Difference between revisions of "Part:BBa K3504011"
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<partinfo>BBa_K3504011 short</partinfo>
 
<partinfo>BBa_K3504011 short</partinfo>
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<p style="color:red">NOTICE: Parts  in our range for this season have been created as a part of our Phase I design of our project. These parts HAVE NOT been tested or characterized in the lab due to COVID-19-related precautionary measures. We have enriched our new parts pages with data from literature and results from our modeling and simulations. If you are intending on using this part or others in our range, please keep in mind these limitations and update these parts with data from your experimentation. Feel free to reach us at: igem.afcm@gmail.com for further inquiries.</p><br/>
 
==Part Description==
 
==Part Description==
 
A multi-epitope vaccine formed of highly expressed and specific TNBC neo-epitopes and specifically chosen according to egyptian population alleles which can work as a generalized vaccine and also personalized vaccine which would illicit an immune response specific to TNBC tumor cells
 
A multi-epitope vaccine formed of highly expressed and specific TNBC neo-epitopes and specifically chosen according to egyptian population alleles which can work as a generalized vaccine and also personalized vaccine which would illicit an immune response specific to TNBC tumor cells
 
==Usage==
 
==Usage==
−
Immune-modulating adjuvants and PADRE (Pan HLA-DR epitopes) sequence were added with epitopes sequence to enhance the immunogenicity. All the epitopes, adjuvants and PADRE sequence were joined by linkers. Through the help of the EAAAK linker at the start (to the MEV N-terminal) the adjuvant (45 amino acid long β-defensin) was bound. EAAK linker is found to increase stability and reduces connection with other protein areas with efficient detachment. There is a possibility that the immunogenicity could increase with an adjuvant. Based on the interactions’ compatibility epitopes were merged together sequentially with AAY and GPGPG linkers, respectively. In the construction of multiepitope vaccines AAY and GPGPG have a main task to prevent the production of junctional epitopes and also promote the immunization and the presentation of epitopes. CTL-epitopes were coupled with AAY linkers and HTL epitopes were coupled with GPGPG and that permitted proficient dissociation and epitope identification. A natural link was established among both innate and adaptive immune responses through Heat-shock proteins(hsp) by merging the idyllic properties of antigen carriage (chaperoning), targeting and activation of antigen-presenting cells (APC), including dendritic cells (DC). The uptake of hsp complexes by DC allows proficient capture and presentation of pathogen-specific antigens and also permits the mounting of a specific immune response by the production of CD4+ T-cell responses.  To improve the vaccine efficacy and potency non-natural pan DR (PADRE) 13 amino acid epitope (AKFVAAWTLKAAA) that induce CD4+ T-cells were also combined along with the adjuvants. Heat Shock Protein (hsp) was retrieved from the database to design a multi-epitope subunit vaccine containing a CTL, HTL and BCL epitopes of varying length. Heat-shock proteins (hsp) provide a natural link between innate and adaptive immune responses by combining the ideal properties of antigen carriage (chaperoning), targeting and activation of antigen-presenting cells (APC), including dendritic cells (DC). The uptake of hsp complexes by DC enables efficient capture and presentation of pathogen-specific antigens and the mounting of a specific immune response through the generation of CD4+ T-cell responses.
+
Immune-modulating adjuvants and PADRE (Pan HLA-DR epitopes) sequence were added with epitopes sequence to enhance the immunogenicity. All the epitopes, adjuvants and PADRE sequence were joined by linkers.  
  
−
References :
+
Through the help of the EAAAK linker at the start (to the MEV N-terminal) the adjuvant (45 amino acid long β-defensin) was bound. EAAK linker is found to increase stability and reduces connection with other protein areas with efficient detachment. There is a possibility that the immunogenicity could increase with an adjuvant. Based on the interactions’ compatibility epitopes were merged together sequentially with AAY and GPGPG linkers, respectively. In the construction of multiepitope vaccines AAY and GPGPG have a main task to prevent the production of junctional epitopes and also promote the immunization and the presentation of epitopes. CTL-epitopes were coupled with AAY linkers and HTL epitopes were coupled with GPGPG and that permitted proficient dissociation and epitope identification.(1), (5)
  
−
Tahir ul Qamar, Muhammad, et al. “Multiepitope-Based Subunit Vaccine Design and Evaluation against Respiratory Syncytial Virus Using Reverse Vaccinology Approach.” Vaccines, vol. 8, no. 2, 1 June 2020, p. 288, www.mdpi.com/2076-393X/8/2/288/htm, 10.3390/vaccines8020288. Accessed 22 Oct. 2020.
+
A natural link was established among both innate and adaptive immune responses through Heat-shock proteins(hsp) by merging the idyllic properties of antigen carriage (chaperoning), targeting and activation of antigen-presenting cells (APC), including dendritic cells (DC). The uptake of hsp complexes by DC allows proficient capture and presentation of pathogen-specific antigens and also permits the mounting of a specific immune response by the production of CD4+ T-cell responses.(7)
  
−
McNulty, Shaun, et al. “Heat-Shock Proteins as Dendritic Cell-Targeting Vaccines - Getting Warmer.” Immunology, vol. 139, no. 4, 2 July 2013, pp. 407–415, 10.1111/imm.12104. Accessed 18 Nov. 2019.
+
To improve the vaccine efficacy and potency non-natural pan DR (PADRE) 13 amino acid epitope (AKFVAAWTLKAAA) that induce CD4+ T-cells were also combined along with the adjuvants. Heat Shock Protein (hsp) was retrieved from the database to design a multi-epitope subunit vaccine containing a CTL, HTL and BCL epitopes of varying length.(6)
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+
−
Solanki, Vandana, et al. “Prioritization of Potential Vaccine Targets Using Comparative Proteomics and Designing of the Chimeric Multi-Epitope Vaccine against Pseudomonas Aeruginosa.” Scientific Reports, vol. 9, no. 1, 27 Mar. 2019, 10.1038/s41598-019-41496-4. Accessed 22 May 2020.
+
  
 
==Characterization==
 
==Characterization==
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==Improvements==
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[[Image:C-IMMSIM_1.png|thumb|right|Figure(1): Using C-IMMSIM simulation models to describe both Humoral and Cellular response of our predicted epitopes in our 1st proposed multi-epitope DNA vaccine for TNBC, Showing Antigen & Immunoglobulins level, B-cell Populations with various isotypes as well as Memory & Not Memory B-Cells and CD4 T-Cell Population & the regulatory T-Cells.]]
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[[Image:C-IMMSIM1.png|thumb|right|Figure(1): Shows the total count of B-cells, Memory B-cells, not Memory B-cells, B isotype IgM, B isotype IgG1 and B isotype IgG2.]]
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[[Image:C-IMMSIM_2.png|thumb|left|Figure(2): Using C-IMMSIM simulation models to describe both Humoral and Cellular response of our predicted epitopes in our 1st proposed multi-epitope DNA vaccine for TNBC,Showing the CD8 T-Cell Population and NKCs & DCs & MQs & Epithelial Populations.]]
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[[Image:C-IMMSIM1a.png|thumb|right|Figure(2): Shows the total count of Plasma B-Cells with its various isotypes.]]
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<br /><br /><br /><br /><br /><br /><br /><br /><br /><br /><br /><br /><br /><br /><br /><br /><br /><br /><br /><br /><br /><br /><br /><br /><br /><br /><br /><br /><br />
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==References==
 +
1-Tahir ul Qamar, Muhammad, et al. “Multiepitope-Based Subunit Vaccine Design and Evaluation against Respiratory Syncytial Virus Using Reverse Vaccinology Approach.” Vaccines, vol. 8, no. 2, 1 June 2020, p. 288, www.mdpi.com/2076-393X/8/2/288/htm, 10.3390/vaccines8020288. Accessed 22 Oct. 2020.
 +
 
 +
2-McNulty, Shaun, et al. “Heat-Shock Proteins as Dendritic Cell-Targeting Vaccines - Getting Warmer.” Immunology, vol. 139, no. 4, 2 July 2013, pp. 407–415, 10.1111/imm.12104. Accessed 18 Nov. 2019.
 +
 
 +
3-Solanki, Vandana, et al. “Prioritization of Potential Vaccine Targets Using Comparative Proteomics and Designing of the Chimeric Multi-Epitope Vaccine against Pseudomonas Aeruginosa.” Scientific Reports, vol. 9, no. 1, 27 Mar. 2019, 10.1038/s41598-019-41496-4. Accessed 22 May 2020.
 +
 
 +
4-Castiglione, F., &amp; Bernaschi, M. (2004, April 30). C-ImmSim∗ : Playing with the immune response. Retrieved October 26, 2020, from https://www.math.ucsd.edu/~helton/MTNSHISTORY/CONTENTS/2004LEUVEN/CDROM/papers/316.pdf
 +
 
 +
5-Tahir Ul Qamar, M., Shokat, Z., Muneer, I., Ashfaq, U., Javed, H., Anwar, F., . . . Saari, N. (2020, June 8). Multiepitope-Based Subunit Vaccine Design and Evaluation against Respiratory Syncytial Virus Using Reverse Vaccinology Approach. Retrieved October 26, 2020, from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7350008/
 +
 
 +
6-Ghaffari-Nazari, H., Tavakkol-Afshari, J., Jaafari, M., Tahaghoghi-Hajghorbani, S., Masoumi, E., &amp; Jalali, S. (2015, November 10). Improving Multi-Epitope Long Peptide Vaccine Potency by Using a Strategy that Enhances CD4+ T Help in BALB/c Mice. Retrieved October 26, 2020, from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4640540/
 +
 
 +
7-McNulty, S., Colaco, C., Blandford, L., Bailey, C., Baschieri, S., &amp; Todryk, S. (2013, August). Heat-shock proteins as dendritic cell-targeting vaccines--getting warmer. Retrieved October 26, 2020, from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3719058/
 +
 
 +
 
 
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<span class='h3bb'>Sequence and Features</span>
 
<span class='h3bb'>Sequence and Features</span>

Latest revision as of 20:15, 26 October 2020


Multi-Epitope TNBC Vaccine Version (1)

NOTICE: Parts in our range for this season have been created as a part of our Phase I design of our project. These parts HAVE NOT been tested or characterized in the lab due to COVID-19-related precautionary measures. We have enriched our new parts pages with data from literature and results from our modeling and simulations. If you are intending on using this part or others in our range, please keep in mind these limitations and update these parts with data from your experimentation. Feel free to reach us at: igem.afcm@gmail.com for further inquiries.


Part Description

A multi-epitope vaccine formed of highly expressed and specific TNBC neo-epitopes and specifically chosen according to egyptian population alleles which can work as a generalized vaccine and also personalized vaccine which would illicit an immune response specific to TNBC tumor cells

Usage

Immune-modulating adjuvants and PADRE (Pan HLA-DR epitopes) sequence were added with epitopes sequence to enhance the immunogenicity. All the epitopes, adjuvants and PADRE sequence were joined by linkers.

Through the help of the EAAAK linker at the start (to the MEV N-terminal) the adjuvant (45 amino acid long β-defensin) was bound. EAAK linker is found to increase stability and reduces connection with other protein areas with efficient detachment. There is a possibility that the immunogenicity could increase with an adjuvant. Based on the interactions’ compatibility epitopes were merged together sequentially with AAY and GPGPG linkers, respectively. In the construction of multiepitope vaccines AAY and GPGPG have a main task to prevent the production of junctional epitopes and also promote the immunization and the presentation of epitopes. CTL-epitopes were coupled with AAY linkers and HTL epitopes were coupled with GPGPG and that permitted proficient dissociation and epitope identification.(1), (5)

A natural link was established among both innate and adaptive immune responses through Heat-shock proteins(hsp) by merging the idyllic properties of antigen carriage (chaperoning), targeting and activation of antigen-presenting cells (APC), including dendritic cells (DC). The uptake of hsp complexes by DC allows proficient capture and presentation of pathogen-specific antigens and also permits the mounting of a specific immune response by the production of CD4+ T-cell responses.(7)

To improve the vaccine efficacy and potency non-natural pan DR (PADRE) 13 amino acid epitope (AKFVAAWTLKAAA) that induce CD4+ T-cells were also combined along with the adjuvants. Heat Shock Protein (hsp) was retrieved from the database to design a multi-epitope subunit vaccine containing a CTL, HTL and BCL epitopes of varying length.(6)

Characterization

Figure(1): Using C-IMMSIM simulation models to describe both Humoral and Cellular response of our predicted epitopes in our 1st proposed multi-epitope DNA vaccine for TNBC, Showing Antigen & Immunoglobulins level, B-cell Populations with various isotypes as well as Memory & Not Memory B-Cells and CD4 T-Cell Population & the regulatory T-Cells.
Figure(2): Using C-IMMSIM simulation models to describe both Humoral and Cellular response of our predicted epitopes in our 1st proposed multi-epitope DNA vaccine for TNBC,Showing the CD8 T-Cell Population and NKCs & DCs & MQs & Epithelial Populations.






























References

1-Tahir ul Qamar, Muhammad, et al. “Multiepitope-Based Subunit Vaccine Design and Evaluation against Respiratory Syncytial Virus Using Reverse Vaccinology Approach.” Vaccines, vol. 8, no. 2, 1 June 2020, p. 288, www.mdpi.com/2076-393X/8/2/288/htm, 10.3390/vaccines8020288. Accessed 22 Oct. 2020.

2-McNulty, Shaun, et al. “Heat-Shock Proteins as Dendritic Cell-Targeting Vaccines - Getting Warmer.” Immunology, vol. 139, no. 4, 2 July 2013, pp. 407–415, 10.1111/imm.12104. Accessed 18 Nov. 2019.

3-Solanki, Vandana, et al. “Prioritization of Potential Vaccine Targets Using Comparative Proteomics and Designing of the Chimeric Multi-Epitope Vaccine against Pseudomonas Aeruginosa.” Scientific Reports, vol. 9, no. 1, 27 Mar. 2019, 10.1038/s41598-019-41496-4. Accessed 22 May 2020.

4-Castiglione, F., & Bernaschi, M. (2004, April 30). C-ImmSim∗ : Playing with the immune response. Retrieved October 26, 2020, from https://www.math.ucsd.edu/~helton/MTNSHISTORY/CONTENTS/2004LEUVEN/CDROM/papers/316.pdf

5-Tahir Ul Qamar, M., Shokat, Z., Muneer, I., Ashfaq, U., Javed, H., Anwar, F., . . . Saari, N. (2020, June 8). Multiepitope-Based Subunit Vaccine Design and Evaluation against Respiratory Syncytial Virus Using Reverse Vaccinology Approach. Retrieved October 26, 2020, from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7350008/

6-Ghaffari-Nazari, H., Tavakkol-Afshari, J., Jaafari, M., Tahaghoghi-Hajghorbani, S., Masoumi, E., & Jalali, S. (2015, November 10). Improving Multi-Epitope Long Peptide Vaccine Potency by Using a Strategy that Enhances CD4+ T Help in BALB/c Mice. Retrieved October 26, 2020, from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4640540/

7-McNulty, S., Colaco, C., Blandford, L., Bailey, C., Baschieri, S., & Todryk, S. (2013, August). Heat-shock proteins as dendritic cell-targeting vaccines--getting warmer. Retrieved October 26, 2020, from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3719058/


Sequence and Features


Assembly Compatibility:
  • 10
    INCOMPATIBLE WITH RFC[10]
    Illegal PstI site found at 120
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal PstI site found at 120
    Illegal NotI site found at 44
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    INCOMPATIBLE WITH RFC[23]
    Illegal PstI site found at 120
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal PstI site found at 120
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal BsaI.rc site found at 584
    Illegal BsaI.rc site found at 935
    Illegal SapI.rc site found at 853