Feasibility of using genetic linkage analysis to identify the genes encoding T cell-defined minor histocompatibility antigens.

We have evaluated the utility of genetic linkage analysis to identify genes that encode minor histocompatibility antigens using vaccinia virus vectors as a simple and convenient method for transient expression of class I MHC molecules in lymphoblastoid cell lines. As a test case, we used a CTL clone that recognizes HA-8, a minor histocompatibility antigen encoded by the KIAA0020 gene and presented by HLA-A*0201. EBV-transformed B cell lines from individuals in three large pedigrees from the CEPH reference family collection were infected with a recombinant vaccinia virus vector encoding an HLA-A*0201 transgene, which led to high level expression of the MHC restricting allele HLA-A*0201 on the cell surface. HA-8 expression in the vaccinia-infected target cells was then determined using standard in vitro cytotoxicity assays. Pairwise linkage analysis of the segregation of HA-8 expression in these pedigrees demonstrated that the HA-8 gene was tightly linked with a cluster of marker loci located on the distal portion of chromosome 9p. Analysis of 9p marker haplotypes for individuals in the three families identified several individuals with recombinant haplotypes, and these recombination events were used to refine the precision of the HA-8 gene localization further. The data collectively indicate that the HA-8 gene is localized to a 10.3 cM (corresponding to 3.9 Mb) interval of distal 9p that is thought to encode at least 11 genes, including KIAA0020. These results demonstrate that linkage analysis can be used to map minor histocompatibility genes with high precision and accuracy. Over the next years, refinement and annotation of the human genome sequence will undoubtedly increase the utility of linkage analysis as a tool for identifying minor histocompatibility antigen genes.

Localization to chromosome 22 of a gene encoding a human minor histocompatibility antigen.

In human allogeneic bone marrow transplantation, graft-vs-host disease and graft rejection can occur even if the patient and donor are genotypically matched by inheritance for HLA. By definition, these allogeneic reactions are due to disparities in minor histocompatibility Ags (minor HAs). Minor HAs are presented to T lymphocytes as peptides bound to HLA molecules, and appear to be encoded by genes throughout the genome. We derived T lymphocyte clones from the PBL of a patient suffering from chronic graft-vs-host disease after bone marrow transplant from his HLA-identical sister. Clones reactive against minor HAs were selected on the basis of reactivity with pretransplant patient cells, and absence of reactivity with donor cells. One clone (MD2) was found to use HLA-B7 as a restricting element. A plasmid vector (pHEBo) containing cDNA encoding the HLA-B7 molecule was transfected into lymphoblastoid cell lines derived from two large families that previously had been saturation mapped for hundreds of polymorphic loci. When clone MD2 was tested against family K1362, it was found to be reactive with three of four grandparents, both parents, and eight of eleven offspring. The same clone was tested with family K1331, with two of three tested grandparents reactive, one of two parents, and nine of eleven offspring. Computer analysis showed that both family segregation patterns linked to an area on the long arm of chromosome 22, localizing the gene encoding this minor HA near the platelet-derived growth factor-beta and IL-2Rbeta genes.

Molecular cloning and physical and genetic mapping of a novel human Na+/H+ exchanger (NHE5/SLC9A5) to chromosome 16q22.1.

A human genomic clone for a novel fifth member of the Na+/H+ exchanger (NHE) family, NHE5 (gene symbol SLC9A5), has been isolated and partially sequenced. The deduced amino acid sequence of two exons, containing 154 codons, exhibits 59-73% identity to the other members of the NHE family, with closest similarity to NHE3. Northern blot analysis demonstrated that the NHE5 gene is expressed in brain, testis, spleen, and skeletal muscle. Fluorescence in situ hybridization analysis of a cosmid containing NHE5 to human metaphase chromosomes localized the NHE5 gene to the cytogenetic interval 16q21-q22. A panel of somatic cell hybrids containing various portions of chromosome 16 was used to refine further the placement of NHE5 within band 16q22.1. A polymorphic dinucleotide (GT/CA)n repeat contained in the NHE5 cosmid was identified and developed into a microsatellite PCR marker. This was typed in a subset of the CEPH (Centre d'Etude du Polymorphisme Humain) families to place it on a genetic map of the human genome. Pairwise linkage analysis of this marker showed that it was linked to marker D16S421 with a maximal lod score of 35.21 at a recombination fraction (theta) of 0.000, in complete concordance with its chromosomal localization by physical mapping. Multipoint linkage analysis placed NHE5 between the flanking markers D16S421 and D16S512. The cloning of this new member of the sodium hydrogen exchanger family, its chromosomal localization, and the discovery of a polymorphic marker for it now make it feasible to study the possible involvement of this gene in disorders of Na+/H+ transport.

Molecular cloning and physical and genetic mapping of the human anion exchanger isoform 3 (SLC2C) gene to chromosome 2q36.

A human clone corresponding to the gene encoding anion exchanger isoform 3 (AE3) (approved gene symbol SLC2C) has been isolated and partially sequenced. Oligonucleotide primers based on this sequence were used in a polymerase chain reaction to specifically amplify a segment of the human gene from a panel of human-rodent somatic cell hybrids, allowing the assignment of AE3 to chromosome 2. To map AE3 more precisely to a cytogenetic band on chromosome 2, the AE3 cosmid was used as a probe in fluorescence in situ hybridization to human metaphase chromosomes. Fractional length measurements were made, and AE3 mapped at high resolution to the cytogenetic band 2q36. A polymorphic dinucleotide (GT/CA)n repeat marker was developed from sequences in the AE3 cosmid and typed on a subset of the CEPH families. Multipoint linkage analysis placed the AE3 gene between D2S128 and D2S126 on a genetic map of chromosome 2, corroborating the chromosomal localization of AE3 obtained by physical mapping methods.