Recent developments in systems biology and genetic engineering toward design of vaccines for TB

References

• Glaziou P, Sismanidis C, Floyd K, et al. Global epidemiology of tuberculosis. Cold Spring Harb Perspect Med. 2014;5(2):a017798.
   PubMed Web of Science ®Google Scholar
• Wei M, Zhao Y, Qian Z, et al. Pneumonia caused by Mycobacterium tuberculosis. Microb Infect. 2020;22:278–284.
   PubMed Web of Science ®Google Scholar
• Mishra R, Krishan S, Siddiqui AN, et al. Potential role of adjuvant drugs on efficacy of first line oral antitubercular therapy: drug repurposing. Tuberculosis. 2020;120:101902.
   PubMedGoogle Scholar
• Migliori GB, Tiberi S, Zumla A, et al. MDR/XDR-TB management of patients and contacts: challenges facing the new decade. The 2020 clinical update by the Global Tuberculosis Network. Int J Infect Dis. 2020;92:S15–S25.
   Web of Science ®Google Scholar
• Schlipköter U, Flahault A. Communicable diseases: achievements and challenges for public health. Public Health Rev. 2010;32:90–119.
   PubMedGoogle Scholar
• Myllymäki H, Niskanen M, Oksanen KE, et al. Animal models in tuberculosis research – where is the beef?. Expert Opin Drug Discov. 2015;10(8):871–883.
   PubMed Web of Science ®Google Scholar
• Shahmohammadi S, Saffar MJ, Rezai MS. BCG-osis after BCG vaccination in immunocompromised children: case series and review. J Pediatr Rev. 2014;2:62–74.
   Google Scholar
• Nuttall JJ, Eley BS. BCG vaccination in HIV-infected children. Tuberc Res Treat. 2011;2011:712736.
   PubMedGoogle Scholar
• Kanekiyo M, Ellis D, King NP. New vaccine design and delivery technologies. J Infect Dis. 2019;219(Suppl. 1):S88–S96.
   PubMedGoogle Scholar
• Comas I, Gagneux S. A role for systems epidemiology in tuberculosis research. Trends Microbiol. 2011;19(10):492–500.
   PubMedGoogle Scholar
• Patronov A, Doytchinova I. T-cell epitope vaccine design by immunoinformatics. Open Biol. 2013;3(1):120139.
   PubMed Web of Science ®Google Scholar
• Soria-Guerra RE, Nieto-Gomez R, Govea-Alonso DO, et al. An overview of bioinformatics tools for epitope prediction: implications on vaccine development. J Biomed Inform. 2015;53:405–414.
   PubMed Web of Science ®Google Scholar
• Oli AN, Obialor WO, Ifeanyichukwu MO, et al. Immunoinformatics and vaccine development: an overview. Immunotargets Ther. 2020;9:13–30.
   PubMed Web of Science ®Google Scholar
• Kennedy RB, Poland GA. The top five “game changers” in vaccinology: toward rational and directed vaccine development. OMICS. 2011;15(9):533–537.
   PubMed Web of Science ®Google Scholar
• Sunita Sajid A, Singh Y, Shukla P. Computational tools for modern vaccine development. Hum Vaccin Immunother. 2020;16:723–735.
   PubMed Web of Science ®Google Scholar
• Söllner J, Heinzel A, Summer G, et al. Concept and application of a computational vaccinology workflow. Immunome Res. 2010;6(Suppl. 2):S7.
   PubMedGoogle Scholar
• Lamont RJ, Koo H, Hajishengallis G. The oral microbiota: dynamic communities and host interactions. Nat Rev Microbiol. 2018;16(12):745–759.
   PubMed Web of Science ®Google Scholar
• Bruggeman FJ, Westerhoff HV. The nature of systems biology. Trends Microbiol. 2007;15(1):45–50.
   PubMed Web of Science ®Google Scholar
• Oberg AL, Kennedy RB, Li P, et al. Systems biology approaches to new vaccine development. Curr Opin Immunol. 2011;23(3):436–443.
   PubMed Web of Science ®Google Scholar
• Lambert ND, Ovsyannikova IG, Pankratz VS, et al. Understanding the immune response to seasonal influenza vaccination in older adults: a systems biology approach. Expert Rev Vaccines. 2012;11(8):985–994.
   PubMed Web of Science ®Google Scholar
• He Y, Racz R, Sayers S, et al. Updates on the web-based VIOLIN vaccine database and analysis system. Nucleic Acids Res. 2014;42(Database issue):D1124–D1132.
   PubMedGoogle Scholar
• Nagpal G, Usmani SS, Raghava GP. A web resource for designing subunit vaccine against major pathogenic species of bacteria. Front Immunol. 2018;9:2280.
   PubMedGoogle Scholar
• Ksiazek M, Mizgalska D, Eick S, et al. KLIKK proteases of Tannerella forsythia: putative virulence factors with a unique domain structure. Front Microbiol. 2015;6:312.
   PubMed Web of Science ®Google Scholar
• Vivona S, Bernante F, Filippini F. NERVE: new enhanced reverse vaccinology environment. BMC Biotechnol. 2006;6:35.
   PubMedGoogle Scholar
• Zaharieva N, Dimitrov I, Flower DR, et al. VaxiJen dataset of bacterial immunogens: an update. Curr Comput Aided Drug Des. 2019;15(5):398–400.
   PubMedGoogle Scholar
• María RR, Arturo CJ, Alicia JA, et al. The impact of bioinformatics on vaccine design and development. In: Farhat Afrin, Hassan Hemeg, Hani Ozbak, editors. Vaccines. Rijeka, Croatia: InTech; 2017.
   Google Scholar
• Bateman A, Coin L, Durbin R, et al. The Pfam protein families database. Nucleic Acids Res. 2004;32:138–141.
   PubMed Web of Science ®Google Scholar
• Yu NY, Wagner JR, Laird MR, et al. PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes. Bioinformatics. 2010;26(13):1608–1615.
   PubMed Web of Science ®Google Scholar
• Dimitrov I, Bangov I, Flower DR, et al. AllerTOP v.2—a server for in silico prediction of allergens. J Mol Model. 2014;20(6):2278.
   PubMed Web of Science ®Google Scholar
• Garg VK, Avashthi H, Tiwari A, et al. MFPPI – multi FASTA ProtParam interface. Bioinformation. 2016;12(2):74–77.
   PubMed Web of Science ®Google Scholar
• Agarwal P, Meena S, Meena LS. Comprehensive analysis of GTP cyclohydrolase I activity in Mycobacterium tuberculosis H37Rv via in silico studies. Biotechnol Appl Biochem. 2020.
   PubMedGoogle Scholar
• Park J, Bae S. Cpf1-Database: web-based genome-wide guide RNA library design for gene knockout screens using CRISPR-Cpf1. Bioinformatics. 2018;34(6):1077–1079.
   PubMed Web of Science ®Google Scholar
• Tomar N, De RK. Tools, databases, and applications of immunoinformatics. In: Gulshan Wadhwa, P. Shanmughavel, Atul Kumar Singh, et al. editors. Current trends in bioinformatics: an insight. Singapore: Springer; 2018. p. 159–174.
   Google Scholar
• Zhou Y, Cui J, Du H. Autoantibody-targeted TAAs in pancreatic cancer: a comprehensive analysis. Pancreatology. 2019;19(5):760–768.
   PubMedGoogle Scholar
• Heidari-Japelaghi R, Haddad R, Valizadeh M, et al. Elastin-like polypeptide fusions for high-level expression and purification of human IFN-γ in Escherichia coli. Anal Biochem. 2019;585:113401.
   PubMedGoogle Scholar
• Sharma D, Surolia A. Computational tools to study and understand the intricate biology of mycobacteria. Tuberculosis. 2011;91(3):273–276.
   PubMedGoogle Scholar
• Brusic V, Petrovsky N. Immunoinformatics and its relevance to understanding human immune disease. Expert Rev Clin Immunol. 2005;1(1):145–157.
   PubMedGoogle Scholar
• De Groot AS. Immunomics: discovering new targets for vaccines and therapeutics. Drug Discov Today. 2006;11(5–6):203–209.
   PubMed Web of Science ®Google Scholar
• Bahrami AA, Payandeh Z, Khalili S, et al. Immunoinformatics: in silico approaches and computational design of a multi-epitope, immunogenic protein. Int Rev Immunol. 2019;38(6):307–322.
   PubMed Web of Science ®Google Scholar
• Lazarus R, Vercelli D, Palmer LJ, et al. Single nucleotide polymorphisms in innate immunity genes: abundant variation and potential role in complex human disease. Immunol Rev. 2002;190:9–25.
   PubMedGoogle Scholar
• Frazer KA, Ballinger DG, Cox DR, et al. A second generation human haplotype map of over 3.1 million SNPs. Nature. 2007;449(7164):851–861.
   PubMed Web of Science ®Google Scholar
• Poland GA, Ovsyannikova IG, Jacobson RM. Personalized vaccines: the emerging field of vaccinomics. Expert Opin Biol Ther. 2008;8(11):1659–1667.
   PubMed Web of Science ®Google Scholar
• Eichelbaum M, Ingelman-Sundberg M, Evans WE. Pharmacogenomics and individualized drug therapy. Annu Rev Med. 2006;57:119–137.
   PubMed Web of Science ®Google Scholar
• Azad AK, Lloyd C, Sadee W, et al. Challenges of immune response diversity in the human population concerning new tuberculosis diagnostics, therapies, and vaccines. Front Cell Infect Microbiol. 2020;10:139.
   PubMedGoogle Scholar
• Sundell J, Bienvenu E, Janzén D, et al. Model-based assessment of variability in isoniazid pharmacokinetics and metabolism in patients co-infected with tuberculosis and HIV: implications for a novel dosing strategy. Clin Pharmacol Ther. 2020;108(1):73–80.
   PubMedGoogle Scholar
• Hein DW, Millner LM. Arylamine N-acetyltransferase acetylation polymorphisms: paradigm for pharmacogenomic-guided therapy—a focused review. Expert Opin Drug Metab Toxicol. 2020;17(1):9–21.
   PubMedGoogle Scholar
• Carpenter AE, Sabatini DM. Systematic genome-wide screens of gene function. Nat Rev Genet. 2004;1:11–22.
   Google Scholar
• Grandi G. Antibacterial vaccine design using genomics and proteomics. Trends Biotechnol. 2001;19(5):181–188.
   PubMed Web of Science ®Google Scholar
• Rappuoli R, Black S, Lambert PH. Vaccine discovery and translation of new vaccine technology. Lancet. 2011;378(9788):360–368.
   PubMed Web of Science ®Google Scholar
• Holt KE, Parkhill J, Mazzoni CJ, et al. High-throughput sequencing provides insights into genome variation and evolution in Salmonella typhi. Nat Genet. 2008;40(8):987–993.
   PubMedGoogle Scholar
• Land M, Hauser L, Jun SR, et al. Insights from 20 years of bacterial genome sequencing. Funct Integr Genomics. 2015;15(2):141–161.
   PubMed Web of Science ®Google Scholar
• Kapopoulou A, Lew JM, Cole ST. The MycoBrowser portal: a comprehensive and manually annotated resource for mycobacterial genomes. Tuberculosis. 2011;91(1):8–13.
   PubMed Web of Science ®Google Scholar
• Rosser A, Stover C, Pareek M, et al. Resuscitation-promoting factors are important determinants of the pathophysiology in Mycobacterium tuberculosis infection. Crit Rev Microbiol. 2017;43(5):621–630.
   PubMed Web of Science ®Google Scholar
• Naidoo N, Pawitan Y, Soong R, et al. Human genetics and genomics a decade after the release of the draft sequence of the human genome. Hum Genomics. 2011;5(6):577–622.
   PubMedGoogle Scholar
• Cosma CL, Sherman DR, Ramakrishnan L. The secret lives of the pathogenic mycobacteria. Annu Rev Microbiol. 2003;57:641–676.
   PubMed Web of Science ®Google Scholar
• Naz K, Naz A, Ashraf ST, et al. PanRV: pangenome-reverse vaccinology approach for identifications of potential vaccine candidates in microbial pangenome. BMC Bioinform. 2019;20:123.
   PubMed Web of Science ®Google Scholar
• Serruto D, Serino L, Masignani V, et al. Genome-based approaches to develop vaccines against bacterial pathogens. Vaccine. 2009;27(25–26):3245–3250.
   PubMed Web of Science ®Google Scholar
• Coscolla M, Gagneux S. Consequences of genomic diversity in Mycobacterium tuberculosis. Semin Immunol. 2014;26(6):431–444.
   PubMed Web of Science ®Google Scholar
• He Y, Rappuoli R, De Groot AS, et al. Emerging vaccine informatics. J Biomed Biotechnol. 2010;2010:218590.
   PubMedGoogle Scholar
• Ni Cheallaigh C, Keane J, Lavelle EC, et al. Autophagy in the immune response to tuberculosis: clinical perspectives. Clin Exp Immunol. 2011;164(3):291–300.
   PubMed Web of Science ®Google Scholar
• Wallis J, Shenton DP, Carlisle RC. Novel approaches for the design, delivery and administration of vaccine technologies. Clin Exp Immunol. 2019;196(2):189–204.
   PubMed Web of Science ®Google Scholar
• Shanmugham B, Pan A. Identification and characterization of potential therapeutic candidates in emerging human pathogen Mycobacterium abscessus: a novel hierarchical in silico approach. PLOS One. 2013;8(3):e59126.
   PubMed Web of Science ®Google Scholar
• Li S, Rouphael N, Duraisingham S, et al. Molecular signatures of antibody responses derived from a systems biology study of five human vaccines. Nat Immunol. 2014;15(2):195–204.
   PubMed Web of Science ®Google Scholar
• Gaucher D, Therrien R, Kettaf N, et al. Yellow fever vaccine induces integrated multilineage and polyfunctional immune responses. J Exp Med. 2008;205(13):3119–3131.
   PubMed Web of Science ®Google Scholar
• Querec TD, Akondy RS, Lee EK, et al. Systems biology approach predicts immunogenicity of the yellow fever vaccine in humans. Nat Immunol. 2009;10(1):116–125.
   PubMed Web of Science ®Google Scholar
• Lowe R, Shirley N, Bleackley M, et al. Transcriptomics technologies. PLoS Comput Biol. 2017;13(5):e1005457.
   PubMed Web of Science ®Google Scholar
• Santoro F, Pettini E, Kazmin D, et al. Transcriptomics of the vaccine immune response: priming with adjuvant modulates recall innate responses after boosting. Front Immunol. 2018;9:1248.
   PubMedGoogle Scholar
• Roy S, Schmeier S, Kaczkowski B, et al. Transcriptional landscape of Mycobacterium tuberculosis infection in macrophages. Sci Rep. 2018;8(1):1–3.
   PubMedGoogle Scholar
• Nakaya HI, Pulendran B. Vaccinology in the era of high-throughput biology. Philos Trans R Soc Lond B Biol Sci. 2015;370(1671):20140146.
   PubMedGoogle Scholar
• Sundaramurthi JC, Brindha S, Shobitha SR, et al. In silico identification of potential antigenic proteins and promiscuous CTL epitopes in Mycobacterium tuberculosis. Infect Genet Evol. 2012;12(6):1312–1318.
   PubMed Web of Science ®Google Scholar
• Pezeshki A, Ovsyannikova IG, McKinney BA, et al. The role of systems biology approaches in determining molecular signatures for the development of more effective vaccines. Expert Rev Vaccines. 2019;18(3):253–267.
   PubMed Web of Science ®Google Scholar
• Blischak JD, Tailleux L, Myrthil M, et al. Predicting susceptibility to tuberculosis based on gene expression profiling in dendritic cells. Sci Rep. 2017;7(1):1.
   PubMedGoogle Scholar
• Lin WN, Tay MZ, Lu R, et al. The role of single-cell technology in the study and control of infectious diseases. Cells. 2020;9(6):1440.
   Google Scholar
• Brown AJ, Snapkov I, Akbar R, et al. Augmenting adaptive immunity: progress and challenges in the quantitative engineering and analysis of adaptive immune receptor repertoires. Mol Syst Des Eng. 2019;4(4):701–736.
   Google Scholar
• Chen G, Ning B, Shi T. Single-cell RNA-Seq technologies and related computational data analysis. Front Genet. 2019;10:317.
   PubMed Web of Science ®Google Scholar
• Shao D, Okuse K, Djamgoz MB. Protein–protein interactions involving voltage-gated sodium channels: post-translational regulation, intracellular trafficking and functional expression. Int J Biochem Cell Biol. 2009;41(7):1471–1481.
   PubMedGoogle Scholar
• Noe A, Cargill TN, Nielsen CM, et al. The application of single-cell RNA sequencing in vaccinology. J Immunol Res. 2020;2020:8624963.
   PubMed Web of Science ®Google Scholar
• Nuss AM, Beckstette M, Pimenova M, et al. Tissue dual RNA-seq allows fast discovery of infection-specific functions and riboregulators shaping host–pathogen transcriptomes. Proc Natl Acad Sci U S A. 2017;114(5):E791–E800.
   PubMedGoogle Scholar
• Wang CC, Zhu B, Fan X, et al. Systems approach to tuberculosis vaccine development. Respirology. 2013;18(3):412–420.
   PubMedGoogle Scholar
• Cortes EA, Kaveh D, Nunez-Garcia J, et al. Mycobacterium bovis-BCG vaccination induces specific pulmonary transcriptome biosignatures in mice. PLOS One. 2010;5(6):e11319.
   PubMedGoogle Scholar
• Zárate-Bladés CR, Bonato VL, da Silveira EL, et al. Comprehensive gene expression profiling in lungs of mice infected with Mycobacterium tuberculosis following DNAhsp65 immunotherapy. J Gene Med. 2009;11(1):66–78.
   PubMed Web of Science ®Google Scholar
• Sia JK, Rengarajan J. Immunology of Mycobacterium tuberculosis infections. Microbiol Spectr. 2019;7(4).
   PubMedGoogle Scholar
• Gupta SK, Shukla P. Advanced technologies for improved expression of recombinant proteins in bacteria: perspectives and applications. Crit Rev Biotechnol. 2016;36(6):1089–1098.
   PubMed Web of Science ®Google Scholar
• Wu HJ, Wang AH, Jennings MP. Discovery of virulence factors of pathogenic bacteria. Curr Opin Chem Biol. 2008;12(1):93–101.
   PubMed Web of Science ®Google Scholar
• Vance RE, Isberg RR, Portnoy DA. Patterns of pathogenesis: discrimination of pathogenic and nonpathogenic microbes by the innate immune system. Cell Host Microbe. 2009;6(1):10–21.
   PubMed Web of Science ®Google Scholar
• Weiner J 3rd, Kaufmann SH. Recent advances towards tuberculosis control: vaccines and biomarkers. J Intern Med. 2014;275(5):467–480.
   PubMed Web of Science ®Google Scholar
• Mattow J, Schaible UE, Schmidt F, et al. Comparative proteome analysis of culture supernatant proteins from virulent Mycobacterium tuberculosis H37Rv and attenuated M. bovis BCG Copenhagen. Electrophoresis. 2003;24(19–20):3405–3420.
   PubMedGoogle Scholar
• Målen H, Berven FS, Fladmark KE, et al. Comprehensive analysis of exported proteins from Mycobacterium tuberculosis H37Rv. Proteomics. 2007;7(10):1702–1718.
   PubMed Web of Science ®Google Scholar
• Sable SB, Verma I, Khuller GK. Multicomponent antituberculous subunit vaccine based on immunodominant antigens of Mycobacterium tuberculosis. Vaccine. 2005;23(32):4175–4184.
   PubMedGoogle Scholar
• Pajon R, Yero D, Lage A, et al. Computational identification of beta-barrel outer-membrane proteins in Mycobacterium tuberculosis predicted proteomes as putative vaccine candidates. Tuberculosis. 2006;86(3–4):290–302.
   PubMed Web of Science ®Google Scholar
• McMurry J, Sbai H, Gennaro ML, et al. Analyzing Mycobacterium tuberculosis proteomes for candidate vaccine epitopes. Tuberculosis. 2005;85(1–2):95–105.
   PubMed Web of Science ®Google Scholar
• Parvizpour S, Pourseif MM, Razmara J, et al. Epitope-based vaccine design: a comprehensive overview of bioinformatics approaches. Drug Discov Today. 2020;25(6):1034–1042.
   PubMed Web of Science ®Google Scholar
• Fookolaee SP, Talebishelimaki S, Rad MT, et al. In silico prediction of B cell epitopes of the hemolysis-associated protein 1 for vaccine design against leptospirosis. J Curr Biomed Rep. 2020;1(1):32–37.
   Google Scholar
• Vita R, Mahajan S, Overton JA, et al. The immune epitope database (IEDB): 2018 update. Nucleic Acids Res. 2019;47(D1):D339–D343.
   PubMed Web of Science ®Google Scholar
• Akhter M, Arif S, Khaliq A, et al. Designing fusion molecules from antigens of Mycobacterium tuberculosis for detection of multiple antibodies in plasma of TB patients. Tuberculosis. 2020;124:101981.
   PubMedGoogle Scholar
• Gautam P, Meena LS. Revelation of point mutations effect in Mycobacterium tuberculosis MfpA protein that involved in mycobacterial DNA supercoiling and fluoroquinolone resistance. Biotechnol Appl Biochem. 2020;67(5):814–823.
   Google Scholar
• Zhou C, Chen Z, Zhang L, et al. SEPPA 3.0-enhanced spatial epitope prediction enabling glycoprotein antigens. Nucleic Acids Res. 2019;47(W1):W388–W394.
   PubMedGoogle Scholar
• Bazhan SI, Antonets DV, Karpenko LI, et al. In silico designed ebola virus T-cell multi-epitope DNA vaccine constructions are immunogenic in mice. Vaccines. 2019;7(2):34.
   Web of Science ®Google Scholar
• Paul S, Croft NP, Purcell AW, et al. Benchmarking predictions of MHC class I restricted T cell epitopes in a comprehensively studied model system. PLoS Comput Biol. 2020;16(5):e1007757.
   PubMedGoogle Scholar
• Raoufi E, Hemmati M, Eftekhari S, et al. Epitope prediction by novel immunoinformatics approach: a state-of-the-art review. Int J Pept Res Ther. 2019;20:1–9.
   Google Scholar
• Shams N, Gandabeh ZS, Nazifi N, et al. Computational design of different epitope-based vaccines against Salmonella typhi. Int J Pept Res Ther. 2020;26(3):1527–1523.
   Web of Science ®Google Scholar
• Dorosti H, Eslami M, Negahdaripour M, et al. Vaccinomics approach for developing multi-epitope peptide pneumococcal vaccine. J Biomol Struct Dyn. 2019;37(13):3524–3535.
   PubMed Web of Science ®Google Scholar
• Ramana J, Mehla K. Immunoinformatics and epitope prediction. Methods Mol Biol. 2020;2131:155–171.
   PubMedGoogle Scholar
• Mora M, Veggi D, Santini L, et al. Reverse vaccinology. Drug Discov Today. 2003;8(10):459–464.
   PubMed Web of Science ®Google Scholar
• Rinaudo CD, Telford JL, Rappuoli R, et al. Vaccinology in the genome era. J Clin Invest. 2009;119(9):2515–2525.
   PubMed Web of Science ®Google Scholar
• Sesterhenn F, Galloux M, Vollers SS, et al. Boosting subdominant neutralizing antibody responses with a computationally designed epitope-focused immunogen. PLoS Biol. 2019;17(2):e3000164.
   PubMedGoogle Scholar
• Dhanda SK, Mahajan S, Paul S, et al. IEDB-AR: immune epitope database-analysis resource in 2019. Nucleic Acids Res. 2019;47(W1):W502–W506.
   PubMed Web of Science ®Google Scholar
• Farrell D, Jones G, Pirson C, et al. Integrated computational prediction and experimental validation identifies promiscuous T cell epitopes in the proteome of Mycobacterium bovis. Microb Genom. 2016;2(8):e000071.
   PubMedGoogle Scholar
• Ong E, He Y, Yang Z. Epitope promiscuity and population coverage of Mycobacterium tuberculosis protein antigens in current subunit vaccines under development. Infect Genet Evol. 2020;80:104186.
   PubMed Web of Science ®Google Scholar
• Verma S, Singhvi N, Singh Y, et al. Computational approaches in epitope design using DNA binding proteins as vaccine candidate in Mycobacterium tuberculosis. Infect Genet Evol. 2020;11:104357.
   Google Scholar
• Salemi O, Noormohammadi Z, Bahrami F, et al. Cloning, expression and purification of Espc, Espb and Espc/Espb proteins of Mycobacterium tuberculosis ESX-1 secretion system. Rep Biochem Mol Biol. 2020;8(4):465–472.
   PubMedGoogle Scholar
• Ortega-Tirado D, Arvizu-Flores AA, Velazquez C, et al. The role of immunoinformatics in the development of T-cell peptide-based vaccines against Mycobacterium tuberculosis. Expert Rev Vaccines. 2020.
   PubMedGoogle Scholar
• Zhu YH, Gao YF, Chen F, et al. Identification of novel T cell epitopes from efflux pumps of Mycobacterium tuberculosis. Immunol Lett. 2011;140(1–2):68–73.
   PubMedGoogle Scholar
• Wang Y, Sun M, He M, et al. Weak binder for MHC molecule is a potent Mycobacterium tuberculosis-specific CTL epitope in the context of HLA-A24 allele. Microb Pathog. 2012;53(3–4):162–167.
   PubMedGoogle Scholar
• Lv H, Gao Y, Wu Y, et al. Identification of a novel cytotoxic T lymphocyte epitope from CFP21, a secreted protein of Mycobacterium tuberculosis. Immunol Lett. 2010;133(2):94–98.
   PubMed Web of Science ®Google Scholar
• Scriba TJ, Netea MG, Ginsberg AM. Key recent advances in TB vaccine development and understanding of protective immune responses against Mycobacterium tuberculosis. Semin Immunol. 2020;50:101431.
   PubMed Web of Science ®Google Scholar
• Movahedi AR, Hampson DJ. New ways to identify novel bacterial antigens for vaccine development. Vet Microbiol. 2008;131(1–2):1–3.
   PubMedGoogle Scholar
• Tucci P, Portela M, Chetto CR, et al. Integrative proteomic and glycoproteomic profiling of Mycobacterium tuberculosis culture filtrate. PLOS One. 2020;15(3):e0221837.
   PubMed Web of Science ®Google Scholar
• Jungblut PR, Schaible UE, Mollenkopf HJ, et al. Comparative proteome analysis of Mycobacterium tuberculosis and Mycobacterium bovis BCG strains: towards functional genomics of microbial pathogens. Mol Microbiol. 1999;33(6):1103–1117.
   PubMed Web of Science ®Google Scholar
• Manjasetty BA, Büssow K, Panjikar S, et al. Current methods in structural proteomics and its applications in biological sciences. 3 Biotech. 2012;2(2):89–113.
   Google Scholar
• Dietrich J, Aagaard C, Leah R, et al. Exchanging ESAT6 with TB10.4 in an Ag85B fusion molecule-based tuberculosis subunit vaccine: efficient protection and ESAT6-based sensitive monitoring of vaccine efficacy. J Immunol. 2005;174(10):6332–6339.
   PubMed Web of Science ®Google Scholar
• Chim N, Habel JE, Johnston JM, et al. The TB structural genomics consortium: a decade of progress. Tuberculosis. 2011;91(2):155–172.
   PubMed Web of Science ®Google Scholar
• Sweeney KA, Dao DN, Goldberg MF, et al. A recombinant Mycobacterium smegmatis induces potent bactericidal immunity against Mycobacterium tuberculosis. Nat Med. 2011;17(10):1261–1268.
   PubMed Web of Science ®Google Scholar
• Ahn SK, Tran V, Leung A, et al. Recombinant BCG overexpressing phoP-phoR confers enhanced protection against tuberculosis. Mol Ther. 2018;26(12):2863–2874.
   PubMed Web of Science ®Google Scholar
• Levillain F, Kim H, Kwon KW, et al. Preclinical assessment of a new live attenuated Mycobacterium tuberculosis Beijing-based vaccine for tuberculosis. Vaccine. 2020;38(6):1416–1423.
   PubMedGoogle Scholar
• Marinova D, Gonzalo-Asensio J, Aguilo N, et al. MTBVAC from discovery to clinical trials in tuberculosis-endemic countries. Expert Rev Vaccines. 2017;16(6):565–576.
   PubMed Web of Science ®Google Scholar
• Choi HG, Choi S, Back YW, Paik S, et al. Rv2299c, a novel dendritic cell-activating antigen of Mycobacterium tuberculosis, fused-ESAT-6 subunit vaccine confers improved and durable protection against the hypervirulent strain HN878 in mice. Oncotarget. 2017;8(12):19947–19967.
   PubMedGoogle Scholar
• Shey RA, Ghogomu SM, Esoh KK, et al. In-silico design of a multi-epitope vaccine candidate against onchocerciasis and related filarial diseases. Sci Rep. 2019;9(1):1–8.
   PubMed Web of Science ®Google Scholar
• Köster S, Klevorn T, Papavinasasundaram K, et al. Consequence of enhanced LC3-trafficking for a live, attenuated M. tuberculosis vaccine. Vaccine. 2018;36(7):939–944.
   PubMedGoogle Scholar
• Kurtz SL, Gardina PJ, Myers TG, et al. Whole genome profiling refines a panel of correlates to predict vaccine efficacy against Mycobacterium tuberculosis. Tuberculosis. 2020;120:101895.
   PubMedGoogle Scholar
• Tang J, Cai Y, Liang J, et al. In vivo electroporation of a codon-optimized BERopt DNA vaccine protects mice from pathogenic Mycobacterium tuberculosis aerosol challenge. Tuberculosis. 2018;113:65–75.
   PubMed Web of Science ®Google Scholar
• Barrangou R, Birmingham A, Wiemann S, et al. Advances in CRISPR-Cas9 genome engineering: lessons learned from RNA interference. Nucleic Acids Res. 2015;43(7):3407–3419.
   PubMed Web of Science ®Google Scholar
• Weninger A, Killinger M, Vogl T. Key methods for synthetic biology: genome engineering and DNA assembly. In: Synthetic biology. Cham: Springer; 2016. p. 101–141.
   Google Scholar
• Araldi RP, Khalil C, Grignet PH, et al. Medical applications of clustered regularly interspaced short palindromic repeats (CRISPR/Cas) tool: a comprehensive overview. Gene. 2020;745:144636.
   PubMedGoogle Scholar
• Savic N, Ringnalda FC, Lindsay H, et al. Covalent linkage of the DNA repair template to the CRISPR-Cas9 nuclease enhances homology-directed repair. Elife. 2018;7:e33761.
   PubMed Web of Science ®Google Scholar
• Barrangou R, Marraffini LA. CRISPR-Cas systems: prokaryotes upgrade to adaptive immunity. Mol Cell. 2014;54(2):234–244.
   PubMed Web of Science ®Google Scholar
• Rahman K, Jamal M, Chen X, et al. Reprogramming the endogenous type III-A CRISPR-Cas system for genome editing, RNA interference and CRISPRi screening in Mycobacterium tuberculosis. bioRxiv. 2020.
   Google Scholar
• Drexler I, Staib C, Sutter G. Modified vaccinia virus Ankara as antigen delivery system: how can we best use its potential? Curr Opin Biotechnol. 2004;15(6):506–512.
   PubMedGoogle Scholar
• Kern A, Tilley E, Hunter IS, et al. Engineering primary metabolic pathways of industrial micro-organisms. J Biotechnol. 2007;129(1):6–29.
   PubMed Web of Science ®Google Scholar
• Lee SY, Kim HU, Park JH, et al. Metabolic engineering of microorganisms: general strategies and drug production. Drug Discov Today. 2009;14(1–2):78–88.
   PubMedGoogle Scholar
• Sutherland JS, Lalor MK, Black GF, et al. Analysis of host responses to Mycobacterium tuberculosis antigens in a multi-site study of subjects with different TB and HIV infection states in sub-Saharan Africa. PLOS One. 2013;8(9):e74080.
   PubMedGoogle Scholar
• Ferraris DM, Miggiano R, Rossi F, et al. Mycobacterium tuberculosis molecular determinants of infection, survival strategies, and vulnerable targets. Pathogens. 2018;7:17.
   Google Scholar
• Williams NC, O’Neill LA. A role for the krebs cycle intermediate citrate in metabolic reprogramming in innate immunity and inflammation. Front Immunol. 2018;9:141.
   PubMed Web of Science ®Google Scholar
• Kaur G, Pandey B, Kumar A, et al. Drug targeted virtual screening and molecular dynamics of LipU protein of Mycobacterium tuberculosis and Mycobacterium leprae. J Biomol Struct Dyn. 2019;37(5):1254–1269.
   PubMed Web of Science ®Google Scholar
• Novoa-Aponte L, Soto Ospina CY. Mycobacterium tuberculosis P-type ATPases: possible targets for drug or vaccine development. Biomed Res Int. 2014;2014:1–9.
   Google Scholar
• Ng TW, Saavedra-Ávila NA, Kennedy SC, et al. Current efforts and future prospects in the development of live mycobacteria as vaccines. Expert Rev Vaccines. 2015;14(11):1493–1507.
   PubMed Web of Science ®Google Scholar
• Dangi AK, Sharma B, Hill RT, et al. Bioremediation through microbes: systems biology and metabolic engineering approach. Crit Rev Biotechnol. 2019;39(1):79–98.
   PubMed Web of Science ®Google Scholar
• Pavlou AK, Reichert JM. Recombinant protein therapeutics—success rates, market trends and values to 2010. Nat Biotechnol. 2004;12:1513–1519.
   Google Scholar
• Bloss CS, Jeste DV, Schork NJ. Genomics for disease treatment and prevention. Psychiatr Clin North Am. 2011;34(1):147–166.
   PubMedGoogle Scholar
• Bruce C, Stone K, Gulcicek E, et al. Proteomics and the analysis of proteomic data: 2013 overview of current protein-profiling technologies. Curr Protoc Bioinformatics. 2013;41:13–21.
   Google Scholar
• Morozova O, Hirst M, Marra MA. Applications of new sequencing technologies for transcriptome analysis. Annu Rev Genomics Hum Genet. 2009;10:135–151.
   PubMed Web of Science ®Google Scholar
• Macer DR. Ethical, legal and social issues of genetically modified disease vectors in public health. Geneva, Switzerland: World Health Organization; 2003.
   Google Scholar
• Garcia-Ruiz E, HamediRad M, Zhao H. Pathway design, engineering, and optimization. In: Huimin Zhao, An-Ping Zeng, editors. Synthetic biology–metabolic engineering. Cham: Springer; 2016. p. 77–116.
   Google Scholar