Promiscuous gene expression (PGE), formerly referred to as ectopic expression, is a process specific to the thymus that plays a pivotal role in the establishment of central tolerance. This phenomenon enables generation of self-antigens, so called tissue-restricted antigens (TRAs), which are in the body expressed only by one or few specific tissues (antigens rank among TRAs if they are expressed by less than five tissues from the sixty tested ). These antigens are represented for example by insulin from the pancreas or defensins from the gastrointestinal tract. Antigen-presenting cells (APCs) of the thymus, namely medullary thymic epithelial cells (mTECs), dendritic cells (DCs) and B cells are capable to present peptides derived from TRAs to developing T cells (thymus is the major origin of T cell development) and hereby test, whether their T cell receptors (TCRs) engage self entities and therefore their occurrence in the body can potentially lead to the development of autoimmune disease. In that case, thymic APCs either induce apoptosis in these autoreactive T cells (negative selection) or they deviate them to become T regulatory cells (Treg selection), which suppress self-reactive T cells in the body that escaped negative selection in the thymus. Thus, PGE is crucial for tissues protection against autoimmunity.
Characteristics of PGE in distinct cell types
The usual level of gene expression in the peripheral tissues (e.g. spleen, kidney, liver etc.) reaches about 60% of the mouse coding genome. Some peripheral tissues, including lungs, brain and testis, reveal the repertoire of expressed genes about 10% broader. Importantly, PGE in the thymus, which is mediated by unique subset of epithelial cells called mTECs, triggers expression of vast majority of the genes from the whole genome (~85%). Such a broad repertoire of expressed genes wasn't shown in any other tissue of the body.
mTECs
The process of PGE in the thymus was discovered in late 80's however, it took a decade to find that the cell subset that mediates PGE and therefore provides a "library" of TRAs are mTECs. These cells were shown to uniquely express a protein called autoimmune regulator (Aire), which drives the expression of approximately 40% TRAs, referred to as Aire-dependent, and is so far the only well characterized driver of PGE. Defects in the expression of Aire lead to multiorgan autoimmunity in mice and cause a severe autoimmune syndrome called APECED in human. Because Aire is not the exclusive PGE regulator, more than half of TRAs are Aire-independent and it isn't still known how their PGE is orchestrated.
mTECs are very heterogenous population and at least should be subdivided to MHCII low expressing subset (mTECsLO) and MHCII high expressing subset (mTECsHI) which is considered to be mature. Aire is expressed only by 30% from the latter.
PGE was found to act in a stochastic manner, which means that each mTEC expresses distinct set of Aire-dependent and Aire-independent TRAs. Despite its stochasticity, TRAs are co-expressed in clusters which however, rather mirror their co-localization on chromosomes than co-expression patterns from particular tissues. Even though TRAs involved in each cluster were found to be consistent, the PGE of whole cluster is transient and changes during mTEC development. Moreover, these clusters are highly variable between individuals. PGE is distinct from the expression of TRAs in the peripheral tissues also by its monoalelic or bialelic course. On the other hand, the level of TRA expression and numbers of alternative-splicing protein variants in the thymus correspond to the peripheral tissues.
PGE is highly conserved between mice and human.
B cells
Although thymic B cells were shown to induce either negative selection or Treg selection, their importance for the establishment of central tolerance remains elusive. It is assumed however, that B cells in the thymus are licensed by CD40-CD40L interaction with autoreactive T cells to activate the expression of Aire and upregulate levels of MHCII and CD80. Moreover, Aire drives the PGE of Aire-dependent TRAs in B cells and because their repertoire is non-overlaping with that of mTECs it should broaden the scope of peripheral antigens displayed in the thymus.