AIRE mõju geeniekspressioonile – transkriptsiooni regulatsiooni mehhanismi uuringud koekultuuri rakkudes

Väitekirja elektrooniline versioon ei sisalda publikatsiooneProbleemi kirjaldus. Immuunsüsteemi põhiline ülesanne on võidelda haigustekitajatega, mis üritavad tungida organismi, et seda kahjustada. Samaväärselt oluline on immuunsüsteemi võime hoiduda kehaomaste või väljastpoolt tulevate kahjutute molekulide vastu suunatud immuunreaktsioonist. Seda nähtust nimetatakse immuuntolerantsuseks. Immuuntolerantsuse kujunemisel on suur roll harknäärmel, mis vastutab kehaomaste valkude suhtes tundlike T-rakkude kõrvaldamise eest. Suuresti sõltub see protsess ühest valgust nimega autoimmuunsuse regulaator (AIRE). AIRE olemasolul avalduvad harknäärmes kehaomased valgud, mis viiakse kokku arenevate T-rakkudega. T-rakk, millel tekib tugev reaktsioon nende valkude suhtes, sureb enne, kui jõuab harknäärmest lahkuda. Kui harknäärmes puudub AIRE, jäävad ohtlikud T-rakud ellu, siirduvad vere- ning lümfiringe kaudu teistesse kudedesse ja vallandavad autoimmuunrünnaku, mis hävitab koe, põhjustades seeläbi raskeid haiguseid. Tulemus ja kasutegur. Käesolevas doktoritöös uurisime, kuidas mõjutab AIRE funktsiooni see, kui valgule lisada biokeemilisel viisil atsetüülrühmasid. Leidsime, et muutuvad AIRE paiknemine rakutuumas, valgu stabiilsus ning võime aktiveerida kehaomaste valkude avaldumist. Lisaks analüüsisime AIRE valgus esinevat mutatsiooni, mis põhjustab inimestel AIRE-puudulikkusest tingitud autoimmuunhaigust. Selgus, et mutatsioon lõhub AIRE valgu struktuuri ning kuigi AIRE on rakus olemas, ei pääse ta rakutuuma, et kehaomaste valkude avaldumist aktiveerida. Doktoritöö viimases osas keskendusime muutustele genoomi struktuuris, mis kaasnevad AIRE poolt aktiveeritud kehaomaste valkude avaldumisega. Avastasime vastupidiselt ootustele, et muutused toimuvad kehaomaste valkude geenidest kaugel olevates genoomiosades, viidates sellele, et AIRE-l on seni teadaolevast palju laialdasem mõju genoomi ülesehitusele. Kokkuvõtvalt, uurides AIRE valku mõjutavaid tegureid ning AIRE enda toimet genoomi struktuurile, suudame paremini mõista immuuntolerantsuse ning autoimmuunhaiguste tekkemehhanisme.Description of the problem. The main function of the immune system is to fight off pathogens that try to invade and harm the body. At the same time, the immune system has to block any immune reactions against harmless antigens stemming from the organism itself or from the environment. This phenomenon is called immune tolerance. The thymus plays a major role in establishing tolerance towards self-antigens by eliminating autoreactive T-cells. This process is primarily controlled by a single protein called autoimmune regulator (AIRE). AIRE promotes the expression of self-antigens that are presented to developing T-cells in the thymus. T-cell that strongly react to the self-antigens, will die before they leave the thymus. If AIRE is absent from the thymus, then the self-reactive T-cells will survive and migrate to other tissues, which can be targeted and destroyed by these T-cells causing an autoimmune disease. Result and benefit. In this thesis, we investigated the effect of acetylation of the AIRE protein. We found that it alters the localisation and stability of the protein and eventually affects the expression of self-antigens. Additionally, we analysed a mutation in the AIRE protein that causes AIRE-deficiency and autoimmunity in humans. We conclude that the mutation destroys AIRE protein structure, and although AIRE is still present in the cells, it cannot move into the nucleus to activate the expression of self-antigens. In the final part of the thesis we explored the changes in the structure of the genome that coincide with the AIRE-dependent activation of self-antigen expression. Contrary to expectations, the genomic alterations occurred far away from self-antigen coding genes suggesting that AIRE has a much broader impact on the gene regulatory processes in the nucleus than previously anticipated. In summary, uncovering factors that affect AIRE function and how AIRE itself contributes to the genomic organisation expand our understanding of the molecular mechanisms behind immune tolerance and autoimmunity

Multimodal human thymic profiling reveals trajectories and cellular milieu for T agonist selection

To prevent autoimmunity, thymocytes expressing self-reactive T cell receptors (TCRs) are negatively selected, however, divergence into tolerogenic, agonist selected lineages represent an alternative fate. As thymocyte development, selection, and lineage choices are dependent on spatial context and cell-to-cell interactions, we have performed Cellular Indexing of Transcriptomes and Epitopes by sequencing (CITE-seq) and spatial transcriptomics on paediatric human thymu​​s. Thymocytes expressing markers of strong TCR signalling diverged from the conventional developmental trajectory prior to CD4+ or CD8+ lineage commitment, while markers of different agonist selected T cell populations (CD8αα(I), CD8αα(II), T(agonist), Treg(diff), and Treg) exhibited variable timing of induction. Expression profiles of chemokines and co-stimulatory molecules, together with spatial localisation, supported that dendritic cells, B cells, and stromal cells contribute to agonist selection, with different subsets influencing thymocytes at specific developmental stages within distinct spatial niches. Understanding factors influencing agonist T cells is needed to benefit from their immunoregulatory effects in clinical use

Autoimmune regulator is acetylated by transcription coactivator CBP/p300

The Autoimmune Regulator (AIRE) is a regulator of transcription in the thymic medulla, where it controls the expression of a large set of peripheral-tissue specific genes. AIRE interacts with the transcriptional coactivator and acetyltransferase CBP and synergistically cooperates with it in transcriptional activation. Here, we aimed to study a possible role of AIRE acetylation in the modulation of its activity. We found that AIRE is acetylated in tissue culture cells and this acetylation is enhanced by overexpression of CBP and the CBP paralog p300. The acetylated lysines were located within nuclear localization signal and SAND domain. AIRE with mutations that mimicked acetylated K243 and K253 in the SAND domain had reduced transactivation activity and accumulated into fewer and larger nuclear bodies, whereas mutations that mimicked the unacetylated lysines were functionally similar to wild-type AIRE. Analogously to CBP, p300 localized to AIRE-containing nuclear bodies, however, the overexpression of p300 did not enhance the transcriptional activation of AIRE-regulated genes. Further studies showed that overexpression of p300 stabilized the AIRE protein. Interestingly, gene expression profiling revealed that AIRE, with mutations mimicking K243/K253 acetylation in SAND, was able to activate gene expression, although the affected genes were different and the activation level was lower from those regulated by wild-type AIRE. Our results suggest that the AIRE acetylation can influence the selection of AIRE activated genes

SP140L, an Evolutionarily Recent Member of the SP100 Family, Is an Autoantigen in Primary Biliary Cirrhosis

The SP100 family members comprise a set of closely related genes on chromosome 2q37.1. The widely expressed SP100 and the leukocyte-specific proteins SP110 and SP140 have been associated with transcriptional regulation and various human diseases. Here, we have characterized the SP100 family member SP140L. The genome sequence analysis showed the formation of SP140L gene through rearrangements of the two neighboring genes, SP100 and SP140, during the evolution of higher primates. The SP140L expression is interferon-inducible with high transcript levels in B cells and other peripheral blood mononuclear cells. Subcellularly, SP140L colocalizes with SP100 and SP140 in nuclear structures that are devoid of SP110, PML, or p300 proteins. Similarly to SP100 and SP140 protein, we detected serum autoantibodies to SP140L in patients with primary biliary cirrhosis using luciferase immunoprecipitation system and immunoblotting assays. In conclusion, our results show that SP140L is phylogenetically recent member of SP100 proteins and acts as an autoantigen in primary biliary cirrhosis patients

Interferon signature in patients with STAT1 gain‐of‐function mutation is epigenetically determined

International audienceSTAT1 gain-of-function (GOF) variants lead to defective Th17 cell development and chronic mucocutaneous candidiasis (CMC), but frequently also to autoimmunity. Stimulation of cells with STAT1 inducing cytokines like interferons (IFN) result in hyperphosphorylation and delayed dephosphorylation of GOF STAT1. However, the mechanism how the delayed dephosphorylation exactly causes the increased expression of STAT1-dependent genes, and how the intracellular signal transduction from cytokine receptors is affected, remains unknown. In this study we show that the circulating levels of IFN-α were not persistently elevated in STAT1 GOF patients. Nevertheless, the expression of interferon signature genes was evident even in the patient with low or undetectable serum IFN-α levels. Chromatin immunoprecipitation (ChIP) experiments revealed that the active chromatin mark trimethylation of lysine 4 of histone 3 (H3K4me3), was significantly enriched in areas associated with interferon-stimulated genes in STAT1 GOF cells in comparison to cells from healthy donors. This suggests that the chromatin binding of GOF STAT1 variant promotes epigenetic changes compatible with higher gene expression and elevated reactivity to type I interferons, and possibly predisposes for interferon-related autoimmunity. The results also suggest that epigenetic rewiring may be responsible for treatment failure of Janus kinase 1/2 (JAK1/2) inhibitors in certain patients

DNA-PK contributes to the phosphorylation of AIRE: Importance in transcriptional activity

The autoimmune regulator (AIRE) protein is a key mediator of the central tolerance for tissue specific antigens and is involved in transcriptional control of many antigens in thymic medullary epithelial cells (mTEC). Mutations in the AIRE gene cause a rare disease named autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED). Here we report using GST pull-down assay, mass-spectrometry and co-immunoprecipitation that a heterotrimeric complex of DNA-Dependent Protein Kinase (DNA-PK), consisting of Ku70, Ku80 and DNA-PK catalytic subunit (DNA-PKcs), is a novel interaction partner for AIRE. In vitro phosphorylation assays show that the residues Thr68 and Ser156 are DNA-PK phosphorylation sites in AIRE. In addition, we demonstrate that DNA-PKcs is expressed in AIRE positive mTEC cell population and that introduction of mutations into the AIRE phosphorylation sites decrease the capacity of AIRE to activate transcription from reporter promoters. In conclusion, our results suggest that phosphorylation of the AIRE protein at Thr68 and Ser156 by DNA-PK influences AIRE transactivation ability and might have impact on other aspects of the functional regulation of the AIRE protein