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Daw Elbait G, Daou M, Abuoudah M, Elmekawy A, Hasan SW, Everett DB, Alsafar H, Henschel A, Yousef AF. Comparison of qPCR and metagenomic sequencing methods for quantifying antibiotic resistance genes in wastewater. PLoS One 2024; 19:e0298325. [PMID: 38578803 PMCID: PMC10997137 DOI: 10.1371/journal.pone.0298325] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 05/29/2023] [Accepted: 01/18/2024] [Indexed: 04/07/2024] Open
Abstract
Surveillance methods of circulating antibiotic resistance genes (ARGs) are of utmost importance in order to tackle what has been described as one of the greatest threats to humanity in the 21st century. In order to be effective, these methods have to be accurate, quickly deployable, and scalable. In this study, we compare metagenomic shotgun sequencing (TruSeq DNA sequencing) of wastewater samples with a state-of-the-art PCR-based method (Resistomap HT-qPCR) on four wastewater samples that were taken from hospital, industrial, urban and rural areas. ARGs that confer resistance to 11 antibiotic classes have been identified in these wastewater samples using both methods, with the most abundant observed classes of ARGs conferring resistance to aminoglycoside, multidrug-resistance (MDR), macrolide-lincosamide-streptogramin B (MLSB), tetracycline and beta-lactams. In comparing the methods, we observed a strong correlation of relative abundance of ARGs obtained by the two tested methods for the majority of antibiotic classes. Finally, we investigated the source of discrepancies in the results obtained by the two methods. This analysis revealed that false negatives were more likely to occur in qPCR due to mutated primer target sites, whereas ARGs with incomplete or low coverage were not detected by the sequencing method due to the parameters set in the bioinformatics pipeline. Indeed, despite the good correlation between the methods, each has its advantages and disadvantages which are also discussed here. By using both methods together, a more robust ARG surveillance program can be established. Overall, the work described here can aid wastewater treatment plants that plan on implementing an ARG surveillance program.
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Affiliation(s)
- Gihan Daw Elbait
- Department of Biological Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Mariane Daou
- Department of Biological Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Miral Abuoudah
- Department of Biological Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Ahmed Elmekawy
- Center for Membranes and Advanced Water Technology (CMAT), Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Shadi W. Hasan
- Center for Membranes and Advanced Water Technology (CMAT), Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department of Chemical Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Dean B. Everett
- Department of Pathology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Center for Biotechnology (BTC), Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Infection Research Unit, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Habiba Alsafar
- Center for Biotechnology (BTC), Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Emirates Bio-research Center, Ministry of Interior, Abu Dhabi, United Arab Emirates
- Department of Biomedical Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Andreas Henschel
- Department of Electrical Engineering and Computer Science, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Ahmed F. Yousef
- Department of Biological Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Center for Membranes and Advanced Water Technology (CMAT), Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Center for Biotechnology (BTC), Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
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Zhang S, Yun D, Yang H, Eckstein M, Elbait GD, Zhou Y, Lu Y, Yang H, Zhang J, Dörflein I, Britzen-Laurent N, Pfeffer S, Stemmler MP, Dahl A, Mukhopadhyay D, Chang D, He H, Zeng S, Lan B, Frey B, Hampel C, Lentsch E, Gollavilli PN, Büttner C, Ekici AB, Biankin A, Schneider-Stock R, Ceppi P, Grützmann R, Pilarsky C. Roflumilast inhibits tumor growth and migration in STK11/LKB1 deficient pancreatic cancer. Cell Death Discov 2024; 10:124. [PMID: 38461159 PMCID: PMC10924943 DOI: 10.1038/s41420-024-01890-y] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 02/22/2024] [Accepted: 02/26/2024] [Indexed: 03/11/2024] Open
Abstract
Pancreatic cancer is a malignant tumor of the digestive system. It is highly aggressive, easily metastasizes, and extremely difficult to treat. This study aimed to analyze the genes that might regulate pancreatic cancer migration to provide an essential basis for the prognostic assessment of pancreatic cancer and individualized treatment. A CRISPR knockout library directed against 915 murine genes was transfected into TB 32047 cell line to screen which gene loss promoted cell migration. Next-generation sequencing and PinAPL.py- analysis was performed to identify candidate genes. We then assessed the effect of serine/threonine kinase 11 (STK11) knockout on pancreatic cancer by wound-healing assay, chick agnosia (CAM) assay, and orthotopic mouse pancreatic cancer model. We performed RNA sequence and Western blotting for mechanistic studies to identify and verify the pathways. After accelerated Transwell migration screening, STK11 was identified as one of the top candidate genes. Further experiments showed that targeted knockout of STK11 promoted the cell migration and increased liver metastasis in mice. Mechanistic analyses revealed that STK11 knockout influences blood vessel morphogenesis and is closely associated with the enhanced expression of phosphodiesterases (PDEs), especially PDE4D, PDE4B, and PDE10A. PDE4 inhibitor Roflumilast inhibited STK11-KO cell migration and tumor size, further demonstrating that PDEs are essential for STK11-deficient cell migration. Our findings support the adoption of therapeutic strategies, including Roflumilast, for patients with STK11-mutated pancreatic cancer in order to improve treatment efficacy and ultimately prolong survival.
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Affiliation(s)
- Shuman Zhang
- Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Duo Yun
- Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Hao Yang
- Experimental Tumor pathology, Institute of Pathology, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Markus Eckstein
- Institute of Pathology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Gihan Daw Elbait
- Department of Biology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Yaxing Zhou
- Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Yanxi Lu
- Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Hai Yang
- Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Jinping Zhang
- Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Isabella Dörflein
- Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Nathalie Britzen-Laurent
- Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Susanne Pfeffer
- Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Marc P Stemmler
- Department of Experimental Medicine 1, Nikolaus-Fiebiger Center for Molecular Medicine, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Andreas Dahl
- DRESDEN-concept Genome Center a DFG NGS Competence Center; TU Dresden, 01307, Dresden, Germany
| | - Debabrata Mukhopadhyay
- Departments of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Jacksonville, USA
| | - David Chang
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, UK
- West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, UK
| | - Hang He
- Department of Pancreatic Surgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, China
| | - Siyuan Zeng
- Department of Breast and Thyroid Surgery, Hunan Provincial People's Hospital (The First Affiliated Hospital of Hunan Normal University), Changsha, China
| | - Bin Lan
- Department of Interventional Radiology and Vascular Surgery, Hunan Provincial People's Hospital (The First Affiliated Hospital of Hunan Normal University), Changsha, 410002, China
| | - Benjamin Frey
- Translational Radiobiology, Department of Radiation Oncology, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Chuanpit Hampel
- Experimental Tumor pathology, Institute of Pathology, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Eva Lentsch
- Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Paradesi Naidu Gollavilli
- Department of Biochemistry and Molecular Biology (BMB), University of Southern Denmark, Odense, Denmark
| | - Christian Büttner
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Arif B Ekici
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Andrew Biankin
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, UK
- West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, UK
| | - Regine Schneider-Stock
- Experimental Tumor pathology, Institute of Pathology, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Paolo Ceppi
- Department of Biochemistry and Molecular Biology (BMB), University of Southern Denmark, Odense, Denmark
| | - Robert Grützmann
- Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Christian Pilarsky
- Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Erlangen, Germany.
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Al-Aamri A, Kamarul Azman S, Daw Elbait G, Alsafar H, Henschel A. Critical assessment of on-premise approaches to scalable genome analysis. BMC Bioinformatics 2023; 24:354. [PMID: 37735350 PMCID: PMC10512525 DOI: 10.1186/s12859-023-05470-2] [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: 05/27/2023] [Accepted: 09/08/2023] [Indexed: 09/23/2023] Open
Abstract
BACKGROUND Plummeting DNA sequencing cost in recent years has enabled genome sequencing projects to scale up by several orders of magnitude, which is transforming genomics into a highly data-intensive field of research. This development provides the much needed statistical power required for genotype-phenotype predictions in complex diseases. METHODS In order to efficiently leverage the wealth of information, we here assessed several genomic data science tools. The rationale to focus on on-premise installations is to cope with situations where data confidentiality and compliance regulations etc. rule out cloud based solutions. We established a comprehensive qualitative and quantitative comparison between BCFtools, SnpSift, Hail, GEMINI, and OpenCGA. The tools were compared in terms of data storage technology, query speed, scalability, annotation, data manipulation, visualization, data output representation, and availability. RESULTS Tools that leverage sophisticated data structures are noted as the most suitable for large-scale projects in varying degrees of scalability in comparison to flat-file manipulation (e.g., BCFtools, and SnpSift). Remarkably, for small to mid-size projects, even lightweight relational database. CONCLUSION The assessment criteria provide insights into the typical questions posed in scalable genomics and serve as guidance for the development of scalable computational infrastructure in genomics.
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Affiliation(s)
- Amira Al-Aamri
- Department of Electrical Engineering and Computer Science, College of Engineering, Khalifa University, P.O. Box 127788, Abu Dhabi, United Arab Emirates
| | - Syafiq Kamarul Azman
- Department of Electrical Engineering and Computer Science, College of Engineering, Khalifa University, P.O. Box 127788, Abu Dhabi, United Arab Emirates
| | - Gihan Daw Elbait
- Department of Biology, College of Arts and Sciences, Khalifa University, P.O. Box 127788, Abu Dhabi, United Arab Emirates
- Center for Biotechnology (BTC), Khalifa University, P.O. Box 127788, Abu Dhabi, United Arab Emirates
| | - Habiba Alsafar
- Center for Biotechnology (BTC), Khalifa University, P.O. Box 127788, Abu Dhabi, United Arab Emirates
- Department of Biomedical Engineering, Khalifa University, P.O. Box 127788, Abu Dhabi, United Arab Emirates
| | - Andreas Henschel
- Department of Electrical Engineering and Computer Science, College of Engineering, Khalifa University, P.O. Box 127788, Abu Dhabi, United Arab Emirates.
- Center for Biotechnology (BTC), Khalifa University, P.O. Box 127788, Abu Dhabi, United Arab Emirates.
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4
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Hassan S, Wang T, Shi K, Huang Y, Urbina Lopez ME, Gan K, Chen M, Willemen N, Kalam H, Luna-Ceron E, Cecen B, Elbait GD, Li J, Garcia-Rivera LE, Gurian M, Banday MM, Yang K, Lee MC, Zhuang W, Johnbosco C, Jeon O, Alsberg E, Leijten J, Shin SR. Self-oxygenation of engineered living tissues orchestrates osteogenic commitment of mesenchymal stem cells. Biomaterials 2023; 300:122179. [PMID: 37315386 PMCID: PMC10330822 DOI: 10.1016/j.biomaterials.2023.122179] [Citation(s) in RCA: 3] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 04/12/2023] [Accepted: 05/25/2023] [Indexed: 06/16/2023]
Abstract
Oxygenating biomaterials can alleviate anoxic stress, stimulate vascularization, and improve engraftment of cellularized implants. However, the effects of oxygen-generating materials on tissue formation have remained largely unknown. Here, we investigate the impact of calcium peroxide (CPO)-based oxygen-generating microparticles (OMPs) on the osteogenic fate of human mesenchymal stem cells (hMSCs) under a severely oxygen deficient microenvironment. To this end, CPO is microencapsulated in polycaprolactone to generate OMPs with prolonged oxygen release. Gelatin methacryloyl (GelMA) hydrogels containing osteogenesis-inducing silicate nanoparticles (SNP hydrogels), OMPs (OMP hydrogels), or both SNP and OMP (SNP/OMP hydrogels) are engineered to comparatively study their effect on the osteogenic fate of hMSCs. OMP hydrogels associate with improved osteogenic differentiation under both normoxic and anoxic conditions. Bulk mRNAseq analyses suggest that OMP hydrogels under anoxia regulate osteogenic differentiation pathways more strongly than SNP/OMP or SNP hydrogels under either anoxia or normoxia. Subcutaneous implantations reveal a stronger host cell invasion in SNP hydrogels, resulting in increased vasculogenesis. Furthermore, time-dependent expression of different osteogenic factors reveals progressive differentiation of hMSCs in OMP, SNP, and SNP/OMP hydrogels. Our work demonstrates that endowing hydrogels with OMPs can induce, improve, and steer the formation of functional engineered living tissues, which holds potential for numerous biomedical applications, including tissue regeneration and organ replacement therapy.
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Affiliation(s)
- Shabir Hassan
- Division of Engineering in Medicine, Department of Medicine, Harvard Medical School, and Brigham and Women's Hospital, Cambridge, MA, 02139, USA; Department of Biology, College of Arts and Sciences, Khalifa University (Main Campus), Abu Dhabi, P.O. Box, 127788, United Arab Emirates; Advanced Materials Chemistry Center (AMCC), Khalifa University (SAN Campus), Abu Dhabi, P.O. Box, 127788, United Arab Emirates
| | - Ting Wang
- Division of Engineering in Medicine, Department of Medicine, Harvard Medical School, and Brigham and Women's Hospital, Cambridge, MA, 02139, USA; Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, 210029, China
| | - Kun Shi
- Division of Engineering in Medicine, Department of Medicine, Harvard Medical School, and Brigham and Women's Hospital, Cambridge, MA, 02139, USA; Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yike Huang
- Division of Engineering in Medicine, Department of Medicine, Harvard Medical School, and Brigham and Women's Hospital, Cambridge, MA, 02139, USA
| | - Maria Elizabeth Urbina Lopez
- Division of Engineering in Medicine, Department of Medicine, Harvard Medical School, and Brigham and Women's Hospital, Cambridge, MA, 02139, USA
| | - Kaifeng Gan
- Division of Engineering in Medicine, Department of Medicine, Harvard Medical School, and Brigham and Women's Hospital, Cambridge, MA, 02139, USA
| | - Mo Chen
- Division of Engineering in Medicine, Department of Medicine, Harvard Medical School, and Brigham and Women's Hospital, Cambridge, MA, 02139, USA
| | - Niels Willemen
- Division of Engineering in Medicine, Department of Medicine, Harvard Medical School, and Brigham and Women's Hospital, Cambridge, MA, 02139, USA; Leijten Lab, Department of Developmental Bioengineering, Faculty of Science and Technology, TechMed Centre, University Twente, Enschede, 7522 NB, the Netherlands
| | - Haroon Kalam
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02139, USA
| | - Eder Luna-Ceron
- Division of Engineering in Medicine, Department of Medicine, Harvard Medical School, and Brigham and Women's Hospital, Cambridge, MA, 02139, USA
| | - Berivan Cecen
- Division of Engineering in Medicine, Department of Medicine, Harvard Medical School, and Brigham and Women's Hospital, Cambridge, MA, 02139, USA
| | - Gihan Daw Elbait
- Department of Biology, College of Arts and Sciences, Khalifa University (Main Campus), Abu Dhabi, P.O. Box, 127788, United Arab Emirates
| | - Jinghang Li
- Division of Engineering in Medicine, Department of Medicine, Harvard Medical School, and Brigham and Women's Hospital, Cambridge, MA, 02139, USA
| | - Luis Enrique Garcia-Rivera
- Division of Engineering in Medicine, Department of Medicine, Harvard Medical School, and Brigham and Women's Hospital, Cambridge, MA, 02139, USA
| | - Melvin Gurian
- Leijten Lab, Department of Developmental Bioengineering, Faculty of Science and Technology, TechMed Centre, University Twente, Enschede, 7522 NB, the Netherlands
| | - Mudassir Meraj Banday
- Department of Medicine, Harvard Medical School, and Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Kisuk Yang
- Center for Nanomedicine, Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA; Division of Bioengineering, College of Life Sciences and Bioengineering, Incheon National University, Incheon, 22012, Republic of Korea
| | - Myung Chul Lee
- Division of Engineering in Medicine, Department of Medicine, Harvard Medical School, and Brigham and Women's Hospital, Cambridge, MA, 02139, USA
| | - Weida Zhuang
- Division of Engineering in Medicine, Department of Medicine, Harvard Medical School, and Brigham and Women's Hospital, Cambridge, MA, 02139, USA
| | - Castro Johnbosco
- Leijten Lab, Department of Developmental Bioengineering, Faculty of Science and Technology, TechMed Centre, University Twente, Enschede, 7522 NB, the Netherlands
| | - Oju Jeon
- Department of Biomedical Engineering, University of Illinois Chicago, Chicago, IL, 60612, USA
| | - Eben Alsberg
- Department of Biomedical Engineering, University of Illinois Chicago, Chicago, IL, 60612, USA; Departments of Orthopaedic Surgery, Pharmacology and Regenerative Medicine, and Mechanical and Industrial Engineering, University of Illinois Chicago, Chicago, IL, 60612, USA
| | - Jeroen Leijten
- Leijten Lab, Department of Developmental Bioengineering, Faculty of Science and Technology, TechMed Centre, University Twente, Enschede, 7522 NB, the Netherlands.
| | - Su Ryon Shin
- Division of Engineering in Medicine, Department of Medicine, Harvard Medical School, and Brigham and Women's Hospital, Cambridge, MA, 02139, USA.
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5
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Jelinek HF, Mousa M, Alkaabi N, Alefishat E, Daw Elbait G, Kannout H, AlHumaidan H, Selvaraj FA, Imambaccus H, Weber S, Uddin M, Abdulkarim F, Mahboub B, Tay G, Alsafar H. Allelic Variants Within the ABO Blood Group Phenotype Confer Protection Against Critical COVID-19 Hospital Presentation. Front Med (Lausanne) 2022; 8:759648. [PMID: 35096865 PMCID: PMC8793802 DOI: 10.3389/fmed.2021.759648] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 08/16/2021] [Accepted: 12/13/2021] [Indexed: 12/13/2022] Open
Abstract
Introduction: Coronavirus disease 2019 (COVID-19) disease severity differs widely due to numerous factors including ABO gene-derived susceptibility or resistance. The objective of this study was to investigate the association of the ABO blood group and genetic variations of the ABO gene with COVID-19 severity in a heterogeneous hospital population sample from the United Arab Emirates, with the use of an epidemiological and candidate gene approach from a genome-wide association study (GWAS). Methods: In this cross-sectional study, a total of 646 participants who tested positive for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were recruited from multiple hospitals and population-based (quarantine camps) recruitment sites from March 2020 to February 2021. The participants were divided into two groups based on the severity of COVID-19: noncritical (n = 453) and critical [intensive care unit (ICU) patients] (n = 193), as per the COVID-19 Reporting and Data System (CO-RADS) classification. The multivariate logistic regression analysis demonstrated the association of ABO blood type as well as circulating anti-A antibodies and anti-B antibodies as well as A and B antigens, in association with critical COVID-19 hospital presentation. A candidate gene analysis approach was conducted from a GWAS where we examined 240 single nucleotide polymorphisms (SNPs) (position in chr9: 136125788-136150617) in the ABO gene, in association with critical COVID-19 hospital presentation. Results: Patients with blood group O [odds ratio (OR): 0.51 (0.33, 0.79); p = 0.003] were less likely to develop critical COVID-19 symptoms. Eight alleles have been identified to be associated with a protective effect of blood group O in ABO 3'untranslated region (UTR): rs199969472 (p = 0.0052), rs34266669 (p = 0.0052), rs76700116 (p = 0.0052), rs7849280 (p = 0.0052), rs34039247 (p = 0.0104), rs10901251 (p = 0.0165), rs9411475 (p = 0.0377), and rs13291798 (p = 0.0377). Conclusion: Our findings suggest that there are novel allelic variants that link genetic variants of the ABO gene and ABO blood groups contributing to the reduced risk of critical COVID-19 disease. This study is the first study to combine genetic and serological evidence of the involvement of the ABO blood groups and the ABO gene allelic associations with COVID-19 severity within the Middle Eastern population.
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Affiliation(s)
- Herbert F. Jelinek
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department of Biomedical Engineering, College of Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Center of Heath Engineering Innovation, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Mira Mousa
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Nuffield Department of Women's and Reproduction Health, Oxford University, Oxford, United Kingdom
| | - Nawal Alkaabi
- Department of Pediatric Infectious Disease, Sheikh Khalifa Medical City, Abu Dhabi, United Arab Emirates
| | - Eman Alefishat
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department of Pharmacology, College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Gihan Daw Elbait
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Hussein Kannout
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Hiba AlHumaidan
- Department of Laboratory Medicine Services, Sheikh Khalifa Medical City, Abu Dhabi, United Arab Emirates
| | | | - Hala Imambaccus
- Department of Laboratory Medicine Services, Sheikh Khalifa Medical City, Abu Dhabi, United Arab Emirates
| | - Stefan Weber
- Department of Laboratory Medicine Services, Sheikh Khalifa Medical City, Abu Dhabi, United Arab Emirates
| | - Maimunah Uddin
- Department of Pediatric Infectious Disease, Sheikh Khalifa Medical City, Abu Dhabi, United Arab Emirates
| | - Fatema Abdulkarim
- Dubai Health Authority, Rashid Hospital, Dubai, United Arab Emirates
| | - Bassam Mahboub
- Dubai Health Authority, Rashid Hospital, Dubai, United Arab Emirates
| | - Guan Tay
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Division of Psychiatry, Faculty of Health and Medical Sciences, University of Western Australia, Crawley, WA, Australia
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
| | - Habiba Alsafar
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department of Biomedical Engineering, College of Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department of Genetics and Molecular Biology, College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
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6
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Daw Elbait G, Henschel A, Tay GK, Al Safar HS. A Population-Specific Major Allele Reference Genome From The United Arab Emirates Population. Front Genet 2021; 12:660428. [PMID: 33968136 PMCID: PMC8102833 DOI: 10.3389/fgene.2021.660428] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 02/01/2021] [Accepted: 03/19/2021] [Indexed: 12/30/2022] Open
Abstract
The ethnic composition of the population of a country contributes to the uniqueness of each national DNA sequencing project and, ideally, individual reference genomes are required to reduce the confounding nature of ethnic bias. This work represents a representative Whole Genome Sequencing effort of an understudied population. Specifically, high coverage consensus sequences from 120 whole genomes and 33 whole exomes were used to construct the first ever population specific major allele reference genome for the United Arab Emirates (UAE). When this was applied and compared to the archetype hg19 reference, assembly of local Emirati genomes was reduced by ∼19% (i.e., some 1 million fewer calls). In compiling the United Arab Emirates Reference Genome (UAERG), sets of annotated 23,038,090 short (novel: 1,790,171) and 137,713 structural (novel: 8,462) variants; their allele frequencies (AFs) and distribution across the genome were identified. Population-specific genetic characteristics including loss-of-function variants, admixture, and ancestral haplogroup distribution were identified and reported here. We also detect a strong correlation between F ST and admixture components in the UAE. This baseline study was conceived to establish a high-quality reference genome and a genetic variations resource to enable the development of regional population specific initiatives and thus inform the application of population studies and precision medicine in the UAE.
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Affiliation(s)
- Gihan Daw Elbait
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Andreas Henschel
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department of Electrical Engineering and Computer Science, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Guan K. Tay
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department of Biomedical Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Division of Psychiatry, Faculty of Health and Medical Sciences, The University of Western Australia, Crawley, WA, Australia
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
| | - Habiba S. Al Safar
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department of Biomedical Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department of Genetics and Molecular Biology, College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
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Daw Elbait G, Henschel A, Tay GK, Al Safar HS. Whole Genome Sequencing of Four Representatives From the Admixed Population of the United Arab Emirates. Front Genet 2020; 11:681. [PMID: 32754195 PMCID: PMC7367215 DOI: 10.3389/fgene.2020.00681] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 02/02/2020] [Accepted: 06/03/2020] [Indexed: 01/21/2023] Open
Abstract
Whole genome sequences (WGS) of four nationals of the United Arab Emirates (UAE) at an average coverage of 33X have been completed and described. The selection of suitable subpopulation representatives was informed by a preceding comprehensive population structure analysis. Representatives were chosen based on their central location within the subpopulation on a principal component analysis (PCA) and the degree to which they were admixed. Novel genomic variations among the different subgroups of the UAE population are reported here. Specifically, the WGS analysis identified 4,161,067-4,798,806 variants in the four individual samples, where approximately 80% were single nucleotide polymorphisms (SNPs) and 20% were insertions or deletions (indels). An average of 2.75% was found to be novel variants according to dbSNP (build 151). This is the first report of structural variants (SV) from WGS data from UAE nationals. There were 15,677-20,339 called SVs, of which around 13.5% were novel. The four samples shared 1,399,178 variants, each with distinct variants as follows: 1,085,524 (for the individual denoted as UAE S011), 1,228,559 (UAE S012), 791,072 (UAE S013), and 906,818 (UAE S014). These results show a previously unappreciated population diversity in the region. The synergy of WGS and genotype array data was demonstrated through variant annotation of the former using 2.3 million allele frequencies for the local population derived from the latter technology platform. This novel approach of combining breadth and depth of array and WGS technologies has guided the choice of population genetic representatives and provides complementary, regionalized allele frequency annotation to new genomes comprising millions of loci.
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Affiliation(s)
- Gihan Daw Elbait
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Andreas Henschel
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.,Department of Computer Science, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Guan K Tay
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.,Department of Biomedical Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.,Division of Psychiatry, Faculty of Health and Medical Sciences, The University of Western Australia, Crawley, WA, Australia.,School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
| | - Habiba S Al Safar
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.,Department of Biomedical Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.,Department of Genetics and Molecular Biology, Collage of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
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8
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Tay GK, Henschel A, Daw Elbait G, Al Safar HS. Genetic Diversity and Low Stratification of the Population of the United Arab Emirates. Front Genet 2020; 11:608. [PMID: 32595703 PMCID: PMC7304494 DOI: 10.3389/fgene.2020.00608] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [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: 02/02/2020] [Accepted: 05/19/2020] [Indexed: 01/09/2023] Open
Abstract
With high consanguinity rates on the Arabian Peninsula, it would not have been unexpected if the population of the United Arab Emirates (UAE) was shown to be relatively homogenous. However, this study of 1000 UAE nationals provided a contrasting perspective, one of a relatively heterogeneous population. Located at the apex of Europe, Asia, and Africa, the observed diversity could be explained by a plethora of migration patterns since the first Out-of-Africa movement. A strategy to explore the extent of genetic variation of the population of the UAE is presented. The first step involved a comprehensive population stratification study that was instructive for subsequent whole genome sequencing (WGS) of suitable representatives (which is described elsewhere). When these UAE data were compared to previous smaller studies from the region, the findings were consistent with a population that is a diverse and admixed group of people. However, rather than sharp and distinctive clusters, cluster analysis reveals low levels of stratification throughout the population. UAE emirates exhibit high within-Emirate-distance/among-Emirate distance ratios. Supervised admixture analysis showed a continuous gradient of ancestral populations, suggesting that admixture on the south eastern tip of the Arabian Peninsula occurred gradually. When visualized using a unique technique that combined admixture ratios and principal component analysis (PCA), unappreciated diversity was revealed while mitigating projection bias of conventional PCA. We observe low population stratification in the UAE in terms of homozygosity versus separation cluster coefficients. This holds for the UAE in a global context as well as for isolated cluster analysis of the Emirati birthplaces. However, the subtle clustering observed in the Emirates reflects geographic proximity and historic migration events. The analytical strategy used here highlights the complementary nature of data from genotype array and WGS for anthropological studies. Specifically, genotype array data were instructive to select representative subjects for WGS. Furthermore, from the 2.3 million allele frequencies obtained from genotype arrays, we identified 46,481 loci with allele frequencies that were significantly different with respect to other world populations. This comparison of allele frequencies facilitates variant prioritization in common diseases. In addition, these loci bear great potential as biomarkers in anthropological and forensic studies.
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Affiliation(s)
- Guan K Tay
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.,Department of Biomedical Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.,Faculty of Health and Medical Sciences, UWA Medical School, The University of Western Australia, Crawley, WA, Australia.,School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
| | - Andreas Henschel
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.,Department of Computer Science, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Gihan Daw Elbait
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Habiba S Al Safar
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.,Department of Biomedical Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.,Department of Genetics and Molecular Biology, College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
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AlSafar HS, Al-Ali M, Elbait GD, Al-Maini MH, Ruta D, Peramo B, Henschel A, Tay GK. Introducing the first whole genomes of nationals from the United Arab Emirates. Sci Rep 2019; 9:14725. [PMID: 31604968 PMCID: PMC6789106 DOI: 10.1038/s41598-019-50876-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 09/20/2019] [Indexed: 12/30/2022] Open
Abstract
Whole Genome Sequencing (WGS) provides an in depth description of genome variation. In the era of large-scale population genome projects, the assembly of ethnic-specific genomes combined with mapping human reference genomes of underrepresented populations has improved the understanding of human diversity and disease associations. In this study, for the first time, whole genome sequences of two nationals of the United Arab Emirates (UAE) at >27X coverage are reported. The two Emirati individuals were predominantly of Central/South Asian ancestry. An in-house customized pipeline using BWA, Picard followed by the GATK tools to map the raw data from whole genome sequences of both individuals was used. A total of 3,994,521 variants (3,350,574 Single Nucleotide Polymorphisms (SNPs) and 643,947 indels) were identified for the first individual, the UAE S001 sample. A similar number of variants, 4,031,580 (3,373,501 SNPs and 658,079 indels), were identified for UAE S002. Variants that are associated with diabetes, hypertension, increased cholesterol levels, and obesity were also identified in these individuals. These Whole Genome Sequences has provided a starting point for constructing a UAE reference panel which will lead to improvements in the delivery of precision medicine, quality of life for affected individuals and a reduction in healthcare costs. The information compiled will likely lead to the identification of target genes that could potentially lead to the development of novel therapeutic modalities.
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Affiliation(s)
- Habiba S AlSafar
- Center of Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.,Department of Biomedical Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.,College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Mariam Al-Ali
- Center of Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.,Department of Biomedical Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Gihan Daw Elbait
- Center of Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | | | - Dymitr Ruta
- Etisalat-British Telecom Innovation Center, Abu Dhabi, United Arab Emirates
| | | | - Andreas Henschel
- Center of Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.,Department of Computer Science, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Guan K Tay
- Center of Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates. .,Department of Biomedical Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates. .,College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates. .,School of Psychiatry and Clinical Neurosciences, University of Western Australia, Nedlands, Australia. .,School of Medical and Health Sciences, Edith Cowan University, Joondalup, Australia.
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