of the variants studied in the two groups. In this study, we performed extensive bioinformatics analysis for biomarker prioritization followed by experimental validation of proposed selected markers. Although there is no statistical difference in the frequencies of these variants between RPL and controls, the expression analysis results suggest that TDGF1 and CFC1 genes might play a role in RPL. In addition, systems biology analyzes raise the hypothesis that genes in other signaling pathways that may be related to RPL as good candidates for future studies.Abbreviations RPL: recurrent pregnancy loss; EGF-CFC1: Epidermal Growth Factors - Cripto/FRL-1; GEO: Gene Omnibus Expression; KEGG: Kyoto Encyclopedia of Genes and Genomes.
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Affiliation(s)
- João Matheus Bremm
- Post-graduate Program in Genetics and Molecular Biology, Department of Genetics, Biosciences Institute, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Juliano André Boquett
- Post-graduate Program in Genetics and Molecular Biology, Department of Genetics, Biosciences Institute, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Post-graduate Program in Child and Adolescent Health, Faculty of Medicine, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Marcus Silva Michels
- Post-graduate Program in Genetics and Molecular Biology, Department of Genetics, Biosciences Institute, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Thayne Woycinck Kowalski
- Post-graduate Program in Genetics and Molecular Biology, Department of Genetics, Biosciences Institute, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Laboratory of Genomic Medicine, Experimental Research Center, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Flávia Gobetti Gomes
- Post-graduate Program in Genetics and Molecular Biology, Department of Genetics, Biosciences Institute, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Fernanda Sales Luiz Vianna
- Post-graduate Program in Genetics and Molecular Biology, Department of Genetics, Biosciences Institute, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Post-Graduate Program in Medicine: Medical Sciences, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Laboratory of Genomic Medicine, Experimental Research Center, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Maria Teresa Vieira Sanseverino
- Post-graduate Program in Genetics and Molecular Biology, Department of Genetics, Biosciences Institute, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,School of Medicine, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil.,Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Lucas Rosa Fraga
- Post-Graduate Program in Medicine: Medical Sciences, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Laboratory of Genomic Medicine, Experimental Research Center, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil.,Department of Morphological Science, Institute of Health Sciences, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
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Identification of novel candidate genes in heterotaxy syndrome patients with congenital heart diseases by whole exome sequencing. Biochim Biophys Acta Mol Basis Dis 2020; 1866:165906. [PMID: 32738303 DOI: 10.1016/j.bbadis.2020.165906] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 07/14/2020] [Accepted: 07/25/2020] [Indexed: 12/13/2022]
Abstract
Heterotaxy syndrome (HS) involves dysfunction of multiple systems resulting from abnormal left-right (LR) body patterning. Most HS patients present with complex congenital heart diseases (CHD), the disability and mortality of HS patients are extremely high. HS has great heterogeneity in phenotypes and genotypes, which have rendered gene discovery challenging. The aim of this study was to identify novel genes that underlie pathogenesis of HS patients with CHD. Whole exome sequencing was performed in 25 unrelated HS cases and 100 healthy controls; 19 nonsynonymous variants in 6 novel candidate genes (FLNA, ITGA1, PCNT, KIF7, GLI1, KMT2D) were identified. The functions of candidate genes were further analyzed in zebrafish model by CRISPR/Cas9 technique. Genome-editing was successfully introduced into the gene loci of flna, kmt2d and kif7, but the phenotypes were heterogenous. Disruption of each gene disturbed normal cardiac looping while kif7 knockout had a more prominent effect on liver budding and pitx2 expression. Our results revealed three potential HS pathogenic genes with probably different molecular mechanisms.
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Li Z, Zhang F, Wang Y, Qiu Y, Wu Y, Lu Y, Yang L, Qu WJ, Wang H, Zhou W, Tian W. PhenoPro: a novel toolkit for assisting in the diagnosis of Mendelian disease. Bioinformatics 2019; 35:3559-3566. [PMID: 30843052 DOI: 10.1093/bioinformatics/btz100] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Revised: 12/29/2018] [Accepted: 02/13/2019] [Indexed: 01/27/2023] Open
Abstract
Abstract
Motivation
Whole-exome sequencing (WES) is now being used in clinical practice for the diagnosis of the causal genes of Mendelian diseases. In order to make the diagnosis, however, the clinical phenotypes [e.g. Human Phenotype Ontology (HPO) terms] of a patient are needed for prioritizing the variants called from the WES data of the patient. Computational tools are therefore needed to standardize and accelerate this process.
Results
Here, we introduce a tool named PhenoPro for prioritizing the causal gene of Mendelian disease given both the HPO terms assigned to and the variants called from the WES data of a patient. PhenoPro has been benchmarked using both simulated patients and 287 real diagnosed patients of Chinese ancestry, and shows significant improvements over five previous tools. Moreover, the addition of an internal variant data of Chinese ancestry and the variant data from the patients’ parents can further improve PhenoPro’s performance. To make PhenoPro a fully automated tool, we also include a natural language processing component for automated HPO term assignment from clinical reports, and demonstrate that the natural language processing is as effective as manual HPO assignment using real clinical reports. In conclusion, PhenoPro can be used as a pre-screening tool to assist in the diagnosis of Mendelian disease genes.
Availability and implementation
The web server of PhenoPro is freely available at http://app.tianlab.cn.
Supplementary information
Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Zixiu Li
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Shanghai, China
- Department of Biostatistics and Computational Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Feng Zhang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Shanghai, China
- Department of Biostatistics and Computational Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Yukai Wang
- Department of Biostatistics and Computational Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Yue Qiu
- Department of Biostatistics and Computational Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Yang Wu
- Department of Biostatistics and Computational Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Yulan Lu
- The Molecular Genetic Diagnosis Center, Shanghai Key Lab of Birth Defect, Translational Medicine Research Center of Children Development and Diseases, Pediatrics Research Institute, Shanghai, China
- Children’s Hospital of Fudan University, Shanghai, China
| | - Lin Yang
- The Molecular Genetic Diagnosis Center, Shanghai Key Lab of Birth Defect, Translational Medicine Research Center of Children Development and Diseases, Pediatrics Research Institute, Shanghai, China
- Children’s Hospital of Fudan University, Shanghai, China
| | | | - Huijun Wang
- The Molecular Genetic Diagnosis Center, Shanghai Key Lab of Birth Defect, Translational Medicine Research Center of Children Development and Diseases, Pediatrics Research Institute, Shanghai, China
- Children’s Hospital of Fudan University, Shanghai, China
| | - Wenhao Zhou
- The Molecular Genetic Diagnosis Center, Shanghai Key Lab of Birth Defect, Translational Medicine Research Center of Children Development and Diseases, Pediatrics Research Institute, Shanghai, China
- Children’s Hospital of Fudan University, Shanghai, China
| | - Weidong Tian
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Shanghai, China
- Department of Biostatistics and Computational Biology, School of Life Sciences, Fudan University, Shanghai, China
- Children’s Hospital of Fudan University, Shanghai, China
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Salehi Karlslätt K, Pettersson M, Jäntti N, Szafranski P, Wester T, Husberg B, Ullberg U, Stankiewicz P, Nordgren A, Lundin J, Lindstrand A, Nordenskjöld A. Rare copy number variants contribute pathogenic alleles in patients with intestinal malrotation. Mol Genet Genomic Med 2019; 7:e549. [PMID: 30632303 PMCID: PMC6418355 DOI: 10.1002/mgg3.549] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 12/05/2018] [Accepted: 12/05/2018] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Intestinal malrotation is a potentially life-threatening congenital anomaly due to the risk of developing midgut volvulus. The reported incidence is 0.2%-1% and both apparently hereditary and sporadic cases have been reported. Intestinal malrotation is associated with a few syndromes with known genotype but the genetic contribution in isolated intestinal malrotation has not yet been reported. Rare copy number variants (CNVs) have been implicated in many congenital anomalies, and hence we sought to investigate the potential contribution of rare CNVs in intestinal malrotation. METHODS Analysis of array comparative genomic hybridization (aCGH) data from 47 patients with symptomatic intestinal malrotation was performed. RESULTS We identified six rare CNVs in five patients. Five CNVs involved syndrome loci: 7q11.23 microduplication, 16p13.11 microduplication, 18q terminal deletion, HDAC8 (Cornelia de Lange syndrome type 5 and FOXF1) as well as one intragenic deletion in GALNT14, not previously implicated in human disease. CONCLUSION In the present study, we identified rare CNVs contributing pathogenic or potentially pathogenic alleles in five patients with syndromic intestinal malrotation, suggesting that CNV screening is indicated in intestinal malrotation with associated malformations or neurological involvements. In addition, we identified intestinal malrotation in two known syndromes (Cornelia de Lange type 5 and 18q terminal deletion syndrome) that has not previously been associated with gastrointestinal malformations.
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Affiliation(s)
- Karin Salehi Karlslätt
- Department of Women's and Children's Health and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Pediatrics, Karolinska University Hospital, Stockholm, Sweden
| | - Maria Pettersson
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Nina Jäntti
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Przemyslaw Szafranski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Tomas Wester
- Department of Pediatric Surgery, Karolinska University Hospital, Stockholm, Sweden.,Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Britt Husberg
- Department of General Surgery, Ersta Hospital, Stockholm, Sweden
| | - Ulla Ullberg
- Department of Pediatric Radiology, Karolinska University Hospital, Stockholm, Sweden
| | - Pawel Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Johanna Lundin
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Agneta Nordenskjöld
- Department of Women's and Children's Health and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Pediatric Surgery, Karolinska University Hospital, Stockholm, Sweden
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