Profiling the bloodstream form and procyclic form Trypanosoma brucei cell cycle using single cell transcriptomics
Abstract
African trypanosomes proliferate as bloodstream forms and procyclic forms in the mammal and tsetse fly midgut, respectively. This allows them to colonise the host environment upon infection and ensure life cycle progression. Yet, understanding of the mechanisms that regulate and drive the cell replication cycle of these forms is limited. Using single cell transcriptomics on unsynchronised cell populations, we have obtained high resolution cell cycle regulated transcriptomes of both procyclic and slender bloodstream form Trypanosoma brucei without prior cell sorting or synchronisation. Additionally, we describe an efficient freeze-thawing protocol that allows single cell transcriptomic analysis of cryopreserved T. brucei. Computational reconstruction of the cell cycle using periodic pseudotime inference allowed the dynamic expression patterns of cycling genes to be profiled for both life cycle forms. Comparative analyses identify a core cycling transcriptome highly conserved between forms, as well as several genes where transcript levels dynamics are form-specific. Comparing transcript expression patterns with protein abundance revealed that the majority of genes with periodic cycling transcript and protein levels exhibit a relative delay between peak transcript and protein expression. This work reveals novel detail of the cell cycle regulated transcriptomes of both forms, which are available for further interrogation via an interactive webtool.
Data availability
The transcriptome data generated in this study have been deposited in the EuropeanNucleotide Archive with project accession number PRJEB58781. The processed transcript count data and cell metadata generated in this study are available at Zenodo (10.5281/zenodo.7508131). BSF and PCF cell cycle transcriptomes can also explored using the interactive cell atlas (https://cellatlas-cxg.mvls.gla.ac.uk/Tbrucei.cellcycle.bsf/ and https://cellatlas-cxg.mvls.gla.ac.uk/Tbrucei.cellcycle.pcf/).
Article and author information
Author details
Funding
Wellcome Trust (218648/Z/19/Z)
- Emma M Briggs
Wellcome Trust (104111/Z/14/ZR)
- Thomas D Otto
Wellcome Trust (221717/Z/20/Z)
- Keith R Matthews
Wellcome Trust (220058/Z/19/Z)
- Guy R Oldrieve
- Keith R Matthews
Biotechnology and Biological Sciences Research Council (BB/R017166/1)
- Catarina A Marques
Biotechnology and Biological Sciences Research Council (BB/W001101/1)
- Catarina A Marques
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Malcolm J McConville, The University of Melbourne, Australia
Version history
- Preprint posted: January 9, 2023 (view preprint)
- Received: January 20, 2023
- Accepted: May 10, 2023
- Accepted Manuscript published: May 11, 2023 (version 1)
- Version of Record published: May 25, 2023 (version 2)
Copyright
© 2023, Briggs et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
Metrics
-
- 1,168
- views
-
- 176
- downloads
-
- 7
- citations
Views, downloads and citations are aggregated across all versions of this paper published by eLife.
Download links
Downloads (link to download the article as PDF)
Open citations (links to open the citations from this article in various online reference manager services)
Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)
Further reading
-
- Cell Biology
- Developmental Biology
The energy-burning capability of beige adipose tissue is a potential therapeutic tool for reducing obesity and metabolic disease, but this capacity is decreased by aging. Here, we evaluate the impact of aging on the profile and activity of adipocyte stem and progenitor cells (ASPCs) and adipocytes during the beiging process in mice. We found that aging increases the expression of Cd9 and other fibro-inflammatory genes in fibroblastic ASPCs and blocks their differentiation into beige adipocytes. Fibroblastic ASPC populations from young and aged mice were equally competent for beige differentiation in vitro, suggesting that environmental factors suppress adipogenesis in vivo. Examination of adipocytes by single nucleus RNA-sequencing identified compositional and transcriptional differences in adipocyte populations with aging and cold exposure. Notably, cold exposure induced an adipocyte population expressing high levels of de novo lipogenesis (DNL) genes, and this response was severely blunted in aged animals. We further identified Npr3, which encodes the natriuretic peptide clearance receptor, as a marker gene for a subset of white adipocytes and an aging-upregulated gene in adipocytes. In summary, this study indicates that aging blocks beige adipogenesis and dysregulates adipocyte responses to cold exposure and provides a resource for identifying cold and aging-regulated pathways in adipose tissue.
-
- Cell Biology
Current studies on cultured meat mainly focus on the muscle tissue reconstruction in vitro, but lack the formation of intramuscular fat, which is a crucial factor in determining taste, texture, and nutritional contents. Therefore, incorporating fat into cultured meat is of superior value. In this study, we employed the myogenic/lipogenic transdifferentiation of chicken fibroblasts in 3D to produce muscle mass and deposit fat into the same cells without the co-culture or mixture of different cells or fat substances. The immortalized chicken embryonic fibroblasts were implanted into the hydrogel scaffold, and the cell proliferation and myogenic transdifferentiation were conducted in 3D to produce the whole-cut meat mimics. Compared to 2D, cells grown in 3D matrix showed elevated myogenesis and collagen production. We further induced fat deposition in the transdifferentiated muscle cells and the triglyceride content could be manipulated to match and exceed the levels of chicken meat. The gene expression analysis indicated that both lineage-specific and multifunctional signalings could contribute to the generation of muscle/fat matrix. Overall, we were able to precisely modulate muscle, fat, and extracellular matrix contents according to balanced or specialized meat preferences. These findings provide new avenues for customized cultured meat production with desired intramuscular fat contents that can be tailored to meet the diverse demands of consumers.