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Tambi R, Zehra B, Nandkishore S, Sharafat S, Kader F, Nassir N, Mohamed N, Ahmed A, Abdel Hameid R, Alasrawi S, Brueckner M, Kuebler WM, Chung WK, Alsheikh-Ali A, Di Donato RM, Uddin M, Berdiev BK. Single-cell reconstruction and mutation enrichment analysis identifies dysregulated cardiomyocyte and endothelial cells in congenital heart disease. Physiol Genomics 2023; 55:634-646. [PMID: 37811720 DOI: 10.1152/physiolgenomics.00070.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 09/19/2023] [Accepted: 10/03/2023] [Indexed: 10/10/2023] Open
Abstract
Congenital heart disease (CHD) is one of the most prevalent neonatal congenital anomalies. To catalog the putative candidate CHD risk genes, we collected 16,349 variants [single-nucleotide variants (SNVs) and Indels] impacting 8,308 genes in 3,166 CHD cases for a comprehensive meta-analysis. Using American College of Medical Genetics (ACMG) guidelines, we excluded the 0.1% of benign/likely benign variants and the resulting dataset consisted of 83% predicted loss of function variants and 17% missense variants. Seventeen percent were de novo variants. A stepwise analysis identified 90 variant-enriched CHD genes, of which six (GPATCH1, NYNRIN, TCLD2, CEP95, MAP3K19, and TTC36) were novel candidate CHD genes. Single-cell transcriptome cluster reconstruction analysis on six CHD tissues and four controls revealed upregulation of the top 10 frequently mutated genes primarily in cardiomyocytes. NOTCH1 (highest number of variants) and MYH6 (highest number of recurrent variants) expression was elevated in endocardial cells and cardiomyocytes, respectively, and 60% of these gene variants were associated with tetralogy of Fallot and coarctation of the aorta, respectively. Pseudobulk analysis using the single-cell transcriptome revealed significant (P < 0.05) upregulation of both NOTCH1 (endocardial cells) and MYH6 (cardiomyocytes) in the control heart data. We observed nine different subpopulations of CHD heart cardiomyocytes of which only four were observed in the control heart. This is the first comprehensive meta-analysis combining genomics and CHD single-cell transcriptomics, identifying the most frequently mutated CHD genes, and demonstrating CHD gene heterogeneity, suggesting that multiple genes contribute to the phenotypic heterogeneity of CHD. Cardiomyocytes and endocardial cells are identified as major CHD-related cell types.NEW & NOTEWORTHY Congential heart disease (CHD) is one of the most prevalent neonatal congenital anomalies. We present a comprehensive analysis combining genomics and CHD single-cell transcriptome. Our study identifies 90 potential candidate CHD risk genes of which 6 are novel. The risk genes have heterogenous expression suggestive of multiple genes contributing to the phenotypic heterogeneity of CHD. Cardiomyocytes and endocardial cells are identified as major CHD-related cell types.
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Affiliation(s)
- Richa Tambi
- Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Binte Zehra
- Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Sharon Nandkishore
- Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Shermin Sharafat
- Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Faiza Kader
- Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Nasna Nassir
- Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Nesrin Mohamed
- Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Awab Ahmed
- Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Reem Abdel Hameid
- Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Samah Alasrawi
- Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
- Al Jalila Children's Hospital, Dubai, United Arab Emirates
| | - Martina Brueckner
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut, United States
- Department of Pediatrics, Yale University, New Haven, Connecticut, United States
| | - Wolfgang M Kuebler
- Institute of Physiology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Wendy K Chung
- Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, United States
| | - Alawi Alsheikh-Ali
- Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | | | - Mohammed Uddin
- Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
- Cellular Intelligence Lab, GenomeArc Incorporated, Toronto, Ontario, Canada
| | - Bakhrom K Berdiev
- Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
- Cellular Intelligence Lab, GenomeArc Incorporated, Toronto, Ontario, Canada
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