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Methods to determine the transcriptomes of trypanosomes in mixtures with mammalian cells: the effects of parasite purification and selective cDNA amplification.

ABSTRACT: Patterns of gene expression in cultured Trypanosoma brucei bloodstream and procyclic forms have been extensively characterized, and some comparisons have been made with trypanosomes grown to high parasitaemias in laboratory rodents. We do not know, however, to what extent these transcriptomes resemble those in infected Tsetse flies - or in humans or cattle, where parasitaemias are substantially lower. For clinical and field samples it is difficult to characterize parasite gene expression because of the large excess of host cell RNA. We have here examined two potential solutions to this problem for bloodstream form trypanosomes, assaying transcriptomes by high throughput cDNA sequencing (RNASeq). We first purified the parasites from blood of infected rats. We found that a red blood cell lysis procedure affected the transcriptome substantially more than purification using a DEAE cellulose column, but that too introduced significant distortions and variability. As an alternative, we specifically amplified parasite sequences from a mixture containing a 1000-fold excess of human RNA. We first purified polyadenylated RNA, then made trypanosome-specific cDNA by priming with a spliced leader primer. Finally, the cDNA was amplified using nested primers. The amplification procedure was able to produce samples in which 20% of sequence reads mapped to the trypanosome genome. Synthesis of the second cDNA strand with a spliced leader primer, followed by amplification, is sufficiently reproducible to allow comparison of different samples so long as they are all treated in the same way. However, SL priming distorted the abundances of the cDNA products and definitely cannot be used, by itself, to measure absolute mRNA levels. The amplification method might be suitable for clinical samples with low parasitaemias, and could also be adapted for other Kinetoplastids and to samples from infected vectors.

SUBMITTER: Mulindwa J

PROVIDER: S-EPMC3990519 | biostudies-literature | 2014 Apr

REPOSITORIES: biostudies-literature

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Methods to determine the transcriptomes of trypanosomes in mixtures with mammalian cells: the effects of parasite purification and selective cDNA amplification.

Mulindwa Julius J Fadda Abeer A Merce Clementine C Matovu Enoch E Enyaru John J Clayton Christine C

PLoS neglected tropical diseases 20140417 4

Patterns of gene expression in cultured Trypanosoma brucei bloodstream and procyclic forms have been extensively characterized, and some comparisons have been made with trypanosomes grown to high parasitaemias in laboratory rodents. We do not know, however, to what extent these transcriptomes resemble those in infected Tsetse flies - or in humans or cattle, where parasitaemias are substantially lower. For clinical and field samples it is difficult to characterize parasite gene expression because ...[more]

PMID: 24743343

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Project description:BackgroundTrypanosomatids are a group of protozoan parasites that includes the etiologic agents of important human illnesses as Chagas disease, sleeping sickness and leishmaniasis. These parasites have a significant distinction from other eukaryotes concerning mRNA structure, since all mature mRNAs have an identical species-specific sequence of 39 nucleotides at the 5' extremity, named spliced leader (SL). Considering this peculiar aspect of trypanosomatid mRNA, the aim of the present work was to develop a Trypanosoma cruzi specific in vitro transcription (IVT) linear mRNA amplification method in order to improve parasite transcriptomics analyses.MethodsWe designed an oligonucleotide complementary to the last 21 bases of T. cruzi SL sequence, bearing an upstream T7 promoter (T7SL primer), which was used to direct the synthesis of second-strand cDNA. Original mRNA was then amplified by IVT using T7 RNA polymerase. T7SL-amplified RNA from two distinct T. cruzi stages (epimastigotes and trypomastigotes) were deep sequenced in SOLiD platform. Usual poly(A) + RNA and and T7-oligo(dT) amplified RNA (Eberwine method) were also sequenced. RNA-Seq reads were aligned to our new and improved T. cruzi Dm28c genome assembly (PacBio technology) and resulting transcriptome pattern from these three RNA preparation methods were compared, mainly concerning the conservation of mRNA transcritional levels and DEGs detection between epimastigotes and trypomastigotes.ResultsT7SL IVT method detected more potential differentially expressed genes in comparison to either poly(A) + RNA or T7dT IVT, and was also able to produce reliable quantifications of the parasite transcriptome down to 3 ng of total RNA. Furthermore, amplification of parasite mRNA in HeLa/epimastigote RNA mixtures showed that T7SL IVT generates transcriptome quantification with similar detection of differentially expressed genes when parasite RNA mass was only 0.1% of the total mixture (R = 0.78 when compared to poly(A) + RNA).ConclusionsThe T7SL IVT amplification method presented here allows the detection of more potential parasite differentially expressed genes (in comparison to poly(A) + RNA) in host-parasite mixtures or samples with low amount of RNA. This method is especially useful for trypanosomatid transcriptomics because it produces less bias than PCR-based mRNA amplification. Additionally, by simply changing the complementary region of the T7SL primer, the present method can be applied to any trypanosomatid species.

Project description:Approximately 20% of sleeping sickness patients exhibit respiratory complications which are commonly attributed to secondary bacterial infections, with an unknown role of the parasite. Using a Glossina morsitans tsetse fly initiated Trypansoma brucei infection in mice we found that parasites rapidly and permanently colonize the lungs, representing one of the major target organs next to the adipose tissue. Trypanosomes were found by immunofluorescence staining and scanning electron microscopy to occupy the extravascular spaces surrounding the blood vessels of the alveoli and bronchi. Parasites were even found in the lung cartilage. Trypanosomes were often observed as nests of multiplying parasites exhibiting close interactions with collagen and highly active secretion of extracellular vesicles that are engaged in intercellular communication. The local immune response was analysed by flow cytometry after 10 and 21 days of infection and was characterized by a substantial increase of CD11b+ Ly6C+ monocytes, CD11b+ Ly6C+ F4/80+ macrophages and CD11b+ CD11c+ dendritic cells. CD11b+ Ly6G+ neutrophils only accumulated prominently at the late infection time point. Interestingly, parasite presence resulted in a significant reduction of B220+ IgM+ B cells, CD11b+ CD11clo/- SiglecF+ eosinophils and TcR-β- NK1.1+ natural killer cells. Digital transcriptomics revealed infection-induced upregulation of Il-10, IFN-ɣ- and IFN-α-responses, IL-2-, IL-6- and TNF-signalling, a Th1 pro-inflammatory signature, negative immune checkpoint regulators and a predominant M1 macrophage polarization. Il12a and genes associated with complement and the B cell receptor were downregulated. No infection-associated pulmonary dysfunction could be detected by in vivo lung function measurements, mirroring the limited pulmonary complications during sleeping sickness. However, the substantial reduction of eosinophils, B cells and NK cells may render individuals more susceptible to opportunistic infections. Collectively, these observations provide essential insights in the peculiar parasite biology, immunological reactions and physiological function of a largely overlooked target organ which may trigger new diagnostic approaches for sleeping sickness.

Dataset Information

Methods to determine the transcriptomes of trypanosomes in mixtures with mammalian cells: the effects of parasite purification and selective cDNA amplification.

Publications

Methods to determine the transcriptomes of trypanosomes in mixtures with mammalian cells: the effects of parasite purification and selective cDNA amplification.

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