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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

Brief illustration of finding diagnostic epitopes in four steps (DEIFS).Motivated by the intrinsic limitations of protein biomarkers (a), epitope based diagnoses were proposed and realized by DEIFS (b): 1. Library construction, protein candidates were selected and translated to 30/15 aa overlapped peptide library; 2.Two-round screening, 30/15 aa overlapped peptide library was screened by training group serum and was narrowed by three-mode analysis. Selected peptides were subjected to 15/12 aa overlapped second round screening for epitope pinning; 3. Optimization of epitopes combination. Peptides were further narrowed by SAM and Cluster algorithm and were optimized for diagnosis by the Dsum principle; 4. Validation, chimeric peptides were created from diagnostic ECPs for rapid diagnostic testing. The whole process could be performed in three months and could shift between high content and high density modes according to the need. Figure 2, 3, 4, 5 will give more details of each of the four steps. (c) Performance of the epitope diagnosis based on DEIFS. Sensitivity and specificity at 94.7% and 99.1%, respectively, were achieved.
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f1: Brief illustration of finding diagnostic epitopes in four steps (DEIFS).Motivated by the intrinsic limitations of protein biomarkers (a), epitope based diagnoses were proposed and realized by DEIFS (b): 1. Library construction, protein candidates were selected and translated to 30/15 aa overlapped peptide library; 2.Two-round screening, 30/15 aa overlapped peptide library was screened by training group serum and was narrowed by three-mode analysis. Selected peptides were subjected to 15/12 aa overlapped second round screening for epitope pinning; 3. Optimization of epitopes combination. Peptides were further narrowed by SAM and Cluster algorithm and were optimized for diagnosis by the Dsum principle; 4. Validation, chimeric peptides were created from diagnostic ECPs for rapid diagnostic testing. The whole process could be performed in three months and could shift between high content and high density modes according to the need. Figure 2, 3, 4, 5 will give more details of each of the four steps. (c) Performance of the epitope diagnosis based on DEIFS. Sensitivity and specificity at 94.7% and 99.1%, respectively, were achieved.

Mentions: For diseases of unknown causes (e.g., autoimmune diseases), proteomics1234 are often involved in searching for biomarkers, and random peptide/peptoid microarrays have also achieved occasional success256. Conversely, for infectious diseases caused by a parasite, bacteria or virus it is clear where to look for biomarkers: either antigens from pathogens or antibodies in serum. Although parasitological detection (e.g., thick smears or PCR) is still the gold standard for the diagnosis of infectious disease, the high technical requirements of the operators and the time-consuming process make it unsuitable for large-scale disease surveillance. The protein biomarker-based rapid diagnostic test (RDT) is more commonly used. The diagnosis of P. falciparum malaria was typically based on the detection of a P. falciparum-specific antigen, namely, the histidine rich protein II (P. falciparum HRPII)78 with matched monoclonal antibodies (mAbs; Fig. 1a). This traditional strategy relies heavily on the discovery of species-specific antigens, which could be a long and costly journey full of uncertainties18910. Furthermore, both genetic and immunogenic variation could cause false negatives for such antigen-based immunoassays. For example, approximately 5% of P. falciparum does not naturally express the P. falciparum HRPII gene811. We identified that 7.6% of patients actually carry HRPII antibodies (Extended Data Fig. 1), and they are also negative for HRPII detection, which leads to a total of 12.6% intrinsic false-negative results. Another diagnostic biomarker of malaria, lactate dehydrogenase, was also found to have neutralizing antibodies (Extended Data Fig. 1), implying that all protein biomarkers face such intrinsic false-negative problems due to the existence of neutralizing antibodies.


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)

Brief illustration of finding diagnostic epitopes in four steps (DEIFS).Motivated by the intrinsic limitations of protein biomarkers (a), epitope based diagnoses were proposed and realized by DEIFS (b): 1. Library construction, protein candidates were selected and translated to 30/15 aa overlapped peptide library; 2.Two-round screening, 30/15 aa overlapped peptide library was screened by training group serum and was narrowed by three-mode analysis. Selected peptides were subjected to 15/12 aa overlapped second round screening for epitope pinning; 3. Optimization of epitopes combination. Peptides were further narrowed by SAM and Cluster algorithm and were optimized for diagnosis by the Dsum principle; 4. Validation, chimeric peptides were created from diagnostic ECPs for rapid diagnostic testing. The whole process could be performed in three months and could shift between high content and high density modes according to the need. Figure 2, 3, 4, 5 will give more details of each of the four steps. (c) Performance of the epitope diagnosis based on DEIFS. Sensitivity and specificity at 94.7% and 99.1%, respectively, were achieved.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f1: Brief illustration of finding diagnostic epitopes in four steps (DEIFS).Motivated by the intrinsic limitations of protein biomarkers (a), epitope based diagnoses were proposed and realized by DEIFS (b): 1. Library construction, protein candidates were selected and translated to 30/15 aa overlapped peptide library; 2.Two-round screening, 30/15 aa overlapped peptide library was screened by training group serum and was narrowed by three-mode analysis. Selected peptides were subjected to 15/12 aa overlapped second round screening for epitope pinning; 3. Optimization of epitopes combination. Peptides were further narrowed by SAM and Cluster algorithm and were optimized for diagnosis by the Dsum principle; 4. Validation, chimeric peptides were created from diagnostic ECPs for rapid diagnostic testing. The whole process could be performed in three months and could shift between high content and high density modes according to the need. Figure 2, 3, 4, 5 will give more details of each of the four steps. (c) Performance of the epitope diagnosis based on DEIFS. Sensitivity and specificity at 94.7% and 99.1%, respectively, were achieved.
Mentions: For diseases of unknown causes (e.g., autoimmune diseases), proteomics1234 are often involved in searching for biomarkers, and random peptide/peptoid microarrays have also achieved occasional success256. Conversely, for infectious diseases caused by a parasite, bacteria or virus it is clear where to look for biomarkers: either antigens from pathogens or antibodies in serum. Although parasitological detection (e.g., thick smears or PCR) is still the gold standard for the diagnosis of infectious disease, the high technical requirements of the operators and the time-consuming process make it unsuitable for large-scale disease surveillance. The protein biomarker-based rapid diagnostic test (RDT) is more commonly used. The diagnosis of P. falciparum malaria was typically based on the detection of a P. falciparum-specific antigen, namely, the histidine rich protein II (P. falciparum HRPII)78 with matched monoclonal antibodies (mAbs; Fig. 1a). This traditional strategy relies heavily on the discovery of species-specific antigens, which could be a long and costly journey full of uncertainties18910. Furthermore, both genetic and immunogenic variation could cause false negatives for such antigen-based immunoassays. For example, approximately 5% of P. falciparum does not naturally express the P. falciparum HRPII gene811. We identified that 7.6% of patients actually carry HRPII antibodies (Extended Data Fig. 1), and they are also negative for HRPII detection, which leads to a total of 12.6% intrinsic false-negative results. Another diagnostic biomarker of malaria, lactate dehydrogenase, was also found to have neutralizing antibodies (Extended Data Fig. 1), implying that all protein biomarkers face such intrinsic false-negative problems due to the existence of neutralizing antibodies.

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