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AI and the Bioscience and Clinical Considerations for Immunology
Published in Louis J. Catania, AI for Immunology, 2021
One other critical element to mention at the beginning of any immunology discussion is the intimate relationship between the science of immunology and genetics, a relationship referred to as immunogenics, immunogenetics, and immunogenomics. The immune system and its activity is effectively dictated and controlled by the human genome. AI is playing an enormous role in our better understanding of this complex relationship both in health and disease. Research and advances in our understanding of the immune system and autoimmune diseases, cancers, infectious diseases, and beyond are indelibly related to immunogenetics. As such, there will be a future volume in this “AI for Everything” series addressing genetics. In this volume on “AI for Immunology,” by necessity, there will be some discussion on genetics as related to immunogenetics.
HLA and autoimmunity
Published in Irun R. Cohen, Perspectives on Autoimmunity, 2020
Rene R. P. de Vries, J. J. van Rood
We will start the second part of this chapter with a question: What has immunogenetics to offer for the prevention or treatment of autoimmune diseases? This question may be answered by using the HLA class I and II Ir genes just described as an example. The aim of the immunogenetic approach to an autoimmune disease is to unravel the following chain of events: polymorphic Ir-genes (1) contain the information for Ir gene products (2) which regulate the immune response and differ among individuals. These differences lead to differences in immune reactivity among individuals (3), which in their turn cause differential susceptibility to or expression of autoimmune diseases (4). Possibilities for intervention at each level (1 through 4) are feasible and may lead to preventive or therapeutic applications. The power of this approach lies particularly in the use of Ir gene differences among healthy individuals as a probe for a mechanism leading to autoimmune disease, in a similar way as the study of immune-deficient individuals led to a better insight into how the immune system prevents disease. The potential usefulness of this approach is illustrated in several animal models discussed in other chapters of this book (Chapters 11 and 12). Here we will discuss the state of the art in humans.
Tolerance and autoimmunity
Published in Gabriel Virella, Medical Immunology, 2019
George C. Tsokos, Gabriel Virella
These postulates are supported by immunogenetic studies in different animals and humans with different manifestations of autoimmunity. Those studies suggest that linkages between specific TCR V-region genes and specific autoimmune diseases may actually exist (for example, insulin-dependent diabetes mellitus, multiple sclerosis, and SLE). Even in identical twins, however, concordance for a particular autoimmune disease never exceeds 40%, suggesting that the presence of autoimmunity-associated TCR V-region genes is not sufficient to cause disease by itself. Indeed, with certain exceptions, human autoimmune diseases are multigenic, and the number of the involved genes has not been determined.
Advancements of next generation sequencing in the field of Rheumatoid Arthritis
Published in Egyptian Journal of Basic and Applied Sciences, 2023
Ankita Pati, Dattatreya Kar, Jyoti Ranjan Parida, Ananya Kuanar
Literature gap has been highlighted through recent research, which has shown that non-coding RNAs and super-enhancers may be overrepresented in rheumatoid arthritis genetic loci, implying fresh perspectives into the disease process [98]. A considerable gap has been observed in the area of immunogenetic correlation determination through NGS technology through sequencing genetic diversity [99]. Complications in the NGS technology for RA have been developed through demonstration of specific alleles such as HLA-DRB [100]. A potential gap has been observed from the correlation of the immunogenetic responses as well as the genetic variation analysis from genome. Additional HLA-DRB1 alleles provide illness resistance in contrast to the HLA-DRB1 alleles that lead to RA risks, which has a limitation in NGS processes due to high variability [101]. Such beneficial HLA-DRB1 alleles have been classified pertaining to different methods and are more common in healthy controls than in RA patients. In this way, protection can be provided against rheumatoid arthritis if it is predominantly connected with the HLA-DRB1 alleles.
Recent trends in next generation immunoinformatics harnessed for universal coronavirus vaccine design
Published in Pathogens and Global Health, 2023
Chin Peng Lim, Boon Hui Kok, Hui Ting Lim, Candy Chuah, Badarulhisam Abdul Rahman, Abu Bakar Abdul Majeed, Michelle Wykes, Chiuan Herng Leow, Chiuan Yee Leow
The Allele Frequency Net Database (AFND) is an open resource storing the frequency data on the polymorphisms of immune-related genes such as human leukocyte antigen (HLA) system, killer-cell immunoglobulin-like receptors (KIR), MHC class I chain-related genes (MIC) and cytokine gene polymorphisms. AFND collects information and data from four main sources, which are, (i) peer-reviewed publications, (ii) analysed populations by International HLA and Immunogenetics Workshops (IHWSs), (iii) individual submissions and (iv) short publication reports (SPR) in Human Immunology Journal. The allele, gene, genotype or haplotype frequencies for the abovementioned loci can be searched in this database [92]. AutoPeptiDB is another database, composed of 103 high-resolution peptide-protein complexes. The binding affinity of short peptides and proteins is calculated based on the data arising from these complexes in this database. The peptide–protein interactions being considered, generally take place in cellular activities such as signal transduction, protein transport, antigen binding and enzyme-substrate inhibition. There are no two protein monomers that share more than 70% sequence identity in this dataset [93].
HLA and amyotrophic lateral sclerosis: a systematic review and meta-analysis
Published in Amyotrophic Lateral Sclerosis and Frontotemporal Degeneration, 2023
R. J. Nona, J. M. Greer, R. D. Henderson, P. A. McCombe
The immune system comprises many different cells, cellular mediators such as cytokines, and antibodies, all of which are subject to genetic variation. A recent large genome-wide association study (GWAS) and meta-analysis has reported an association of ALS with the human leukocyte antigen (HLA) region (18). The HLA region, also referred to as the major histocompatibility complex (MHC) region, is an immunogenetic region located on the short arm (p21) of chromosome 6. It consists of 3 broad regions, class I (which encodes for the HLA-A, HLA-B and HLA-C molecules, amongst others), the class III region (which encodes a variety of molecules, including members of the TNF and complement families), and the class II regions (which primarily encodes the HLA-DR, HLA-DQ, and HLA-DP molecules). The HLA-A, -B, and -C molecules are involved in antigen presentation to CD8+ cytotoxic T lymphocytes, whereas the HLA-DR, -DP, and -DQ molecules present antigen to CD4+ helper T lymphocytes (19). Genetic alterations and polymorphisms of these genes have been associated with several neurodegenerative diseases (20). The region of the HLA identified in the recent ALS GWAS is in a non-coding area of the class II region (identified by rs9275477), between the genes encoding the HLA-DQ beta chain and a non-classical HLA-DQ alpha chain, close to the pseudogene MTC03P1. However, there is strong linkage disequilibrium across the HLA region, so this may just be a marker that tags the actual causal variant(s).