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Transcription Profiling of Malaria-Naïve and Semi-immune Colombian Volunteers in a Plasmodium vivax Sporozoite Challenge.

Rojas-Peña ML, Vallejo A, Herrera S, Gibson G, Arévalo-Herrera M - PLoS Negl Trop Dis (2015)

Bottom Line: There was no evidence for transcriptional changes prior to the appearance of blood stage parasites at day 12 or 13, at which time there was a strong interferon response and, unexpectedly, down-regulation of transcripts related to inflammation and innate immunity.This differential expression was confirmed with RNASeq, which also suggested perturbations of aspects of T cell function and erythropoiesis.Despite differences in clinical symptoms between the semi-immune and malaria naïve individuals, only subtle differences in their transcriptomes were observed, although 175 genes showed significantly greater induction or repression in the naïve volunteers from Cali.

View Article: PubMed Central - PubMed

Affiliation: Center for Integrative Genomics, School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America.

ABSTRACT

Background: Continued exposure to malaria-causing parasites in endemic regions of malaria induces significant levels of acquired immunity in adult individuals. A better understanding of the transcriptional basis for this acquired immunological response may provide insight into how the immune system can be boosted during vaccination, and into why infected individuals differ in symptomology.

Methodology/principal findings: Peripheral blood gene expression profiles of 9 semi-immune volunteers from a Plasmodium vivax malaria prevalent region (Buenaventura, Colombia) were compared to those of 7 naïve individuals from a region with no reported transmission of malaria (Cali, Colombia) after a controlled infection mosquito bite challenge with P. vivax. A Fluidigm nanoscale quantitative RT-PCR array was used to survey altered expression of 96 blood informative transcripts at 7 timepoints after controlled infection, and RNASeq was used to contrast pre-infection and early parasitemia timepoints. There was no evidence for transcriptional changes prior to the appearance of blood stage parasites at day 12 or 13, at which time there was a strong interferon response and, unexpectedly, down-regulation of transcripts related to inflammation and innate immunity. This differential expression was confirmed with RNASeq, which also suggested perturbations of aspects of T cell function and erythropoiesis. Despite differences in clinical symptoms between the semi-immune and malaria naïve individuals, only subtle differences in their transcriptomes were observed, although 175 genes showed significantly greater induction or repression in the naïve volunteers from Cali.

Conclusion/significance: Gene expression profiling of whole blood reveals the type and duration of the immune response to P. vivax infection, and highlights a subset of genes that may mediate adaptive immunity.

No MeSH data available.


Related in: MedlinePlus

Differential expression in whole-blood RNASeq data set.Volcano plots of statistical significance vs. magnitude of differential expression for the contrasts between timepoint in (A) and by location in (B), highlighting significant genes for the timepoint effect in orange. Y axis shows the significance as–log10 P value, and x-axis shows the magnitude of the difference log2 units (highlighting significant genes at NLP>5 for the timepoint contrast). (C) Heat map showing two-way hierarchical clustering of transcripts (columns) in each sample (rows) of 175 genes that show a significant timepoint-by-location interaction effect at p<0.05. Red cells indicate high expression, blue low, gray intermediate. Green sample labels represent Baseline (Pre-challenge) and red labels represent Diagnosis day, solid points represent Cali (N, naïve), and open circles represent Buenaventura (S, semi-immune). Approximately unbiased bootstrap support (AU) values computed with pvclust are indicated beside three deep nodes.
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pntd.0003978.g004: Differential expression in whole-blood RNASeq data set.Volcano plots of statistical significance vs. magnitude of differential expression for the contrasts between timepoint in (A) and by location in (B), highlighting significant genes for the timepoint effect in orange. Y axis shows the significance as–log10 P value, and x-axis shows the magnitude of the difference log2 units (highlighting significant genes at NLP>5 for the timepoint contrast). (C) Heat map showing two-way hierarchical clustering of transcripts (columns) in each sample (rows) of 175 genes that show a significant timepoint-by-location interaction effect at p<0.05. Red cells indicate high expression, blue low, gray intermediate. Green sample labels represent Baseline (Pre-challenge) and red labels represent Diagnosis day, solid points represent Cali (N, naïve), and open circles represent Buenaventura (S, semi-immune). Approximately unbiased bootstrap support (AU) values computed with pvclust are indicated beside three deep nodes.

Mentions: Consistent with timepoint rather than population explaining a large proportion of the variance, gene-specific differential expression analysis revealed more than 250 transcripts up- or down-regulated at the experiment-wide threshold of p<10-5 (Fig 4A), but only two transcripts more highly expressed in Buenaventura and none in Cali (Fig 4B). Approximately 50 genes show more than 2-fold up-regulation at Diagnosis relative to Baseline yet are less significant than many of the orange-colored genes (Fig 4A, green-colored genes). The reason is that these genes are even more highly upregulated in a subset of individuals, namely the naïve (Cali) volunteers. In fact, 175 genes show a significant timepoint-by-population interaction effect at p<0.05 (ANOVA, Fig 4C; S6 Table). These are represented in the heat-map in Fig 4C, showing two-way hierarchical clustering of transcripts in samples, two-thirds of the genes are actually down regulated at Diagnosis day (red sample labels, top). Interestingly, there was a marked distinction between the two timepoints (Fig 4C) in the sense that the Baseline samples were intermingled with respect to whether they were from the naïve or semi-immune populations, whereas the Diagnosis ones showed a near-perfect separation with respect to pre-immune exposure (bootstrap support 78%). In other words, most of the genes showing an interaction effect were more strongly up- or down regulated in the naïve than semi-immune individuals. An exception was a Baseline sample from a Cali volunteer (number 306), which clustered with the Diagnosis set but still showed a robust response to malaria infection along with moderate thrombocytopenia and leukopenia, as did Cali 310 who was not an outlier.)


Transcription Profiling of Malaria-Naïve and Semi-immune Colombian Volunteers in a Plasmodium vivax Sporozoite Challenge.

Rojas-Peña ML, Vallejo A, Herrera S, Gibson G, Arévalo-Herrera M - PLoS Negl Trop Dis (2015)

Differential expression in whole-blood RNASeq data set.Volcano plots of statistical significance vs. magnitude of differential expression for the contrasts between timepoint in (A) and by location in (B), highlighting significant genes for the timepoint effect in orange. Y axis shows the significance as–log10 P value, and x-axis shows the magnitude of the difference log2 units (highlighting significant genes at NLP>5 for the timepoint contrast). (C) Heat map showing two-way hierarchical clustering of transcripts (columns) in each sample (rows) of 175 genes that show a significant timepoint-by-location interaction effect at p<0.05. Red cells indicate high expression, blue low, gray intermediate. Green sample labels represent Baseline (Pre-challenge) and red labels represent Diagnosis day, solid points represent Cali (N, naïve), and open circles represent Buenaventura (S, semi-immune). Approximately unbiased bootstrap support (AU) values computed with pvclust are indicated beside three deep nodes.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4526565&req=5

pntd.0003978.g004: Differential expression in whole-blood RNASeq data set.Volcano plots of statistical significance vs. magnitude of differential expression for the contrasts between timepoint in (A) and by location in (B), highlighting significant genes for the timepoint effect in orange. Y axis shows the significance as–log10 P value, and x-axis shows the magnitude of the difference log2 units (highlighting significant genes at NLP>5 for the timepoint contrast). (C) Heat map showing two-way hierarchical clustering of transcripts (columns) in each sample (rows) of 175 genes that show a significant timepoint-by-location interaction effect at p<0.05. Red cells indicate high expression, blue low, gray intermediate. Green sample labels represent Baseline (Pre-challenge) and red labels represent Diagnosis day, solid points represent Cali (N, naïve), and open circles represent Buenaventura (S, semi-immune). Approximately unbiased bootstrap support (AU) values computed with pvclust are indicated beside three deep nodes.
Mentions: Consistent with timepoint rather than population explaining a large proportion of the variance, gene-specific differential expression analysis revealed more than 250 transcripts up- or down-regulated at the experiment-wide threshold of p<10-5 (Fig 4A), but only two transcripts more highly expressed in Buenaventura and none in Cali (Fig 4B). Approximately 50 genes show more than 2-fold up-regulation at Diagnosis relative to Baseline yet are less significant than many of the orange-colored genes (Fig 4A, green-colored genes). The reason is that these genes are even more highly upregulated in a subset of individuals, namely the naïve (Cali) volunteers. In fact, 175 genes show a significant timepoint-by-population interaction effect at p<0.05 (ANOVA, Fig 4C; S6 Table). These are represented in the heat-map in Fig 4C, showing two-way hierarchical clustering of transcripts in samples, two-thirds of the genes are actually down regulated at Diagnosis day (red sample labels, top). Interestingly, there was a marked distinction between the two timepoints (Fig 4C) in the sense that the Baseline samples were intermingled with respect to whether they were from the naïve or semi-immune populations, whereas the Diagnosis ones showed a near-perfect separation with respect to pre-immune exposure (bootstrap support 78%). In other words, most of the genes showing an interaction effect were more strongly up- or down regulated in the naïve than semi-immune individuals. An exception was a Baseline sample from a Cali volunteer (number 306), which clustered with the Diagnosis set but still showed a robust response to malaria infection along with moderate thrombocytopenia and leukopenia, as did Cali 310 who was not an outlier.)

Bottom Line: There was no evidence for transcriptional changes prior to the appearance of blood stage parasites at day 12 or 13, at which time there was a strong interferon response and, unexpectedly, down-regulation of transcripts related to inflammation and innate immunity.This differential expression was confirmed with RNASeq, which also suggested perturbations of aspects of T cell function and erythropoiesis.Despite differences in clinical symptoms between the semi-immune and malaria naïve individuals, only subtle differences in their transcriptomes were observed, although 175 genes showed significantly greater induction or repression in the naïve volunteers from Cali.

View Article: PubMed Central - PubMed

Affiliation: Center for Integrative Genomics, School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America.

ABSTRACT

Background: Continued exposure to malaria-causing parasites in endemic regions of malaria induces significant levels of acquired immunity in adult individuals. A better understanding of the transcriptional basis for this acquired immunological response may provide insight into how the immune system can be boosted during vaccination, and into why infected individuals differ in symptomology.

Methodology/principal findings: Peripheral blood gene expression profiles of 9 semi-immune volunteers from a Plasmodium vivax malaria prevalent region (Buenaventura, Colombia) were compared to those of 7 naïve individuals from a region with no reported transmission of malaria (Cali, Colombia) after a controlled infection mosquito bite challenge with P. vivax. A Fluidigm nanoscale quantitative RT-PCR array was used to survey altered expression of 96 blood informative transcripts at 7 timepoints after controlled infection, and RNASeq was used to contrast pre-infection and early parasitemia timepoints. There was no evidence for transcriptional changes prior to the appearance of blood stage parasites at day 12 or 13, at which time there was a strong interferon response and, unexpectedly, down-regulation of transcripts related to inflammation and innate immunity. This differential expression was confirmed with RNASeq, which also suggested perturbations of aspects of T cell function and erythropoiesis. Despite differences in clinical symptoms between the semi-immune and malaria naïve individuals, only subtle differences in their transcriptomes were observed, although 175 genes showed significantly greater induction or repression in the naïve volunteers from Cali.

Conclusion/significance: Gene expression profiling of whole blood reveals the type and duration of the immune response to P. vivax infection, and highlights a subset of genes that may mediate adaptive immunity.

No MeSH data available.


Related in: MedlinePlus