scholarly journals Trans-Species Polymorphism in Immune Genes: General Pattern or MHC-Restricted Phenomenon?

2015 ◽  
Vol 2015 ◽  
pp. 1-10 ◽  
Author(s):  
Martin Těšický ◽  
Michal Vinkler
Keyword(s):  
Balancing Selection ◽  
General Pattern ◽  
Evolutionary Medicine ◽  
Present Species ◽  
Evolutionary Pattern ◽  
Immune Genes ◽  
Adaptive Introgression ◽  
Histocompatibility Complex ◽  
Innate Immune Genes ◽  
Immune Related Genes

Immunity exhibits extraordinarily high levels of variation. Evolution of the immune system in response to host-pathogen interactions in particular ecological contexts appears to be frequently associated with diversifying selection increasing the genetic variability. Many studies have documented that immunologically relevant polymorphism observed today may be tens of millions years old and may predate the emergence of present species. This pattern can be explained by the concept of trans-species polymorphism (TSP) predicting the maintenance and sharing of favourable functionally important alleles of immune-related genes between species due to ongoing balancing selection. Despite the generality of this concept explaining the long-lasting adaptive variation inherited from ancestors, current research in TSP has vastly focused only on major histocompatibility complex (MHC). In this review we summarise the evidence available on TSP in human and animal immune genes to reveal that TSP is not a MHC-specific evolutionary pattern. Further research should clearly pay more attention to the investigation of TSP in innate immune genes and especially pattern recognition receptors which are promising candidates for this type of evolution. More effort should also be made to distinguish TSP from convergent evolution and adaptive introgression. Identification of balanced TSP variants may represent an accurate approach in evolutionary medicine to recognise disease-resistance alleles.

scholarly journals The Evolution of Innate Immune Genes: Purifying and Balancing Selection on β-Defensins in Waterfowl

2016 ◽  
Vol 33 (12) ◽  
pp. 3075-3087 ◽  
Author(s):  
Joanne R. Chapman ◽  
Olof Hellgren ◽  
Anu S. Helin ◽  
Robert H. S. Kraus ◽  
Ruth L. Cromie ◽  
...  
Keyword(s):  
Balancing Selection ◽  
Innate Immune ◽  
Immune Genes ◽  
Innate Immune Genes

scholarly journals A new theory of MHC evolution: beyond selection on the immune genes

2008 ◽  
Vol 276 (1657) ◽  
pp. 657-665 ◽  
Author(s):  
Cock van Oosterhout
Keyword(s):  
Balancing Selection ◽  
Gene Diversity ◽  
Purifying Selection ◽  
Recombination Rates ◽  
Immune Genes ◽  
Mhc Genes ◽  
Histocompatibility Complex ◽  
Species Evolution ◽  
Hla Haplotypes ◽  
Mhc Evolution

The major histocompatibility complex (MHC) is a dense region of immune genes with high levels of polymorphism, which are arranged in haplotype blocks. Traditional models of balancing selection (i.e. overdominance and negative frequency dependence) were developed to study the population genetics of single genes. However, the MHC is a multigene family surrounded by linked (non-neutral) polymorphisms, and not all of its features are well explained by these models. For example, (i) the high levels of polymorphism in small populations, (ii) the unexpectedly large genetic differentiation between populations, (iii) the shape of the allelic genealogy associated with trans-species evolution, and (iv) the close associations between particular MHC (human leucocyte antigen, HLA) haplotypes and the approximately 100 pathologies in humans. Here, I propose a new model of MHC evolution named Associative Balancing Complex evolution that can explain these phenomena. The model proposes that recessive deleterious mutations accumulate as a ‘sheltered load’ nearby MHC genes. These mutations can accumulate because (i) they are rarely expressed as homozygotes given the high MHC gene diversity and (ii) purifying selection is inefficient with low recombination rates (cf. Muller's ratchet). Once fixed, these mutations add to balancing selection and further reinforce linkage through epistatic selection against recombinants.

scholarly journals Expression Changes of MHC and Other Immune Genes in Frog Skin during Ontogeny

Animals ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 91
Author(s):  
Quintin Lau ◽  
Takeshi Igawa ◽  
Shohei Komaki ◽  
Yoko Satta
Keyword(s):  
Mhc Class I ◽  
Larval Stage ◽  
Mrna Level ◽  
Class I ◽  
Immune Genes ◽  
Larval Stages ◽  
Histocompatibility Complex ◽  
Immune Related Genes ◽  
Go Terms ◽  
Rana Ornativentris

Anuran amphibians undergo major physiological and immunological changes following metamorphosis. Genes of the major histocompatibility complex (MHC) code for receptors important for vertebrate adaptive immunity. We used qPCR to measure skin MHC expression in six different ontological stages of Rana ornativentris (n = 10 per stage); normalized MHC class I and II expression at the mRNA level was significantly higher in stage 28 (mid-larval) compared to stages 24/25 (early-larval) tadpoles. Subsequent transcriptomic analyses of three tadpole (early-, mid-, and late-larval) stages of R. ornativentris and model species Xenopus tropicalis focused on mRNA expression of immune-related genes in the skin. Normalized expression of most MHC class I and II transcripts in both species were significantly higher in mid- and late-larval stages compared to early-larval stage. In addition, gene ontology (GO) analyses of differentially expressed transcripts revealed several immune-related GO terms that were significantly upregulated from the mid-larval stage. Our study provides evidence that both MHC class I and II is expressed during development in both R. ornativentris and X. tropicalis.

1080 Milk yield genotype impacts expression of hepatic innate immune genes during the transition period in Holsteins

2016 ◽  
Vol 94 (suppl_5) ◽  
pp. 518-518
Author(s):  
G. T. Cousillas ◽  
W. J. Weber ◽  
B. Walcheck ◽  
D. E. Kerr ◽  
T. H. Elsasser ◽  
...  
Keyword(s):  
Milk Yield ◽  
Transition Period ◽  
Innate Immune ◽  
Immune Genes ◽  
Innate Immune Genes

Recombination, Balancing Selection and Phylogenies in MHC and Self-Incompatibility Genes

Genetics ◽  
2001 ◽  
Vol 159 (4) ◽  
pp. 1833-1844 ◽  
Author(s):  
Mikkel H Schierup ◽  
Anders M Mikkelsen ◽  
Jotun Hein
Keyword(s):  
Major Histocompatibility Complex ◽  
Phylogenetic Tree ◽  
Balancing Selection ◽  
Nucleotide Sequences ◽  
Recombination Process ◽  
Self Incompatibility ◽  
Selection Coefficient ◽  
Histocompatibility Complex ◽  
A Site ◽  
Possible Cause

AbstractUsing a coalescent model of multiallelic balancing selection with recombination, the genealogical process as a function of recombinational distance from a site under selection is investigated. We find that the shape of the phylogenetic tree is independent of the distance to the site under selection. Only the timescale changes from the value predicted by Takahata's allelic genealogy at the site under selection, converging with increasing recombination to the timescale of the neutral coalescent. However, if nucleotide sequences are simulated over a recombining region containing a site under balancing selection, a phylogenetic tree constructed while ignoring such recombination is strongly affected. This is true even for small rates of recombination. Published studies of multiallelic balancing selection, i.e., the major histocompatibility complex (MHC) of vertebrates, gametophytic and sporophytic self-incompatibility of plants, and incompatibility of fungi, all observe allelic genealogies with unexpected shapes. We conclude that small absolute levels of recombination are compatible with these observed distortions of the shape of the allelic genealogy, suggesting a possible cause of these observations. Furthermore, we illustrate that the variance in the coalescent with recombination process makes it difficult to locate sites under selection and to estimate the selection coefficient from levels of variability.

scholarly journals Identification and development of an independent immune-related genes prognostic model for breast cancer

BMC Cancer ◽  
2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Lin Chen ◽  
Yuxiang Dong ◽  
Yitong Pan ◽  
Yuhan Zhang ◽  
Ping Liu ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Regression Analysis ◽  
Cox Regression ◽  
Gene Set Enrichment Analysis ◽  
Risk Scores ◽  
Validation Dataset ◽  
Immune Gene ◽  
Cox Regression Analysis ◽  
Immune Genes ◽  
Immune Related Genes

Abstract Background Breast cancer is one of the main malignant tumors that threaten the lives of women, which has received more and more clinical attention worldwide. There are increasing evidences showing that the immune micro-environment of breast cancer (BC) seriously affects the clinical outcome. This study aims to explore the role of tumor immune genes in the prognosis of BC patients and construct an immune-related genes prognostic index. Methods The list of 2498 immune genes was obtained from ImmPort database. In addition, gene expression data and clinical characteristics data of BC patients were also obtained from the TCGA database. The prognostic correlation of the differential genes was analyzed through Survival package. Cox regression analysis was performed to analyze the prognostic effect of immune genes. According to the regression coefficients of prognostic immune genes in regression analysis, an immune risk scores model was established. Gene set enrichment analysis (GSEA) was performed to probe the biological correlation of immune gene scores. P < 0.05 was considered to be statistically significant. Results In total, 556 immune genes were differentially expressed between normal tissues and BC tissues (p < 0. 05). According to the univariate cox regression analysis, a total of 66 immune genes were statistically significant for survival risk, of which 30 were associated with overall survival (P < 0.05). Finally, a 15 immune genes risk scores model was established. All patients were divided into high- and low-groups. KM survival analysis revealed that high immune risk scores represented worse survival (p < 0.001). ROC curve indicated that the immune genes risk scores model had a good reliability in predicting prognosis (5-year OS, AUC = 0.752). The established risk model showed splendid AUC value in the validation dataset (3-year over survival (OS) AUC = 0.685, 5-year OS AUC = 0.717, P = 0.00048). Moreover, the immune risk signature was proved to be an independent prognostic factor for BC patients. Finally, it was found that 15 immune genes and risk scores had significant clinical correlations, and were involved in a variety of carcinogenic pathways. Conclusion In conclusion, our study provides a new perspective for the expression of immune genes in BC. The constructed model has potential value for the prognostic prediction of BC patients and may provide some references for the clinical precision immunotherapy of patients.

Flagellin induces innate immune genes in bronchial epithelial cells in vivo: Role of TET2

2021 ◽  
Author(s):  
Wanhai Qin ◽  
Xanthe Brands ◽  
Cornelis Veer ◽  
Alex F. Vos ◽  
Brendon P. Scicluna ◽  
...  
Keyword(s):  
Epithelial Cells ◽  
Bronchial Epithelial Cells ◽  
Innate Immune ◽  
Bronchial Epithelial ◽  
Immune Genes ◽  
Innate Immune Genes

scholarly journals Thymic transcriptome analysis after Newcastle disease virus inoculation in chickens and the influence of host small RNAs on NDV replication

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Liangxing Guo ◽  
Zhaokun Mu ◽  
Furong Nie ◽  
Xuanniu Chang ◽  
Haitao Duan ◽  
...  
Keyword(s):  
Innate Immunity ◽  
Newcastle Disease Virus ◽  
Disease Virus ◽  
Newcastle Disease ◽  
Viral Disease ◽  
Immune Genes ◽  
Comprehensive Information ◽  
Virulent Newcastle Disease Virus ◽  
Chicken Thymus ◽  
Innate Immune Genes

AbstractNewcastle disease (ND), caused by virulent Newcastle disease virus (NDV), is a contagious viral disease affecting various birds and poultry worldwide. In this project, differentially expressed (DE) circRNAs, miRNAs and mRNAs were identified by high-throughput RNA sequencing (RNA-Seq) in chicken thymus at 24, 48, 72 or 96 h post LaSota NDV vaccine injection versus pre-inoculation group. The vital terms or pathways enriched by vaccine-influenced genes were tested through KEGG and GO analysis. DE genes implicated in innate immunity were preliminarily screened out through GO, InnateDB and Reactome Pathway databases. The interaction networks of DE innate immune genes were established by STRING website. Considering the high expression of gga-miR-6631-5p across all the four time points, DE circRNAs or mRNAs with the possibility to bind to gga-miR-6631-5p were screened out. Among DE genes that had the probability to interact with gga-miR-6631-5p, 7 genes were found to be related to innate immunity. Furthermore, gga-miR-6631-5p promoted LaSota NDV replication by targeting insulin induced gene 1 (INSIG1) in DF-1 chicken fibroblast cells. Taken together, our data provided the comprehensive information about molecular responses to NDV LaSota vaccine in Chinese Partridge Shank Chickens and elucidated the vital roles of gga-miR-6631-5p/INSIG1 axis in LaSota NDV replication.

scholarly journals A SNP assay for assessing diversity in immune genes in the honey bee (Apis mellifera L.)

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Dora Henriques ◽  
Ana R. Lopes ◽  
Nor Chejanovsky ◽  
Anne Dalmon ◽  
Mariano Higes ◽  
...  
Keyword(s):  
Apis Mellifera ◽  
Honey Bee ◽  
Large Scale ◽  
Medium Density ◽  
Nucleotide Polymorphisms ◽  
Functional Variation ◽  
Immune Genes ◽  
Wide Range ◽  
Scale Range ◽  
Innate Immune Genes

AbstractWith a growing number of parasites and pathogens experiencing large-scale range expansions, monitoring diversity in immune genes of host populations has never been so important because it can inform on the adaptive potential to resist the invaders. Population surveys of immune genes are becoming common in many organisms, yet they are missing in the honey bee (Apis mellifera L.), a key managed pollinator species that has been severely affected by biological invasions. To fill the gap, here we identified single nucleotide polymorphisms (SNPs) in a wide range of honey bee immune genes and developed a medium-density assay targeting a subset of these genes. Using a discovery panel of 123 whole-genomes, representing seven A. mellifera subspecies and three evolutionary lineages, 180 immune genes were scanned for SNPs in exons, introns (< 4 bp from exons), 3’ and 5´UTR, and < 1 kb upstream of the transcription start site. After application of multiple filtering criteria and validation, the final medium-density assay combines 91 quality-proved functional SNPs marking 89 innate immune genes and these can be readily typed using the high-sample-throughput iPLEX MassARRAY system. This medium-density-SNP assay was applied to 156 samples from four countries and the admixture analysis clustered the samples according to their lineage and subspecies, suggesting that honey bee ancestry can be delineated from functional variation. In addition to allowing analysis of immunogenetic variation, this newly-developed SNP assay can be used for inferring genetic structure and admixture in the honey bee.

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