Differential gene expression in CD3 epsilon- and RAG1-deficient thymuses: definition of a set of genes potentially involved in thymocyte maturation

A set of 3000 mouse thymus cDNAs was analyzed by extensive measurement of e xpression using complex-probe hybridization of DNA arrays ("quantitative di fferential screening"). The complex probes were initially prepared using to tal thymus RNA isolated from C57BL/6 wild-type (WT), CD3 epsilon- and RAG1- deficient mice. Over 100 clones displaying over-or under-expression by at l east a factor of two between WT and knockout (KO) thymuses were further ana lyzed by measuring hybridization signatures with probes from a wide range o f KO thymuses, cell types, organs, and embryonic thymuses. A restricted set of clones was selected by virtue of their expression spectra (modulation i n KO thymuses and thymocytes, lymphoid cell specificity, and differential e xpression during embryonic thymus development), sequenced at one extremity, and compared to sequences in databases. Clones corresponding to previously identified genes (e.g., Tcr beta, Tcf1 or CD25) showed expression patterns that were consistent with existing data, Ten distinct clones corresponding to new genes were subjected to further study: Northern blot hybridization, in situ hybridization on thymus sections, and partial or complete mRNA seq uence determination. Among these genes, we report a new serine peptidase hi ghly expressed in cortical epithelial cells that we have named thymus-speci fic serine peptidase (TSSP), and an acidic protein ex-pressed in thymocytes and of unknown function that we have named thymus-expressed acidic protein (TEAP). This approach identifies new molecules likely to be involved in th ymocyte differentiation and function.