1
|
Kasprzyk-Hordern B, Adams B, Adewale ID, Agunbiade FO, Akinyemi MI, Archer E, Badru FA, Barnett J, Bishop IJ, Di Lorenzo M, Estrela P, Faraway J, Fasona MJ, Fayomi SA, Feil EJ, Hyatt LJ, Irewale AT, Kjeldsen T, Lasisi AKS, Loiselle S, Louw TM, Metcalfe B, Nmormah SA, Oluseyi TO, Smith TR, Snyman MC, Sogbanmu TO, Stanton-Fraser D, Surujlal-Naicker S, Wilson PR, Wolfaardt G, Yinka-Banjo CO. Wastewater-based epidemiology in hazard forecasting and early-warning systems for global health risks. ENVIRONMENT INTERNATIONAL 2022; 161:107143. [PMID: 35176575 PMCID: PMC8842583 DOI: 10.1016/j.envint.2022.107143] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 01/20/2022] [Accepted: 02/07/2022] [Indexed: 05/17/2023]
Abstract
With the advent of the SARS-CoV-2 pandemic, Wastewater-Based Epidemiology (WBE) has been applied to track community infection in cities worldwide and has proven succesful as an early warning system for identification of hotspots and changingprevalence of infections (both symptomatic and asymptomatic) at a city or sub-city level. Wastewater is only one of environmental compartments that requires consideration. In this manuscript, we have critically evaluated the knowledge-base and preparedness for building early warning systems in a rapidly urbanising world, with particular attention to Africa, which experiences rapid population growth and urbanisation. We have proposed a Digital Urban Environment Fingerprinting Platform (DUEF) - a new approach in hazard forecasting and early-warning systems for global health risks and an extension to the existing concept of smart cities. The urban environment (especially wastewater) contains a complex mixture of substances including toxic chemicals, infectious biological agents and human excretion products. DUEF assumes that these specific endo- and exogenous residues, anonymously pooled by communities' wastewater, are indicative of community-wide exposure and the resulting effects. DUEF postulates that the measurement of the substances continuously and anonymously pooled by the receiving environment (sewage, surface water, soils and air), can provide near real-time dynamic information about the quantity and type of physical, biological or chemical stressors to which the surveyed systems are exposed, and can create a risk profile on the potential effects of these exposures. Successful development and utilisation of a DUEF globally requires a tiered approach including: Stage I: network building, capacity building, stakeholder engagement as well as a conceptual model, followed by Stage II: DUEF development, Stage III: implementation, and Stage IV: management and utilization. We have identified four key pillars required for the establishment of a DUEF framework: (1) Environmental fingerprints, (2) Socioeconomic fingerprints, (3) Statistics and modelling and (4) Information systems. This manuscript critically evaluates the current knowledge base within each pillar and provides recommendations for further developments with an aim of laying grounds for successful development of global DUEF platforms.
Collapse
Affiliation(s)
| | - B Adams
- Department of Mathematical Sciences, University of Bath, BA2 7AY, UK
| | - I D Adewale
- Department of Electrical and Electronics Engineering, University of Lagos, 100213 Akoka, Lagos, Nigeria
| | - F O Agunbiade
- Department of Chemistry, Faculty of Science, University of Lagos, Akoka, Lagos, Nigeria
| | - M I Akinyemi
- Department of Mathematics, University of Lagos, Akoka, Lagos, Nigeria
| | - E Archer
- Department of Microbiology, Stellenbosch University, 7600 Stellenbosch, South Africa
| | - F A Badru
- Department of Social Work, University of Lagos, Akoka, Lagos, Nigeria
| | - J Barnett
- Department of Psychology, University of Bath, BA2 7AY, UK
| | - I J Bishop
- Earthwatch Europe, Mayfield House, 256 Banbury Road, Summertown, Oxford OX2 7DE, UK
| | - M Di Lorenzo
- Department of Chemical Engineering, University of Bath, BA2 7AY Bath, UK
| | - P Estrela
- Department of Electronic and Electrical Engineering, University of Bath, BA2 7AY, UK
| | - J Faraway
- Department of Mathematical Sciences, University of Bath, BA2 7AY, UK
| | - M J Fasona
- Department of Geography, University of Lagos, Akoka, Lagos, Nigeria
| | - S A Fayomi
- Research for Sustainable Development Unit, Peculiar Grace Youth Empowerment Initiative, Shasha, Lagos, Nigeria
| | - E J Feil
- Department of Biology and Biochemistry, University of Bath, BA2 7AY, UK
| | - L J Hyatt
- Amazon Web Services, 60 Holborn Viaduct, Holborn, London EC1A 2FD, United Kingdom
| | - A T Irewale
- Research for Sustainable Development Unit, Peculiar Grace Youth Empowerment Initiative, Shasha, Lagos, Nigeria
| | - T Kjeldsen
- Department of Architecture and Civil Engineering, University of Bath, BA2 7AY, UK
| | - A K S Lasisi
- Environmental Assessment Department, Lagos State Ministry of Environment and Water Resources, Lagos, Nigeria
| | - S Loiselle
- Earthwatch Europe, Mayfield House, 256 Banbury Road, Summertown, Oxford OX2 7DE, UK
| | - T M Louw
- Department of Process Engineering, Stellenbosch University, Stellenbosch, South Africa
| | - B Metcalfe
- Department of Electronic and Electrical Engineering, University of Bath, BA2 7AY, UK
| | - S A Nmormah
- Centre for Human Development (CHD), Lagos, Nigeria
| | - T O Oluseyi
- Department of Chemistry, Faculty of Science, University of Lagos, Akoka, Lagos, Nigeria
| | - T R Smith
- Department of Mathematical Sciences, University of Bath, BA2 7AY, UK
| | - M C Snyman
- TecLab SP, Collaborator of Stellenbosch University Water Institute, Stellenbosch 64B. W, South Africa
| | - T O Sogbanmu
- Ecotoxicology and Conservation Unit, Department of Zoology, Faculty of Science, University of Lagos, Akoka, Lagos, Nigeria
| | | | - S Surujlal-Naicker
- Scientific Services Branch, Water and Sanitation Department, City of Cape Town Metropolitan Municipality, Cape Town, South Africa
| | - P R Wilson
- Department of Electronic and Electrical Engineering, University of Bath, BA2 7AY, UK
| | - G Wolfaardt
- Department of Microbiology, Stellenbosch University, 7600 Stellenbosch, South Africa
| | - C O Yinka-Banjo
- Department of Computer Sciences, University of Lagos, Akoka, Lagos, Nigeria
| |
Collapse
|
2
|
Nabeel-Shah S, Garg J, Saettone A, Ashraf K, Lee H, Wahab S, Ahmed N, Fine J, Derynck J, Pu S, Ponce M, Marcon E, Zhang Z, Greenblatt JF, Pearlman RE, Lambert JP, Fillingham J. Functional characterization of RebL1 highlights the evolutionary conservation of oncogenic activities of the RBBP4/7 orthologue in Tetrahymena thermophila. Nucleic Acids Res 2021; 49:6196-6212. [PMID: 34086947 PMCID: PMC8216455 DOI: 10.1093/nar/gkab413] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/22/2021] [Accepted: 05/04/2021] [Indexed: 12/18/2022] Open
Abstract
Retinoblastoma-binding proteins 4 and 7 (RBBP4 and RBBP7) are two highly homologous human histone chaperones. They function in epigenetic regulation as subunits of multiple chromatin-related complexes and have been implicated in numerous cancers. Due to their overlapping functions, our understanding of RBBP4 and 7, particularly outside of Opisthokonts, has remained limited. Here, we report that in the ciliate protozoan Tetrahymena thermophila a single orthologue of human RBBP4 and 7 proteins, RebL1, physically interacts with histone H4 and functions in multiple epigenetic regulatory pathways. Functional proteomics identified conserved functional links for Tetrahymena RebL1 protein as well as human RBBP4 and 7. We found that putative subunits of multiple chromatin-related complexes including CAF1, Hat1, Rpd3, and MuvB, co-purified with RebL1 during Tetrahymena growth and conjugation. Iterative proteomics analyses revealed that the cell cycle regulatory MuvB-complex in Tetrahymena is composed of at least five subunits including evolutionarily conserved Lin54, Lin9 and RebL1 proteins. Genome-wide analyses indicated that RebL1 and Lin54 (Anqa1) bind within genic and intergenic regions. Moreover, Anqa1 targets primarily promoter regions suggesting a role for Tetrahymena MuvB in transcription regulation. RebL1 depletion inhibited cellular growth and reduced the expression levels of Anqa1 and Lin9. Consistent with observations in glioblastoma tumors, RebL1 depletion suppressed DNA repair protein Rad51 in Tetrahymena, thus underscoring the evolutionarily conserved functions of RBBP4/7 proteins. Our results suggest the essentiality of RebL1 functions in multiple epigenetic regulatory complexes in which it impacts transcription regulation and cellular viability.
Collapse
Affiliation(s)
- Syed Nabeel-Shah
- Department of Chemistry and Biology, Ryerson University, 350 Victoria St., Toronto M5B 2K3, Canada
| | - Jyoti Garg
- Department of Chemistry and Biology, Ryerson University, 350 Victoria St., Toronto M5B 2K3, Canada.,Department of Biology, York University, 4700 Keele St., Toronto M3J 1P3, Canada
| | - Alejandro Saettone
- Department of Chemistry and Biology, Ryerson University, 350 Victoria St., Toronto M5B 2K3, Canada
| | - Kanwal Ashraf
- Department of Biology, York University, 4700 Keele St., Toronto M3J 1P3, Canada
| | - Hyunmin Lee
- Department of Computer Science, University of Toronto, Toronto M5S 1A8, Canada.,Donnelly Centre, University of Toronto, Toronto M5S 3E1, Canada
| | - Suzanne Wahab
- Department of Chemistry and Biology, Ryerson University, 350 Victoria St., Toronto M5B 2K3, Canada
| | - Nujhat Ahmed
- Donnelly Centre, University of Toronto, Toronto M5S 3E1, Canada.,Department of Molecular Genetics, University of Toronto, Toronto M5S 1A8, Canada
| | - Jacob Fine
- Department of Biology, York University, 4700 Keele St., Toronto M3J 1P3, Canada
| | - Joanna Derynck
- Department of Chemistry and Biology, Ryerson University, 350 Victoria St., Toronto M5B 2K3, Canada
| | - Shuye Pu
- Donnelly Centre, University of Toronto, Toronto M5S 3E1, Canada
| | - Marcelo Ponce
- SciNet HPC Consortium, University of Toronto, 661 University Avenue, Suite 1140, Toronto M5G 1M1, Canada
| | - Edyta Marcon
- Donnelly Centre, University of Toronto, Toronto M5S 3E1, Canada
| | - Zhaolei Zhang
- Department of Computer Science, University of Toronto, Toronto M5S 1A8, Canada.,Donnelly Centre, University of Toronto, Toronto M5S 3E1, Canada.,Department of Molecular Genetics, University of Toronto, Toronto M5S 1A8, Canada
| | - Jack F Greenblatt
- Donnelly Centre, University of Toronto, Toronto M5S 3E1, Canada.,Department of Molecular Genetics, University of Toronto, Toronto M5S 1A8, Canada
| | - Ronald E Pearlman
- Department of Biology, York University, 4700 Keele St., Toronto M3J 1P3, Canada
| | - Jean-Philippe Lambert
- Department of Molecular Medicine, Cancer Research Center, Big Data Research Center, Université Laval, Quebec City, Canada; CHU de Québec Research Center, CHUL, 2705 Laurier Boulevard, Quebec City G1V 4G2, Canada
| | - Jeffrey Fillingham
- Department of Chemistry and Biology, Ryerson University, 350 Victoria St., Toronto M5B 2K3, Canada
| |
Collapse
|
3
|
Wahab S, Saettone A, Nabeel-Shah S, Dannah N, Fillingham J. Exploring the Histone Acetylation Cycle in the Protozoan Model Tetrahymena thermophila. Front Cell Dev Biol 2020; 8:509. [PMID: 32695779 PMCID: PMC7339932 DOI: 10.3389/fcell.2020.00509] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 05/28/2020] [Indexed: 12/22/2022] Open
Abstract
The eukaryotic histone acetylation cycle is composed of three classes of proteins, histone acetyltransferases (HATs) that add acetyl groups to lysine amino acids, bromodomain (BRD) containing proteins that are one of the most characterized of several protein domains that recognize acetyl-lysine (Kac) and effect downstream function, and histone deacetylases (HDACs) that catalyze the reverse reaction. Dysfunction of selected proteins of these three classes is associated with human disease such as cancer. Additionally, the HATs, BRDs, and HDACs of fungi and parasitic protozoa present potential drug targets. Despite their importance, the function and mechanisms of HATs, BRDs, and HDACs and how they relate to chromatin remodeling (CR) remain incompletely understood. Tetrahymena thermophila (Tt) provides a highly tractable single-celled free-living protozoan model for studying histone acetylation, featuring a massively acetylated somatic genome, a property that was exploited in the identification of the first nuclear/type A HAT Gcn5 in the 1990s. Since then, Tetrahymena remains an under-explored model for the molecular analysis of HATs, BRDs, and HDACs. Studies of HATs, BRDs, and HDACs in Tetrahymena have the potential to reveal the function of HATs and BRDs relevant to both fundamental eukaryotic biology and to the study of disease mechanisms in parasitic protozoa.
Collapse
Affiliation(s)
| | | | | | | | - Jeffrey Fillingham
- Department of Chemistry and Biology, Ryerson University, Toronto, ON, Canada
| |
Collapse
|