Foxn1 regulates key target genes essential for T cell development in postnatal thymic epithelial cells

Thymic epithelial cell differentiation, growth and function depend on the expression of the transcription factor Foxn1, however its target genes have never been physically identified. Using novel static and inducible genetic model systems and chromatin studies, we provide now a genome wide map of direct Foxn1 target genes for postnatal thymic epithelia and define the Foxn1 binding motif. We detail the function of Foxn1 in these cells and demonstrate that in addition to the transcriptional control of genes involved in the attraction and lineage commitment of T cell precursors, Foxn1 regulates the expression of genes involved in antigen processing and thymocyte selection. Thus, critical events in thymic lympho-stromal cross-talk and T cell selection are indispensably choreographed by Foxn1.

Dynamic spatio-temporal contribution of single β5t+ cortical epithelial precursors to the thymus medulla

Intrathymic T‐cell development is critically dependent on cortical and medullary thymic epithelial cells (TECs). Both epithelial subsets originate during early thymus organogenesis from progenitor cells that express the thymoproteasome subunit β5t, a typical feature of cortical TECs. Using in vivo lineage fate mapping, we demonstrate in mice that β5t⁺ TEC progenitors give rise to the medullary TEC compartment early in life but significantly limit their contribution once the medulla has completely formed. Lineage‐tracing studies at single cell resolution demonstrate for young mice that the postnatal medulla is expanded from individual β5t⁺ cortical progenitors located at the cortico‐medullary junction. These results therefore not only define a developmental window during which the expansion of medulla is efficiently enabled by progenitors resident in the thymic cortex, but also reveal the spatio‐temporal dynamics that control the growth of the thymic medulla.

Aire-expressing thymic medullary epithelial cells originate from β5t-expressing progenitor cells

The thymus provides multiple microenvironments that are essential for the development and repertoire selection of T lymphocytes. The thymic cortex induces the generation and positive selection of T lymphocytes, whereas the thymic medulla establishes self-tolerance among the positively selected T lymphocytes. Cortical thymic epithelial cells (cTECs) and medullary TECs (mTECs) constitute the major stromal cells that structurally form and functionally characterize the cortex and the medulla, respectively. cTECs and mTECs are both derived from the endodermal epithelium of the third pharyngeal pouch. However, the molecular and cellular characteristics of the progenitor cells for the distinct TEC lineages are unclear. Here we report the preparation and characterization of mice that express the recombinase Cre instead of β5t, a proteasome subunit that is abundant in cTECs and not detected in other cell types, including mTECs. By crossing β5t-Cre knock-in mice with loxP-dependent GFP reporter mice, we found that β5t-Cre-mediated recombination occurs specifically in TECs but not in any other cell types in the mouse. Surprisingly, in addition to cTECs, β5t-Cre-loxP-mediated GFP expression was detected in almost all mTECs. These results indicate that the majority of mTECs, including autoimmune regulator-expressing mTECs, are derived from β5t-expressing progenitor cells.

MicroRNAs control the maintenance of thymic epithelia and their competence for T lineage commitment and thymocyte selection

Thymic epithelial cells provide unique cues for the lifelong selection and differentiation of a repertoire of functionally diverse T cells. Rendered microRNA (miRNA) deficient, these stromal cells in the mouse lose their capacity to instruct the commitment of hematopoietic precursors to a T cell fate, to effect thymocyte positive selection, and to achieve promiscuous gene expression required for central tolerance induction. Over time, the microenvironment created by miRNA-deficient thymic epithelia assumes the cellular composition and structure of peripheral lymphoid tissue, where thympoiesis fails to be supported. These findings emphasize a global role for miRNA in the maintenance and function of the thymic epithelial cell scaffold and establish a novel mechanism how these cells control peripheral tissue Ag expression to prompt central immunological tolerance.

Prediction of protein functional residues from sequence by probability density estimation

MOTIVATION

The prediction of ligand-binding residues or catalytically active residues of a protein may give important hints that can guide further genetic or biochemical studies. Existing sequence-based prediction methods mostly rank residue positions by evolutionary conservation calculated from a multiple sequence alignment of homologs. A problem hampering more wide-spread application of these methods is the low per-residue precision, which at 20% sensitivity is around 35% for ligand-binding residues and 20% for catalytic residues.

RESULTS

We combine information from the conservation at each site, its amino acid distribution, as well as its predicted secondary structure (ss) and relative solvent accessibility (rsa). First, we measure conservation by how much the amino acid distribution at each site differs from the distribution expected for the predicted ss and rsa states. Second, we include the conservation of neighboring residues in a weighted linear score by analytically optimizing the signal-to-noise ratio of the total score. Third, we use conditional probability density estimation to calculate the probability of each site to be functional given its conservation, the observed amino acid distribution, and the predicted ss and rsa states. We have constructed two large data sets, one based on the Catalytic Site Atlas and the other on PDB SITE records, to benchmark methods for predicting functional residues. The new method FRcons predicts ligand-binding and catalytic residues with higher precision than alternative methods over the entire sensitivity range, reaching 50% and 40% precision at 20% sensitivity, respectively.

AVAILABILITY

Server: http://frpred.tuebingen.mpg.de. Data sets: ftp://ftp.tuebingen.mpg.de/pub/protevo/FRpred/.

Mapping of Dermatophagoides farinae mite allergens by two-dimensional immunoblotting

BACKGROUND

Allergens from the house dust mite Dermatophagoides farinae are responsible for frequent respiratory allergic disorders, but only 3 groups of these allergens are well characterized.

OBJECTIVE

This study was performed to complete the repertoire of D farinae allergens using two-dimensional (2-D) electrophoresis.

METHODS

D farinae mite allergens, extracted from whole cultures in the presence of a mild detergent, were separated by 2-D electrophoresis with subsequent immunoblotting. IgE-binding proteins were detected with individual mite-sensitive patient sera and the anti-D pteronyssinus human serum pool. Allergens were identified by an inhibition immunoblot test, by means of specific mAbs, or by biochemical characterization. The internal peptides of 2 allergens were microsequenced.

RESULTS

2-D immunoblotting with individual patient sera showed a marked heterogeneity in the isoelectric point of the allergens, as well as differences in the individual IgE-binding patterns. In addition to identification of allergens Der f 1, Der f 2, and Der f 3, new allergens have been characterized as Der f 4, Der f 5, and 2 high molecular mass allergens. Microsequencing of peptides from the latter allergens revealed significant homologies with allergen Mag 3 from D farinae and with a chitinase from prawn Penaeus japonicus.

CONCLUSION

2-D electrophoresis with subsequent immunoblotting and protein microsequencing allowed characterization of a more complete repertoire of D farinae allergens and their multiple isoforms, and identification of six new allergens.