In-silico identification of subunit vaccine candidates against lung cancer-associated oncogenic viruses

Globally, ~20% of cancer malignancies are associated with virus infections. Lung cancer is the most prevalent cancer and has a 10% 5-year survival rate when diagnosed at stage IV. Cancer vaccines and oncolytic immunotherapy are promising treatment strategies for better clinical outcomes in advanced-stage cancer patients. Here, we used a reverse vaccinology approach to devise subunit vaccine candidates against lung cancer-causing oncogenic viruses. Protein components (945) from nine oncogenic virus species were systematically analyzed to identify epitope-based subunit vaccine candidates. Best vaccine candidates were identified based on their predicted ability to stimulate humoral and cell-mediated immunity and avoid self-tolerance. Using a rigorous integrative approach, we identified 125 best antigenic epitopes with predicted B-cell, T-cell, and/or MHC-binding capability and vaccine adjuvant potential. Thirty-two of these antigenic epitopes were predicted to have IL-4/IFN-gamma inducing potential and IL-10 non-inducing potential and were predicted to bind 15 MHC-type I and 49 MHC-type II alleles. All 32 epitopes were non-allergenic and 31 were non-toxic. The identified epitopes showed good conservancy and likely bind a broad class of human HLA alleles, indicating promiscuous potential. The majority of best antigenic epitopes were derived from Human papillomavirus and Epstein-Barr virus proteins. Of the 32 epitopes, 25 promiscuous epitopes were related to E1 and E6 envelope genes and were present in multiple viral strains/species, potentially providing heterologous immunity. Further validating our results, 38 antigenic epitopes were also present in the largest experimentally-validated epitope resource, Immune Epitope Database and Analysis Resource. We further narrowed the selection to 29 antigenic epitopes with the highest immunogenic/immune-boosting potential. These epitopes possess tremendous therapeutic potential as vaccines against lung cancer-causing viruses and should be validated in future experiments. All findings are available at https://webs.iiitd.edu.in/raghava/vlcvirus/.

Epitope promiscuity and population coverage of Mycobacterium tuberculosis protein antigens in current subunit vaccines under development

Tuberculosis (TB) is the leading infectious cause of death worldwide and claimed over 1.6 million lives in 2017. Furthermore, one-third of the world population is estimated to be latently infected with Mycobacterium tuberculosis (MTB). A safe and effective MTB vaccine that can prevent both the primary infection and the reactivation of latent tuberculosis infection (LTBI), and that can protect against all forms of TB in adults and adolescents is urgently needed. In this study, using computational approaches, we predicted the capacity of the epitopes to be presented by the HLA molecules for ten MTB protein antigens (Mtb39a, Mtb32a, Ag85B, ESAT-6, TB10.4, Rv2660, Rv2608, Rv3619, Rv3620, and Rv1813) constituting five MTB subunit vaccines (M72, H1, H4, H56, and ID93) that are currently in clinical trials. We also assessed the promiscuity of the predicted epitopes based on a reference set of alleles and supertype alleles, and estimated the population coverage of the ten antigens in three high TB burden countries (China, India, and South Africa). Among the ten antigens evaluated, Rv2608 was found to have the highest number of promiscuous epitopes predicted to bind the most MHC-I and MHC-II supertype alleles, highest predicted immunogenicity, and the broadest population coverage in three high burden countries. Between the two latency-related antigens (Rv1813 and Rv2660), Rv1813 was predicted to have a better epitope diversity and promiscuity, immunogenicity, and population coverage. As a result, the ID93 vaccine consisted of Rv2608, Rv1813, Rv3619, and Rv3620 was predicted to have the best potential for preventing both active and latent TB infection. Our results highlighted the importance and usefulness of a systematic and comprehensive assessment of protein antigens using computational approaches in MTB vaccine development.

Novel lipopeptides of ESAT-6 induce strong protective immunity against Mycobacterium tuberculosis: Routes of immunization and TLR agonists critically impact vaccine's efficacy

Mycobacterium tuberculosis (Mtb), the bacterial cause of tuberculosis, is a leading infectious agent worldwide. The development of a new vaccine against Mtb is essential to control global spread of tuberculosis, since the current vaccine BCG is not very effective and antibiotic resistance is a serious, burgeoning problem. ESAT-6 is a secreted protein of Mtb, which is absent in BCG but has been implicated in inducing protective immunity against Mtb. Peptide based subunit vaccines are attractive due to their safety and high specificity in eliciting immune responses, but small synthetic peptides are usually not very immunogenic. We have designed a novel subunit vaccine for Mtb by using simple lipid (palmitic acid) modified derivatives of peptides from ESAT-6 protein corresponding to dominant human T cell epitopes and examined their ability to stimulate protective immunity against Mtb by intranasal and subcutaneous immunization in mice. We also investigated how individual TLR agonists as adjuvants (PolyI:C, MPL and GDQ) contribute to enhancing the induced immune responses and resulting protective efficacy of our vaccine. We observed that single C-terminal palmitoyl-lysine modified lipopeptides derived from ESAT-6 induce significant cellular immune responses on their own upon mucosal and subcutaneous immunizations. Intriguingly, a combination of immunogenic lipopeptides of ESAT-6 antigen exhibited local (pulmonary) and systemic immune responses along with efficient protective efficacy when administered intranasally or subcutaneously. Surprisingly, combination of ESAT-6 derived lipopeptides with a TLR-4 agonist (MPL) enhanced protection, whereas TLR-3 (Poly I:C) and TLR-7/8 agonists (gardiquimod, GDQ) led to reduced protection associated with specific local and systemic immune modulation. Our studies demonstrate the potential of ESAT-6 derived lipopeptides as a promising vaccine candidate against Mtb, and emphasize that selection of adjuvant is critical for the success of vaccines. These findings demonstrate the promise of synthetic lipopeptides as the basis of a subunit vaccine for TB.