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Published on: April 6, 2022
Identification of microRNA genes in three opisthorchiids
Vladimir Y Ovchinnikov1, Dmitry A Afonnikov2, Gennady V Vasiliev3
1Department of Human and Animal Genetics, Institute of Cytology and Genetics, Novosibirsk, Russian Federation.
Background:
Opisthorchis felineus, O. viverrini, and Clonorchis sinensis (family Opisthorchiidae) are parasitic flatworms that pose a serious threat to humans in some countries and cause opisthorchiasis/clonorchiasis. Chronic disease may lead to a risk of carcinogenesis in the biliary ducts. MicroRNAs (miRNAs) are small noncoding RNAs that control gene expression at post-transcriptional level and are implicated in the regulation of various cellular processes during the parasite- host interplay. However, to date, the miRNAs of opisthorchiid flukes, in particular those essential for maintaining their complex biology and parasitic mode of existence, have not been satisfactorily described.
Methodology/Principal Findings:
Using a SOLiD deep sequencing-bioinformatic approach, we identified 43 novel and 18 conserved miRNAs for O. felineus (miracidia, metacercariae and adult worms), 20 novel and 16 conserved miRNAs for O. viverrini (adult worms), and 33 novel and 18 conserved miRNAs for C. sinensis (adult worms). The analysis of the data revealed differences in the expression level of conserved miRNAs among the three species and among three the developmental stages of O. felineus. Analysis of miRNA genes revealed two gene clusters, one cluster-like region and one intronic miRNA in the genome. The presence and structure of the two gene clusters were validated using a PCR-based approach in the three flukes.
Conclusions:
This study represents a comprehensive description of miRNAs in three members of the family Opistorchiidae, significantly expands our knowledge of miRNAs in multicellular parasites and provides a basis for understanding the structural and functional evolution of miRNAs in these metazoan parasites. Results of this study also provides novel resources for deeper understanding the complex parasite biology, for further research on the pathogenesis and molecular events of disease induced by the liver flukes. The present data may also facilitate the development of novel approaches for the prevention and treatment of opisthorchiasis/clonorchiasis.
Insights
This study identifies novel microRNAs (miRNAs) in liver flukes like Opisthorchis felineus, expanding knowledge of these parasitic flatworms. Understanding these miRNAs is crucial for combating opisthorchiasis and clonorchiasis.
Area of Science:
- Parasitology
- Molecular Biology
- Genomics
Background:
- Opisthorchis felineus, O. viverrini, and Clonorchis sinensis are liver flukes causing opisthorchiasis/clonorchiasis, with chronic infection risking biliary duct cancer.
- MicroRNAs (miRNAs) regulate gene expression and are vital in parasite-host interactions, but their role in opisthorchid flukes remains poorly understood.
Purpose of the Study:
- To comprehensively identify and characterize microRNAs (miRNAs) in three medically important liver fluke species: Opisthorchis felineus, Opisthorchis viverrini, and Clonorchis sinensis.
- To investigate the presence and genomic organization of miRNA genes within these parasites.
Main Methods:
- Deep sequencing (SOLiD) and bioinformatics analysis were employed to identify known and novel miRNAs across different developmental stages of O. felineus and in adult O. viverrini and C. sinensis.
- PCR-based approaches were used to validate the genomic structure, including gene clusters, of identified miRNAs.
Main Results:
- Discovery of 43 novel and 18 conserved miRNAs in O. felineus, 20 novel and 16 conserved miRNAs in O. viverrini, and 33 novel and 18 conserved miRNAs in C. sinensis.
- Identification of differential expression of conserved miRNAs among species and developmental stages, alongside the discovery of miRNA gene clusters and intronic miRNAs.
- Validation of the presence and structure of two miRNA gene clusters using PCR.
Conclusions:
- This study provides the most extensive description of miRNAs in Opisthorchiidae family members to date, significantly advancing the understanding of miRNA biology in multicellular parasites.
- The findings offer valuable resources for studying parasite biology, disease pathogenesis, and developing novel strategies for preventing and treating opisthorchiasis/clonorchiasis.
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