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Stimulation of Innate and Adaptive Immunity by Using Filamentous Bacteriophage fd Targeted to DEC-205.

D'Apice L, Costa V, Sartorius R, Trovato M, Aprile M, De Berardinis P - J Immunol Res (2015)

Bottom Line: The filamentous bacteriophage fd, codisplaying antigenic determinants and a single chain antibody fragment directed against the dendritic cell receptor DEC-205, is a promising vaccine candidate for its safety and its ability to elicit innate and adaptive immune response in absence of adjuvants.By using a system vaccinology approach based on RNA-Sequencing (RNA-Seq) analysis, we describe a relevant gene modulation in dendritic cells pulsed with anti-DEC-205 bacteriophages fd.RNA-Seq data analysis indicates that the bacteriophage fd virions are sensed as a pathogen by dendritic cells; they activate the danger receptors that trigger an innate immune response and thus confer a strong adjuvanticity that is needed to obtain a long-lasting adaptive immune response.

View Article: PubMed Central - PubMed

Affiliation: Institute of Protein Biochemistry (IBP), National Council of Research, 80131 Naples, Italy.

ABSTRACT
The filamentous bacteriophage fd, codisplaying antigenic determinants and a single chain antibody fragment directed against the dendritic cell receptor DEC-205, is a promising vaccine candidate for its safety and its ability to elicit innate and adaptive immune response in absence of adjuvants. By using a system vaccinology approach based on RNA-Sequencing (RNA-Seq) analysis, we describe a relevant gene modulation in dendritic cells pulsed with anti-DEC-205 bacteriophages fd. RNA-Seq data analysis indicates that the bacteriophage fd virions are sensed as a pathogen by dendritic cells; they activate the danger receptors that trigger an innate immune response and thus confer a strong adjuvanticity that is needed to obtain a long-lasting adaptive immune response.

No MeSH data available.


Related in: MedlinePlus

RNA-Seq data analysis of BMDC in presence and absence of fdsc-αDEC. MA plot of expressed genes (a) and pie chart (b) of the differentially expressed genes classified according to their FDR value. Genes with FDR < 0.0005 and fold change >±2 are shown in blue. For these genes, pathway analysis is reported in (c).
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fig3: RNA-Seq data analysis of BMDC in presence and absence of fdsc-αDEC. MA plot of expressed genes (a) and pie chart (b) of the differentially expressed genes classified according to their FDR value. Genes with FDR < 0.0005 and fold change >±2 are shown in blue. For these genes, pathway analysis is reported in (c).

Mentions: To gain insights into the molecular mechanisms through which fdsc–αDEC induces a strong cell-mediated immune response, we used RNA-Sequencing to analyze the transcriptional profiles of BMDCs in vitro challenged with fdsc–αDEC phage particles. The gene expression pattern of these cells was compared to the one of control untreated BMDCs (i.e., cells treated only with PBS). Two technical replicates for each condition were performed. Approximately 55 million reads (95% of them uniquely mapped on the reference genome) per replicate were produced. Expression values for both control and fdsc-αDEC-treated DCs were measured as FPKM (fragments per kilobase of transcript per million mapped reads). Technical replicates revealed a very highly correlation. Using RNA-Sequencing we could simultaneously measure gene expression levels of (virtually) all genes expressed in mouse DCs. Setting an arbitrary threshold (FPKM = 1) for gene expression, we found about ten thousand genes expressed at significant levels in both conditions. Then, we compared gene expression levels between the two conditions. This analysis revealed that approximately 3800 genes (FDR < 0.01) were differentially expressed (DE) in DCs after exposure to fdsc-αDEC compared to control cells (Figure 3(a)). As reported in Figures 3(a) and 3(b), we selected different FDR intervals. Genes with a FDR value between 0.05 and 0.005 are classified in the first group and represent the 30% of the DE genes (in red in Figures 3(a) and 3(b)); the second group includes the 18% of the total DE genes with FDR between 0.005 and 0.0005 (in green in Figures 3(a) and 3(b)), while the most significant DE genes, with FDR under 0.0005, represent the 52% of the total DE genes (in grey in Figures 3(a) and 3(b)). Among them, we further selected DE genes with a fold change (FC) >±2 in DCs exposed to fdsc-αDEC versus control cells. All further analyses were performed on this group of DE genes named DEG (differentially expressed Genes, shown in blue in Figures 3(a) and 3(b)). Most of these DEG were significantly upregulated in DCs upon treatment with the fdsc-αDEC, whereas only very few of them were downmodulated. To understand if these genes with a significant upregulation were related to specific cells function and/or pathways, we interrogated the Database for Annotation, Visualization and Integrated Discovery (DAVID). The most enriched biological pathways (using KEGG database) are shown in Figure 3(c). Interestingly, the exposure of DCs to fdsc-αDEC significantly upregulated many genes involved in inflammatory pathways linked to innate immunity.


Stimulation of Innate and Adaptive Immunity by Using Filamentous Bacteriophage fd Targeted to DEC-205.

D'Apice L, Costa V, Sartorius R, Trovato M, Aprile M, De Berardinis P - J Immunol Res (2015)

RNA-Seq data analysis of BMDC in presence and absence of fdsc-αDEC. MA plot of expressed genes (a) and pie chart (b) of the differentially expressed genes classified according to their FDR value. Genes with FDR < 0.0005 and fold change >±2 are shown in blue. For these genes, pathway analysis is reported in (c).
© Copyright Policy - open-access
Related In: Results  -  Collection

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fig3: RNA-Seq data analysis of BMDC in presence and absence of fdsc-αDEC. MA plot of expressed genes (a) and pie chart (b) of the differentially expressed genes classified according to their FDR value. Genes with FDR < 0.0005 and fold change >±2 are shown in blue. For these genes, pathway analysis is reported in (c).
Mentions: To gain insights into the molecular mechanisms through which fdsc–αDEC induces a strong cell-mediated immune response, we used RNA-Sequencing to analyze the transcriptional profiles of BMDCs in vitro challenged with fdsc–αDEC phage particles. The gene expression pattern of these cells was compared to the one of control untreated BMDCs (i.e., cells treated only with PBS). Two technical replicates for each condition were performed. Approximately 55 million reads (95% of them uniquely mapped on the reference genome) per replicate were produced. Expression values for both control and fdsc-αDEC-treated DCs were measured as FPKM (fragments per kilobase of transcript per million mapped reads). Technical replicates revealed a very highly correlation. Using RNA-Sequencing we could simultaneously measure gene expression levels of (virtually) all genes expressed in mouse DCs. Setting an arbitrary threshold (FPKM = 1) for gene expression, we found about ten thousand genes expressed at significant levels in both conditions. Then, we compared gene expression levels between the two conditions. This analysis revealed that approximately 3800 genes (FDR < 0.01) were differentially expressed (DE) in DCs after exposure to fdsc-αDEC compared to control cells (Figure 3(a)). As reported in Figures 3(a) and 3(b), we selected different FDR intervals. Genes with a FDR value between 0.05 and 0.005 are classified in the first group and represent the 30% of the DE genes (in red in Figures 3(a) and 3(b)); the second group includes the 18% of the total DE genes with FDR between 0.005 and 0.0005 (in green in Figures 3(a) and 3(b)), while the most significant DE genes, with FDR under 0.0005, represent the 52% of the total DE genes (in grey in Figures 3(a) and 3(b)). Among them, we further selected DE genes with a fold change (FC) >±2 in DCs exposed to fdsc-αDEC versus control cells. All further analyses were performed on this group of DE genes named DEG (differentially expressed Genes, shown in blue in Figures 3(a) and 3(b)). Most of these DEG were significantly upregulated in DCs upon treatment with the fdsc-αDEC, whereas only very few of them were downmodulated. To understand if these genes with a significant upregulation were related to specific cells function and/or pathways, we interrogated the Database for Annotation, Visualization and Integrated Discovery (DAVID). The most enriched biological pathways (using KEGG database) are shown in Figure 3(c). Interestingly, the exposure of DCs to fdsc-αDEC significantly upregulated many genes involved in inflammatory pathways linked to innate immunity.

Bottom Line: The filamentous bacteriophage fd, codisplaying antigenic determinants and a single chain antibody fragment directed against the dendritic cell receptor DEC-205, is a promising vaccine candidate for its safety and its ability to elicit innate and adaptive immune response in absence of adjuvants.By using a system vaccinology approach based on RNA-Sequencing (RNA-Seq) analysis, we describe a relevant gene modulation in dendritic cells pulsed with anti-DEC-205 bacteriophages fd.RNA-Seq data analysis indicates that the bacteriophage fd virions are sensed as a pathogen by dendritic cells; they activate the danger receptors that trigger an innate immune response and thus confer a strong adjuvanticity that is needed to obtain a long-lasting adaptive immune response.

View Article: PubMed Central - PubMed

Affiliation: Institute of Protein Biochemistry (IBP), National Council of Research, 80131 Naples, Italy.

ABSTRACT
The filamentous bacteriophage fd, codisplaying antigenic determinants and a single chain antibody fragment directed against the dendritic cell receptor DEC-205, is a promising vaccine candidate for its safety and its ability to elicit innate and adaptive immune response in absence of adjuvants. By using a system vaccinology approach based on RNA-Sequencing (RNA-Seq) analysis, we describe a relevant gene modulation in dendritic cells pulsed with anti-DEC-205 bacteriophages fd. RNA-Seq data analysis indicates that the bacteriophage fd virions are sensed as a pathogen by dendritic cells; they activate the danger receptors that trigger an innate immune response and thus confer a strong adjuvanticity that is needed to obtain a long-lasting adaptive immune response.

No MeSH data available.


Related in: MedlinePlus