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Computational Biology and Bioinformatics in Anti-SARS-CoV-2 Drug Development
Published in Debmalya Barh, Kenneth Lundstrom, COVID-19, 2022
Jaiswal et al. emphasized the importance of using systems biology approaches and integration of multiple omics (transcriptomics, proteomics, genomics, lipidomics, immunomics, and in silico computational modeling) while dealing with analysis of host–virus interactions in search of potential therapeutic targets against the COVID-19 [118].
Emerging Trends and Future Directions for AI in Immunology
Published in Louis J. Catania, AI for Immunology, 2021
The Harvard T.H. Chan School of Public Health and the Human Vaccines Project announced the Human Immunomics Initiative (HII), a joint project that aims to revolutionize the understanding of the human immune system and accelerate the creation of effective vaccines, diagnostics, and treatments. HII will specifically focus on determining the principles of effective immunity in aging populations, the world’s largest growing demographic that has an immense disease burden and high morbidity and mortality in the current COVID-19 pandemic.1
Proteomics-inspired precision medicine for treating and understanding multiple myeloma
Published in Expert Review of Precision Medicine and Drug Development, 2020
Matthew Ho, Giada Bianchi, Kenneth C. Anderson
Cancer immunomics is the study of the interaction between the immune system and cancer antigens using genome-wide approaches such as genomics, proteomics, and bioinformatics [183]. The successful design of T-mAbs (including BiTEs and ADCs) hinges on the identification of highly immunogenic tumor-associated antigens (TAAs) that are expressed on MM cells but not on normal cells [184]. Genome-wide cDNA microarray analysis provides unbiased and comprehensive gene expression profiles that can be interrogated to identify TAAs that are consistently highly expressed in MM cells but not normal tissues [184]. Mu et al. utilized a proteomics-based approach to look for potential TAAs [185]. Firstly, rabbits were immunized with ARH-77 human plasmacytoma cells and allowed to mount a humoral response. Tumor-specific polyclonal antibodies (PAb) were then isolated using an affinity chromatography system. 2D-gel electrophoresis and Western blot were performed using the ARH-77 cell lysates. The tumor-specific PAb was then used to bind and identify the protein band that corresponded to the antigens of PAb. Protein bands that reacted positively with PAb were excised and subject to MALDI-TOF MS/MS analysis [185]. Using this method, the group identified severe potential TAAs including HSP90A, ENO1, and ADPH [185].
Immunoinformatics: In Silico Approaches and Computational Design of a Multi-epitope, Immunogenic Protein
Published in International Reviews of Immunology, 2019
Armina Alagheband Bahrami, Zahra Payandeh, Saeed Khalili, Alireza Zakeri, Mojgan Bandehpour
Immunomics is a relatively new science with effective methods and approaches to search and study the immune system. Immunology, Proteomics, Genomics, Informatics, and Medicine are scientific fields involved in Immunomics. Contemporary, immunomics is focused on the design of newer and more advanced algorithms for discovery and design of new vaccines. There is a direct linear relationship between the progress of databases and immunoinformatics. Immunological databases are the basis for the development of computational tools. These tools in turn accelerate and facilitate the recognition of immune responses [4]. Previously, the advancement of vaccines relied on immunological and biochemical experiments, including ELISA, NMR, immunofluorescence, western blot, and immunohistochemistry which were time-consuming and cost-effective. However, using immunoinformatics tools such as databases and various softwares have largely circumvented these disadvantages. Prediction of immunogenic epitopes and the virtual immunogenicity assessment have contributed to vaccine design efforts, prevention of diseases, and their diagnosis and treatment [4].
Genetic and epigenetic strategies for advancing ovarian cancer immunotherapy
Published in Expert Opinion on Biological Therapy, 2019
Youngwoo Cho, Lara Milane, Mansoor M. Amiji
In OC carcinogenesis, the immune system is believed to be an important mediator with its possible role in ovulation and chronic inflammation [15]. Indeed, candidate gene studies performed by several group of researchers have revealed that polymorphisms in multiple immune-related genes show correlation with OC development: single nucleotide polymorphisms of NFKB1, NOD2, CASP8, BRCA1/2, and PTGS2 were significantly associated reduced risk of OC development while those of IL1A and IL18 were significantly associated with increased risk [15]. Zhang et al. have demonstrated that T-cell infiltration in OC was correlated with increased survival in patients with increased expression of monokines and chemokines [4]. Other studies have demonstrated that OC with high and low CD8 T-cell infiltration show differential gene expressions of interferon (IFN) regulatory factor 1 and C-X-C chemokine receptor 6 [16,17]. Recently, in order to further incorporate the role of the immune system in our understanding of the established disease, a new field of study, namely immunomics, has emerged. This novel scholarly inquiry aims to analyze the interface between host and (pathogen) proteome using genome-wide approaches [18]. An increasing number of studies are emerging that advance our knowledge of OC immunomics.