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Special Issue Editors

Special Issue Information

Dear Colleagues,

In last 3 years we have seen the power of omics for the COVID-19 vaccine development. Different types of omics are adding great values to solve diseases and find better cures. Omics technologies include genomics, transcriptomics, proteomics, metabolomics, and immunomics. These technologies have been used in vaccine research, which can be summarized using the term “vaccinomics.” These omics technologies combined with advanced bioinformatics analysis form the core of “systems vaccinology.” Omics technologies provide powerful methods in vaccine target identification. The genomics‐based reverse vaccinology starts with predicting vaccine protein candidates through in silico bioinformatics analysis of genome sequences. Systematic transcriptomics and proteomics analyses facilitate rational vaccine target identification by detesting genome‐wide gene expression profiles. Immunomics is the study of the set of antigens recognized by host immune systems and has also been used for efficient vaccine target prediction. In this special issue I would like to bring together this all-discreet information at one place.

(1) System biology approach for immune characterization and vaccine development
(2) Analysis of high throughput data for faster vaccine development (data handling and development of predictive models)
(3) Integrating systems biology approaches into clinical trials of vaccines
(4) Immunoinformatics modelling and vaccine development (mathematical and computational modelling)
(5) Various High-throughput technologies for immune characterization and Covid vaccine development
(6) Role of system biology approach in anti-tuberculosis vaccine development
(7) Development of cancer vaccines using various high throughput technologies
(8) Role of immuno-metabolomics in vaccines characterization and development
(9) Challenges in system biology based approach for vaccine development
(10) Future prospective of vaccine development using next generation technologies.

Dr. Vijay Soni
Dr. Yogesh Chawla
Guest Editors

Manuscript Submission Information

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Keywords

omics
system biology
proteomics
genomics
transcriptomics
metabolomics
vaccines

Published Papers (2 papers)

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Research

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20 pages, 2881 KiB

Open AccessArticle

Surface-Exposed Protein Moieties of Burkholderia cenocepacia J2315 in Microaerophilic and Aerobic Conditions

by António M. M. Seixas, Carolina Silva, Joana M. M. Marques, Patrícia Mateus, Manuel J. Rodríguez-Ortega, Joana R. Feliciano, Jorge H. Leitão and Sílvia A. Sousa

Vaccines 2024, 12(4), 398; https://doi.org/10.3390/vaccines12040398 - 09 Apr 2024

Viewed by 414

Abstract

Burkholderia cepacia complex infections remain life-threatening to cystic fibrosis patients, and due to the limited eradication efficiency of current treatments, novel antimicrobial therapies are urgently needed. Surface proteins are among the best targets to develop new therapeutic strategies since they are exposed to the host’s immune system. A surface-shaving approach was performed using Burkholderia cenocepacia J2315 to quantitatively compare the relative abundance of surface-exposed proteins (SEPs) expressed by the bacterium when grown under aerobic and microaerophilic conditions. After trypsin incubation of live bacteria and identification of resulting peptides by liquid chromatography coupled with mass spectrometry, a total of 461 proteins with ≥2 unique peptides were identified. Bioinformatics analyses revealed a total of 53 proteins predicted as localized at the outer membrane (OM) or extracellularly (E). Additionally, 37 proteins were predicted as moonlight proteins with OM or E secondary localization. B-cell linear epitope bioinformatics analysis of the proteins predicted to be OM and E-localized revealed 71 SEP moieties with predicted immunogenic epitopes. The protegenicity higher scores of proteins BCAM2761, BCAS0104, BCAL0151, and BCAL0849 point out these proteins as the best antigens for vaccine development. Additionally, 10 of the OM proteins also presented a high probability of playing important roles in adhesion to host cells, making them potential targets for passive immunotherapeutic approaches. The immunoreactivity of three of the OM proteins identified was experimentally demonstrated using serum samples from cystic fibrosis patients, validating our strategy for identifying immunoreactive moieties from surface-exposed proteins of potential interest for future immunotherapies development. Full article

(This article belongs to the Special Issue Vaccinomics: Omics-System Biology Approach in Vaccine Development)

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Review

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20 pages, 2070 KiB

Open AccessReview

Mycobacterium smegmatis, a Promising Vaccine Vector for Preventing TB and Other Diseases: Vaccinomics Insights and Applications

by Weile Xie, Longlong Wang, Dan Luo, Vijay Soni, Eric H. Rosenn and Zhe Wang

Vaccines 2023, 11(8), 1302; https://doi.org/10.3390/vaccines11081302 - 31 Jul 2023

Cited by 1 | Viewed by 1535

Abstract

Mycobacterium smegmatis (M.sm) is frequently used as an alternative model organism in Mycobacterium tuberculosis (M.tb) studies. While containing high sequence homology with M.tb, it is considered non-pathogenic in humans. As such it has been used to study M.tb and other infections in vivo and more recently been explored for potential therapeutic applications. A body of previous research has highlighted the potential of using genetically modified M.sm displaying rapid growth and unique immunostimulatory characteristics as an effective vaccine vector. Novel systems biology techniques can further serve to optimize these delivery constructs. In this article, we review recent advancements in vaccinomics tools that support the efficacy of a M.sm-based vaccine vector. Moreover, the integration of systems biology and molecular omics techniques in these pioneering studies heralds a potential accelerated pipeline for the development of next-generation recombinant vaccines against rapidly developing diseases. Full article

(This article belongs to the Special Issue Vaccinomics: Omics-System Biology Approach in Vaccine Development)

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