IMMUNOLOGICAL ASPECTS Immunoinformatics study on highly expressed Mycobacterium tuberculosis genes during infection Le Thuy Nguyen Thi a , Maria Elena Sarmiento b , Romel Calero c , Frank Camacho d , Fatima Reyes d , Md Murad Hossain b , Gustavo Sierra Gonzalez c , Mohd Nor Norazmi b, e , Armando Acosta e, * a Biotechnology Centre of Ho Chi Minh City,176 Hai Ba Trung Street, Ho Chi Minh City, Viet Nam b PPSK, Health Campus, Universiti Sains Malaysia, Malaysia c Finlay Institute, Cuba d Universidad de Concepcion, Chile e INFORMM, Health Campus, Universiti Sains Malaysia, Malaysia article info Article history: Received 16 January 2014 Received in revised form 4 June 2014 Accepted 8 June 2014 Keywords: Mycobacterium tuberculosis Gene expression Epitope prediction summary The most important targets for vaccine development are the proteins that are highly expressed by the microorganisms during infection in-vivo. A number of Mycobacterium tuberculosis (Mtb) proteins are also reported to be expressed in-vivo at different phases of infection. In the present study, we analyzed multiple published databases of gene expression profiles of Mtb in-vivo at different phases of infection in animals and humans and selected 38 proteins that are highly expressed in the active, latent and reac- tivation phases. We predicted T- and B-cell epitopes from the selected proteins using HLAPred for T-cell epitope prediction and BCEPred combined with ABCPred for B-cell epitope prediction. For each selected proteins, regions containing both T- and B-cell epitopes were identified which might be considered as important candidates for vaccine design against tuberculosis. © 2014 Elsevier Ltd. All rights reserved. 1. Introduction Tuberculosis (TB) still remains a major health problem world- wide. Mycobacterium tuberculosis (Mtb), the causative organism of TB in humans infects 9 million individuals and kills 1.4 million people annually [1,2]. The World Health Organization (WHO) has estimated that one-third of the world's population has already been infected with Mtb [1,2]. The attenuated live Mycobacterium. bovis bacille calmetteeguerin (BCG) is the vaccine in use for the pre- vention of TB [3]. However, the variable efficacy of BCG vaccine against TB in adults, and the emergence of multi-drug resistant and extensively drug resistant Mtb strains have made the development of new or improved TB vaccines more urgent [3,4]. The complete genome sequences of Mtb, BCG and other mycobacteria have provided an enormous flow of valuable information that can be useful for designing new vaccine strategies [5e17]. The application of in silico techniques in vaccine design is an exciting approach for the discovery of new vaccines as well as for the improvement of existing vaccines [18]. Over the past decade, a number of bioinformatics tools have been developed that use genomic sequence data to predict which parts of a microbe that the immune system will react to, the so-called epitopes, which are the most ideal components of vaccines [19]. After deciphering the complete genome sequence of Mtb and with the use of highly specific and sensitive technologies, such as microarrays and quantitative real-time polymerase chain reaction (RT-PCR), the expression in-vivo of genes of Mtb has been studied [17,20e38]. Understanding how Mtb regulates its different gene functions ac- cording to environmental changes will probably lead to the un- derstanding of many interesting aspects of the growth patterns of the organism, including activation, latency and reactivation of TB [20e38]. The combination of in-vivo and in silico studies allows focusing on a smaller group of relevant antigens to be used in vaccine development [18,19]. In this study, we selected Mtb genes that are highly expressed in-vivo in order to establish a pre-selected pool of antigens for the search of potential protective epitopes. * Corresponding author. INFORMM, Health Campus, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia. Tel.: þ60 9 767 2402, þ60 9 767 2403, þ60 9 767 2404; fax: þ60 9 764 8673. E-mail addresses: lenacns83@yahoo.com (L.T. Nguyen Thi), sarmari14@gmail. com (M.E. Sarmiento), rcalero@finlay.edu.cu (R. Calero), frank.camacho@gmail. com (F. Camacho), fatima8526@gmail.com (F. Reyes), mmhossaink140@yahoo. com (M.M. Hossain), gsierra@finlay.edu.cu (G.S. Gonzalez), norazmimn@usm.my (M.N. Norazmi), ducmar13@gmail.com (A. Acosta). Contents lists available at ScienceDirect Tuberculosis journal homepage: http://intl.elsevierhealth.com/journals/tube http://dx.doi.org/10.1016/j.tube.2014.06.004 1472-9792/© 2014 Elsevier Ltd. All rights reserved. Tuberculosis xxx (2014) 1e7 Please cite this article in press as: Nguyen Thi LT, et al., Immunoinformatics study on highly expressed Mycobacterium tuberculosis genes during infection, Tuberculosis (2014), http://dx.doi.org/10.1016/j.tube.2014.06.004