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Chimeric peptide constructs comprising linear B-cell epitopes: application to the serodiagnosis of infectious diseases.

Lu Y, Li Z, Teng H, Xu H, Qi S, He J, Gu D, Chen Q, Ma H - Sci Rep (2015)

Bottom Line: However, the long-predicted diagnostic value of epitopes has not been realized.Using DEIFS for malaria, we identified 6 epitopes from 8 peptides and combined them into 3 chimeric peptide constructs.In addition to applications in diagnosis, DEIFS could also be used in the diagnosis of virus and bacterium infections, discovery of vaccine candidates, evaluation of vaccine potency, and study of disease progression.

View Article: PubMed Central - PubMed

Affiliation: Nano-Bio-Chem Centre, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123, P. R. China.

ABSTRACT
Linear B-cell epitopes are ideal biomarkers for the serodiagnosis of infectious diseases. However, the long-predicted diagnostic value of epitopes has not been realized. Here, we demonstrated a method, diagnostic epitopes in four steps (DEIFS), that delivers a combination of epitopes for the serodiagnosis of infectious diseases with a high success rate. Using DEIFS for malaria, we identified 6 epitopes from 8 peptides and combined them into 3 chimeric peptide constructs. Along with 4 other peptides, we developed a rapid diagnostic test (RDT), which is able to differentiate Plasmodium falciparum (P. falciparum) from Plasmodium vivax (P. vivax) infections with 95.6% overall sensitivity and 99.1% overall specificity. In addition to applications in diagnosis, DEIFS could also be used in the diagnosis of virus and bacterium infections, discovery of vaccine candidates, evaluation of vaccine potency, and study of disease progression.

No MeSH data available.


Related in: MedlinePlus

Three-mode analysis and two round screening strategy for ECPs identification.(a) For instance, 010, 011 and 111 modes were, respectively, indicated with red, blue and green boxes. (b) A peptide with the 010 mode or 011/110 mode indicated a single epitope in the 30 aa peptide. A peptide with the 111 mode indicated that the protein contains more than a single epitope in the 30 aa peptide. (c) For each serum, each peptide obtained an SNR value after seroscreening (as an example, protein Px was resolved into 4 peptides and reacted with 4 serums, which are Se1, Se2, Se3 and Se4). The SNR matrix of protein Px was converted to (d) 1/0 matrix at the beginning of the three-mode analysis. (e) After modes identification, the 1/0 matrix was converted to (f) a mode type matrix, which was then (g) statistically analyzed to (h) visualize treatment. The line chart with dots represents coverage of 3 different modes, which were 010 (h, red line), 011/110 (h, blue line) and 111 (h, green line). The area chart (h, gray area) represents the total coverage of all 3 modes. The three-mode analysis revealed epitope containing peptides (ECPs). The three-mode analysis of P28 (i), P18 (j) and P07 (k) are typical instances revealing ECPs from three different modes. Selected ECPs were subjected to a second-round screening (15/12 aa) for epitope pinning. Different modes showed different epitope locations: type 010 in the middle (l), type 011/110 in the common parts of two adjacent 30 aa peptides (m) and type 111 represented a series of epitopes repeatedly located in 3 consecutive peptides (n). The identified epitope sequences were selected to make chimeric peptides.
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f3: Three-mode analysis and two round screening strategy for ECPs identification.(a) For instance, 010, 011 and 111 modes were, respectively, indicated with red, blue and green boxes. (b) A peptide with the 010 mode or 011/110 mode indicated a single epitope in the 30 aa peptide. A peptide with the 111 mode indicated that the protein contains more than a single epitope in the 30 aa peptide. (c) For each serum, each peptide obtained an SNR value after seroscreening (as an example, protein Px was resolved into 4 peptides and reacted with 4 serums, which are Se1, Se2, Se3 and Se4). The SNR matrix of protein Px was converted to (d) 1/0 matrix at the beginning of the three-mode analysis. (e) After modes identification, the 1/0 matrix was converted to (f) a mode type matrix, which was then (g) statistically analyzed to (h) visualize treatment. The line chart with dots represents coverage of 3 different modes, which were 010 (h, red line), 011/110 (h, blue line) and 111 (h, green line). The area chart (h, gray area) represents the total coverage of all 3 modes. The three-mode analysis revealed epitope containing peptides (ECPs). The three-mode analysis of P28 (i), P18 (j) and P07 (k) are typical instances revealing ECPs from three different modes. Selected ECPs were subjected to a second-round screening (15/12 aa) for epitope pinning. Different modes showed different epitope locations: type 010 in the middle (l), type 011/110 in the common parts of two adjacent 30 aa peptides (m) and type 111 represented a series of epitopes repeatedly located in 3 consecutive peptides (n). The identified epitope sequences were selected to make chimeric peptides.

Mentions: The first round of seroscreening used peptides of 30 amino acid (aa) in length with 15 aa overlapping (abbreviated as 30/15 aa thereafter). A heat map was obtained by converting the resulting SNR value to grayscale (Fig. 2b–d). Significance Analysis of Microarray (SAM), which is widely used in DNA microarray analysis, performed poorly for the peptide microarrays when used directly on the large-scale original data of the peptide microarrays (Extended Data Table 3). Here we introduced a “three-mode analysis” method (Fig. 3), which facilitated the identification of epitope containing peptides (ECPs).


Chimeric peptide constructs comprising linear B-cell epitopes: application to the serodiagnosis of infectious diseases.

Lu Y, Li Z, Teng H, Xu H, Qi S, He J, Gu D, Chen Q, Ma H - Sci Rep (2015)

Three-mode analysis and two round screening strategy for ECPs identification.(a) For instance, 010, 011 and 111 modes were, respectively, indicated with red, blue and green boxes. (b) A peptide with the 010 mode or 011/110 mode indicated a single epitope in the 30 aa peptide. A peptide with the 111 mode indicated that the protein contains more than a single epitope in the 30 aa peptide. (c) For each serum, each peptide obtained an SNR value after seroscreening (as an example, protein Px was resolved into 4 peptides and reacted with 4 serums, which are Se1, Se2, Se3 and Se4). The SNR matrix of protein Px was converted to (d) 1/0 matrix at the beginning of the three-mode analysis. (e) After modes identification, the 1/0 matrix was converted to (f) a mode type matrix, which was then (g) statistically analyzed to (h) visualize treatment. The line chart with dots represents coverage of 3 different modes, which were 010 (h, red line), 011/110 (h, blue line) and 111 (h, green line). The area chart (h, gray area) represents the total coverage of all 3 modes. The three-mode analysis revealed epitope containing peptides (ECPs). The three-mode analysis of P28 (i), P18 (j) and P07 (k) are typical instances revealing ECPs from three different modes. Selected ECPs were subjected to a second-round screening (15/12 aa) for epitope pinning. Different modes showed different epitope locations: type 010 in the middle (l), type 011/110 in the common parts of two adjacent 30 aa peptides (m) and type 111 represented a series of epitopes repeatedly located in 3 consecutive peptides (n). The identified epitope sequences were selected to make chimeric peptides.
© Copyright Policy - open-access
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4543967&req=5

f3: Three-mode analysis and two round screening strategy for ECPs identification.(a) For instance, 010, 011 and 111 modes were, respectively, indicated with red, blue and green boxes. (b) A peptide with the 010 mode or 011/110 mode indicated a single epitope in the 30 aa peptide. A peptide with the 111 mode indicated that the protein contains more than a single epitope in the 30 aa peptide. (c) For each serum, each peptide obtained an SNR value after seroscreening (as an example, protein Px was resolved into 4 peptides and reacted with 4 serums, which are Se1, Se2, Se3 and Se4). The SNR matrix of protein Px was converted to (d) 1/0 matrix at the beginning of the three-mode analysis. (e) After modes identification, the 1/0 matrix was converted to (f) a mode type matrix, which was then (g) statistically analyzed to (h) visualize treatment. The line chart with dots represents coverage of 3 different modes, which were 010 (h, red line), 011/110 (h, blue line) and 111 (h, green line). The area chart (h, gray area) represents the total coverage of all 3 modes. The three-mode analysis revealed epitope containing peptides (ECPs). The three-mode analysis of P28 (i), P18 (j) and P07 (k) are typical instances revealing ECPs from three different modes. Selected ECPs were subjected to a second-round screening (15/12 aa) for epitope pinning. Different modes showed different epitope locations: type 010 in the middle (l), type 011/110 in the common parts of two adjacent 30 aa peptides (m) and type 111 represented a series of epitopes repeatedly located in 3 consecutive peptides (n). The identified epitope sequences were selected to make chimeric peptides.
Mentions: The first round of seroscreening used peptides of 30 amino acid (aa) in length with 15 aa overlapping (abbreviated as 30/15 aa thereafter). A heat map was obtained by converting the resulting SNR value to grayscale (Fig. 2b–d). Significance Analysis of Microarray (SAM), which is widely used in DNA microarray analysis, performed poorly for the peptide microarrays when used directly on the large-scale original data of the peptide microarrays (Extended Data Table 3). Here we introduced a “three-mode analysis” method (Fig. 3), which facilitated the identification of epitope containing peptides (ECPs).

Bottom Line: However, the long-predicted diagnostic value of epitopes has not been realized.Using DEIFS for malaria, we identified 6 epitopes from 8 peptides and combined them into 3 chimeric peptide constructs.In addition to applications in diagnosis, DEIFS could also be used in the diagnosis of virus and bacterium infections, discovery of vaccine candidates, evaluation of vaccine potency, and study of disease progression.

View Article: PubMed Central - PubMed

Affiliation: Nano-Bio-Chem Centre, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123, P. R. China.

ABSTRACT
Linear B-cell epitopes are ideal biomarkers for the serodiagnosis of infectious diseases. However, the long-predicted diagnostic value of epitopes has not been realized. Here, we demonstrated a method, diagnostic epitopes in four steps (DEIFS), that delivers a combination of epitopes for the serodiagnosis of infectious diseases with a high success rate. Using DEIFS for malaria, we identified 6 epitopes from 8 peptides and combined them into 3 chimeric peptide constructs. Along with 4 other peptides, we developed a rapid diagnostic test (RDT), which is able to differentiate Plasmodium falciparum (P. falciparum) from Plasmodium vivax (P. vivax) infections with 95.6% overall sensitivity and 99.1% overall specificity. In addition to applications in diagnosis, DEIFS could also be used in the diagnosis of virus and bacterium infections, discovery of vaccine candidates, evaluation of vaccine potency, and study of disease progression.

No MeSH data available.


Related in: MedlinePlus