antigenic selection
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Immunoglobulin (IG) gene repertoire restrictions strongly support antigen selection in the pathogenesis of chronic lymphocytic leukemia (CLL). Given the emerging multifarious interactions between CLL and bystander T cells, we sought to determine whether antigen(s) are also selecting T cells in CLL. We performed a large-scale, next-generation sequencing (NGS) study of the T-cell repertoire, focusing on major stereotyped subsets representing CLL subgroups with undisputed antigenic drive, but also included patients carrying non-subset IG rearrangements to seek for T-cell immunogenetic signatures ubiquitous in CLL. Considering the inherent limitations of NGS, we deployed bioinformatics algorithms for qualitative curation of T-cell receptor rearrangements, and included multiple types of controls. Overall, we document the clonal architecture of the T-cell repertoire in CLL. These T-cell clones persist and further expand overtime, and can be shared by different patients, most especially patients belonging to the same stereotyped subset. Notably, these shared clonotypes appear to be disease-specific, as they are found in neither public databases nor healthy controls. Altogether, these findings indicate that antigen drive likely underlies T-cell expansions in CLL and may be acting in a CLL subset-specific context. Whether these are the same antigens interacting with the malignant clone or tumor-derived antigens remains to be elucidated.
- MeSH
- antigeny nádorové MeSH
- buněčné mikroprostředí MeSH
- CD8-pozitivní T-lymfocyty imunologie MeSH
- chronická lymfatická leukemie imunologie MeSH
- genová přestavba T-lymfocytů MeSH
- geny pro imunoglobuliny MeSH
- lidé MeSH
- senioři MeSH
- T-lymfocyty imunologie MeSH
- vysoce účinné nukleotidové sekvenování MeSH
- Check Tag
- lidé MeSH
- senioři MeSH
- Publikační typ
- časopisecké články MeSH
Apical membrane antigen-1 (AMA-1) of Plasmodium vivax Grassi et Feletti, 1890 is a promising malaria vaccine candidate. However, antigenic variation is a major problem to design a universal malaria vaccine. Hence, detailed understanding of the pvama-1 gene polymorphism can provide conductive information on this potential vaccine component. Therefore, this study investigated the extent of genetic polymorphisms at domain I (DI), DII and partial DIII of AMA-1 among Iranian P. vivax isolates. Out of 107 blood samples, 92 were analysed based on the quality of the sequencing data. The sequences were classified into 53 haplotypes. Amino acid changes were observed at 31 positions that 17 were located at DI, 11 were at DII and the rest of them (3 positions) were at DIII. Thus, codon polymorphisms at DI were found to be higher than DII. Also, five of these polymorphic codons (D242E, T374P, S389R, Y391F, I395F) were novel and have not been reported yet. Neutrality analysis by using the dN-dS difference (the difference between the rate of non-synonymous and synonymous mutations) showed a negative diversifying selection at DI, DII and across the length of both domains. The potential B-cell epitopes were found in 5 regions of the PvAMA-1 with 10 mutation sites (E145A, K188N, E189N/K/D, K190Q/E, P210S, E227V, D242E, R249H, G253E, K352E), whereas only one mutation (G288E) has been detected in intrinsically unstructured/disordered regions. Fixation index (Fst) estimation between Iranian and Indian isolates (0.0131) indicated a significant low genetic differentiation. Distribution of the polymorphic sites and IURs mapped on a three dimensional structure of PvAMA-1 showed that these regions were located at two opposite faces of the molecule. In conclusion, the results have significant value in the design and development of a malaria vaccine based on this antigen.
- MeSH
- antigeny protozoální genetika metabolismus MeSH
- fylogeneze MeSH
- genetická variace MeSH
- konformace proteinů MeSH
- lidé MeSH
- malárie vivax epidemiologie parazitologie MeSH
- membránové proteiny genetika metabolismus MeSH
- molekulární sekvence - údaje MeSH
- Plasmodium vivax genetika MeSH
- protozoální DNA genetika MeSH
- protozoální proteiny genetika metabolismus MeSH
- regulace genové exprese MeSH
- sekvence aminokyselin MeSH
- selekce (genetika) MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Írán MeSH
- MeSH
- HLA antigeny analýza MeSH
- isoelektrická fokusace metody MeSH
- lidé MeSH
- transplantace kostní dřeně MeSH
- Check Tag
- lidé MeSH
BACKGROUND: The mammalian Major Histocompatibility Complex (MHC) is a genetic region containing highly polymorphic genes with immunological functions. MHC class I and class II genes encode antigen-presenting molecules expressed on the cell surface. The MHC class II sub-region contains genes expressed in antigen presenting cells. The antigen binding site is encoded by the second exon of genes encoding antigen presenting molecules. The exon 2 sequences of these MHC genes have evolved under the selective pressure of pathogens. Interspecific differences can be observed in the class II sub-region. The family Equidae includes a variety of domesticated, and free-ranging species inhabiting a range of habitats exposed to different pathogens and represents a model for studying this important part of the immunogenome. While equine MHC class II DRA and DQA loci have received attention, the genetic diversity and effects of selection on DRB and DQB loci have been largely overlooked. This study aimed to provide the first in-depth analysis of the MHC class II DRB and DQB loci in the Equidae family. RESULTS: Three DRB and two DQB genes were identified in the genomes of all equids. The genes DRB2, DRB3 and DQB3 showed high sequence conservation, while polymorphisms were more frequent at DRB1 and DQB1 across all species analyzed. DQB2 was not found in the genome of the Asiatic asses Equus hemionus kulan and E. h. onager. The bioinformatic analysis of non-zero-coverage-bases of DRB and DQB genes in 14 equine individual genomes revealed differences among individual genes. Evidence for recombination was found for DRB1, DRB2, DQB1 and DQB2 genes. Trans-species allele sharing was identified in all genes except DRB1. Site-specific selection analysis predicted genes evolving under positive selection both at DRB and DQB loci. No selected amino acid sites were identified in DQB3. CONCLUSIONS: The organization of the MHC class II sub-region of equids is similar across all species of the family. Genomic sequences, along with phylogenetic trees suggesting effects of selection as well as trans-species polymorphism support the contention that pathogen-driven positive selection has shaped the MHC class II DRB/DQB sub-regions in the Equidae.
- MeSH
- Equidae klasifikace genetika MeSH
- fylogeneze MeSH
- hlavní histokompatibilní komplex genetika MeSH
- molekulární evoluce * MeSH
- polymorfismus genetický * MeSH
- rekombinace genetická MeSH
- selekce (genetika) * MeSH
- vznik druhů (genetika) MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
Among bird species, the most studied major histocompatibility complex (MHC) is the chicken MHC. Although the number of studies on MHC in free-ranging species is increasing, the knowledge on MHC variation in species closely related to chicken is required to understand the peculiarities of bird MHC evolution. Here we describe the variation of MHC class IIB (MHCIIB) exon 2 in a population of the Grey partridge (Perdix perdix), a species of high conservation concern throughout Europe and an emerging galliform model in studies of sexual selection. We found 12 alleles in 108 individuals, but in comparison to other birds surprisingly many sites show signatures of historical positive selection. Individuals displayed between two to four alleles both on genomic and complementary DNA, suggesting the presence of two functional MHCIIB loci. Recombination and gene conversion appear to be involved in generating MHCIIB diversity in the Grey partridge; two recombination breakpoints and several gene conversion events were detected. In phylogenetic analysis of galliform MHCIIB, the Grey partridge alleles do not cluster together, but are scattered through the tree instead. Thus, our results indicate that the Grey partridge MHCIIB is comparable to most other galliforms in terms of copy number and population polymorphism.
- MeSH
- alely MeSH
- druhová specificita MeSH
- exony genetika MeSH
- fylogeneze MeSH
- Galliformes genetika MeSH
- genová konverze * MeSH
- MHC antigeny II. třídy chemie genetika MeSH
- molekulární sekvence - údaje MeSH
- polymorfismus genetický * MeSH
- pravděpodobnostní funkce MeSH
- regulace genové exprese MeSH
- rekombinace genetická genetika MeSH
- sekvence aminokyselin MeSH
- sekvence nukleotidů MeSH
- sekvenční seřazení MeSH
- selekce (genetika) * MeSH
- substituce aminokyselin genetika MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- MeSH
- CD antigeny MeSH
- myši transgenní MeSH
- myši MeSH
- selekce (genetika) MeSH
- T-lymfocyty MeSH
- thymus MeSH
- zvířata MeSH
- Check Tag
- myši MeSH
- zvířata MeSH
BACKGROUND: The interferon-induced transmembrane (IFITM) protein family comprises a class of restriction factors widely characterised in humans for their potent antiviral activity. Their biological activity is well documented in several animal species, but their genetic variation and biological mechanism is less well understood, particularly in avian species. RESULTS: Here we report the complete sequence of the domestic chicken Gallus gallus IFITM locus from a wide variety of chicken breeds to examine the detailed pattern of genetic variation of the locus on chromosome 5, including the flanking genes ATHL1 and B4GALNT4. We have generated chIFITM sequences from commercial breeds (supermarket-derived chicken breasts), indigenous chickens from Nigeria (Nsukka) and Ethiopia, European breeds and inbred chicken lines from the Pirbright Institute, totalling of 206 chickens. Through mapping of genetic variants to the latest chIFITM consensus sequence our data reveal that the chIFITM locus does not show structural variation in the locus across the populations analysed, despite spanning diverse breeds from different geographic locations. However, single nucleotide variants (SNVs) in functionally important regions of the proteins within certain groups of chickens were detected, in particular the European breeds and indigenous birds from Ethiopia and Nigeria. In addition, we also found that two out of four SNVs located in the chIFITM1 (Ser36 and Arg77) and chIFITM3 (Val103) proteins were simultaneously under positive selection. CONCLUSIONS: Together these data suggest that IFITM genetic variation may contribute to the capacities of different chicken populations to resist virus infection.
- MeSH
- diferenciační antigeny genetika MeSH
- genetické lokusy * MeSH
- genetické markery * MeSH
- genom MeSH
- jednonukleotidový polymorfismus * MeSH
- kur domácí MeSH
- mapování chromozomů MeSH
- molekulární evoluce * MeSH
- sekvence aminokyselin MeSH
- sekvenční analýza DNA MeSH
- sekvenční homologie MeSH
- selekce (genetika) * MeSH
- variabilita počtu kopií segmentů DNA MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- srovnávací studie MeSH
