1
|
Al-Jawabreh R, Lastik D, McKenzie D, Reynolds K, Suleiman M, Mousley A, Atkinson L, Hunt V. Advancing Strongyloides omics data: bridging the gap with Caenorhabditis elegans. Philos Trans R Soc Lond B Biol Sci 2024; 379:20220437. [PMID: 38008117 PMCID: PMC10676819 DOI: 10.1098/rstb.2022.0437] [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: 06/27/2023] [Accepted: 08/31/2023] [Indexed: 11/28/2023] Open
Abstract
Among nematodes, the free-living model organism Caenorhabditis elegans boasts the most advanced portfolio of high-quality omics data. The resources available for parasitic nematodes, including Strongyloides spp., however, are lagging behind. While C. elegans remains the most tractable nematode and has significantly advanced our understanding of many facets of nematode biology, C. elegans is not suitable as a surrogate system for the study of parasitism and it is important that we improve the omics resources available for parasitic nematode species. Here, we review the omics data available for Strongyloides spp. and compare the available resources to those for C. elegans and other parasitic nematodes. The advancements in C. elegans omics offer a blueprint for improving omics-led research in Strongyloides. We suggest areas of priority for future research that will pave the way for expansions in omics resources and technologies. This article is part of the Theo Murphy meeting issue 'Strongyloides: omics to worm-free populations'.
Collapse
Affiliation(s)
- Reem Al-Jawabreh
- Department of Life Sciences, University of Bath, Bath, BA2 7AY, UK
| | - Dominika Lastik
- Department of Life Sciences, University of Bath, Bath, BA2 7AY, UK
| | | | - Kieran Reynolds
- Department of Life Sciences, University of Bath, Bath, BA2 7AY, UK
| | - Mona Suleiman
- Department of Life Sciences, University of Bath, Bath, BA2 7AY, UK
| | | | | | - Vicky Hunt
- Department of Life Sciences, University of Bath, Bath, BA2 7AY, UK
| |
Collapse
|
2
|
Al-Jawabreh R, Anderson R, Atkinson LE, Bickford-Smith J, Bradbury RS, Breloer M, Bryant AS, Buonfrate D, Cadd LC, Crooks B, Deiana M, Grant W, Hallem E, Hedtke SM, Hunt V, Khieu V, Kikuchi T, Kounosu A, Lastik D, van Lieshout L, Liu Y, McSorley HJ, McVeigh P, Mousley A, Murcott B, Nevin WD, Nosková E, Pomari E, Reynolds K, Ross K, Streit A, Suleiman M, Tiberti N, Viney M. Strongyloides questions-a research agenda for the future. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230004. [PMID: 38008122 PMCID: PMC10676812 DOI: 10.1098/rstb.2023.0004] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 09/29/2023] [Indexed: 11/28/2023] Open
Abstract
The Strongyloides genus of parasitic nematodes have a fascinating life cycle and biology, but are also important pathogens of people and a World Health Organization-defined neglected tropical disease. Here, a community of Strongyloides researchers have posed thirteen major questions about Strongyloides biology and infection that sets a Strongyloides research agenda for the future. This article is part of the Theo Murphy meeting issue 'Strongyloides: omics to worm-free populations'.
Collapse
Affiliation(s)
| | - Roy Anderson
- Department of Infectious Disease Epidemiology, Imperial College London, London SW7 2BX, UK
| | - Louise E. Atkinson
- School of Biological Sciences, Queen's University Belfast, Belfast BT9 5DL, UK
| | | | | | - Minka Breloer
- Bernhard Nocht Institute for Tropical Medicine, Hamburg 20359, Germany
| | - Astra S. Bryant
- Department of Physiology and Biophysics, University of Washington, Seattle 98195, USA
| | - Dora Buonfrate
- Department of Infectious Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona 37024, Italy
| | - Luke C. Cadd
- School of Biological Sciences, Queen's University Belfast, Belfast BT9 5DL, UK
| | - Bethany Crooks
- School of Biological Sciences, Queen's University Belfast, Belfast BT9 5DL, UK
| | - Michela Deiana
- Department of Infectious Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona 37024, Italy
| | - Warwick Grant
- Department of Environment and Genetics, La Trobe University, Bundoora, Victoria 3083, Australia
| | - Elissa Hallem
- Department of Microbiology, Immunology, and Molecular Genetics, Molecular Biology Institute, University of California Los Angeles, Los Angeles 90095, USA
| | - Shannon M. Hedtke
- Department of Environment and Genetics, La Trobe University, Bundoora, Victoria 3083, Australia
| | - Vicky Hunt
- Life Sciences Department, University of Bath, Bath BA2 7AY, UK
| | - Virak Khieu
- National Centre for Parasitology, Entomology and Malaria Control, Cambodia Ministry of Health, Cambodia
| | - Taisei Kikuchi
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8652, Japan
| | - Asuka Kounosu
- Division of Parasitology, Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, Miyazaki 889-1692, Japan
| | - Dominika Lastik
- Life Sciences Department, University of Bath, Bath BA2 7AY, UK
| | - Lisette van Lieshout
- Leiden University Center for Infectious Diseases, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Yuchen Liu
- Department of Evolution, Ecology & Behaviour, University of Liverpool, Liverpool L69 7ZB, UK
| | - Henry J. McSorley
- Division of Cell Signalling and Immunology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Paul McVeigh
- School of Biological Sciences, Queen's University Belfast, Belfast BT9 5DL, UK
| | - Angela Mousley
- School of Biological Sciences, Queen's University Belfast, Belfast BT9 5DL, UK
| | - Ben Murcott
- Life Sciences Department, University of Bath, Bath BA2 7AY, UK
| | - William David Nevin
- Department of Infectious Diseases, Imperial College London, London SW7 2BX, UK
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK
| | - Eva Nosková
- Department of Botany and Zoology, Faculty of Science, Masaryk University, 611 37 Brno, Czech Republic
- Institute of Vertebrate Biology, Czech Academy of Sciences, 603 65 Brno, Czech Republic
| | - Elena Pomari
- Department of Infectious Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona 37024, Italy
| | - Kieran Reynolds
- Life Sciences Department, University of Bath, Bath BA2 7AY, UK
| | - Kirstin Ross
- Environmental Health, College of Science and Engineering, Flinders University, South Australia 5042, Australia
| | - Adrian Streit
- Department of Integrative Evolutionary Biology, Max Planck Institute for Biology Tübingen, Tübingen 72076, Germany
| | - Mona Suleiman
- Life Sciences Department, University of Bath, Bath BA2 7AY, UK
| | - Natalia Tiberti
- Department of Infectious Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona 37024, Italy
| | - Mark Viney
- Department of Evolution, Ecology & Behaviour, University of Liverpool, Liverpool L69 7ZB, UK
| |
Collapse
|
3
|
Murcott B, Pawluk RJ, Protasio AV, Akinmusola RY, Lastik D, Hunt VL. stepRNA: Identification of Dicer cleavage signatures and passenger strand lengths in small RNA sequences. Front Bioinform 2022; 2:994871. [DOI: 10.3389/fbinf.2022.994871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 10/26/2022] [Indexed: 11/22/2022] Open
Abstract
The enzyme Dicer is a component of many small RNA (sRNA) pathways involved in RNA processing for post-transcriptional regulation, anti-viral response and control of transposable elements. Cleavage of double-stranded RNA by Dicer produces a signature overhanging sequence at the 3’ end of the sRNA sequence relative to a complementary passenger strand in a RNA duplex. There is a need for reliable tools to computationally search for Dicer cleavage signatures to help characterise families of sRNAs. This is increasingly important due to the rising popularity of sRNA sequencing, especially in non-model organisms. Here, we present stepRNA, a fast, local tool that identifies (i) overhang signatures strongly indicative of Dicer cleavage in RNA sequences, and (ii) the length of the passenger strand in sRNAs duplexes. We demonstrate the use of stepRNA with simulated and biological datasets to detect Dicer cleavage signatures in experimentally validated examples. Compared to currently available tools, stepRNA is more accurate, requires only sRNA sequence data rather than a reference genome, and provides information about other important features such as passenger strand length. stepRNA is freely available at https://github.com/Vicky-Hunt-Lab/stepRNA and is easily installable.
Collapse
|