Functional genomics to unveil the early intra-mammalian development of schistosomes
Lead Research Organisation:
UNIVERSITY OF OXFORD
Abstract
Schistosomiasis, the infection with parasitic flatworms in the genus Schistosoma spp., remains a major Neglected Tropical Disease affecting >250 million people worldwide. My research team employs molecular, cellular and ‘omics’ technologies to unveil unexplored schistosome developmental biology and its interaction with the hosts. Unusual among parasitic flatworms, schistosomes have evolved male and female individuals. Genetically determined males and females are indistinguishable across most developmental stages; however, phenotypic sexual dimorphism becomes apparent by adulthood within the mammalian host. Worms undergo separate but concurrent sexual differentiation that eventually allows intersexual pairing, a critical step for female maturation, egg production and life cycle propagation. Understanding the sexual biology of schistosomes may lead to strategies to block transmission.
During the Future Leaders Fellowship (FLF) we have not only achieved most of the aims across the two original Work Packages (WP-I: Aims 1 and 2; WP-II: Aims 3 and 4), but also unexpected discoveries led the team towards new research lines. In WP-I, single cell RNA-sequencing (scRNA-seq) identified sex-specific/biased cell clusters, genes and pathways at the single cell level. We selected two key developmental transitions in the life cycle of Schistosoma mansoni: (1) from free-living larva (cercaria) to the first intra-mammalian parasitic stage (schistosomulum); and (2) from sexually monomorphic to sexually dimorphic intra-mammalian stages. ‘Novel’ and ‘existing’ sex-biased genes (the latter based on comparative genomic studies), were prioritised, cloned and sequenced. Additionally, proteomic and small RNA-seq analyses complemented the scRNA-seq findings, shining light into gene expression regulation during schistosome sexual development. For WP-I years 5-7 we proposed to (Aim 5) validate sex-biased cell clusters and characterise sex-biased genes (e.g., Transcription Factors) across the two selected life cycle transitions; (Aim 6) identify sex-specific splicing isoforms during development by single cell long-read sequencing; (Aim 7) study chromatin conformation by ATAC-seq from matched developmental stages.
For WP-II (technology innovation), we first optimised a protocol based on a ‘long-term media’ (LTM) complemented with Human Serum (HS) for in vitro schistosome sexual differentiation. Unexpectedly, these in vitro developed parasites digested haemoglobin more efficiently than control parasites. We performed scRNA-seq to define parasite TFs underlying the in vitro sexual differentiation, and proteomics of the LTM to identify factors contributing to parasite development. Second, we established a reliable protocol for medium/long- term preservation of schistosome eggs, that allows parasite material distribution across research laboratories reducing the overall number of animals used for life cycle maintenance. For WP-II years 5-7 we aim to: (Aim 8) compare/contrast the transcriptome landscape at single cell level between in vitro and in vivo developed schistosomes; (Aim 9) functional characterise key genes, e.g. TF, by RNAi in in vitro-developed parasites; (Aim 10) analyse the metabolomic/lipidomic profile of HS used to complement the LTM and test the effect of HS fractions on parasite development
This FLF allowed the establishment of my independent research team first at Aberystwyth University, and since October 2024 at the Department of Biology, University of Oxford where I am training new generation of scientists. My research program based on cutting-edge technologies comprehensively addresses knowledge gaps in fundamental schistosome biology and helminthology at large. Parasitic worms are agents of devastating human, veterinary and agriculture diseases, for which treatments are always in need. In the long-term, outcomes from my research program will contribute to the development of novel control strategies to alleviate the worldwide infectious disease burden.
During the Future Leaders Fellowship (FLF) we have not only achieved most of the aims across the two original Work Packages (WP-I: Aims 1 and 2; WP-II: Aims 3 and 4), but also unexpected discoveries led the team towards new research lines. In WP-I, single cell RNA-sequencing (scRNA-seq) identified sex-specific/biased cell clusters, genes and pathways at the single cell level. We selected two key developmental transitions in the life cycle of Schistosoma mansoni: (1) from free-living larva (cercaria) to the first intra-mammalian parasitic stage (schistosomulum); and (2) from sexually monomorphic to sexually dimorphic intra-mammalian stages. ‘Novel’ and ‘existing’ sex-biased genes (the latter based on comparative genomic studies), were prioritised, cloned and sequenced. Additionally, proteomic and small RNA-seq analyses complemented the scRNA-seq findings, shining light into gene expression regulation during schistosome sexual development. For WP-I years 5-7 we proposed to (Aim 5) validate sex-biased cell clusters and characterise sex-biased genes (e.g., Transcription Factors) across the two selected life cycle transitions; (Aim 6) identify sex-specific splicing isoforms during development by single cell long-read sequencing; (Aim 7) study chromatin conformation by ATAC-seq from matched developmental stages.
For WP-II (technology innovation), we first optimised a protocol based on a ‘long-term media’ (LTM) complemented with Human Serum (HS) for in vitro schistosome sexual differentiation. Unexpectedly, these in vitro developed parasites digested haemoglobin more efficiently than control parasites. We performed scRNA-seq to define parasite TFs underlying the in vitro sexual differentiation, and proteomics of the LTM to identify factors contributing to parasite development. Second, we established a reliable protocol for medium/long- term preservation of schistosome eggs, that allows parasite material distribution across research laboratories reducing the overall number of animals used for life cycle maintenance. For WP-II years 5-7 we aim to: (Aim 8) compare/contrast the transcriptome landscape at single cell level between in vitro and in vivo developed schistosomes; (Aim 9) functional characterise key genes, e.g. TF, by RNAi in in vitro-developed parasites; (Aim 10) analyse the metabolomic/lipidomic profile of HS used to complement the LTM and test the effect of HS fractions on parasite development
This FLF allowed the establishment of my independent research team first at Aberystwyth University, and since October 2024 at the Department of Biology, University of Oxford where I am training new generation of scientists. My research program based on cutting-edge technologies comprehensively addresses knowledge gaps in fundamental schistosome biology and helminthology at large. Parasitic worms are agents of devastating human, veterinary and agriculture diseases, for which treatments are always in need. In the long-term, outcomes from my research program will contribute to the development of novel control strategies to alleviate the worldwide infectious disease burden.