# Aire, a zinc-finger protein that controls autoimmunity

> **NIH NIH R01** · HARVARD MEDICAL SCHOOL · 2022 · $423,750

## Abstract

T cell tolerance depends heavily on the thymus, reflecting negative selection of effector T cells (Teffs)
and positive selection of regulatory T cells (Tregs). Medullary thymic epithelial cells (mTECs) are major players
in both of these processes. Beyond transcribing the genes encoding molecules needed for their maintenance
and function, mTECs express transcripts derived from much of the protein-coding genome, notably mRNAs
specifying proteins characteristic of mature peripheral cell-types (peripheral-tissue antigens or PTAs). While
the whole mTEC compartment expresses a large repertoire of PTA transcripts, an individual mTEC makes only
a small subset of them. Aire drives expression of most thymic PTA transcripts by a mechanism thought to
entail super-enhancer activation and remodeling of 3D chromatin structure. Hence, the reigning model to
account for the mTEC PTA repertoire focuses on quasi-random de-repression of gene transcription, with no
discernible biological logic. However, our unpublished scATAC-seq and multi-pronged downstream studies
argue for a different model: in fact, Aire promotes both the ectopic expression of PTA transcripts (in Aire-stage
mTECs) and the ectopic differentiation of peripheral cell-types (from post-Aire mTECs). While previous scRNA-
seq studies did uncover some ectopic mTEC clusters, our ATAC-seq approach substantially broadened these
observations and revealed the underlying logic: a diversity of ectopic mTEC subtypes, largely downstream of
Aire expression, are marked by the lineage-defining transcription factors (TFs), chromatin accessibility
landscapes and transcriptional programs of peripheral cell-types. While it is well established that the ectopic
transcripts characteristic of Aire-expressing mTECs play an important role in T cell tolerance, almost nothing is
known about the influence of post-Aire ectopic mTEC subtypes. Thus, the major goal of this project is to
elucidate the impact of ectopic mTEC subtypes on T cell tolerance, which will be addressed in three
Specific Aims: a. To determine whether ectopic mTEC subtypes induce T cell tolerance. Our initial approach
relies on the lineage-defining TF logic mentioned above and on exploiting a fluorescent-protein (FP)-targeting
strategy. Preliminary data demonstrate that specific targeting of eYFP to the M-cell mTEC subtype inhibits the
CD4+ T cell response to immunization with an eYFP peptide. We will extend this finding in several directions --
evaluating the mechanism, thymus dependence, Aire dependence, generality & implications for autoimmunity.
b. To examine the landscape and function of ectopic mTEC subtypes in perinatal mice. As this is a critical
window for induction of T cell tolerance, we will perform scRNA-seq, scATAC-seq and functional comparisons
of mTECs from perinatal and adult mice to query the range and relative importance of ectopic mTEC subtypes
at the two ages. c. To determine whether extrinsic signaling to ectopic mTEC subtypes expands their...

## Key facts

- **NIH application ID:** 10520994
- **Project number:** 2R01DK060027-21
- **Recipient organization:** HARVARD MEDICAL SCHOOL
- **Principal Investigator:** DIANE J MATHIS
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $423,750
- **Award type:** 2
- **Project period:** 2002-03-01 → 2027-04-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10520994

## Citation

> US National Institutes of Health, RePORTER application 10520994, Aire, a zinc-finger protein that controls autoimmunity (2R01DK060027-21). Retrieved via AI Analytics 2026-06-11 from https://api.ai-analytics.org/grant/nih/10520994. Licensed CC0.

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