Effects of the MHC on hormonal induction of mammary tumors and function of hypophyseal isografts in the mouse

What has GWAS done for HLA and disease associations?

The major histocompatibility complex (MHC) is located in chromosome 6p21 and contains crucial regulators of immune response, including human leucocyte antigen (HLA) genes, alongside other genes with nonimmunological roles. More recently, a repertoire of noncoding RNA genes, including expressed pseudogenes, has also been identified. The MHC is the most gene dense and most polymorphic part of the human genome. The region exhibits haplotype-specific linkage disequilibrium patterns, contains the strongest cis- and trans-eQTLs/meQTLs in the genome and is known as a hot spot for disease associations. Another layer of complexity is provided to the region by the extreme structural variation and copy number variations. While the HLA-B gene has the highest number of alleles, the HLA-DR/DQ subregion is structurally most variable and shows the highest number of disease associations. Reliance on a single reference sequence has complicated the design, execution and analysis of GWAS for the MHC region and not infrequently, the MHC region has even been excluded from the analysis of GWAS data. Here, we contrast features of the MHC region with the rest of the genome and highlight its complexities, including its functional polymorphisms beyond those determined by single nucleotide polymorphisms or single amino acid residues. One of the several issues with customary GWAS analysis is that it does not address this additional layer of polymorphisms unique to the MHC region. We highlight alternative approaches that may assist with the analysis of GWAS data from the MHC region and unravel associations with all functional polymorphisms beyond single SNPs. We suggest that despite already showing the highest number of disease associations, the true extent of the involvement of the MHC region in disease genetics may not have been uncovered.

The novel gene G17, located in the human major histocompatibility complex, encodes PBX2, a homeodomain-containing protein

Recent characterization of the class III region of the human major histocompatibility complex (MHC), located in chromosome 6p21.3, has revealed that it is very gene dense and contains at least 47 transcriptional units. One of these is the gene G17, which lies 250 kb telomeric of the class II gene DRA. DNA sequence analysis of 5.5 kb of DNA corresponding to the G17 gene has revealed that it encodes PBX2, a homeodomain-containing protein with extensive similarity to PBX1 (which is involved in t(1;19) chromosomal translocations in acute pre-B-cell leukemias). Comparison of the genomic DNA sequence with the published PBX2 cDNA sequence, which are 99.7% identical, indicates that the G17 gene is split into 9 exons, with the intron/exon boundaries conforming to the normal pattern (AG/.../GT) for splice sites. Of the 9 differences observed between the PBX2 cDNA sequence and the G17 genomic sequence, only 1 is contained in the coding sequence and alters the derived amino acid sequence. This results in an Ile (PBX2)-Met (G17) substitution at amino acid 393 near the C-terminus. The PBX2 gene was originally localized only to human chromosome 3q22-q23. However, comparison of genomic and cosmid Southern blots clearly indicates that another copy(ies) of the PBX2 (G17) gene exist(s) in the genome. PCR amplification of exons III and IX of the G17 (PBX2) gene, corresponding to the coding and 3' untranslated regions, respectively, using as template genomic DNA from a panel of monochromosomal somatic human-rodent cell hybrids, gave specific products in hybrids that contain human chromosomes 6, 3, and 1. These results confirm that copies of the PBX2 gene are located on human chromosomes 6 and 3 and indicate that a gene homologous to PBX2 could exist on human chromosome 1. Further PCR analysis of the genes and reverse transcribed mRNA from the hybrid cell lines has revealed that the copies of the PBX2 gene on human chromosomes 6 and 1 are expressed, while the copy on human chromosome 3 may be a processed pseudogene.

A susceptibility gene for alveolar lung tumors in the mouse maps between Hsp70.3 and G7 within the H2 complex

Lung tumor susceptibility (LTS) in the mouse is influenced by multiple loci within the H2 complex. We compared the LTS of two H2 congenic strains with intra H2 recombinations, B10.A(1R) and B10.A(2R), whose genetic difference has been reduced to a region of approximately 50 kilobases within the C4-H2D interval, between Hsp70.3 and G7. After transplacental induction with N-ethyl-N-nitrosourea the load of alveolar lung tumors in strain B10.A(2R) is significantly higher than in strain B10.A(1R) (P < 0.001). For papillary tumors no significant differences were observed. We conclude that the alveolar lung tumor load is influenced by an LTS gene located within the Hsp70.3-G7 interval.