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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

Optimization of the epitope combination.(a) SAM plot of 153 selected peptides from P. falciparum infected and healthy samples. A total of 72 peptides with significantly different SNR in infected and healthy samples are shown in red circles. (b) The heat map of these 72 peptides was clustered, and 8 peptides were selected from each cluster. (c) Violin plot of 3 selected peptides (P25-040, P23-027, and P34-088). (d) ROC curve of each of the 3 peptides and all 8 peptides. Although these peptides have high specificity (99.2%, 93.6%, and 98.0%), none has satisfactory sensitivity (66.5%, 79.9%, and 75.4%).
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f4: Optimization of the epitope combination.(a) SAM plot of 153 selected peptides from P. falciparum infected and healthy samples. A total of 72 peptides with significantly different SNR in infected and healthy samples are shown in red circles. (b) The heat map of these 72 peptides was clustered, and 8 peptides were selected from each cluster. (c) Violin plot of 3 selected peptides (P25-040, P23-027, and P34-088). (d) ROC curve of each of the 3 peptides and all 8 peptides. Although these peptides have high specificity (99.2%, 93.6%, and 98.0%), none has satisfactory sensitivity (66.5%, 79.9%, and 75.4%).

Mentions: After reducing 2038 peptides to 153 ECPs by the three-mode analysis (Extended Data Table 3), SAM succeeded in extracting peptides that show different responsive rates for different serum subgroups (Fig. 4a): a total of 72 ECPs were selected as highly responsive peptides in P. falciparum-positive samples and were clustered (Fig. 4b). ECPs with the highest coverage of positive serum from each cluster group were selected. For further optimization, we calculated the total coverage of these ECPs. Eight ECPs (Table 1) were finally identified as diagnostic candidates. The 8 selected ECPs from multiple proteins performed poorly based on the traditional SNR cutoff value (Fig. 4c,d and Extended Data Figs 4 and 5 and Table 4), where SNR ≥ 2 indicated a positive result. None of the 8 ECPs can provide a satisfactory sensitivity (>90%) of diagnosis. Only 2 of the 8 ECPs could achieve 100% specificity, which was attributed to mimotopes or molecular mimics due to the complexity of the antibodies in the serum. If we used the traditional strategy of multiplexing, i.e., any one of the 8 ECPs being positive indicates that the serum is positive21, one would find an increased sensitivity of 97.2% but a poor specificity of 86.4%. We believe that this contradiction between sensitivity and specificity has hindered the realization of the long-predicted diagnostic value of epitopes. A binarization/digitization strategy was developed to enable the 8 selected ECPs to achieve diagnostic function, a solution for the third and fourth problems.


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)

Optimization of the epitope combination.(a) SAM plot of 153 selected peptides from P. falciparum infected and healthy samples. A total of 72 peptides with significantly different SNR in infected and healthy samples are shown in red circles. (b) The heat map of these 72 peptides was clustered, and 8 peptides were selected from each cluster. (c) Violin plot of 3 selected peptides (P25-040, P23-027, and P34-088). (d) ROC curve of each of the 3 peptides and all 8 peptides. Although these peptides have high specificity (99.2%, 93.6%, and 98.0%), none has satisfactory sensitivity (66.5%, 79.9%, and 75.4%).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4543967&req=5

f4: Optimization of the epitope combination.(a) SAM plot of 153 selected peptides from P. falciparum infected and healthy samples. A total of 72 peptides with significantly different SNR in infected and healthy samples are shown in red circles. (b) The heat map of these 72 peptides was clustered, and 8 peptides were selected from each cluster. (c) Violin plot of 3 selected peptides (P25-040, P23-027, and P34-088). (d) ROC curve of each of the 3 peptides and all 8 peptides. Although these peptides have high specificity (99.2%, 93.6%, and 98.0%), none has satisfactory sensitivity (66.5%, 79.9%, and 75.4%).
Mentions: After reducing 2038 peptides to 153 ECPs by the three-mode analysis (Extended Data Table 3), SAM succeeded in extracting peptides that show different responsive rates for different serum subgroups (Fig. 4a): a total of 72 ECPs were selected as highly responsive peptides in P. falciparum-positive samples and were clustered (Fig. 4b). ECPs with the highest coverage of positive serum from each cluster group were selected. For further optimization, we calculated the total coverage of these ECPs. Eight ECPs (Table 1) were finally identified as diagnostic candidates. The 8 selected ECPs from multiple proteins performed poorly based on the traditional SNR cutoff value (Fig. 4c,d and Extended Data Figs 4 and 5 and Table 4), where SNR ≥ 2 indicated a positive result. None of the 8 ECPs can provide a satisfactory sensitivity (>90%) of diagnosis. Only 2 of the 8 ECPs could achieve 100% specificity, which was attributed to mimotopes or molecular mimics due to the complexity of the antibodies in the serum. If we used the traditional strategy of multiplexing, i.e., any one of the 8 ECPs being positive indicates that the serum is positive21, one would find an increased sensitivity of 97.2% but a poor specificity of 86.4%. We believe that this contradiction between sensitivity and specificity has hindered the realization of the long-predicted diagnostic value of epitopes. A binarization/digitization strategy was developed to enable the 8 selected ECPs to achieve diagnostic function, a solution for the third and fourth problems.

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