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. 2023 Jun 15;11(3):e0014723.
doi: 10.1128/spectrum.00147-23. Epub 2023 Apr 25.

Chemical Inhibition of Bromodomain Proteins in Insect-Stage African Trypanosomes Perturbs Silencing of the Variant Surface Glycoprotein Repertoire and Results in Widespread Changes in the Transcriptome

Affiliations

Chemical Inhibition of Bromodomain Proteins in Insect-Stage African Trypanosomes Perturbs Silencing of the Variant Surface Glycoprotein Repertoire and Results in Widespread Changes in the Transcriptome

Ethan C Ashby et al. Microbiol Spectr. .

Abstract

The eukaryotic protozoan parasite Trypanosoma brucei is transmitted by the tsetse fly to both humans and animals, where it causes a fatal disease called African trypanosomiasis. While the parasite lacks canonical DNA sequence-specific transcription factors, it does possess histones, histone modifications, and proteins that write, erase, and read histone marks. Chemical inhibition of chromatin-interacting bromodomain proteins has previously been shown to perturb bloodstream specific trypanosome processes, including silencing of the variant surface glycoprotein (VSG) genes and immune evasion. Transcriptomic changes that occur in bromodomain-inhibited bloodstream parasites mirror many of the changes that occur as parasites developmentally progress from the bloodstream to the insect stage. We performed transcriptome sequencing (RNA-seq) time courses to determine the effects of chemical bromodomain inhibition in insect-stage parasites using the compound I-BET151. We found that treatment with I-BET151 causes large changes in the transcriptome of insect-stage parasites and also perturbs silencing of VSG genes. The transcriptomes of bromodomain-inhibited parasites share some features with early metacyclic-stage parasites in the fly salivary gland, implicating bromodomain proteins as important for regulating transcript levels for developmentally relevant genes. However, the downregulation of surface procyclin protein that typically accompanies developmental progression is absent in bromodomain-inhibited insect-stage parasites. We conclude that chemical modulation of bromodomain proteins causes widespread transcriptomic changes in multiple trypanosome life cycle stages. Understanding the gene-regulatory processes that facilitate transcriptome remodeling in this highly diverged eukaryote may shed light on how these mechanisms evolved. IMPORTANCE The disease African trypanosomiasis imposes a severe human and economic burden for communities in sub-Saharan Africa. The parasite that causes the disease is transmitted to the bloodstream of a human or ungulate via the tsetse fly. Because the environments of the fly and the bloodstream differ, the parasite modulates the expression of its genes to accommodate two different lifestyles in these disparate niches. Perturbation of bromodomain proteins that interact with histone proteins around which DNA is wrapped (chromatin) causes profound changes in gene expression in bloodstream-stage parasites. This paper reports that gene expression is also affected by chemical bromodomain inhibition in insect-stage parasites but that the genes affected differ depending on life cycle stage. Because trypanosomes diverged early from model eukaryotes, an understanding of how trypanosomes regulate gene expression may lend insight into how gene-regulatory mechanisms evolved. This could also be leveraged to generate new therapeutic strategies.

Keywords: Trypanosoma brucei; bromodomain proteins; epigenetics; gene regulation; molecular parasitology; parasite.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

FIG 1
FIG 1
VSG genes and ESAGs are the among the most highly upregulated genes following I-BET151 treatment in insect-stage parasites. (A) PCA of RNA-seq samples for I-BET151-treated parasites at indicated time points. (B) PCA of RNA-seq samples from indicated tsetse fly organs using data from the work of Savage et al. (28). MG, midgut; PV, proventriculus; SA, salivary gland. (C) MA plot for parasites treated for 12 h with I-BET151 compared with untreated parasites. Red dots indicate differentially expressed genes, identified by DESeq, with a Benjamini-Hochberg-adjusted P value of <0.05 and a fold change of >2.
FIG 2
FIG 2
I-BET151 treatment in insect-stage parasites increases transcript levels of VSG genes and ESAGs that are silenced in wild-type parasites. (A) (Left) Median transcript levels for each indicated gene subset over 24 h of I-BET151 treatment. Shading represents the inner quartile range at each time point. (Right) Schematic of VSG gene locations in the genome. (B) MA plot for VSG gene subsets and ESAGs in parasites treated for 12 h with I-BET151 compared with untreated parasites. Dashed lines demarcate 2-fold differences in treated parasites compared to untreated parasites. (C) (Left) Transcript levels for 6 individual VSG genes with metacyclic promoters over 24 h of I-BET151 treatment. (Right) Transcript levels for 4 VSG genes in samples taken from the indicated organs of tsetse flies using data from the work of Savage et al. (28).
FIG 3
FIG 3
Transcript levels for some gene sets associated with insect-stage developmental progression are also altered following I-BET151 treatment. Violin plot for transcript levels of adenylate cyclases and transporters that are downregulated during insect-stage developmental progression and transcript levels of ISG and RBP genes that are upregulated during developmental progression. Data are plotted as log2(I-BET151 [12 h]/untreated [0 h]) and log2(salivary gland/midgut) using data on parasites harvested from the midgut and salivary gland from the work of Savage et al. (28). Data for all gene sets shown were statistically significant using GSEA (Table S1). Numbers to the right of the x axis labels indicate the numbers of genes in the gene set analyzed.
FIG 4
FIG 4
I-BET151-treated parasites share some transcriptomic features of early metacyclic parasites. (A) Violin plot showing transcript levels of indicated gene sets defined by Vigneron et al. (31) in parasites over 24 h of I-BET151 treatment. Numbers over gene sets indicate the numbers of genes in set. Data are plotted as log2(I-BET151-treated/untreated [0 h]) using normalized counts. Blue shading indicates time of I-BET151 treatment. Schematics under the labels represent transcript levels for each group during development as measured by Vigneron et al. (31), where a black node indicates transcript level at the epimastigote stage, a dark gray node represents transcript level in early metacyclic parasites, and a light gray node indicates transcript level in late metacyclic parasites. (B) Normalized transcript levels for the indicated genes following I-BET151 treatment. Each gene set was identified by Vigneron et al. (31) as having altered expression specifically in early-metacyclic-stage parasites.
FIG 5
FIG 5
Differentially expressed genes in I-BET151-treated parasites show distinct patterns of expression. (A) DESeq normalized transcript levels of differentially expressed genes following I-BET151 treatment, clustered based on expression pattern and timing. Transcript levels are scaled such that the mean is 0 and the standard deviation is 1. (B) Violin plot comparing changes in transcript levels for each cluster in panel A following 12 h of I-BET151 treatment or during insect-stage developmental progression using data for midgut, proventriculus, and salivary gland parasites taken from the work of Savage et al. (28). Stars indicate clusters identified as enriched by GSEA with an FDR of <0.1 in the insect-stage-developmental-progression data set.
FIG 6
FIG 6
Genes involved in movement and microtubule-based processes are upregulated in I-BET151 parasites and in parasites transitioning from the midgut to the proventriculus. (A) (Top) Same as in Fig. 5A. Bottom, REVIGO (80) plot of GO enrichment analysis performed on cluster 3. (B) Violin plot for genes identified as enriched by GO analysis of cluster 3. Transcript levels for I-BET151-treated parasites are compared with transcript levels in midgut and proventriculus stage parasites using data from the work of Savage et al. (28).
FIG 7
FIG 7
Diverse biological processes affected by I-BET151 treatment in insect-stage parasites. Violin plot showing transcript levels of parasites treated for 12 h with I-BET151 compared with untreated parasites (0 h) expressed as log2(12-h I-BET151/0-h IBET151) using normalized counts for GO sets with an FDR of <0.1 by GSEA.
FIG 8
FIG 8
Many transcriptomic changes initiated by I-BET151 treatment are life cycle stage specific. UpSet plot showing differentially expressed genes identified by DESeq with a Benjamini-Hochberg-adjusted P value of <0.05 and a fold change of >2 up or down in bloodstream and procyclic-stage parasites. Data from bloodstream parasites were generated from the work of Schulz et al. (23).

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