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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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Safizadeh Shabestari SA, Nassir N, Sopariwala S, Karimov I, Tambi R, Zehra B, Kosaji N, Akter H, Berdiev BK, Uddin M. Overlapping pathogenic de novo CNVs in neurodevelopmental disorders and congenital anomalies impacting constraint genes regulating early development. Hum Genet 2023; 142:1201-1213. [PMID: 36383254 PMCID: PMC10449996 DOI: 10.1007/s00439-022-02482-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 08/21/2022] [Indexed: 11/17/2022]
Abstract
Neurodevelopmental disorders (NDDs) and congenital anomalies (CAs) are rare disorders with complex etiology. In this study, we investigated the less understood genomic overlap of copy number variants (CNVs) in two large cohorts of NDD and CA patients to identify de novo CNVs and candidate genes associated with both phenotypes. We analyzed clinical microarray CNV data from 10,620 NDD and 3176 CA cases annotated using Horizon platform of GenomeArc Analytics and applied rigorous downstream analysis to evaluate overlapping genes from NDD and CA CNVs. Out of 13,796 patients, only 195 cases contained 218 validated de novo CNVs. Eighteen percent (31/170) de novo CNVs in NDD cases and 40% (19/48) de novo CNVs in CA cases contained genomic overlaps impacting developmentally constraint genes. Seventy-nine constraint genes (10.1% non-OMIM entries) were found to have significantly enriched genomic overlap within rare de novo pathogenic deletions (P value = 0.01, OR = 1.58) and 45 constraint genes (13.3% non-OMIM entries) within rare de novo pathogenic duplications (P value = 0.01, OR = 1.97). Analysis of spatiotemporal transcriptome demonstrated both pathogenic deletion and duplication genes to be highly expressed during the prenatal stage in human developmental brain (P value = 4.95 X 10-6). From the list of overlapping genes, EHMT1, an interesting known NDD gene encompassed pathogenic deletion CNVs from both NDD and CA patients, whereas FAM189A1, and FSTL5 are new candidate genes from non-OMIM entries. In summary, we have identified constraint overlapping genes from CNVs (including de novo) in NDD and CA patients that have the potential to play a vital role in common disease etiology.
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Affiliation(s)
| | - Nasna Nassir
- Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
| | | | | | - Richa Tambi
- Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
| | - Binte Zehra
- Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
| | - Noor Kosaji
- Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
| | - Hosneara Akter
- Genetics and Genomic Medicine Centre, NeuroGen Healthcare, Dhaka, Bangladesh
| | - Bakhrom K Berdiev
- Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
| | - Mohammed Uddin
- Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE.
- GenomeArc Inc, Toronto, ON, Canada.
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Kosaji N, Zehra B, Nassir N, Tambi R, Orszulak AR, Lim ET, Berdiev BK, Woodbury-Smith M, Uddin M. Lack of ethnic diversity in single-cell transcriptomics hinders cell type detection and precision medicine inclusivity. Med 2023; 4:217-219. [PMID: 37060896 DOI: 10.1016/j.medj.2023.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 02/10/2023] [Accepted: 03/09/2023] [Indexed: 04/17/2023]
Abstract
Perhaps one of the most revolutionary next generation sequencing technologies is single-cell (SC) transcriptomics, which was recognized by Nature in 2013 as the method of the year. SC-technologies delve deep into genomics at the single-cell level, revealing previously restricted, valuable information on the identity of single cells, particularly highlighting their heterogeneity. Understanding the cellular heterogeneity of complex tissue provides insight about the gene expression and regulation across different biological and environmental conditions. This vast heterogeneity of cells and their markers makes identifying populations and sub-clusters especially difficult, even more so in rare cell types limited by the absence of rare sub-population markers. One particularly overlooked challenge is the lack of adequate ethnic representation in single-cell data. As the availability of cell types and their markers grow exponentially through new discoveries, the need to study ethnically driven heterogeneity becomes more feasible, while offering the opportunity to further elaborate ethnicity-related heterogeneity. In this commentary, we will discuss this major single-cell limitation particularly focusing on the repercussions it has on disease research, therapeutic design, and precision medicine.
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Affiliation(s)
- Noor Kosaji
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
| | - Binte Zehra
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
| | - Nasna Nassir
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
| | - Richa Tambi
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
| | - Adrian R Orszulak
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Elaine T Lim
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Bakhrom K Berdiev
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
| | | | - Mohammed Uddin
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE; Cellular Intelligence (Ci) Lab, GenomeArc Inc., Toronto, ON, Canada.
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Tambi R, Nandkishore S, Sharafat S, Kader F, Nassir N, Binte Ashraf Z, Mohamed N, Ahmed A, Abdel Hameid R, Taylor A, Abou Tayoun A, Alsheikh‐Ali A, Di Donato R, Uddin M, Berdiev B. Single‐Cell Reconstruction of Cellular Heterogeneity of Congenital Heart Disease. FASEB J 2022. [DOI: 10.1096/fasebj.2022.36.s1.r3237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Richa Tambi
- Mohammed Bin Rashid University of Medicine and Health SciencesDubai
| | | | - Shermin Sharafat
- Mohammed Bin Rashid University of Medicine and Health SciencesDubai
| | - Faiza Kader
- Mohammed Bin Rashid University of Medicine and Health SciencesDubai
| | - Nasna Nassir
- Mohammed Bin Rashid University of Medicine and Health SciencesDubai
| | | | - Nesrin Mohamed
- Mohammed Bin Rashid University of Medicine and Health SciencesDubai
| | - Awab Ahmed
- Mohammed Bin Rashid University of Medicine and Health SciencesDubai
| | | | | | - Ahmad Abou Tayoun
- Mohammed Bin Rashid University of Medicine and Health SciencesDubai
- Al Jalila Children's HospitalDubai
| | - Alawi Alsheikh‐Ali
- Mohammed Bin Rashid University of Medicine and Health SciencesDubai
- Dubai Health AuthorityDubai
| | | | - Mohammed Uddin
- Mohammed Bin Rashid University of Medicine and Health SciencesDubai
| | - Bakhrom Berdiev
- Mohammed Bin Rashid University of Medicine and Health SciencesDubai
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Nassir N, Tambi R, Bankapur A, Al Heialy S, Karuvantevida N, Khansaheb HH, Zehra B, Begum G, Hameid RA, Ahmed A, Deesi Z, Alkhajeh A, Uddin KF, Akter H, Safizadeh Shabestari SA, Almidani O, Islam A, Gaudet M, Kandasamy RK, Loney T, Tayoun AA, Nowotny N, Woodbury-Smith M, Rahman P, Kuebler WM, Yaseen Hachim M, Casanova JL, Berdiev BK, Alsheikh-Ali A, Uddin M. Single-cell transcriptome identifies FCGR3B upregulated subtype of alveolar macrophages in patients with critical COVID-19. iScience 2021; 24:103030. [PMID: 34458692 PMCID: PMC8384759 DOI: 10.1016/j.isci.2021.103030] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 06/16/2021] [Accepted: 08/20/2021] [Indexed: 01/08/2023] Open
Abstract
Understanding host cell heterogeneity is critical for unraveling disease mechanism. Utilizing large-scale single-cell transcriptomics, we analyzed multiple tissue specimens from patients with life-threatening COVID-19 pneumonia, compared with healthy controls. We identified a subtype of monocyte-derived alveolar macrophages (MoAMs) where genes associated with severe COVID-19 comorbidities are significantly upregulated in bronchoalveolar lavage fluid of critical cases. FCGR3B consistently demarcated MoAM subset in different samples from severe COVID-19 cohorts and in CCL3L1-upregulated cells from nasopharyngeal swabs. In silico findings were validated by upregulation of FCGR3B in nasopharyngeal swabs of severe ICU COVID-19 cases, particularly in older patients and those with comorbidities. Additional lines of evidence from transcriptomic data and in vivo of severe COVID-19 cases suggest that FCGR3B may identify a specific subtype of MoAM in patients with severe COVID-19 that may present a novel biomarker for screening and prognosis, as well as a potential therapeutic target. Association of MoAM subtype with severe COVID-19 cases presented with comorbidities Upregulated FCGR3B in CCL3L1 positive MoAM cells in severe COVID-19 cases Upregulated FCGR3B within MoAM subtype as a potential marker for COVID-19 severity
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Affiliation(s)
- Nasna Nassir
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
| | - Richa Tambi
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
| | - Asma Bankapur
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
| | - Saba Al Heialy
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
- Meakins-Christie Laboratories, Research Institute of the McGill University Health Center, Montreal, QC, Canada
| | - Noushad Karuvantevida
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
| | - Hamda Hassan Khansaheb
- Dubai Health Authority, Microbiology and Infection Control Unit, Pathology and Genetics Department, Latifa Women and Children Hospital, Dubai, UAE
| | - Binte Zehra
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
| | - Ghausia Begum
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
| | - Reem Abdel Hameid
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
| | - Awab Ahmed
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
| | - Zulfa Deesi
- Dubai Health Authority, Microbiology and Infection Control Unit, Pathology and Genetics Department, Latifa Women and Children Hospital, Dubai, UAE
| | | | - K.M. Furkan Uddin
- Genetics and Genomic Medicine Centre, NeuroGen Children’s Healthcare, Dhaka, Bangladesh
| | - Hosneara Akter
- Genetics and Genomic Medicine Centre, NeuroGen Children’s Healthcare, Dhaka, Bangladesh
| | | | - Omar Almidani
- Nuffield Department of Surgical Science, University of Oxford, Oxford, UK
| | - Amirul Islam
- Genetics and Genomic Medicine Centre, NeuroGen Children’s Healthcare, Dhaka, Bangladesh
- Cellular Intelligence (Ci) Lab, GenomeArc Inc., Toronto, ON, Canada
| | - Mellissa Gaudet
- Meakins-Christie Laboratories, Research Institute of the McGill University Health Center, Montreal, QC, Canada
| | | | - Tom Loney
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
| | - Ahmad Abou Tayoun
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
- Al Jalila Genomics Center, Al Jalila Children’s Hospital, Dubai, UAE
| | - Norbert Nowotny
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
- Institute of Virology, University of Veterinary Medicine Vienna, Vienna, Austria
| | | | - Proton Rahman
- Department of Rheumatology, Memorial University of Newfoundland, St Johns, NL, Canada
| | - Wolfgang M. Kuebler
- Institute of Physiology, Charité - Universitätsmedizin Berlin, Berlin Germany
| | - Mahmood Yaseen Hachim
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University of Paris, Imagine Institute, Paris, France
- Howard Hughes Medical Institute, New York, NY, USA
| | - Bakhrom K. Berdiev
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
| | - Alawi Alsheikh-Ali
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
- Dubai Health Authority, Dubai, UAE
| | - Mohammed Uddin
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
- Cellular Intelligence (Ci) Lab, GenomeArc Inc., Toronto, ON, Canada
- Corresponding author
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Rooj AK, Cormet-Boyaka E, Clark EB, Qadri YJ, Lee W, Boddu R, Agarwal A, Tambi R, Uddin M, Parpura V, Sorscher EJ, Fuller CM, Berdiev BK. Association of cystic fibrosis transmembrane conductance regulator with epithelial sodium channel subunits carrying Liddle's syndrome mutations. Am J Physiol Lung Cell Mol Physiol 2021; 321:L308-L320. [PMID: 34037494 DOI: 10.1152/ajplung.00298.2020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The association of the cystic fibrosis transmembrane conductance regulator (CFTR) and epithelial sodium channel (ENaC) in the pathophysiology of cystic fibrosis (CF) is controversial. Previously, we demonstrated a close physical association between wild-type (WT) CFTR and WT ENaC. We have also shown that the F508del CFTR fails to associate with ENaC unless the mutant protein is rescued pharmacologically or by low temperature. In this study, we present the evidence for a direct physical association between WT CFTR and ENaC subunits carrying Liddle's syndrome mutations. We show that all three ENaC subunits bearing Liddle's syndrome mutations (both point mutations and the complete truncation of the carboxy terminus), could be coimmunoprecipitated with WT CFTR. The biochemical studies were complemented by fluorescence lifetime imaging microscopy (FLIM), a distance-dependent approach that monitors protein-protein interactions between fluorescently labeled molecules. Our measurements revealed significantly increased fluorescence resonance energy transfer between CFTR and all tested ENaC combinations as compared with controls (ECFP and EYFP cotransfected cells). Our findings are consistent with the notion that CFTR and ENaC are within reach of each other even in the setting of Liddle's syndrome mutations, suggestive of a direct intermolecular interaction between these two proteins.
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Affiliation(s)
- Arun K Rooj
- Department of Cell, Developmental & Integrative Biology, The University of Alabama at Birmingham School of Medicine, Birmingham, Alabama
| | | | - Edlira B Clark
- Department of Cell, Developmental & Integrative Biology, The University of Alabama at Birmingham School of Medicine, Birmingham, Alabama
| | - Yawar J Qadri
- Department of Anesthesiology, The Emory University School of Medicine, Atlanta, Georgia
| | - William Lee
- Department of Neurobiology, The University of Alabama at Birmingham School of Medicine, Birmingham, Alabama
| | - Ravindra Boddu
- Department of Medicine, The University of Alabama at Birmingham School of Medicine, Birmingham, Alabama
| | - Anupam Agarwal
- Department of Medicine, The University of Alabama at Birmingham School of Medicine, Birmingham, Alabama
| | - Richa Tambi
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Mohammed Uddin
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Vladimir Parpura
- Department of Neurobiology, The University of Alabama at Birmingham School of Medicine, Birmingham, Alabama
| | - Eric J Sorscher
- Department of Pediatrics, The Emory University School of Medicine, Atlanta, Georgia
| | - Cathy M Fuller
- Department of Cell, Developmental & Integrative Biology, The University of Alabama at Birmingham School of Medicine, Birmingham, Alabama
| | - Bakhrom K Berdiev
- Department of Cell, Developmental & Integrative Biology, The University of Alabama at Birmingham School of Medicine, Birmingham, Alabama.,College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
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7
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Tambi R, Abdel Hameid R, Bankapur A, Nassir N, Begum G, Zehra B, Akter H, Alsheikh‐Ali A, Uddin M, Berdiev B. Single Cell Transcriptomic and Genomic Characterization of Brugada Syndrome Associated Genes. FASEB J 2021. [DOI: 10.1096/fasebj.2021.35.s1.01506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Richa Tambi
- College of MedicineMohammed Bin Rashid University of Medicine and Health SciencesDubai
| | | | - Asma Bankapur
- Mohammed Bin Rashid University of Medicine and Health SciencesDubai
| | - Nasna Nassir
- Mohammed Bin Rashid University of Medicine and Health SciencesDubai
| | - Ghausia Begum
- Mohammed Bin Rashid University of Medicine and Health SciencesDubai
| | - Binte Zehra
- Mohammed Bin Rashid University of Medicine and Health SciencesDubai
| | - Hosneara Akter
- Genetics and Genomic Medicine CentreNeuroGen Children's Genomic ClinicDhaka
- Department of Biochemistry and Molecular BiologyDhaka UniversityDhaka
| | - Alawi Alsheikh‐Ali
- College of MedicineMohammed Bin Rashid University of Medicine and Health SciencesDubai
| | - Mohammed Uddin
- College of MedicineMohammed Bin Rashid University of Medicine and Health SciencesDubai
| | - Bakhrom Berdiev
- College of MedicineMohammed Bin Rashid University of Medicine and Health SciencesDubai
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Abdel Hameid R, Tambi R, Nassir N, Begum G, Zehra B, Akter H, Cormet‐Boyaka E, Kuebler W, Uddin M, Berdiev B. SARS‐CoV‐2 May Hijack GPCR Signaling Pathways to Compromise Lung Ion and Fluid Transport. FASEB J 2021. [PMCID: PMC8239626 DOI: 10.1096/fasebj.2021.35.s1.01520] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The tropism of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2), a virus responsible for the ongoing coronavirus disease 2019 (COVID‐19) pandemic, towards the host cells is determined, at least in part, by the expression and distribution of its cell surface receptor, angiotensin‐converting enzyme 2 (ACE2). The virus further exploits the host cellular machinery to gain access into the cells; its spike protein is cleaved by a host cell surface transmembrane serine protease 2 (TMPRSS2) shortly after binding ACE2 followed by its proteolytic activation at a furin cleavage site. The virus primarily targets the epithelium of the respiratory tract which is covered by a tightly regulated airway surface liquid (ASL) layer that serves as a primary defense mechanism against respiratory pathogens. The volume and viscosity of this fluid layer is regulated and maintained by a coordinated function of different transport pathways in the respiratory epithelium. We argue that SARS‐CoV‐2 may potentially alter evolutionary conserved second‐messenger signaling cascades via activation of G‐protein coupled receptors (GPCRs) or by directly modulating G protein signaling. Such signaling may in turn adversely modulate transepithelial transport processes, especially those involving cystic fibrosis transmembrane conductance regulator (CFTR) and epithelial Na+ channel (ENaC), thereby shifting the delicate balance between anion secretion and sodium absorption that controls homeostasis of this fluid layer. As a result, activation of the secretory pathways including CFTR‐mediated Cl‐ transport may overwhelm the absorptive pathways such as ENaC‐dependent Na+ uptake and initiate a pathophysiological cascade leading to lung edema, one of the most serious and potentially deadly clinical manifestations of COVID‐19.
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Affiliation(s)
| | - Richa Tambi
- Mohammed Bin Rashid University of Medicine and Health SciencesDubai
| | - Nasna Nassir
- Mohammed Bin Rashid University of Medicine and Health SciencesDubai
| | - Ghausia Begum
- Mohammed Bin Rashid University of Medicine and Health SciencesDubai
| | - Binte Zehra
- Mohammed Bin Rashid University of Medicine and Health SciencesDubai
| | - Hosneara Akter
- Genetics and Genomic Medicine CentreNeuroGen Children's Genomic ClinicDhaka
- Department of Biochemistry and Molecular BiologyDhaka UniversityDhaka
| | | | | | - Mohammed Uddin
- Mohammed Bin Rashid University of Medicine and Health SciencesDubai
| | - Bakhrom Berdiev
- Mohammed Bin Rashid University of Medicine and Health SciencesDubai
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9
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Tambi R, Abdel Hameid R, Bankapur A, Nassir N, Begum G, Alsheikh-Ali A, Uddin M, Berdiev BK. Single-cell transcriptomics trajectory and molecular convergence of clinically relevant mutations in Brugada syndrome. Am J Physiol Heart Circ Physiol 2021; 320:H1935-H1948. [PMID: 33797273 DOI: 10.1152/ajpheart.00061.2021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Brugada syndrome (BrS) is a rare, inherited arrhythmia with high risk of sudden cardiac death. To evaluate the molecular convergence of clinically relevant mutations and to identify developmental cardiac cell types that are associated with BrS etiology, we collected 733 mutations represented by 16 sodium, calcium, potassium channels, and regulatory and structural genes related to BrS. Among the clinically relevant mutations, 266 are unique singletons and 88 mutations are recurrent. We observed an over-representation of clinically relevant mutations (∼80%) in SCN5A gene and also identified several candidate genes, including GPD1L, TRPM4, and SCN10A. Furthermore, protein domain enrichment analysis revealed that a large proportion of the mutations impacted ion transport domains in multiple genes, including SCN5A, TRPM4, and SCN10A. A comparative protein domain analysis of SCN5A further established a significant (P = 0.04) enrichment of clinically relevant mutations within ion transport domain, including a significant (P = 0.02) mutation hotspot within 1321-1380 residue. The enrichment of clinically relevant mutations within SCN5A ion transport domain is stronger (P = 0.00003) among early onset of BrS. Our spatiotemporal cellular heart developmental (prenatal to adult) trajectory analysis applying single-cell transcriptome identified the most frequently BrS-mutated genes (SCN5A and GPD1L) are significantly upregulated in the prenatal cardiomyocytes. A more restrictive cellular expression trajectory is prominent in the adult heart ventricular cardiomyocytes compared to prenatal. Our study suggests that genomic and proteomic hotspots in BrS converge into ion transport pathway and cardiomyocyte as a major BrS-associated cell type that provides insight into the complex genetic etiology of BrS.NEW & NOTEWORTHY Brugada syndrome is a rare inherited arrhythmia with high risk of sudden cardiac death. We present the findings for a molecular convergence of clinically relevant mutations and identification of a single-cell transcriptome-derived cardiac cell types that are associated with the etiology of BrS. Our study suggests that genomic and proteomic hotspots in BrS converge into ion transport pathway and cardiomyocyte as a major BrS-associated cell type that provides insight into the complex genetic etiology of BrS.
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Affiliation(s)
- Richa Tambi
- 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
| | - Asma Bankapur
- 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
| | - Ghausia Begum
- Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - 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
| | - Bakhrom K Berdiev
- Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
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Begum G, Albanna A, Bankapur A, Nassir N, Tambi R, Berdiev BK, Akter H, Karuvantevida N, Kellam B, Alhashmi D, Sung WWL, Thiruvahindrapuram B, Alsheikh-Ali A, Scherer SW, Uddin M. Long-Read Sequencing Improves the Detection of Structural Variations Impacting Complex Non-Coding Elements of the Genome. Int J Mol Sci 2021; 22:2060. [PMID: 33669700 PMCID: PMC7923155 DOI: 10.3390/ijms22042060] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/21/2021] [Accepted: 01/27/2021] [Indexed: 12/17/2022] Open
Abstract
The advent of long-read sequencing offers a new assessment method of detecting genomic structural variation (SV) in numerous rare genetic diseases. For autism spectrum disorders (ASD) cases where pathogenic variants fail to be found in the protein-coding genic regions along chromosomes, we proposed a scalable workflow to characterize the risk factor of SVs impacting non-coding elements of the genome. We applied whole-genome sequencing on an Emirati family having three children with ASD using long and short-read sequencing technology. A series of analytical pipelines were established to identify a set of SVs with high sensitivity and specificity. At 15-fold coverage, we observed that long-read sequencing technology (987 variants) detected a significantly higher number of SVs when compared to variants detected using short-read technology (509 variants) (p-value < 1.1020 × 10-57). Further comparison showed 97.9% of long-read sequencing variants were spanning within the 1-100 kb size range (p-value < 9.080 × 10-67) and impacting over 5000 genes. Moreover, long-read variants detected 604 non-coding RNAs (p-value < 9.02 × 10-9), comprising 58% microRNA, 31.9% lncRNA, and 9.1% snoRNA. Even at low coverage, long-read sequencing has shown to be a reliable technology in detecting SVs impacting complex elements of the genome.
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Affiliation(s)
- Ghausia Begum
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai 505055, United Arab Emirates; (G.B.); (A.A.); (A.B.); (N.N.); (R.T.); (B.K.B.); (N.K.); (D.A.); (A.A.-A.)
| | - Ammar Albanna
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai 505055, United Arab Emirates; (G.B.); (A.A.); (A.B.); (N.N.); (R.T.); (B.K.B.); (N.K.); (D.A.); (A.A.-A.)
- Department of Psychiatry, Al Jalila Children’s Specialty Hospital, Dubai 7662, United Arab Emirates
| | - Asma Bankapur
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai 505055, United Arab Emirates; (G.B.); (A.A.); (A.B.); (N.N.); (R.T.); (B.K.B.); (N.K.); (D.A.); (A.A.-A.)
| | - Nasna Nassir
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai 505055, United Arab Emirates; (G.B.); (A.A.); (A.B.); (N.N.); (R.T.); (B.K.B.); (N.K.); (D.A.); (A.A.-A.)
| | - Richa Tambi
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai 505055, United Arab Emirates; (G.B.); (A.A.); (A.B.); (N.N.); (R.T.); (B.K.B.); (N.K.); (D.A.); (A.A.-A.)
| | - Bakhrom K. Berdiev
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai 505055, United Arab Emirates; (G.B.); (A.A.); (A.B.); (N.N.); (R.T.); (B.K.B.); (N.K.); (D.A.); (A.A.-A.)
| | - Hosneara Akter
- Genetics and Genomic Medicine Centre, NeuroGen Children’s Healthcare, Dhaka 1205, Bangladesh;
- Department of Biochemistry and Molecular Biology, Dhaka University, Dhaka 1000, Bangladesh
| | - Noushad Karuvantevida
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai 505055, United Arab Emirates; (G.B.); (A.A.); (A.B.); (N.N.); (R.T.); (B.K.B.); (N.K.); (D.A.); (A.A.-A.)
- Department of Biotechnology, Bharathidasan University, Tiruchirappalli 620024, India
| | - Barbara Kellam
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5S 1A1, Canada; (B.K.); (W.W.L.S.); (B.T.)
| | - Deena Alhashmi
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai 505055, United Arab Emirates; (G.B.); (A.A.); (A.B.); (N.N.); (R.T.); (B.K.B.); (N.K.); (D.A.); (A.A.-A.)
| | - Wilson W. L. Sung
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5S 1A1, Canada; (B.K.); (W.W.L.S.); (B.T.)
| | - Bhooma Thiruvahindrapuram
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5S 1A1, Canada; (B.K.); (W.W.L.S.); (B.T.)
| | - Alawi Alsheikh-Ali
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai 505055, United Arab Emirates; (G.B.); (A.A.); (A.B.); (N.N.); (R.T.); (B.K.B.); (N.K.); (D.A.); (A.A.-A.)
| | - Stephen W. Scherer
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5S 1A1, Canada; (B.K.); (W.W.L.S.); (B.T.)
- Department of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
- McLaughlin Centre and Department of Molecular Genetics, University of Toronto, Toronto, ON M5S, Canada
| | - Mohammed Uddin
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai 505055, United Arab Emirates; (G.B.); (A.A.); (A.B.); (N.N.); (R.T.); (B.K.B.); (N.K.); (D.A.); (A.A.-A.)
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Banerjee Y, Tambi R, Gholami M, Alsheikh-Ali A, Bayoumi R, Lansberg P. Augmenting Flexnerism Via Twitterism: Need for Integrating Social Media Application in Blueprinting Pedagogical Strategies for Undergraduate Medical Education. JMIR Med Educ 2019; 5:e12403. [PMID: 30907736 PMCID: PMC6452274 DOI: 10.2196/12403] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 12/29/2018] [Accepted: 01/03/2019] [Indexed: 05/10/2023]
Abstract
BACKGROUND Flexnerism, or "competency-based medical education," advocates that formal analytic reasoning, the kind of rational thinking fundamental to the basic sciences, especially the natural sciences, should be the foundation of physicians' intellectual training. The complexity of 21st century health care requires rethinking of current (medical) educational paradigms. In this "Millennial Era," promulgation of the tenets of Flexnerism in undergraduate medical education requires a design and blueprint of innovative pedagogical strategies, as the targeted learners are millennials (designated as generation-Y medical students). OBJECTIVE The aim of this proof-of-concept study was to identify the specific social media app platforms that are selectively preferred by generation-Y medical students in undergraduate medical education. In addition, we aimed to explore if these preferred social media apps can be used to design an effective pedagogical strategy in order to disseminate course learning objectives in the preclinical phase of a spiral curriculum. METHODS A cross-sectional survey was conducted by distributing a 17-item questionnaire among the first- and second-year medical students in the preclinical phase at the Mohammed Bin Rashid University of Medicine and Health Science. RESULTS The study identified YouTube and WhatsApp as the social media app platforms preferred by generation-Y medical students in undergraduate medical education. This study also identified the differences between female and male generation-Y medical students in terms of the use of social media apps in medical education, which we believe will assist instructors in designing pedagogical strategies to integrate social media apps. In addition, we determined the perceptions of generation-Y medical students on the implementation of social media apps in medical education. The pedagogical strategy designed using social media apps and implemented in the Biochemistry course was well accepted by generation-Y medical students and can be translated to any course in the preclinical phase of the medical curriculum. Moreover, the identified limitations of this study provide an understanding of the gaps in research in the integration of social media apps in a medical curriculum catering to generation-Y medical students. CONCLUSIONS 21st century medical education requires effective use of social media app platforms to augment competency-based medical education: Augmentation of Flexnerism in the current scenario is possible only by the adaptation of Twitterism.
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Affiliation(s)
- Yajnavalka Banerjee
- Department of Basic Medical Sciences, College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
- Centre for Medical Education, School of Medicine, University of Dundee, Dundee, United Kingdom
| | - Richa Tambi
- Academic Medical Center, Dubai Healthcare City, Department of Basic Medical Sciences, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
- Laboratory for Computational Molecular Design, RIKEN Center for Biosystems Dynamics Research, Osaka, Japan
| | - Mandana Gholami
- Academic Medical Center, Dubai Healthcare City, Bachelor of Medicine & Bachelor of Surgery Program, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Alawi Alsheikh-Ali
- Academic Medical Center, Dubai Healthcare City, Department of Basic Medical Sciences, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Riad Bayoumi
- Department of Basic Medical Sciences, College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Peter Lansberg
- Molecular Genetics Section, Department of Pediatrics, University Medical Center Groningen, Groningen, Netherlands
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Tambi R, Bayoumi R, Lansberg P, Banerjee Y. Blending Gagne's Instructional Model with Peyton's Approach to Design an Introductory Bioinformatics Lesson Plan for Medical Students: Proof-of-Concept Study. JMIR Med Educ 2018; 4:e11122. [PMID: 30361192 PMCID: PMC6231819 DOI: 10.2196/11122] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 06/30/2018] [Accepted: 07/03/2018] [Indexed: 05/25/2023]
Abstract
BACKGROUND With the rapid integration of genetics into medicine, it has become evident that practicing physicians as well as medical students and clinical researchers need to be updated on the fundamentals of bioinformatics. To achieve this, the following gaps need to be addressed: a lack of defined learning objectives for "Bioinformatics for Medical Practitioner" courses, an absence of a structured lesson plan to disseminate the learning objectives, and no defined step-by-step strategy to teach the essentials of bioinformatics in the medical curriculum. OBJECTIVE The objective of this study was to address these gaps to design a streamlined pedagogical strategy for teaching basics of bioinformatics in the undergraduate medical curriculum. METHODS The established instructional design strategies employed in medical education-Gagne's 9 events of instruction-were followed with further contributions from Peyton's four-step approach to design a structured lesson plan in bioinformatics. RESULTS First, we defined the specifics of bioinformatics that a medical student or health care professional should be introduced to use this knowledge in a clinical context. Second, we designed a structured lesson plan using a blended approach from both Gagne's and Peyton's instructional models. Lastly, we delineated a step-by-step strategy employing free Web-based bioinformatics module, combining it with a clinical scenario of familial hypercholesterolemia to disseminate the defined specifics of bioinformatics. Implementation of Schon's reflective practice model indicated that the activity was stimulating for the students with favorable outcomes regarding their basic training in bioinformatics. CONCLUSIONS To the best of our knowledge, the present lesson plan is the first that outlines an effective dissemination strategy for integrating introductory bioinformatics into a medical curriculum. Further, the lesson plan blueprint can be used to develop similar skills in workshops, continuing professional development, or continuing medical education events to introduce bioinformatics to practicing physicians.
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Affiliation(s)
- Richa Tambi
- Department of Basic Medical Sciences, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Riad Bayoumi
- Department of Basic Medical Sciences, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Peter Lansberg
- Department of Pediatrics, University Medical Center Groningen, Groningen, Netherlands
| | - Yajnavalka Banerjee
- Department of Basic Medical Sciences, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
- University of Dundee, Department of Medical Education, University of Dundee, Dundee, United Kingdom
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