Extensive genetic polymorphism in the human tumor necrosis factor region and relation to extended HLA haplotypes

Abstract

We have identified three polymorphic microsatellites (which we call TNFa, TNFb, and TNFc) within a 12-kilobase region of the human major histocompatibility complex (MHC) that includes the tumor necrosis factor (TNF) locus. TNFc is located within the first intron of the TNF-gene and has only 2 alleles. TNFa and TNFb are 3.5 kilobases upstream (telomeric) of the TNF-P gene and have at least 13 and 7 alleles, respectively. TNFa, -b, and -c alleles are in linkage disequilibrium with alleles at other loci within the MHC, including class I, class II, and class m. TNFa, -b, and -c alleles are also associated with extended HLA haplotypes.These TNF polymorphisms will allow a thorough genetic analysis of the involvement of TNF in MHC-linked pathologies.The tumor necrosis factors (TNFs) have been recognized as essential mediators of the inflammatory response (1-3). The genes encoding TNF-a, the major macrophage-monocytederived form, and TNF-,3, which seems to be produced exclusively by lymphocytes, are located within a 7-kilobase (kb) region (4, 5), which we will henceforth designate as the TNF locus. The TNF locus is located within the major histocompatibility complex (MHC) of mouse and human (6, 7). In humans, TNF maps 320 kb centromeric to HLA-B (class I) and 340 kb telomeric to the C2/BF complex (class III) (8,9).The location of TNF within the MHC has prompted much speculation about the role of TNF alleles in the etiology of MHC-linked diseases, in particular those with an inflammatory or autoimmune component. This hypothesis has been difficult to test because of a lack of genetic markers in the locus: an extensive search for restriction fragment length polymorphisms (RFLPs) has yielded a biallelic Nco I RFLP (10-13) and a very rare EcoRI RFLP (14). In spite of its limited information content, the Nco I RFLP has already allowed some tentative associations between TNF alleles and autoimmune diseases (11, 15); recent evidence also suggests that one Nco I allele correlates with increased TNF-a and reduced TNF-13 production (13, 16).Microsatellite mapping is a recently developed technique in which the repeat number of a simple sequence element (usually a CA or CT dinucleotide) occurring at a unique location within the genome is measured after amplification by the PCR and used as an allelic marker (17). We have previously used this technique to define a multiallelic polymorphism within the mouse TNF locus (18). The present study extends this work to humans and defines three polymorphic regions that are in linkage disequilibrium with alleles at other MHC loci.