Thymic Mechanisms of T Cell Tolerance

Abstract

Peripheral-tissue antigen (PTA) expression by medullary thymic epithelial cells (mTECs) eliminates self-reactive T cells from the immune repertoire, protecting against autoimmunity. The transcription factor (TF) Aire plays a major role in inducing PTA expression in mTECs, but how a single TF can control the expression of thousands of biologically disparate genes has remained unclear. In my thesis work, I used genomics approaches, especially single-cell approaches, to study the molecular mechanisms of PTA expression in mTECs. A major fraction of mTECs showed strong Aire-dependency of their cell state and, in the absence of Aire, adopted a distinct gene program marked by IRF8 and CTLA-4. However, another heterogenous subset of mTECs was only indirectly affected by Aire deficiency and instead harbored the chromatin states and transcriptional programs of diverse cell types from peripheral tissues. These peripheral-cell-mimicking mTECs were termed “mimetic cells.” Chromatin, transcriptional and histological analyses showed that mimetic cells maintain a core mTEC identity yet overlay features of their peripheral counterparts. Lineage-defining TFs—including SpiB, Sox8, Hnf4α and Hnf4γ—were key controllers of mimetic cells, binding specifically to chromatin, activating enhancers, promoting mimetic cell accumulation and driving PTA expression. Study of mimetic cells, which reflect the peripheral self, also serendipitously revealed new extra-thymic biology. Finally, proof-of-principle experiments demonstrated that self-antigen expression in mimetic cells sufficed for cognate T cell tolerance. Integrating these data, I propose a two-component model of PTA expression comprised of Aire-expressing mTECs and mimetic cells.