1
|
Marshall DA, Hua N, Buchanan J, Christensen KD, Frederix GWJ, Goranitis I, Ijzerman M, Jansen JP, Lavelle TA, Regier DA, Smith HS, Ungar WJ, Weymann D, Wordsworth S, Phillips KA. Paving the path for implementation of clinical genomic sequencing globally: Are we ready? HEALTH AFFAIRS SCHOLAR 2024; 2:qxae053. [PMID: 38783891 PMCID: PMC11115369 DOI: 10.1093/haschl/qxae053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/18/2024] [Accepted: 04/25/2024] [Indexed: 05/25/2024]
Abstract
Despite the emerging evidence in recent years, successful implementation of clinical genomic sequencing (CGS) remains limited and is challenged by a range of barriers. These include a lack of standardized practices, limited economic assessments for specific indications, limited meaningful patient engagement in health policy decision-making, and the associated costs and resource demand for implementation. Although CGS is gradually becoming more available and accessible worldwide, large variations and disparities remain, and reflections on the lessons learned for successful implementation are sparse. In this commentary, members of the Global Economics and Evaluation of Clinical Genomics Sequencing Working Group (GEECS) describe the global landscape of CGS in the context of health economics and policy and propose evidence-based solutions to address existing and future barriers to CGS implementation. The topics discussed are reflected as two overarching themes: (1) system readiness for CGS and (2) evidence, assessments, and approval processes. These themes highlight the need for health economics, public health, and infrastructure and operational considerations; a robust patient- and family-centered evidence base on CGS outcomes; and a comprehensive, collaborative, interdisciplinary approach.
Collapse
Affiliation(s)
- Deborah A Marshall
- Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Calgary, Alberta T2N 4Z6, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Nicolle Hua
- Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Calgary, Alberta T2N 4Z6, Canada
| | - James Buchanan
- Health Economics and Policy Research Unit, Centre for Evaluation and Methods, Wolfson Institute of Population Health, Queen Mary University of London, London E1 2AB, United Kingdom
| | - Kurt D Christensen
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA 02215, United States
| | - Geert W J Frederix
- Epidemiology and Health Economics, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, 3584 CG Utrecht, The Netherlands
| | - Ilias Goranitis
- Health Economics Unit, Centre for Health Policy, Melbourne School of Population and Global Health, University of Melbourne, Parkville, Victoria 3010, Australia
- Australian Genomics, Parkville, Victoria 3052, Australia
| | - Maarten Ijzerman
- University of Melbourne Centre for Cancer Research, University of Melbourne, Melbourne, Victoria 3000, Australia
- Erasmus School of Health Policy & Management, Eramus University Rotterdam, 3062 PA Rotterdam, The Netherlands
| | - Jeroen P Jansen
- Center for Translational and Policy Research on Precision Medicine (TRANSPERS), Department of Clinical Pharmacy, School of Pharmacy, University of California, San Francisco, San Francisco, CA 94158, United States
| | - Tara A Lavelle
- Center for the Evaluation of Value and Risk in Health, Institute for Clinical Research and Health Policy Studies, Tufts Medical Center, Boston, MA 02111, United States
| | - Dean A Regier
- Canadian Centre for Applied Research in Cancer Control, Cancer Control Research, BC Cancer Research Institute, Vancouver, British Columbia V5Z 1L3, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Hadley S Smith
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA 02215, United States
| | - Wendy J Ungar
- Program of Child Health Evaluative Sciences, The Hospital for Sick Children Research Institute, Toronto, Ontario M5G 0A4, Canada
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario M5T 3M6, Canada
| | - Deirdre Weymann
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Sarah Wordsworth
- Health Economics Research Centre, Nuffield Department of Population Health and NIHR Biomedical Research Centre, University of Oxford, Oxford OX3 7LF, United Kingdom
| | - Kathryn A Phillips
- Center for Translational and Policy Research on Precision Medicine (TRANSPERS), Department of Clinical Pharmacy, School of Pharmacy, University of California, San Francisco, San Francisco, CA 94158, United States
- Health Affairs Scholar Emerging & Global Health Policy, Health Affairs, Washington, DC 20036, United States
| |
Collapse
|
2
|
Dai YF, Wu XM, Wang HC, Li WH, Cai LT, Li JX, Wang F, Sehar S, Shamsi IH. Spatio-Temporal Variation in the Phyllospheric Microbial Biodiversity of Alternaria Alternata-Infected Tobacco Foliage. Front Microbiol 2022; 13:920109. [PMID: 35966692 PMCID: PMC9370072 DOI: 10.3389/fmicb.2022.920109] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 06/22/2022] [Indexed: 11/13/2022] Open
Abstract
Phyllospheric microbial composition of tobacco (Nicotiana tabacum L.) is contingent upon certain factors, such as the growth stage of the plant, leaf position, and cultivar and its geographical location, which influence, either directly or indirectly, the growth, overall health, and production of the tobacco plant. To better understand the spatiotemporal variation of the community and the divergence of phyllospheric microflora, procured from healthy and diseased tobacco leaves infected by Alternaria alternata, the current study employed microbe culturing, high-throughput technique, and BIOLOG ECO. Microbe culturing resulted in the isolation of 153 culturable fungal isolates belonging to 33 genera and 99 bacterial isolates belonging to 15 genera. High-throughput sequencing revealed that the phyllosphere of tobacco was dominantly colonized by Ascomycota and Proteobacteria, whereas, the most abundant fungal and bacterial genera were Alternaria and Pseudomonas. The relative abundance of Alternaria increased in the upper and middle healthy groups from the first collection time to the third, whereas, the relative abundance of Pseudomonas, Sphingomonas, and Methylobacterium from the same positions increased during gradual leaf aging. Non-metric multi-dimensional scaling (NMDs) showed clustering of fungal communities in healthy samples, while bacterial communities of all diseased and healthy groups were found scattered. FUNGuild analysis, from the first collection stage to the third one in both groups, indicated an increase in the relative abundance of Pathotroph-Saprotroph, Pathotroph-Saprotroph-Symbiotroph, and Pathotroph-Symbiotroph. Inclusive of all samples, as per the PICRUSt analysis, the predominant pathway was metabolism function accounting for 50.03%. The average values of omnilog units (OUs) showed relatively higher utilization rates of carbon sources by the microbial flora of healthy leaves. According to the analysis of genus abundances, leaf growth and leaf position were the important drivers of change in structuring the microbial communities. The current findings revealed the complex ecological dynamics that occur in the phyllospheric microbial communities over the course of a spatiotemporal varying environment with the development of tobacco brown spots, highlighting the importance of community succession.
Collapse
Affiliation(s)
- Yuan-feng Dai
- Department of Plant Protection, Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang, China
- Guizhou Provincial Academician Workstation of Microbiology and Health, Guizhou Academy of Tobacco Science, Guiyang, China
- Bijie Tobacco Company, Bijie, China
| | - Xiao-mao Wu
- Department of Plant Protection, Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang, China
- *Correspondence: Xiao-mao Wu
| | - Han-cheng Wang
- Guizhou Provincial Academician Workstation of Microbiology and Health, Guizhou Academy of Tobacco Science, Guiyang, China
- Han-cheng Wang
| | - Wen-hong Li
- Guizhou Institute of Plant Protection, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Liu-ti Cai
- Guizhou Provincial Academician Workstation of Microbiology and Health, Guizhou Academy of Tobacco Science, Guiyang, China
| | - Ji-xin Li
- Guizhou Tobacco Company of CNTC, China National Tobacco Corporation, Guiyang, China
| | - Feng Wang
- Guizhou Provincial Academician Workstation of Microbiology and Health, Guizhou Academy of Tobacco Science, Guiyang, China
- Feng Wang
| | - Shafaque Sehar
- Zhejiang Key Laboratory of Crop Germplasm Resource, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Imran Haider Shamsi
- Zhejiang Key Laboratory of Crop Germplasm Resource, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Imran Haider Shamsi
| |
Collapse
|
3
|
Rabiu Abubakar A, Ahmad R, Rowaiye AB, Rahman S, Iskandar K, Dutta S, Oli AN, Dhingra S, Tor MA, Etando A, Kumar S, Irfan M, Gowere M, Chowdhury K, Akter F, Jahan D, Schellack N, Haque M. Targeting Specific Checkpoints in the Management of SARS-CoV-2 Induced Cytokine Storm. Life (Basel) 2022; 12:life12040478. [PMID: 35454970 PMCID: PMC9031737 DOI: 10.3390/life12040478] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 03/18/2022] [Accepted: 03/21/2022] [Indexed: 02/07/2023] Open
Abstract
COVID-19-infected patients require an intact immune system to suppress viral replication and prevent complications. However, the complications of SARS-CoV-2 infection that led to death were linked to the overproduction of proinflammatory cytokines known as cytokine storm syndrome. This article reported the various checkpoints targeted to manage the SARS-CoV-2-induced cytokine storm. The literature search was carried out using PubMed, Embase, MEDLINE, and China National Knowledge Infrastructure (CNKI) databases. Journal articles that discussed SARS-CoV-2 infection and cytokine storm were retrieved and appraised. Specific checkpoints identified in managing SARS-CoV-2 induced cytokine storm include a decrease in the level of Nod-Like Receptor 3 (NLRP3) inflammasome where drugs such as quercetin and anakinra were effective. Janus kinase-2 and signal transducer and activator of transcription-1 (JAK2/STAT1) signaling pathways were blocked by medicines such as tocilizumab, baricitinib, and quercetin. In addition, inhibition of interleukin (IL)-6 with dexamethasone, tocilizumab, and sarilumab effectively treats cytokine storm and significantly reduces mortality caused by COVID-19. Blockade of IL-1 with drugs such as canakinumab and anakinra, and inhibition of Bruton tyrosine kinase (BTK) with zanubrutinib and ibrutinib was also beneficial. These agents' overall mechanisms of action involve a decrease in circulating proinflammatory chemokines and cytokines and or blockade of their receptors. Consequently, the actions of these drugs significantly improve respiration and raise lymphocyte count and PaO2/FiO2 ratio. Targeting cytokine storms' pathogenesis genetic and molecular apparatus will substantially enhance lung function and reduce mortality due to the COVID-19 pandemic.
Collapse
Affiliation(s)
- Abdullahi Rabiu Abubakar
- Department of Pharmacology and Therapeutics, Faculty of Pharmaceutical Sciences, Bayero University, PMB 3452, Kano 700233, Nigeria;
| | - Rahnuma Ahmad
- Department of Physiology, Medical College for Women and Hospital, Dhaka 1230, Bangladesh;
| | | | - Sayeeda Rahman
- School of Medicine, American University of Integrative Sciences, Bridgetown BB11114, Barbados;
| | - Katia Iskandar
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Lebanese University, Beirut P.O. Box 6573/14, Lebanon;
| | - Siddhartha Dutta
- Department of Pharmacology, All India Institute of Medical Sciences, Rajkot 360001, Gujrat, India;
| | - Angus Nnamdi Oli
- Department of Pharmaceutical Microbiology and Biotechnology, Faculty of Pharmaceutical Sciences, Nnamdi Azikiwe University, PMB 5025, Awka 420110, Nigeria;
| | - Sameer Dhingra
- Department of Pharmacy Practice, National Institute of Pharmaceutical Education and Research (NIPER), Hajipur 844102, Bihar, India;
| | - Maryam Abba Tor
- Department of Health and Biosciences, University of East London, University Way, London E16 2RD, UK;
| | - Ayukafangha Etando
- Department of Medical Laboratory Sciences, Faculty of Health Sciences, Eswatini Medical Christian University, P.O. Box A624 Swazi Plaza Mbabane, Mbabane H101, Hhohho, Eswatini;
| | - Santosh Kumar
- Department of Periodontology and Implantology, Karnavati School of Dentistry, Karnavati University, 907/A, Adalaj Uvarsad Road, Gandhinagar 382422, Gujarat, India;
| | - Mohammed Irfan
- Department of Forensics, Federal University of Pelotas, R. Gomes Carneiro, 1-Centro, Pelotas 96010-610, RS, Brazil;
| | - Marshall Gowere
- Department of Pharmacology, Faculty of Health Sciences, Basic Medical Sciences Building, Prinshof Campus, University of Pretoria, Arcadia 0083, South Africa; (M.G.); (N.S.)
| | - Kona Chowdhury
- Department of Paediatrics, Gonoshasthaya Samaj Vittik Medical College and Hospital, Dhaka 1344, Bangladesh;
| | - Farhana Akter
- Department of Endocrinology, Chittagong Medical College, Chattogram 4203, Bangladesh;
| | - Dilshad Jahan
- Department of Hematology, Asgar Ali Hospital, 111/1/A Distillery Road, Gandaria Beside Dhupkhola, Dhaka 1204, Bangladesh;
| | - Natalie Schellack
- Department of Pharmacology, Faculty of Health Sciences, Basic Medical Sciences Building, Prinshof Campus, University of Pretoria, Arcadia 0083, South Africa; (M.G.); (N.S.)
| | - Mainul Haque
- Unit of Pharmacology, Faculty of Medicine and Defense Health, Universiti Pertahanan Nasional Malaysia (National Defense University of Malaysia), Kem Perdana Sungai Besi, Kuala Lumpur 57000, Malaysia
- Correspondence: or
| |
Collapse
|
4
|
Huang Y, Wang HC, Cai LT, Li W, Pan D, Xiang L, Su X, Li Z, Adil MF, Shamsi IH. Phyllospheric Microbial Composition and Diversity of the Tobacco Leaves Infected by Didymella segeticola. Front Microbiol 2021; 12:699699. [PMID: 34721315 PMCID: PMC8551862 DOI: 10.3389/fmicb.2021.699699] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 09/08/2021] [Indexed: 11/13/2022] Open
Abstract
A Myriad of biotic and abiotic factors inevitably affects the growth and production of tobacco (Nicotiana tabacum L.), which is a model crop and sought-after worldwide for its foliage. Among the various impacts the level of disease severity poses on plants, the influence on the dynamics of phyllospheric microbial diversity is of utmost importance. In China, recurring reports of a phyto-pathogen, Didymella segeticola, a causal agent of tobacco leaf spot, accentuate the need for its in-depth investigation. Here, a high-throughput sequencing technique, IonS5TMXL was employed to analyze tobacco leaves infected by D. segeticola at different disease severity levels, ranging from T1G (least disease index) to T4G (highest disease index), in an attempt to explore the composition and diversity of phyllospheric microbiota. In all healthy and diseased tobacco leaves, the most dominant fungal phylum was Ascomycota with a high prevalence of genus Didymella, followed by Boeremia, Meyerozyma and Alternaria, whereas in the case of bacterial phyla, Proteobacteria was prominent with Pseudomonas being a predominant genus, followed by Pantoea. The relative abundance of fungi, i.e., Didymella and Boeremia (Ascomycota) and bacteria, i.e., Pseudomonas and Pantoea (Proteobacteria) were higher in diseased groups compared to healthy groups. Healthy tissues exhibited relatively rich and diverse fungal communities in contrast with diseased groups. The infection of D. segeticola had a complex and significant effect on fungal as well as bacterial alpha diversity. FUNGuild analysis indicated that the relative abundance of pathotrophs and saprotrophs in diseased tissues proportionally increased with disease severity. PICRUSt analysis of diseased tissues indicated that the relative abundance of bacterial cell motility and membrane transport-related gene sequences elevated with an increase in disease severity from T1G to T3G and then tended to decrease at T4G. Conclusively, the current study shows the typical characteristics of the tobacco leaf microbiome and provides insights into the distinct microbiome shifts on tobacco leaves infected by D. segeticola.
Collapse
Affiliation(s)
- Yu Huang
- Upland Flue-Cured Tobacco Quality and Ecology Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang, China.,College of Agriculture, Guizhou University, Guiyang, China
| | - Han-Cheng Wang
- Upland Flue-Cured Tobacco Quality and Ecology Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang, China
| | - Liu-Ti Cai
- Upland Flue-Cured Tobacco Quality and Ecology Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang, China
| | - Wenhong Li
- Guizhou Institute of Plant Protection, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Daiwei Pan
- Faculty of Science, Wilfrid Laurier University, Waterloo, ON, Canada
| | - Ligang Xiang
- Upland Flue-Cured Tobacco Quality and Ecology Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang, China.,College of Agriculture, Yangtze University, Jingzhou, China
| | - Xiankun Su
- Upland Flue-Cured Tobacco Quality and Ecology Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang, China
| | - Zhong Li
- College of Agriculture, Guizhou University, Guiyang, China
| | - Muhammad Faheem Adil
- Key Laboratory of Crop Germplasm Resource, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Imran Haider Shamsi
- Key Laboratory of Crop Germplasm Resource, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| |
Collapse
|
5
|
Identification of Hub Genes in Tuberculosis via Bioinformatics Analysis. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2021; 2021:8159879. [PMID: 34671419 PMCID: PMC8523273 DOI: 10.1155/2021/8159879] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 09/01/2021] [Indexed: 01/19/2023]
Abstract
Background Tuberculosis (TB) is a serious chronic bacterial infection caused by Mycobacterium tuberculosis (MTB). It is one of the deadliest diseases in the world and a heavy burden for people all over the world. However, the hub genes involved in the host response remain largely unclear. Methods The data set GSE11199 was studied to clarify the potential gene network and signal transduction pathway in TB. The subjects were divided into latent tuberculosis and pulmonary tuberculosis, and the distribution of differentially expressed genes (DEGs) was analyzed between them using GEO2R. We verified the enriched process and pathway of DEGs by making use of the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO). The construction of protein-protein interaction (PPI) network of DEGs was achieved through making use of the Search Tool for the Retrieval of Interacting Genes (STRING), aiming at identifying hub genes. Then, the hub gene expression level in latent and pulmonary tuberculosis was verified by a boxplot. Finally, through making use of Gene Set Enrichment Analysis (GSEA), we further analyzed the pathways related to DEGs in the data set GSE11199 to show the changing pattern between latent and pulmonary tuberculosis. Results We identified 98 DEGs in total in the data set GSE11199, 91 genes upregulated and 7 genes downregulated included. The enrichment of GO and KEGG pathways demonstrated that upregulated DEGs were mainly abundant in cytokine-mediated signaling pathway, response to interferon-gamma, endoplasmic reticulum lumen, beta-galactosidase activity, measles, JAK-STAT signaling pathway, cytokine-cytokine receptor interaction, etc. Based on the PPI network, we obtained 4 hub genes with a higher degree, namely, CTLA4, GZMB, GZMA, and PRF1. The box plot showed that these 4 hub gene expression levels in the pulmonary tuberculosis group were higher than those in the latent group. Finally, through Gene Set Enrichment Analysis (GSEA), it was concluded that DEGs were largely associated with proteasome and primary immunodeficiency. Conclusions This study reveals the coordination of pathogenic genes during TB infection and offers the diagnosis of TB a promising genome. These hub genes also provide new directions for the development of latent molecular targets for TB treatment.
Collapse
|
6
|
Chen QL, Cai L, Wang HC, Cai LT, Goodwin P, Ma J, Wang F, Li Z. Fungal Composition and Diversity of the Tobacco Leaf Phyllosphere During Curing of Leaves. Front Microbiol 2020; 11:554051. [PMID: 33013785 PMCID: PMC7499341 DOI: 10.3389/fmicb.2020.554051] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 08/12/2020] [Indexed: 11/16/2022] Open
Abstract
Rhizopus oryzae causes tobacco pole rot in China during tobacco flue-curing. Flue-curing is a post-harvest process done to prepare tobacco leaves and involves three different stages: the yellowing stage has the lowest temperatures and highest humidity, then the color-fixing stage has higher temperatures and medium humidity, and finally the stem-drying stage has the highest temperatures and lowest humidity. In this study, fungal culturing and IonS5XL high-throughput sequencing techniques were used to reveal the fungal community of the petioles and lamina of tobacco leaves infected with pole rot during flue-curing. A total of 108 fungal isolates belonging to 6 genera were isolated on media. The most common fungal species isolated was the pathogen, R. oryzae, that was most often found equally on petioles and laminas in the color-fixing stage, followed by saprotrophs, mostly Aspergillus spp. High-throughput sequencing revealed saprotrophs with Alternaria being the most abundant genus, followed by Phoma, Cercospora, and Aspergillus, whereas Rhizopus was the tenth most abundant genus, which was mostly found on petioles at the yellowing stage. Both culturable fungal diversity and fungal sequence diversity was higher at stem-drying stage than the yellowing and color-fixing stages, and diversity was higher with leaf lamina than petioles revealing that the changes in fungal composition and diversity during the curing process were similar with both methods. This study demonstrates that the curing process affects the leaf microbiome of tobacco during the curing process, and future work could examine if any of these saprotrophic fungi detected during the curing of tobacco leaves may be potential biocontrol agents for with pole rot in curing chambers.
Collapse
Affiliation(s)
- Qian-Li Chen
- Key Laboratory of Molecular Genetics, Guizhou Academy of Tobacco Science, Guiyang, China
- College of Agriculture, Guizhou University, Guiyang, China
| | - Lin Cai
- College of Plant Protection, Southwest University, Chongqing, China
| | - Han-Cheng Wang
- Key Laboratory of Molecular Genetics, Guizhou Academy of Tobacco Science, Guiyang, China
| | - Liu-Ti Cai
- Key Laboratory of Molecular Genetics, Guizhou Academy of Tobacco Science, Guiyang, China
| | - Paul Goodwin
- School of Environmental Sciences, University of Guelph, Guelph, ON, Canada
| | - Jun Ma
- Qianxinan Branch of Guizhou Tobacco Company, Guiyang, China
| | - Feng Wang
- Key Laboratory of Molecular Genetics, Guizhou Academy of Tobacco Science, Guiyang, China
| | - Zhong Li
- College of Agriculture, Guizhou University, Guiyang, China
| |
Collapse
|
7
|
Oli AN, Obialor WO, Ifeanyichukwu MO, Odimegwu DC, Okoyeh JN, Emechebe GO, Adejumo SA, Ibeanu GC. Immunoinformatics and Vaccine Development: An Overview. Immunotargets Ther 2020; 9:13-30. [PMID: 32161726 PMCID: PMC7049754 DOI: 10.2147/itt.s241064] [Citation(s) in RCA: 107] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 01/25/2020] [Indexed: 12/11/2022] Open
Abstract
The use of vaccines have resulted in a remarkable improvement in global health. It has saved several lives, reduced treatment costs and raised the quality of animal and human lives. Current traditional vaccines came empirically with either vague or completely no knowledge of how they modulate our immune system. Even at the face of potential vaccine design advance, immune-related concerns (as seen with specific vulnerable populations, cases of emerging/re-emerging infectious disease, pathogens with complex lifecycle and antigenic variability, need for personalized vaccinations, and concerns for vaccines' immunological safety -specifically vaccine likelihood to trigger non-antigen-specific responses that may cause autoimmunity and vaccine allergy) are being raised. And these concerns have driven immunologists toward research for a better approach to vaccine design that will consider these challenges. Currently, immunoinformatics has paved the way for a better understanding of some infectious disease pathogenesis, diagnosis, immune system response and computational vaccinology. The importance of this immunoinformatics in the study of infectious diseases is diverse in terms of computational approaches used, but is united by common qualities related to host–pathogen relationship. Bioinformatics methods are also used to assign functions to uncharacterized genes which can be targeted as a candidate in vaccine design and can be a better approach toward the inclusion of women that are pregnant into vaccine trials and programs. The essence of this review is to give insight into the need to focus on novel computational, experimental and computation-driven experimental approaches for studying of host–pathogen interactions and thus making a case for its use in vaccine development.
Collapse
Affiliation(s)
- Angus Nnamdi Oli
- Department of Pharmaceutical Microbiology and Biotechnology, Faculty of Pharmaceutical Sciences, Nnamdi Azikiwe University, Awka, Nigeria
| | - Wilson Okechukwu Obialor
- Department of Pharmaceutical Microbiology and Biotechnology, Faculty of Pharmaceutical Sciences, Nnamdi Azikiwe University, Awka, Nigeria
| | - Martins Ositadimma Ifeanyichukwu
- Department of Immunology, College of Health Sciences, Faculty of Medicine, Nnamdi Azikiwe University, Anambra, Nigeria.,Department of Medical Laboratory Science,Faculty of Health Science and Technology, College of Health Sciences, Nnamdi Azikiwe University,Nnewi Campus, Nnewi, Nigeria
| | - Damian Chukwu Odimegwu
- Department of Pharmaceutical Microbiology and Biotechnology, Faculty of Pharmaceutical Sciences, University of Nigeria Nsukka, Enugu, Nigeria
| | - Jude Nnaemeka Okoyeh
- Department of Biology and Clinical Laboratory Science, Division of Arts and Sciences, Neumann University, Aston, PA 19014-1298, USA
| | - George Ogonna Emechebe
- Department of Pediatrics, Faculty of Clinical Medicine, Chukwuemeka Odumegwu Ojukwu University, Awka, Nigeria
| | - Samson Adedeji Adejumo
- Department of Pharmaceutical Microbiology and Biotechnology, Faculty of Pharmaceutical Sciences, Nnamdi Azikiwe University, Awka, Nigeria
| | - Gordon C Ibeanu
- Department of Pharmaceutical Science, North Carolina Central University, Durham, NC 27707, USA
| |
Collapse
|
8
|
Mboowa G, Mwesigwa S, Katagirya E, Retshabile G, Mlotshwa BC, Williams L, Kekitiinwa A, Kateete D, Wampande E, Wayengera M, Kintu BN, Kisitu GP, Kyobe S, Brown CW, Hanchard NA, Mardon G, Joloba M, Anabwani G, Pettitt E, Tsimako-Johnstone M, Kasvosve I, Maplanka K, Mpoloka SW, Hlatshwayo M, Matshaba M. The Collaborative African Genomics Network (CAfGEN): Applying Genomic technologies to probe host factors important to the progression of HIV and HIV-tuberculosis infection in sub-Saharan Africa. AAS Open Res 2018; 1:3. [PMID: 30714022 PMCID: PMC6358002 DOI: 10.12688/aasopenres.12832.2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2018] [Indexed: 01/25/2023] Open
Abstract
Background: Here, we describe how the Collaborative African Genomics Network ( CAfGEN) of the Human Heredity and Health in Africa (H3Africa) consortium is using genomics to probe host genetic factors important to the progression of HIV and HIV-tuberculosis (TB) coinfection in sub-Saharan Africa. The H3Africa was conceived to facilitate the application of genomics technologies to improve health across Africa.. Methods: CAfGEN is an H3Africa collaborative centre comprising expertise from the University of Botswana; Makerere University; Baylor College of Medicine Children's Clinical Centers of Excellence (COEs) in Botswana, Uganda, and Swaziland; as well as Baylor College of Medicine, Texas. The COEs provide clinical expertise for community engagement, participant recruitment and sample collection while the three University settings facilitate processing and management of genomic samples and provide infrastructure and training opportunities to sustain genomics research. Results: The project has focused on utilizing whole-exome sequencing to identify genetic variants contributing to extreme HIV disease progression phenotypes in children, as well as RNA sequencing and integrated genomics to identify host genetic factors associated with TB disease progression among HIV-positive children. These cohorts, developed using the COEs' electronic medical records, are exceptionally well-phenotyped and present an unprecedented opportunity to assess genetic factors in individuals whose HIV was acquired by a different route than their adult counterparts in the context of a unique clinical course and disease pathophysiology. Conclusions: Our approach offers the prospect of developing a critical mass of well-trained, highly-skilled, continent-based African genomic scientists. To ensure long term genomics research sustainability in Africa, CAfGEN contributes to a wide range of genomics capacity and infrastructure development on the continent, has laid a foundation for genomics graduate programs at its institutions, and continues to actively promote genomics research through innovative forms of community engagement brokered by partnerships with governments and academia to support genomics policy formulation.
Collapse
Affiliation(s)
- Gerald Mboowa
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda.,Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Savannah Mwesigwa
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda.,Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Eric Katagirya
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda.,Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Gaone Retshabile
- Department of Biological Sciences, Faculty of Sciences, University of Botswana, Gaborone, Botswana
| | - Busisiwe C Mlotshwa
- Department of Biological Sciences, Faculty of Sciences, University of Botswana, Gaborone, Botswana
| | - Lesedi Williams
- Department of Biological Sciences, Faculty of Sciences, University of Botswana, Gaborone, Botswana
| | | | - David Kateete
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda.,Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Eddie Wampande
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda.,Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda.,Department of Bio-molecular Resources, College of Veterinary Medicine, Makerere University, Kampala, Uganda
| | - Misaki Wayengera
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda.,Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Betty Nsangi Kintu
- Baylor College of Medicine Children's Foundation-Uganda, Kampala, Uganda
| | - Grace P Kisitu
- Baylor College of Medicine Children's Foundation-Uganda, Kampala, Uganda
| | - Samuel Kyobe
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Chester W Brown
- Genetics Division, Department of Pediatrics , University of Tennessee Health Science Center, Memphis, Memphis, TN, USA.,Le Bonheur Children's Hospital, Memphis, Memphis, TN, USA.,St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Neil A Hanchard
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.,ARS/USDA/Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine , Houston, TX, USA
| | - Graeme Mardon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
| | - Moses Joloba
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda.,Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Gabriel Anabwani
- Botswana-Baylor Children's Clinical Centre of Excellence, Gaborone, Botswana.,Baylor College of Medicine Children's Foundation-Swaziland, Mbabane, Swaziland
| | - Ed Pettitt
- Botswana-Baylor Children's Clinical Centre of Excellence, Gaborone, Botswana
| | - Masego Tsimako-Johnstone
- Department of Biological Sciences, Faculty of Sciences, University of Botswana, Gaborone, Botswana
| | - Ishmael Kasvosve
- Department of Medical Laboratory Sciences, University of Botswana, Gaborone, Botswana
| | - Koketso Maplanka
- Department of Biological Sciences, Faculty of Sciences, University of Botswana, Gaborone, Botswana
| | - Sununguko W Mpoloka
- Department of Biological Sciences, Faculty of Sciences, University of Botswana, Gaborone, Botswana
| | | | - Mogomotsi Matshaba
- Botswana-Baylor Children's Clinical Centre of Excellence, Gaborone, Botswana.,Pediatric Retrovirology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| |
Collapse
|
9
|
Mboowa G, Mwesigwa S, Katagirya E, Retshabile G, Mlotshwa BC, Williams L, Kekitiinwa A, Kateete D, Wampande E, Wayengera M, Kintu BN, Kisitu GP, Kyobe S, Brown CW, Hanchard NA, Mardon G, Joloba M, Anabwani G, Pettitt E, Tsimako-Johnstone M, Kasvosve I, Maplanka K, Mpoloka SW, Hlatshwayo M, Matshaba M. The Collaborative African Genomics Network (CAfGEN): Applying Genomic technologies to probe host factors important to the progression of HIV and HIV-tuberculosis infection in sub-Saharan Africa. AAS Open Res 2018; 1:3. [DOI: 10.12688/aasopenres.12832.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Background: The Human Heredity and Health in Africa consortium (H3Africa) was conceived to facilitate the application of genomics technologies to improve health across Africa. Here, we describe how the Collaborative African Genomics Network (CAfGEN) of the H3Africa consortium is using genomics to probe host genetic factors important to the progression of HIV and HIV-tuberculosis (TB) coinfection in sub-Saharan Africa. Methods: CAfGEN is an H3Africa collaborative centre comprising expertise from the University of Botswana; Makerere University; Baylor College of Medicine Children’s Clinical Centers of Excellence (COEs) in Botswana, Uganda, and Swaziland; as well as Baylor College of Medicine, Texas. The COEs provide clinical expertise for community engagement, participant recruitment and sample collection while the three University settings facilitate processing and management of genomic samples and provide infrastructure and training opportunities to sustain genomics research. Results: The project has focused on utilizing whole-exome sequencing to identify genetic variants contributing to extreme HIV disease progression phenotypes in children, as well as RNA sequencing and integrated genomics to identify host genetic factors associated with TB disease progression among HIV-positive children. These cohorts, developed using the COEs’ electronic medical records, are exceptionally well-phenotyped and present an unprecedented opportunity to assess genetic factors in individuals whose HIV was acquired by a different route than their adult counterparts in the context of a unique clinical course and disease pathophysiology. Conclusions: Our approach offers the prospect of developing a critical mass of well-trained, highly-skilled, continent-based African genomic scientists. To ensure long term genomics research sustainability in Africa, CAfGEN contributes to a wide range of genomics capacity and infrastructure development on the continent, has laid a foundation for genomics graduate programs at its institutions, and continues to actively promote genomics research through innovative forms of community engagement brokered by partnerships with governments and academia to support genomics policy formulation.
Collapse
|