Little is known regarding the functional effects of common autoimmune susceptibility variants on human immune cells. The SNP CT60 (rs3087243; A/G) located in the 3 UTR of the CTLA4 gene has been associated with autoimmune diseases. We examined a cohort of healthy individuals stratified by genotypes at CTLA4 to gain insight into the functional effects of allelic variation on T cell signaling. Using phospho-site-specific mAbs, we tested the hypothesis that the CT60 genotype at CTLA4 is associated with altered T cell antigen receptor (TCR) signaling in naive and/or memory T cells. By normalizing for the extent of the initial TCR signaling event at CD3 , we observed that the relative responsiveness to TCR stimulation as assessed by phosphorylation levels of downstream signaling molecules was altered in naive (CD4 ؉ CD45RA high ) and memory (CD4 ؉ CD45RA low ) T cells obtained from individuals with the disease-susceptibility allele at CTLA4. Thus, allelic variation associated with autoimmune disease can alter the signaling threshold of CD4 ؉ T cells. These experiments provide a rational approach for the dissection of T cell-susceptibility genes in autoimmune diseases.genotype ͉ human ͉ T cell antigen receptor signaling ͉ CTLA4 ͉ autoimmunity T he recent successful completion of several genome-wide association scans, together with the rapid advancement in highthroughput genotyping technologies, have resulted in the discovery of an ever-increasing number of genetic variants associated with susceptibility to human autoimmune diseases (1-5). However, because of the small genetic effects of these variants, compared with the strong genetic effects seen in Mendelian diseases, the study of genotypic variation in relation to phenotypes has been a substantial challenge. One well validated region associated with susceptibility to autoimmune disease harbors the CTLA4 gene on chromosome 2q33. An associated allele in this susceptibility region is the G allele of the SNP CT60 (rs3087243; A/G) in the CTLA4 gene region, which has been associated with risk to type 1 diabetes, Graves disease, autoimmune hypothyroidism, systemic lupus erythematosus, and Addison's disease (6-10).The expression of mRNA isoforms of CTLA4 has been investigated in relation to CTLA4 genotype in healthy controls. Moreover, the genotype-dependent difference in the expression of soluble CTLA4 transcripts appears to be T cell-specific (6, 10). In the nonobese diabetic (NOD) mouse, the orthologous CTLA4 region also is associated with autoimmune diabetes, and, similar to humans, an allelic variant causes the increased expression of a major splice isoform. In the NOD model, the isoform is ligandindependent CTLA-4 (11) and results in strongly inhibited T cell responses, as well as increased susceptibility to disease (12). Together these investigations in both the experimental model and in humans suggest that genetic variation in the CTLA4 gene region may have an important effect on T cell function because of altered T cell signaling.Although CTLA4 is important in aut...