Polymorphisms/mutations of TCR-ζ-chain promoter and 3' untranslated region and selective expression of TCR ζ-chain with an alternatively spliced 3' untranslated region in patients with systemic lupus erythematosus

Abstract A vast majority of systemic lupus erythematosus (SLE) patients display decreased expression of TCR ζ-chain mRNA, a critical signaling molecule implicated in the selection of the TCR repertoire and in the prevention of autoimmunity. To identify the molecular mechanisms involved in the downregulation of TCR ζ-chain transcripts in SLE T cells, we investigated the possibility of polymorphisms/mutations in the promoter and the 3′ untranslated region. PCR, cloning and sequence analysis of the promoter region from the genomic DNA showed significantly higher number of polymorphisms in SLE T cells compared to non-SLE control subjects ( P =0.044). Promoter sequence was also analysed from granulocytes to delineate the possibility of somatic mutations in activated SLE T cells. Promoter polymorphisms were significantly higher in granulocytes of SLE patients compared to non-SLE controls ( P =0.048), suggesting that these polymorphisms were of genomic origin. Nucleotide analysis of the promoter sequence revealed a −76T insertion compared to the published sequence, in all of the SLE samples and controls. RT–PCR analysis of the TCR ζ-chain 3′ untranslated region showed a 344 bp product in addition to the expected 906 bp product. Cloning and sequence analysis of the 344 bp product indicated that it is an alternatively spliced form with both splicing donor and acceptor sites, resulting in deletion of nucleotides 672–1233 of TCR ζ-chain mRNA. Unlike the nomal TCR ζ-chain, the expression of TCR ζ-chain with the alternatively spliced 344 bp 3′ untranslated region was higher in SLE T cells compared to non-SLE controls. The number of mutations/polymorphisms in the 906 bp TCR ζ-chain 3′ untranslated region were significantly higher in SLE T cells compared to non-SLE subjects ( P =0.032). Frequent mutations/polymorphisms and aberrant splicing of the downstream 3′ untranslated region may affect the stability and/or transport of TCR ζ-chain mRNA, leading to its downregulation in SLE T cells.