Biology subjects

Irla, M.

Publications and source records attributed to Irla, M..

5 recordsLinked to original sources

bioRxiv2026

Cross-species chromatin accessibility pinpoints HIVEP3 as a driver of thymic epithelial maturation and self-antigen expression, preventing chronic inflammation

Promiscuous expression of tissue-specific antigens (TSAs) by medullary thymic epithelial cells (mTECs) underpins central T-cell tolerance, relying on NF-{kappa}B-driven mTEC maturation and induction of the autoimmune regulator AIRE. However, a substantial fraction of TSAs is AIRE-independent, implying additional regulators that remain only partially identified. Using cross-species single-cell chromatin accessibility profiling of human and mouse TECs, we find that HIVEP motifs are among the most accessible regulatory elements across the mTEC lineage. Among HIVEP paralogs, HIVEP3 is robustly expressed in mature mTECs across human, mouse and rat; given that rat immunity more closely mirrors human physiology than the mouse, we generated a CRISPR Hivep3-knockout rat line. Hivep3 deletion impairs mTEC maturation, reduces Aire expression and reshapes the TSA repertoire that underlies negative selection and Treg induction, as Hivep3 constrains canonical NF-{kappa}B1 and sustains non-canonical NF-{kappa}B2, the principal mediator of mTEC maturation. Beyond mTECs, Hivep3 deficiency downregulates Foxn1 target genes in cortical TECs and impairs positive selection. In the periphery, Hivep3-KO rats show reduced splenic CD4 T-cells, a shift from naive towards effector-and central-memory phenotypes, increased regulatory T-cells, and a sustained Th1-biased serum profile (elevated IFN-{gamma}, reduced IL-17A) with concurrent systemic metabolic perturbations across all ages. With age, this culminates in chronic inflammation, with multi-organ CD3 T-cell infiltration accompanied by inflammatory lesions. Together, these findings establish HIVEP3 as a previously unrecognised regulator of thymic epithelial function and central tolerance, whose deficiency leads to systemic T-cell-mediated chronic inflammation.

immunology↗

bioRxiv2026

Embryonic lympho-epithelial cell interactions play an essential role in the establishment of adult T cell tolerance

Thymic seeding progenitors (TSP) colonize the embryonic thymus in two successive waves, with the first wave uniquely contributing to lymphoid tissue inducer and invariant {gamma}{delta} T cells that drive primordial medullary thymic epithelial cell (mTEC) maturation. Although recognized during thymic organogenesis, their long-term impact on T cell selection and immune tolerance remains unclear. We show that selective depletion of first-wave TSP alters thymic architecture and TEC composition. This results in reduced mTEC numbers, failure of medullary islets to expand and coalesce, altered dendritic cell composition, and delayed regulatory T cell development. Single-cell transcriptional analysis revealed a decrease in the most immature and expanding compartments and signs of accelerated maturation. It also revealed abnormal TEC differentiation trajectories, expansion of post-Aire and mimetic TEC subsets, and altered expression of tissue-restricted antigen-coding genes. Functionally, first-wave TSP depletion resulted in impaired thymic recovery after injury, and age-associated autoimmunity, with elevated anti-nuclear antibodies and lymphocytic infiltration in peripheral tissues. Thus, first-wave TSP imprint long-lasting control of thymic function and immune tolerance. One sentence summaryEarly embryonic thymic seeding progenitors program thymic epithelial maturation and regulatory T cell development, ensuring long-term immune tolerance and protection from age-associated autoimmunity.

immunology↗

bioRxiv2024

Systems-level analysis provides insights on methanol-based production of L-glutamate and its decarboxylation product γ-aminobutyric acid by Bacillus methanolicus

BackgroundBacillus methanolicus is the next workhorse in biotechnology using methanol, an alternative and economical one-carbon feedstock that can be obtained directly from carbon dioxide, as both carbon and energy source for the production of various value-added chemicals. The wild-type strain B. methanolicus MGA3 naturally overproduces O_SCPLOWLC_SCPLOW-glutamate in methanol-based fed-batch fermentations. ResultsHere we generated, by induced mutagenesis, an evolved B. methanolicus strain exhibiting enhanced O_SCPLOWLC_SCPLOW-glutamate production capability (>150%). To showcase the potential of this evolved strain, further metabolic engineering enabled the production of {gamma}-aminobutyric acid (GABA) directly from O_SCPLOWLC_SCPLOW-glutamate, with a yield of 13.2 g/L from methanol during fed-batch fermentations. By using a systems-level analysis, encompassing whole-genome sequencing, RNA sequencing, fluxome analysis and genome-scale metabolic modelling, we were able to elucidate the metabolic and regulatory adaptations that sustain the biosynthesis of these products. The metabolism of the mutant strain evolved to prioritize energy conservation and efficient carbon utilization. Key metabolic shifts include the downregulation of energy-intensive processes such as flagellation and motility and the rerouting of carbon fluxes towards -ketoglutarate and its derivative, O_SCPLOWLC_SCPLOW-glutamate. Moreover, we observed that transformation of the evolved strain with a GABA biosynthesis plasmid had a positive effect on O_SCPLOWLC_SCPLOW-glutamate production, likely due to an upregulation of various transaminases involved in the O_SCPLOWLC_SCPLOW-glutamate biosynthesis from -ketoglutarate. ConclusionsThese results and insights provide a foundation for further rational metabolic engineering and bioprocess optimization, enhancing the industrial viability of B. methanolicus for sustainable production of O_SCPLOWLC_SCPLOW-glutamate and its derivatives.

systems biology↗

bioRxiv2021

Aire-dependent transcripts escape H3K36me3 and Raver2 induced alternative splicing to sustain central immune tolerance

Aire allows medullary thymic epithelial cells (mTECs) to express and present a large number of self-antigens for central tolerance. Although mTECs express a high diversity of self-antigen splice isoforms, the extent and regulation of alternative splicing events (ASEs) included in their transcripts, notably in those induced by Aire, is unknown. Unexpectedly, and in contrast to Aire-neutral genes, we found that the Aire-sensitive genes exhibit in Aire-positive and negative mTECs, a weak inclusion of ASEs, with about a quarter present in peripheral tissues being excluded from the thymus. We identified Raver2, as a splicing-related factor overrepresented in mTECs and dependent on H3K36me3 marks. We discovered that both Raver2 and methylation of H3K36 promoted ASE inclusion for Aire-neutral genes, leaving Aire-sensitive genes unaffected. Profiling of H3K36me3 revealed its depletion at Aire-sensitive genes, supporting a mechanism, whose setup precedes Aires expression and by which Aire-sensitive genes exhibit weak ASE inclusion through the escape of Raver2s effect. Lack of ASEs in Aire-induced transcripts highlights a role for regulatory T cells in controlling the incomplete Aire-dependent negative selection.

immunology↗

bioRxiv2020

Thymocytes trigger self-antigen-controlling pathways in immature medullary thymic epithelial stages

Interactions of developing T cells with Aire+ medullary thymic epithelial cells expressing high levels of MHCII molecules (mTEChi) are critical for the induction of central tolerance. In turn, thymocytes regulate the cellularity of Aire+ mTEChi. However, it remains unknown whether thymocytes control Aire+ mTEChi-precursors that are contained in mTEClo cells or other mTEClo subsets that have recently been delineated or identified by single-cell transcriptomic analyses. Here, using three distinct transgenic mouse models, in which antigen-presentation between mTECs and CD4+ thymocytes is perturbed, we show by high-throughput RNA-seq that self-reactive CD4+ thymocytes induce in mTEClo the expression of tissue-restricted self-antigens, cytokines, chemokines and adhesion molecules important for T-cell development. This gene activation program is combined with a global increase of the active H3K4me3 histone mark. Finally, we show that these interactions induce key mTEC transcriptional regulators and govern mTEClo subset composition, including Aire+ mTEChi-precursors, post-Aire and tuft-like mTECs. Our genome-wide study thus reveals that self-reactive CD4+ thymocytes control multiple unsuspected facets from immature stages of mTECs, which determines their heterogeneity.

immunology↗