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Ha T, Morgan A, Bartos MN, Beatty K, Cogné B, Braun D, Gerber CB, Gaspar H, Kopps AM, Rieubland C, Hurst ACE, Amor DJ, Nizon M, Pasquier L, Pfundt R, Reis A, Siu VM, Tessarech M, Thompson ML, Vincent M, de Vries BBA, Walsh MB, Wechsler SB, Zweier C, Schnur RE, Guillen Sacoto MJ, Margot H, Masotto B, Palafoll MIV, Nawaz U, Voineagu I, Slavotinek A. De novo variants predicting haploinsufficiency for DIP2C are associated with expressive speech delay. Am J Med Genet A 2024; 194:e63559. [PMID: 38421105 PMCID: PMC11161320 DOI: 10.1002/ajmg.a.63559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/16/2023] [Accepted: 01/04/2024] [Indexed: 03/02/2024]
Abstract
The disconnected (disco)-interacting protein 2 (DIP2) gene was first identified in D. melanogaster and contains a DNA methyltransferase-associated protein 1 (DMAP1) binding domain, Acyl-CoA synthetase domain and AMP-binding sites. DIP2 regulates axonal bifurcation of the mushroom body neurons in D. melanogaster and is required for axonal regeneration in the neurons of C. elegans. The DIP2 homologues in vertebrates, Disco-interacting protein 2 homolog A (DIP2A), Disco-interacting protein 2 homolog B (DIP2B), and Disco-interacting protein 2 homolog C (DIP2C), are highly conserved and expressed widely in the central nervous system. Although there is evidence that DIP2C plays a role in cognition, reports of pathogenic variants in these genes are rare and their significance is uncertain. We present 23 individuals with heterozygous DIP2C variants, all manifesting developmental delays that primarily affect expressive language and speech articulation. Eight patients had de novo variants predicting loss-of-function in the DIP2C gene, two patients had de novo missense variants, three had paternally inherited loss of function variants and six had maternally inherited loss-of-function variants, while inheritance was unknown for four variants. Four patients had cardiac defects (hypertrophic cardiomyopathy, atrial septal defects, and bicuspid aortic valve). Minor facial anomalies were inconsistent but included a high anterior hairline with a long forehead, broad nasal tip, and ear anomalies. Brainspan analysis showed elevated DIP2C expression in the human neocortex at 10-24 weeks after conception. With the cases presented herein, we provide phenotypic and genotypic data supporting the association between loss-of-function variants in DIP2C with a neurocognitive phenotype.
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Affiliation(s)
- Thoa Ha
- Division of Medical Genetics, Department of Pediatrics, University of California, San Francisco, San Francisco, USA
| | - Angela Morgan
- Murdoch Children's Research Institute, Parkville, Victoria, Australia
- University of Melbourne, Parkville, Victoria, Australia
- Royal Children's Hospital, Parkville, Victoria, Australia
| | - Meghan N Bartos
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Katelyn Beatty
- Division of Human Genetics, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Benjamin Cogné
- CHU Nantes, Service de Génétique Médicale, L'institut du Thorax, University Nantes, Nantes, France
| | - Dominique Braun
- Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Céline B Gerber
- Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Harald Gaspar
- Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Anna M Kopps
- Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Claudine Rieubland
- Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Anna C E Hurst
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - David J Amor
- Murdoch Children's Research Institute, Parkville, Victoria, Australia
- University of Melbourne, Parkville, Victoria, Australia
- Royal Children's Hospital, Parkville, Victoria, Australia
| | - Mathilde Nizon
- CHU Nantes, Service de Génétique Médicale, L'institut du Thorax, University Nantes, Nantes, France
| | | | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center and Donders Institute for Brain, Cognition and Behavior, Nijmegen, The Netherlands
| | - André Reis
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
- Centre for Rare Diseases Erlangen (ZSEER), Erlangen, Germany
| | - Victoria Mok Siu
- London Health Sciences Center and Department of Pediatrics, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Marine Tessarech
- Department of Biochemistry and Genetics, Angers University Hospital, Angers, France
| | | | - Marie Vincent
- CHU Nantes, Service de Génétique Médicale, L'institut du Thorax, University Nantes, Nantes, France
| | - Bert B A de Vries
- Department of Human Genetics, Radboud University Medical Center and Donders Institute for Brain, Cognition and Behavior, Nijmegen, The Netherlands
| | | | - Stephanie Burns Wechsler
- Departments of Pediatrics and Human Genetics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Christiane Zweier
- Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | | | | | - Henri Margot
- Université Bordeaux, MRGM INSERM U1211, CHU de Bordeaux, Service de Génétique Médicale, Bordeaux, France
| | - Barbara Masotto
- Hospital Universitari Vall d'Hebron, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | | | - Urwah Nawaz
- Adelaide Medical School and Robinson Research Institute, The University of Adelaide, Adelaide, Australia
| | - Irina Voineagu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Anne Slavotinek
- Division of Medical Genetics, Department of Pediatrics, University of California, San Francisco, San Francisco, USA
- Division of Human Genetics, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
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Zhang X, Zhou C, Hu J, Hu J, Ding Y, Chen S, Wang X, Xu L, Gou Z, Zhang S, Shi W. Six-gene prognostic signature for non-alcoholic fatty liver disease susceptibility using machine learning. Medicine (Baltimore) 2024; 103:e38076. [PMID: 38728481 PMCID: PMC11081587 DOI: 10.1097/md.0000000000038076] [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: 12/28/2023] [Accepted: 04/10/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND nonalcoholic fatty liver disease (NAFLD) is a common liver disease affecting the global population and its impact on human health will continue to increase. Genetic susceptibility is an important factor influencing its onset and progression, and there is a lack of reliable methods to predict the susceptibility of normal populations to NAFLD using appropriate genes. METHODS RNA sequencing data relating to nonalcoholic fatty liver disease was analyzed using the "limma" package within the R software. Differentially expressed genes were obtained through preliminary intersection screening. Core genes were analyzed and obtained by establishing and comparing 4 machine learning models, then a prediction model for NAFLD was constructed. The effectiveness of the model was then evaluated, and its applicability and reliability verified. Finally, we conducted further gene correlation analysis, analysis of biological function and analysis of immune infiltration. RESULTS By comparing 4 machine learning algorithms, we identified SVM as the optimal model, with the first 6 genes (CD247, S100A9, CSF3R, DIP2C, OXCT 2 and PRAMEF16) as predictive genes. The nomogram was found to have good reliability and effectiveness. Six genes' receiver operating characteristic curves (ROC) suggest an essential role in NAFLD pathogenesis, and they exhibit a high predictive value. Further analysis of immunology demonstrated that these 6 genes were closely connected to various immune cells and pathways. CONCLUSION This study has successfully constructed an advanced and reliable prediction model based on 6 diagnostic gene markers to predict the susceptibility of normal populations to NAFLD, while also providing insights for potential targeted therapies.
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Affiliation(s)
- Xiang Zhang
- Zhejiang Chinese Medical University, Hangzhou, China
| | - Chunzi Zhou
- Zhejiang Chinese Medical University, Hangzhou, China
| | - Jingwen Hu
- Zhejiang Chinese Medical University, Hangzhou, China
| | - Jingwen Hu
- Zhejiang Chinese Medical University, Hangzhou, China
| | - Yueping Ding
- The Second Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
| | - Shiqi Chen
- Lishui Hospital of Traditional Chinese Medicine, Lishui, China
| | - Xu Wang
- Shanghai Jinshan TCM-Integrated Hospital, Shanghai, China
| | - Lei Xu
- The Second Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
| | - Zhijun Gou
- Zhejiang Chinese Medical University, Hangzhou, China
| | - Shuqiao Zhang
- First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Weiqun Shi
- The Second Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
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Ul Mudassir B, Agha Z. Novel and known minor alleles of CNTNAP2 gene variants are associated with comorbidity of intellectual disability and epilepsy phenotypes: a case-control association study reveals potential biomarkers. Mol Biol Rep 2024; 51:276. [PMID: 38315301 DOI: 10.1007/s11033-023-09176-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 12/18/2023] [Indexed: 02/07/2024]
Abstract
BACKGROUND Neurodevelopmental disorders are heterogeneous due to underlying multiple shared genetic pathways and risk factors. Intellectual disability, epilepsy and autism spectrum disorder phenotypes overlap which indicates the diverse effects of common genes. Recent studies suggested the probable contribution of CNTNAP2 gene polymorphisms to the comorbidity of these neurological conditions. METHODS AND RESULTS This study was conducted to investigate the role of CNTNAP2 polymorphisms rs147815978 (G>T) and rs2710102 (A>G) as a risk factor for comorbidity of intellectual disability and epilepsy in a group of 345 individuals including 170 patients and 175 healthy controls recruited from various ethnic groups of Pakistani population. Our case-control study group was genotyped by tetra primer ARMS-PCR technique and results were analysed to know the effects of CNTNAP2 rs147815978 (G>T) and rs2710102 (A>G) polymorphisms in the group. The frequency of risk allele T (rs147815978) and risk allele G (rs2710102) for homozygous recessive genotypes (TT/GG) in our study group was 36.47% while odds ratios for risk allele T (rs147815978) was 5.45 (3.90-7.61: 95% CI, P = 0.000) and that for risk allele G (rs2710102) was 2.39 (1.76-3.24: 95% CI, P = 0.0001). Homozygous recessive genotypes (TT/GG) appeared only in cases and not in control group which indicated these as suspected risk genotypes and the significant association (p < 0.05%) of CNTNAP2 gene polymorphisms rs147815978 (G>T) and rs2710102 (A>G) with co-occurrence of intellectual disability and epilepsy phenotypes in our study group which is in HWE (χ2 = 174, P < 0.0001). Logistic regression analysis shows additive (p < 0.0001) and multiplicative (p < 0.001) models which confirms significant association of both the polymorphisms in our data, which are closely located on same haplotype (D' = - 0.168). CONCLUSIONS We propose that CNTNAP2 rs147815978 (G>T) and rs2710102 (A>G) polymorphisms are possible risk loci for overlapping neurodevelopmental disorders in Pakistani population. We propose the role of a previously reported common SNP rs2710102 (A>G) with a rarely reported novel SNP rs147815978 (G>T) for CNTNAP2 gene association with neurodevelopmental disorders in our data. Our study has expanded the knowledge of CNTNAP2 gene polymorphisms as probable biomarkers for susceptibility of co-occurrence of intellectual disability and epilepsy phenotypes in Pakistani population. We hope that our study will open new horizons of CNTNAP2 gene variants research to cure the neurological conditions in Pakistani population where consanguinity is a tradition and prevalence of neurodevelopmental disorders has increased from 1 to 2% during last 5 years.
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Affiliation(s)
- Behjat Ul Mudassir
- Translational Genomics Laboratory, Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Zehra Agha
- Translational Genomics Laboratory, Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan.
- Department of Psychiatry, State University of New York at Buffalo, Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA.
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Alibutud R, Hansali S, Cao X, Zhou A, Mahaganapathy V, Azaro M, Gwin C, Wilson S, Buyske S, Bartlett CW, Flax JF, Brzustowicz LM, Xing J. Structural Variations Contribute to the Genetic Etiology of Autism Spectrum Disorder and Language Impairments. Int J Mol Sci 2023; 24:13248. [PMID: 37686052 PMCID: PMC10487745 DOI: 10.3390/ijms241713248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 08/24/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by restrictive interests and/or repetitive behaviors and deficits in social interaction and communication. ASD is a multifactorial disease with a complex polygenic genetic architecture. Its genetic contributing factors are not yet fully understood, especially large structural variations (SVs). In this study, we aimed to assess the contribution of SVs, including copy number variants (CNVs), insertions, deletions, duplications, and mobile element insertions, to ASD and related language impairments in the New Jersey Language and Autism Genetics Study (NJLAGS) cohort. Within the cohort, ~77% of the families contain SVs that followed expected segregation or de novo patterns and passed our filtering criteria. These SVs affected 344 brain-expressed genes and can potentially contribute to the genetic etiology of the disorders. Gene Ontology and protein-protein interaction network analysis suggested several clusters of genes in different functional categories, such as neuronal development and histone modification machinery. Genes and biological processes identified in this study contribute to the understanding of ASD and related neurodevelopment disorders.
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Affiliation(s)
- Rohan Alibutud
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (R.A.); (S.H.); (X.C.); (A.Z.); (V.M.); (M.A.); (C.G.); (S.W.); (J.F.F.); (L.M.B.)
| | - Sammy Hansali
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (R.A.); (S.H.); (X.C.); (A.Z.); (V.M.); (M.A.); (C.G.); (S.W.); (J.F.F.); (L.M.B.)
| | - Xiaolong Cao
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (R.A.); (S.H.); (X.C.); (A.Z.); (V.M.); (M.A.); (C.G.); (S.W.); (J.F.F.); (L.M.B.)
| | - Anbo Zhou
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (R.A.); (S.H.); (X.C.); (A.Z.); (V.M.); (M.A.); (C.G.); (S.W.); (J.F.F.); (L.M.B.)
| | - Vaidhyanathan Mahaganapathy
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (R.A.); (S.H.); (X.C.); (A.Z.); (V.M.); (M.A.); (C.G.); (S.W.); (J.F.F.); (L.M.B.)
| | - Marco Azaro
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (R.A.); (S.H.); (X.C.); (A.Z.); (V.M.); (M.A.); (C.G.); (S.W.); (J.F.F.); (L.M.B.)
| | - Christine Gwin
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (R.A.); (S.H.); (X.C.); (A.Z.); (V.M.); (M.A.); (C.G.); (S.W.); (J.F.F.); (L.M.B.)
| | - Sherri Wilson
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (R.A.); (S.H.); (X.C.); (A.Z.); (V.M.); (M.A.); (C.G.); (S.W.); (J.F.F.); (L.M.B.)
| | - Steven Buyske
- Department of Statistics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA;
| | - Christopher W. Bartlett
- The Steve Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH 43205, USA;
- Department of Pediatrics, College of Medicine, The Ohio State University, Columbus, OH 43205, USA
| | - Judy F. Flax
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (R.A.); (S.H.); (X.C.); (A.Z.); (V.M.); (M.A.); (C.G.); (S.W.); (J.F.F.); (L.M.B.)
| | - Linda M. Brzustowicz
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (R.A.); (S.H.); (X.C.); (A.Z.); (V.M.); (M.A.); (C.G.); (S.W.); (J.F.F.); (L.M.B.)
- The Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Jinchuan Xing
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (R.A.); (S.H.); (X.C.); (A.Z.); (V.M.); (M.A.); (C.G.); (S.W.); (J.F.F.); (L.M.B.)
- The Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
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