Annotation of immune genes in the extinct thylacine (Thylacinus cynocephalus)
AbstractAdvances in genome sequencing technology have enabled genomes of extinct species to be sequenced. However, given the fragmented nature of these genome assemblies, it is not clear whether it is possible to comprehensively annotate highly variable and repetitive genes such as those involved in immunity. As such, immune genes have only been investigated in a handful of extinct genomes, mainly in human lineages. In 2018 the genome of the thylacine (Thylacinus cynocephalus), a carnivorous marsupial from Tasmania that went extinct in 1936, was sequenced. Here we attempt to characterise the immune repertoire of the thylac...
Source: Immunogenetics - June 1, 2021 Category: Genetics & Stem Cells Source Type: research
Major histocompatibility complex genes and locus organization in the Komodo dragon (Varanus komodoensis)
AbstractWe performed a meta-analysis of the newly assembled Komodo dragon (Varanus komodoensis) genome to characterize the major histocompatibility complex (MHC) of the species. The MHC gene clusters of the Komodo dragon are gene dense, complex, and contain counterparts of many genes of the human MHC. Our analysis identified 20 contigs encompassing ~ 6.9 Mbp of sequence with 223 annotated genes of which many are predicted orthologs to the genes of the human MHC. These MHC contigs range in size from 13.2 kb to 21.5 Mbp, contain an average of one gene per 30 kb, and are thought to occur on at least two chromosomes. Eigh...
Source: Immunogenetics - May 12, 2021 Category: Genetics & Stem Cells Source Type: research
Major histocompatibility complex genes and locus organization in the Komodo dragon ( Varanus komodoensis )
AbstractWe performed a meta-analysis of the newly assembled Komodo dragon (Varanus komodoensis) genome to characterize the major histocompatibility complex (MHC) of the species. The MHC gene clusters of the Komodo dragon are gene dense, complex, and contain counterparts of many genes of the human MHC. Our analysis identified 20 contigs encompassing ~ 6.9 Mbp of sequence with 223 annotated genes of which many are predicted orthologs to the genes of the human MHC. These MHC contigs range in size from 13.2 kb to 21.5 Mbp, contain an average of one gene per 30 kb, and are thought to occur on at least two chromosomes. Eigh...
Source: Immunogenetics - May 12, 2021 Category: Genetics & Stem Cells Source Type: research
Erik Thorsby (1938 –2021)
(Source: Immunogenetics)
Source: Immunogenetics - May 6, 2021 Category: Genetics & Stem Cells Source Type: research
CDR3 and V genes show distinct reconstitution patterns in T cell repertoire post-allogeneic bone marrow transplantation
AbstractRestoration of T cell repertoire diversity after allogeneic bone marrow transplantation (allo-BMT) is crucial for immune recovery. T cell diversity is produced by rearrangements of germline gene segments (V (D) and J) of the T cell receptor (TCR) α and β chains, and selection induced by binding of TCRs to MHC-peptide complexes. Multiple measures were proposed for this diversity. We here focus on the V-gene usage and the CDR3 sequences of the beta chain. We compared multiple T cell repertoires to follow T cell repertoire changes post-allo-B MT in HLA-matched related donor and recipient pairs. Our analyses of the d...
Source: Immunogenetics - April 1, 2021 Category: Genetics & Stem Cells Source Type: research
Correction to: Major histocompatibility complex (MHC) associations with diseases in ethnic groups of the Arabian Peninsula
A correction to this paper has been published:https://doi.org/10.1007/s00251-021-01210-z. (Source: Immunogenetics)
Source: Immunogenetics - April 1, 2021 Category: Genetics & Stem Cells Source Type: research
Plasma cell immunoglobulin heavy chain repertoire dynamics before and after tetanus booster vaccination
AbstractAntibody sequence repertoire analysis of plasma cells (PC) isolated before and 1 week after a vaccine provides time-specific snapshots of the antibody response. Comparison of the immunoglobulin (Ig) sequences pre- and post-vaccination allows analysis of maturation over time and identification of antigen specific Ig. Here we compare the Ig heavy chain (Ig-H) repertoire of circulating PCs isolated from 109 peripheral blood mononuclear cells (PBMC) collected by apheresis 1 week after a tetanus toxoid vaccine booster with the Ig-H repertoire of PCs collected 2 and 11 weeks prior to the booster. A total of 21,060 unique...
Source: Immunogenetics - March 25, 2021 Category: Genetics & Stem Cells Source Type: research
Evidence of genetic epistasis in autoimmune diabetes susceptibility revealed by mouse congenic sublines
AbstractSusceptibility to autoimmune diabetes is a complex genetic trait. Linkage analyses exploiting the NOD mouse, which spontaneously develops autoimmune diabetes, have proved to be a useful tool for the characterization of some of these traits. In a linkage analysis using 3A9 TCR transgenic mice on both B10.BR and NOD.H2k backgrounds, we previously determined that both theIdd2 andIdd13 loci were linked to the proportion of immunoregulatory CD4-CD8- double negative (DN) T cells. In addition toIdd2 andIdd13, five other loci showed weak linkage to the proportion of DN T cells. Of interest, in an interim analysis, a locus ...
Source: Immunogenetics - March 23, 2021 Category: Genetics & Stem Cells Source Type: research
HLA-DRB1 genes and the expression dynamics of HLA CIITA determine the susceptibility to T2DM
AbstractType 2 diabetes mellitus (T2DM) is a disease with polygenic inheritance. The expression of major histocompatibility complex class II genes are regulated by several trans-activators. We have studied the expression of HLA-DRB1, RFX, CIITA-P1, PIV transactivators, immunophenotyping of cells, SNPs in CIITA-168 (A/G) and IFN- γ + 874 (T/A) in T2DM patients and controls (n = 201 each). We observed increased frequencies of DRB1*03, DRB1*04 and DRB1*07 and decreased frequencies of DRB1*10, DRB1*14, and DRB1*15 alleles among patients. Significant up-regulations of HLA-DRB1 genes were observed in patients (p < 0...
Source: Immunogenetics - March 22, 2021 Category: Genetics & Stem Cells Source Type: research
Prediction of ATPase cation transporting 13A2 molecule in Petromyzon marinus and pan-cancer analysis into human tumors from an evolutionary perspective
AbstractThe ATPase cation transporting 13A2 protein (ATP13A2), which maintains the homeostasis of mitochondria and lysosomes, plays a significant role in human neurodegenerative diseases and cancer. Through constructing a lamprey proteome database, employing multiple sequence alignment and phylogenetic analysis, 5 ATP13A2 proteins fromPetromyzon marinus (Pm-ATP13A2) were identified based on the evolutionary perspective. The motif and domain analysis showed that the ATP13A2 protein was conserved. The multiple phosphorylation sites and transmembrane structures highlighted the characteristics of ATP13A2 as the P-ATPase-V cati...
Source: Immunogenetics - March 20, 2021 Category: Genetics & Stem Cells Source Type: research
Analysis of shark NCR3 family genes reveals primordial features of vertebrate NKp30
AbstractNatural killer (NK) cells play major roles in innate immunity against viruses and cancer. Natural killer receptors (NKR) expressed by NK cells recognize foreign- or self-ligands on infected and transformed cells as well as healthy cells. NKR genes are the most rapidly evolving loci in vertebrates, and it is generally difficult to detect orthologues in different taxa. The unique exception is NKp30, an activating NKR in mammals that binds to the self-ligand B7H6. The NKp30-encoding gene,NCR3, has been found in most vertebrates including sharks, the oldest vertebrates with human-type adaptive immunity. NCR3 has a spec...
Source: Immunogenetics - March 19, 2021 Category: Genetics & Stem Cells Source Type: research
The WC1 γδ T cell pathogen receptor of ruminants is preserved in the genome of ancient extinct auroch
AbstractThe work reported here investigated the γδ T cell-specific cell surface receptor known as workshop cluster 1 (WC1) in the extinct Auroch and compared the gene sequences to those in modern cattle breeds. These molecules function as hybrid pattern recognition receptors (PRR), binders of microbial pathogens, and as signaling co-receptors o f the T cell antigen receptor (TCR), directing the immune responses by γδ T cell subsets. Sequences in the Auroch genome included both WC1.1 and WC1.2-like a-patterned scavenger receptor cytsteine–rich (SRCR) domains as well as the more conserved b, c, d, and e-patterned SRCR ...
Source: Immunogenetics - March 12, 2021 Category: Genetics & Stem Cells Source Type: research
Variation and expression of HLA-DPB1 gene in HBV infection
AbstractHepatitis B virus (HBV) affects approximately 68 million people in China, and 10 –15% of adults infected with HBV develop chronic hepatitis B, liver cirrhosis, liver failure or hepatocellular carcinoma (HCC). HLA-DPB1 gene polymorphism and expression have been shown to be associated with HBV infection susceptibility and spontaneous clearance. The aim of this study is to evalua te the role of HLA-DPB1 gene polymorphism in HBV infection. HLA-DPB1 and rs9277535 polymorphisms were investigated in 259 patients with HBV infection and 442 healthy controls (HCs) using sequence-based typing. The mRNA of HLA-DPB1 was measu...
Source: Immunogenetics - March 12, 2021 Category: Genetics & Stem Cells Source Type: research
Correction to: Major histocompatibility complex (MHC) associations with diseases in ethnic groups of the Arabian Peninsula
A correction to this paper has been published:https://doi.org/10.1007/s00251-021-01210-z. (Source: Immunogenetics)
Source: Immunogenetics - March 5, 2021 Category: Genetics & Stem Cells Source Type: research
