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Mouton S, Mougel A, Ustyantsev K, Dissous C, Melnyk O, Berezikov E, Vicogne J. Optimized protocols for RNA interference in Macrostomum lignano. G3 (BETHESDA, MD.) 2024; 14:jkae037. [PMID: 38421640 PMCID: PMC11075559 DOI: 10.1093/g3journal/jkae037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 02/09/2024] [Accepted: 02/13/2024] [Indexed: 03/02/2024]
Abstract
Macrostomum lignano, a marine free-living flatworm, has emerged as a potent invertebrate model in developmental biology for studying stem cells, germline, and regeneration processes. In recent years, many tools have been developed to manipulate this worm and to facilitate genetic modification. RNA interference is currently the most accessible and direct technique to investigate gene functions. It is obtained by soaking worms in artificial seawater containing dsRNA targeting the gene of interest. Although easy to perform, the original protocol calls for daily exchange of dsRNA solutions, usually until phenotypes are observed, which is both time- and cost-consuming. In this work, we have evaluated alternative dsRNA delivery techniques, such as electroporation and osmotic shock, to facilitate the experiments with improved time and cost efficiency. During our investigation to optimize RNAi, we demonstrated that, in the absence of diatoms, regular single soaking in artificial seawater containing dsRNA directly produced in bacteria or synthesized in vitro is, in most cases, sufficient to induce a potent gene knockdown for several days with a single soaking step. Therefore, this new and highly simplified method allows a very significant reduction of dsRNA consumption and lab work. In addition, it enables performing experiments on a larger number of worms at minimal cost.
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Affiliation(s)
- Stijn Mouton
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen 9700AD, The Netherlands
| | - Alexandra Mougel
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019-UMR9017—CIIL—Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Kirill Ustyantsev
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen 9700AD, The Netherlands
| | - Colette Dissous
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019-UMR9017—CIIL—Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Oleg Melnyk
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019-UMR9017—CIIL—Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Eugene Berezikov
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen 9700AD, The Netherlands
| | - Jérôme Vicogne
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019-UMR9017—CIIL—Center for Infection and Immunity of Lille, F-59000 Lille, France
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Formaggioni A, Cavalli G, Hamada M, Sakamoto T, Plazzi F, Passamonti M. The Evolution and Characterization of the RNA Interference Pathways in Lophotrochozoa. Genome Biol Evol 2024; 16:evae098. [PMID: 38713108 PMCID: PMC11114477 DOI: 10.1093/gbe/evae098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 04/24/2024] [Accepted: 04/30/2024] [Indexed: 05/08/2024] Open
Abstract
In animals, three main RNA interference mechanisms have been described so far, which respectively maturate three types of small noncoding RNAs (sncRNAs): miRNAs, piRNAs, and endo-siRNAs. The diversification of these mechanisms is deeply linked with the evolution of the Argonaute gene superfamily since each type of sncRNA is typically loaded by a specific Argonaute homolog. Moreover, other protein families play pivotal roles in the maturation of sncRNAs, like the DICER ribonuclease family, whose DICER1 and DICER2 paralogs maturate respectively miRNAs and endo-siRNAs. Within Metazoa, the distribution of these families has been only studied in major groups, and there are very few data for clades like Lophotrochozoa. Thus, we here inferred the evolutionary history of the animal Argonaute and DICER families including 43 lophotrochozoan species. Phylogenetic analyses along with newly sequenced sncRNA libraries suggested that in all Trochozoa, the proteins related to the endo-siRNA pathway have been lost, a part of them in some phyla (i.e. Nemertea, Bryozoa, Entoprocta), while all of them in all the others. On the contrary, early diverging phyla, Platyhelminthes and Syndermata, showed a complete endo-siRNA pathway. On the other hand, miRNAs were revealed the most conserved and ubiquitous mechanism of the metazoan RNA interference machinery, confirming their pivotal role in animal cell regulation.
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Affiliation(s)
- Alessandro Formaggioni
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Gianmarco Cavalli
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Mayuko Hamada
- Ushimado Marine Institute, Okayama University, Okayama, Japan
| | | | - Federico Plazzi
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Marco Passamonti
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
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Chowdhury S, Sais D, Donnelly S, Tran N. The knowns and unknowns of helminth-host miRNA cross-kingdom communication. Trends Parasitol 2024; 40:176-191. [PMID: 38151361 DOI: 10.1016/j.pt.2023.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/05/2023] [Accepted: 12/05/2023] [Indexed: 12/29/2023]
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs that oversee gene modulation. They are integral to cellular functions and can migrate between species, leading to cross-kingdom gene suppression. Recent breakthroughs in helminth genome studies have sparked curiosity about helminth RNA regulators and their ability to regulate genes across species. Growing data indicate that helminth miRNAs have a significant impact on the host's immune system. Specific miRNAs from helminth parasites can merge with the host's miRNA system, implying that parasites could exploit their host's regulatory machinery and function. This review highlights the role of cross-kingdom helminth-derived miRNAs in the interplay between host and parasite, exploring potential routes for their uptake, processing, and consequences in host interaction.
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Affiliation(s)
- Sumaiya Chowdhury
- The School of Life Sciences, University of Technology, Sydney, Australia; School of Biomedical Engineering, Faculty of Engineering and Information Technology, University of Technology Sydney, Ultimo, NSW, Australia
| | - Dayna Sais
- School of Biomedical Engineering, Faculty of Engineering and Information Technology, University of Technology Sydney, Ultimo, NSW, Australia
| | - Sheila Donnelly
- The School of Life Sciences, University of Technology, Sydney, Australia.
| | - Nham Tran
- School of Biomedical Engineering, Faculty of Engineering and Information Technology, University of Technology Sydney, Ultimo, NSW, Australia.
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Doyle SR. Improving helminth genome resources in the post-genomic era. Trends Parasitol 2022; 38:831-840. [PMID: 35810065 DOI: 10.1016/j.pt.2022.06.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/14/2022] [Accepted: 06/14/2022] [Indexed: 01/02/2023]
Abstract
Rapid advancement in high-throughput sequencing and analytical approaches has seen a steady increase in the generation of genomic resources for helminth parasites. Now, helminth genomes and their annotations are a cornerstone of numerous efforts to compare genetic and transcriptomic variation, from single cells to populations of globally distributed parasites, to genome modifications to understand gene function. Our understanding of helminths is increasingly reliant on these genomic resources, which are primarily static once published and vary widely in quality and completeness between species. This article seeks to highlight the cause and effect of this variation and argues for the continued improvement of these genomic resources - even after their publication - which is necessary to provide a more accurate and complete understanding of the biology of these important pathogens.
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Affiliation(s)
- Stephen R Doyle
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK.
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Domínguez MF, Costábile A, Koziol U, Preza M, Brehm K, Tort JF, Castillo E. Cell repertoire and proliferation of germinative cells of the model cestode Mesocestoides corti. Parasitology 2022; 149:1505-1514. [PMID: 35787303 PMCID: PMC11010542 DOI: 10.1017/s0031182022000956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/23/2022] [Accepted: 06/27/2022] [Indexed: 11/06/2022]
Abstract
The phylum Platyhelminthes shares a unique population of undifferentiated cells responsible for the proliferation capacity needed for cell renewal, growth, tissue repair and regeneration. These cells have been extensively studied in free-living flatworms, whereas in cestodes the presence of a set of undifferentiated cells, known as germinative cells, has been demonstrated in classical morphology studies, but poorly characterized with molecular biology approaches. Furthermore, several genes have been identified as neoblast markers in free-living flatworms that deserve study in cestode models. Here, different cell types of the model cestode Mesocestoides corti were characterized, identifying differentiated and germinative cells. Muscle cells, tegumental cells, calcareous corpuscle precursor cells and excretory system cells were identified, all of which are non-proliferative, differentiated cell types. Besides those, germinative cells were identified as a population of small cells with proliferative capacity in vivo. Primary cell culture experiments in Dulbecco's Modified Eagle Medium (DMEM), Echinococcus hydatid fluid and hepatocyte conditioned media in non-reductive or reductive conditions confirmed that the germinative cells were the only ones with proliferative capacity. Since several genes have been identified as markers of undifferentiated neoblast cells in free-living flatworms, the expression of pumilio and pL10 genes was analysed by qPCR and in situ hybridization, showing that the expression of these genes was stronger in germinative cells but not restricted to this cell type. This study provides the first tools to analyse and further characterise undifferentiated cells in a model cestode.
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Affiliation(s)
- María Fernanda Domínguez
- Departamento de Genética, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Alicia Costábile
- Sección Bioquímica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Uriel Koziol
- Sección Biología Celular, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Matías Preza
- Sección Biología Celular, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Klaus Brehm
- University of Würzburg, Institute of Hygiene and Microbiology, Würzburg, Germany
| | - José F. Tort
- Departamento de Genética, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Estela Castillo
- Sección Bioquímica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
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Fontenla S, Langleib M, de la Torre-Escudero E, Domínguez MF, Robinson MW, Tort J. Role of Fasciola hepatica Small RNAs in the Interaction With the Mammalian Host. Front Cell Infect Microbiol 2022; 11:812141. [PMID: 35155272 PMCID: PMC8824774 DOI: 10.3389/fcimb.2021.812141] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 12/29/2021] [Indexed: 12/21/2022] Open
Abstract
MicroRNAs (miRNAs) are important post-transcriptional regulators of gene expression being involved in many different biological processes and play a key role in developmental timing. Additionally, recent studies have shown that miRNAs released from parasites are capable of regulating the expression of host genes. In the present work, we studied the expression patterns of ncRNAs of various intra-mammalian life-cycle stages of the liver fluke, Fasciola hepatica, as well as those packaged into extracellular vesicles and shed by the adult fluke. The miRNA expression profile of the intra-mammalian stages shows important variations, despite a set of predominant miRNAs that are highly expressed across all stages. No substantial variations in miRNA expression between dormant and activated metacercariae were detected, suggesting that they might not be central players in regulating fluke gene expression during this crucial step in the invasion of the definitive host. We generated a curated pipeline for the prediction of putative target genes that reports only sites conserved between three different prediction approaches. This pipeline was tested against an iso-seq curated database of the 3’ UTR regions of F. hepatica genes to detect miRNA regulation networks within liver fluke. Several functions related to the host immune response or modulation were enriched among the targets of the most highly expressed parasite miRNAs, stressing that they might be key players during the establishment and maintenance of infection. Additionally, we detected fragments derived from the processing of tRNAs, in all developmental stages analyzed, and documented the presence of novel long tRNA fragments enriched in vesicles. We confirmed the presence of at least 5 putative vault RNAs (vtRNAs), that are expressed across different stages and enriched in vesicles. The presence of tRNA fragments and vtRNAs in vesicles raise the possibility that they could be involved in the host-parasite interaction.
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Affiliation(s)
- Santiago Fontenla
- Departamento de Genética, Facultad de Medicina, Universidad de la República (UdelaR), Montevideo, Uruguay
- *Correspondence: Santiago Fontenla, ; José Tort,
| | - Mauricio Langleib
- Departamento de Genética, Facultad de Medicina, Universidad de la República (UdelaR), Montevideo, Uruguay
- Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República (UdelaR), Montevideo, Uruguay
| | | | - Maria Fernanda Domínguez
- Departamento de Genética, Facultad de Medicina, Universidad de la República (UdelaR), Montevideo, Uruguay
| | - Mark W. Robinson
- School of Biological Sciences, Queen’s University Belfast, Belfast, Northern Ireland
| | - José Tort
- Departamento de Genética, Facultad de Medicina, Universidad de la República (UdelaR), Montevideo, Uruguay
- *Correspondence: Santiago Fontenla, ; José Tort,
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Gutierrez J, Platt R, Opazo JC, Ray DA, Hoffmann F, Vandewege M. Evolutionary history of the vertebrate Piwi gene family. PeerJ 2021; 9:e12451. [PMID: 34760405 PMCID: PMC8574217 DOI: 10.7717/peerj.12451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 10/18/2021] [Indexed: 11/28/2022] Open
Abstract
PIWIs are regulatory proteins that belong to the Argonaute family. Piwis are primarily expressed in gonads and protect the germline against the mobilization and propagation of transposable elements (TEs) through transcriptional gene silencing. Vertebrate genomes encode up to four Piwi genes: Piwil1, Piwil2, Piwil3 and Piwil4, but their duplication history is unresolved. We leveraged phylogenetics, synteny and expression analyses to address this void. Our phylogenetic analysis suggests Piwil1 and Piwil2 were retained in all vertebrate members. Piwil4 was the result of Piwil1 duplication in the ancestor of gnathostomes, but was independently lost in ray-finned fishes and birds. Further, Piwil3 was derived from a tandem Piwil1 duplication in the common ancestor of marsupial and placental mammals, but was secondarily lost in Atlantogenata (Xenarthra and Afrotheria) and some rodents. The evolutionary rate of Piwil3 is considerably faster than any Piwi among all lineages, but an explanation is lacking. Our expression analyses suggest Piwi expression has mostly been constrained to gonads throughout vertebrate evolution. Vertebrate evolution is marked by two early rounds of whole genome duplication and many multigene families are linked to these events. However, our analyses suggest Piwi expansion was independent of whole genome duplications.
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Affiliation(s)
- Javier Gutierrez
- Department of Biology, Eastern New Mexico University, Portales, NM, United States of America
| | - Roy Platt
- Host Pathogen Interaction Program, Texas Biomedical Research Institute, San Antonio, TX, United States of America
| | - Juan C Opazo
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile.,Millennium Nucleus of Ion Channel-Associated Diseases (MiNICAD), Valdivia, Chile.,Integrative Biology Group, Universidad Austral de Chile, Valdivia, Chile
| | - David A Ray
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, United States of America
| | - Federico Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Starkville, MS, United States of America.,Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Starkville, MS, United States of America
| | - Michael Vandewege
- Department of Biology, Eastern New Mexico University, Portales, NM, United States of America
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