Molecular genetics and population studies of the KIR and HLA gene complexes

点击翻译按钮获取中文摘要

The classical HLA class I molecules, HLA-A, -B and -C, present antigenic peptides to CD8+ T cells, eliciting an adaptive immune response. The genes encoding these molecules are highly polymorphic, resulting in extensive diversity of the peptide repertoire, both within individuals and at the population level. Peptide loading of HLA class I molecules takes place primarily in the endoplasmic reticulum within the peptide loading complex (PLC). Tapasin is a critical component of the PLC, which performs its peptide "editing" function by association with peptide-empty HLA class I, stabilizing its structure, and promoting dissociation of low affinity peptides. HLA class I allotypes vary in level of cell surface expression in the absence of tapasin. Some allotypes are expressed at very low levels on the surface of tapasin-deficient cells (tapasin-dependent allotypes), while others exhibit normal expression on these cells (tapasin-independent allotypes). The exact molecular determinants of tapasin dependence (TD) remain unknown, although amino acids in the peptide binding groove near the peptide C terminus appear to contribute most to this phenomenon. For example, a single amino acid change (D116Y) located in this region distinguishes the highly tapasin-dependent B4402 allotype from the tapasin-independent B4405 allotype. Tapasin function can be targeted by viruses as a means of downmodulating HLA class I and evading cytotoxic CD8+ T cell (CTL) responses. Similarly, loss of tapasin expression has been observed in various human cancers. Thus, tapasin-independent HLA class I allotypes may be advantageous in terms of eliciting CTL responses against virally infected cells or tumor cells when tapasin function has been diminished. Allotype-specific regulation of the peptide repertoire by tapasin may also affect the quality of CTL responses. We have quantified the level of TD across all common HLA allotypes present in European and African Americans and tested the functional significance of differential HLA class I TD and its impact on disease. Ex vivo examination of cytotoxic T cell responses to the entire HIV-1 proteome from infected subjects indicates that tapasin-dependent allotypes present a more limited set of distinct peptides than do tapasin-independent allotypes, data supported by computational predictions. This suggests that variation in tapasin dependence may impact the strength of the immune responses by altering peptide repertoire size. In support of this model, we observed that individuals carrying HLA class I genotypes characterized by greater tapasin independence progress more slowly to AIDS and maintain lower viral loads, presumably due to increased breadth of peptide presentation. Thus, tapasin dependence level, like HLA zygosity, may serve as a means to restrict or expand breadth of the HLA-I peptide repertoire across humans, ultimately influencing immune responses to pathogens and vaccines. The development of methods for assessing the nature and extent of KIR genomic diversity has been limited by the complexity of the region. Members of this gene family share a high amount of sequence similarity. Also, there is remarkable diversity with respect to KIR gene content at the genomic level. Therefore, it is extremely challenging to determine the absence or presence of KIR genes based on short-read sequencing data. Currently, we are developing a computational approach that allows predictions for KIR gene content based on either whole-genome or whole-exome sequencing data. This approach utilizes same-length sequence fragments (k-mers) that are unique to individual KIR genes. Preliminary results are promising and show that high-confidence predictions of KIR genes based on sequencing data is feasible. This method will allow us to interrogate publicly available datasets for disease association analyses. IgG subclasses, IgG1, IgG2, IgG3, and IgG4, display distinct functional properties due to the differences in their constant H chains, encoded by individual genetic loci, IGHG1, IGHG2, IGHG3, and IGHG4, respectively. These genes form a cluster spanning approximately 150 kb region within the Ig H chain constant (IGHC) locus on human chromosome 14. The Fc portion of the constant region (CH2 and CH3 domains) mediates antibody stability and its effector functions, such as cytotoxicity, phagocytosis, and complement activation. Therefore, polymorphism in this region may directly affect immune responses. For example, the naturally occurring change from arginine to histidine at position 435 in IgG3 causes a dramatic increase in the antibody half-life. Variation in the constant regions has been characterized primarily by serological methods (Gm-Am allotypes) with limited information on nucleotide diversity. This region of the genome is not well covered in genome-wide studies due to high homology between the IGHG genes. We have developed a genotyping method based on Sanger sequencing, which covers all exons of IGHG1, IGHG2, and IGHG3 genes. In addition, we can distinguish hinge exon copy number, which is variable for IGHG3. The method has been applied to several population groups, including healthy whites, HIV infected whites and blacks from the US, as well as healthy blacks from South Africa. We have observed striking differences in frequency distributions among these groups.