Class II transactivator suppresses transcription of thyroid-specific genes

Systems biology analysis reveals distinct molecular signatures associated with immune responsiveness to the BNT162b COVID-19 vaccine

BACKGROUND

Human immune responses to COVID-19 vaccines display a large heterogeneity of induced immunity and the underlying immune mechanisms for this remain largely unknown.

METHODS

Using a systems biology approach, we longitudinally profiled a unique cohort of female high and low responders to the BNT162b vaccine, who were known from previous COVID-19 vaccinations to develop maximum and minimum immune responses to the vaccine. We utilized high dimensional flow cytometry, bulk and single cell mRNA sequencing and 48-plex serum cytokine analyses.

FINDINGS

We revealed early, transient immunological and molecular signatures that distinguished high from low responders and correlated with B and T cell responses measured 14 days later. High responders featured a distinct transcriptional activity of interferon-driven genes and genes connected to enhanced antigen presentation. This was accompanied by a robust cytokine response related to Th1 differentiation. Both transcriptome and serum cytokine signatures were confirmed in two independent confirmatory cohorts.

INTERPRETATION

Collectively, our data contribute to a better understanding of the immunogenicity of mRNA-based COVID-19 vaccines, which might lead to the optimization of vaccine designs for individuals with poor vaccine responses.

FUNDING

German Center for Infection Research, German Center for Lung Research, German Research Foundation, Excellence Strategy EXC 2155 "RESIST" and European Regional Development Fund.

Interactome analysis implicates class II transactivator (CIITA) in depression and other neuroinflammatory disorders

PURPOSE

Inappropriate inflammatory responses within the nervous system (neuroinflammation) have been implicated in several neurological conditions. Class II transactivator (CIITA), a principal regulator of the major histocompatibility complex II (MHCII), is known to play essential roles in inflammation. Hence, CIITA and its interactors could be potentially involved in multiple neurological disorders. However, the molecular mechanisms underlying CIITA-mediated neuroinflammation (NI) are yet to be understood.

MATERIALS AND METHODS

In this regard, we analyzed the potential involvement of CIITA and its interactome in the regulation of neuroinflammation. In the present study, using various computational tools, we aimed (1) to identify NI-related proteins, (2) to filter the critical interactors in the CIITA-NI network, and (3) to analyze the protein-disease interactions and the associated molecular pathways through which CIITA could influence neuroinflammation.

RESULTS

CIITA was found to interact with P T GS2, GSK3B, and NR3C1 and may influence depressive disorders. Further, the IL4/IL13 pathway was found to be potentially underlying the CIITA-interactomemediated effects on neurological disorders. Moreover, CIITA was found to be connected to genes associated with depressive disorder through IL4, wherein CIITA was found to be potentially involved in depressive disorders through IL-4/IL-13 and hippo pathways. However, the present study is based on the existing data on protein interactomes and could be re-evaluated as newer interactions are discovered. Also, the functional mechanisms of CIITA's roles in neuroinflammation must be evaluated further.

CONCLUSION

Notwithstanding these limitations, the results presented here, could form a basis for further experimental studies to assess CIITA as a potential therapeutic target in managing depression and other neuroinflammatory disorders.

Identification of small molecule modulators of class II transactivator-I using computational approaches

Major histocompatibility complex II (MHCII), a mediator of the innate and adaptive immune system, plays a central role in regulating inflammation and its progression. Class II transactivator (CIITA) is a master regulator of MHCII expression and controls antigen presentation followed by T-cell activation. Regulation of inflammation by modulation of CIITA has been suggested as a promising intervention for several disorders, including neuroinflammation, rheumatoid arthritis and other autoimmune diseases. This study aimed to (i) identify possible pharmacological agents which could bind to and inhibit isoform I of CIITA (CIITA-I) and (ii) determine their strength of interactions. The structure of CIITA-I isoform was predicted using phyre2 and refined via 3D refine. Loops were refined using ModBase, followed by quality assessment based on ERRAT value. The refined 3D structure was subjected to docking via Maestro (from Schrodinger) using glide module against small molecule databases. Molecules having the least glide score and favorable ADME properties were subjected to molecular simulation by GROMACS. We used the 3D refined structure of CIITA-I, with a score of 83.4% in ERRAT for docking studies. The ligand 4-(2-((6-oxo-4-phenyl-1,6-dihydropyrimidin-2-yl) thio) acetamido) benzamide (ZINC5154833), showed maximum glide score (-6.591) followed by N-[4-(3-oxo-3-{4-[3-(trifluoromethyl) phenyl] piperazin-1-yl} propyl)-1,3-thiazol-2-yl] benzamide (F5254-0161, glide score -6.41). Simulation studies using GROMACS showed F5254-0161 to have a more stable interaction with CIITA-I. Based on our analysis, we propose ZINC5154833 and F5254-0161 as potential modulators for CIITA-I.Communicated by Ramaswamy H. Sarma.

The genetic architecture of helminth-specific immune responses in a wild population of Soay sheep (Ovis aries)

Much of our knowledge of the drivers of immune variation, and how these responses vary over time, comes from humans, domesticated livestock or laboratory organisms. While the genetic basis of variation in immune responses have been investigated in these systems, there is a poor understanding of how genetic variation influences immunity in natural, untreated populations living in complex environments. Here, we examine the genetic architecture of variation in immune traits in the Soay sheep of St Kilda, an unmanaged population of sheep infected with strongyle gastrointestinal nematodes. We assayed IgA, IgE and IgG antibodies against the prevalent nematode Teladorsagia circumcincta in the blood plasma of > 3,000 sheep collected over 26 years. Antibody levels were significantly heritable (h² = 0.21 to 0.57) and highly stable over an individual’s lifespan. IgA levels were strongly associated with a region on chromosome 24 explaining 21.1% and 24.5% of heritable variation in lambs and adults, respectively. This region was adjacent to two candidate loci, Class II Major Histocompatibility Complex Transactivator (CIITA) and C-Type Lectin Domain Containing 16A (CLEC16A). Lamb IgA levels were also associated with the immunoglobulin heavy constant loci (IGH) complex, and adult IgE levels and lamb IgA and IgG levels were associated with the major histocompatibility complex (MHC). This study provides evidence of high heritability of a complex immunological trait under natural conditions and provides the first evidence from a genome-wide study that large effect genes located outside the MHC region exist for immune traits in the wild.

Understanding how immune responses vary in natural populations can give an insight into how infection affects the ability of hosts and parasites to survive and reproduce, and how this drives evolutionary and ecological dynamics. Yet, very little is known about how immune responses vary over an individual’s lifetime and how genes contribute to this variation under natural conditions. Our study investigates the genetic architecture of variation in three antibody types, IgA, IgE and IgG in a wild population of Soay sheep on the St Kilda archipelago in North-West Scotland. Using data collected over 26 years, we show that antibody levels have a heritable basis in lambs and adults and are stable over an individual’s lifetime. We also identify several genomic regions with large effects on immune responses. Our study offers the first insights into the genetic control of immunity in a wild population, which is essential to understand how immune profiles vary in challenging natural conditions and how natural selection maintains genetic variation in complex immune traits.

Histone Acetylation and the Regulation of Major Histocompatibility Class II Gene Expression

Major histocompatibility complex (MHC) class II molecules are essential for processing and presenting exogenous pathogen antigens to activate CD4⁺ T cells. Given their central role in adaptive immune responses, MHC class II genes are tightly regulated in a tissue- and activation-specific manner. The regulation of MHC class II gene expression involves various transcription factors that interact with conserved proximal cis-acting regulatory promoter elements, as well as MHC class II transactivator that interacts with a variety of chromatin remodeling machineries. Recent studies also identified distal regulatory elements within MHC class II gene locus that provide enormous insight into the long-range coordination of MHC class II gene expression. Novel therapeutic modalities that can modify MHC class II genes at the epigenetic level are emerging and are currently in preclinical and clinical trials. This review will focus on the role of chromatin remodeling, particularly remodeling that involves histone acetylation, in the constitutive and inducible regulation of MHC class II gene expression.

Innate Immune Receptors

For many years innate immunity was regarded as a relatively nonspecific set of mechanisms serving as a first line of defence to contain infections while the more refined adaptive immune response was developing. The discovery of pattern recognition receptors (PRRs) revolutionised the prevailing view of innate immunity, revealing its intimate connection with adaptive immunity and generation of effector and memory T- and B-cell responses. Among the PRRs, families of Toll-like receptors (TLRs), C-type lectin receptors (CLR), retinoic acid-inducible gene-I (RIG-I)-like receptors (RLRs) and nucleotide-binding domain, leucine-rich repeat-containing protein receptors (NLRs), along with a number of cytosolic DNA sensors and the family of absent in melanoma (AIM)-like receptors (ALRs), have been characterised. NLR sensors have been a particular focus of attention, and some NLRs have emerged as key orchestrators of the inflammatory response through the formation of large multiprotein complexes termed inflammasomes. However, several other functions not related to inflammasomes have also been described for NLRs. This chapter introduces the different families of PRRs, their signalling pathways, cross-regulation and their roles in immunosurveillance. The structure and function of NLRs is also discussed with particular focus on the non-inflammasome NLRs.

Identification of a nuclear export sequence in the MHC CIITA

Initiation of an immune response through expression of MHC class II and related genes is under the control of the CIITA. Normally found in both the cytoplasm and nucleus, CIITA is tightly controlled by a variety of posttranslational modifications as well as interactions with other nuclear and cytoplasmic factors, whereas disruption of this dual subcellular localization impairs CIITA functioning and expression of target genes. Although CIITA has well-defined domains necessary for its nuclear import, the region responsible for the translocation of CIITA from the nucleus has not been characterized. In this study, we identify a leucine-rich motif at residues 717-724 that bears strong homology to known nuclear export sequence (NES) domains. Mutation of this region renders CIITA insensitive to treatment with leptomycin B, an inhibitor of nuclear export, whereas fusion of this domain to a heterologous GFP is sufficient to induce its export to the cytoplasm or cause its retention in the nucleus following leptomycin B treatment. Point mutations of specific leucine residues within the NES disrupt the normal subcellular distribution of the full-length CIITA, impair its ability to interact with the nuclear export factor CRM1, and enhance CIITA-induced gene expression from an MHC class II gene promoter. IFN-γ stimulation of class II genes is further enhanced by inhibiting the nuclear export of endogenous CIITA. Collectively, these data demonstrate the first identification of a specific NES within CIITA and place it among the other protein domains that contribute to the posttranslational regulation of CIITA activity.

CIITA and Its Dual Roles in MHC Gene Transcription

Class II transactivator (CIITA) is a transcriptional coactivator that regulates γ-interferon-activated transcription of Major Histocompatibility Complex (MHC) class I and II genes. As such, it plays a critical role in immune responses: CIITA deficiency results in aberrant MHC gene expression and consequently in autoimmune diseases such as Type II bare lymphocyte syndrome. Although CIITA does not bind DNA directly, it regulates MHC transcription in two distinct ways - as a transcriptional activator and as a general transcription factor. As an activator, CIITA nucleates an enhanceosome consisting of the DNA binding transcription factors RFX, cyclic AMP response element binding protein, and NF-Y. As a general transcription factor, CIITA functionally replaces the TFIID component, TAF1. Like TAF1, CIITA possesses acetyltransferase (AT) and kinase activities, both of which contribute to proper transcription of MHC class I and II genes. The substrate specificity and regulation of the CIITA AT and kinase activities also parallel those of TAF1. In addition, CIITA is tightly regulated by its various regulatory domains that undergo phosphorylation and influence its targeted localization. Thus, a complex picture of the mechanisms regulating CIITA function is emerging suggesting that CIITA has dual roles in transcriptional regulation which are summarized in this review.

Fragments of genomic DNA released by injured cells activate innate immunity and suppress endocrine function in the thyroid

Activation of innate and acquired immune responses, which can be induced by infection, inflammation, or tissue injury, may impact the development of autoimmunity. Although stimulation of cells by double-stranded DNA (dsDNA) has been shown to activate immune responses, the role of self-genomic DNA fragments released in the context of sterile cellular injury is not well understood. Using cultured thyroid cells, we show that cell injury prompts the release of genomic DNA into the cytosol, which is associated with the production of type I interferons, inflammatory cytokines, and chemokines. Molecules necessary for antigen processing and presentation to lymphocytes are also induced in thyroid cells by injury. dsDNA strongly suppressed the expression of sodium/iodide symporter and radioiodine uptake. To identify molecules responsible for sensing cytosolic dsDNA, we directly identified the cellular proteins that bound a dsDNA Sepharose column by mass spectrometry. Our analysis identified histone H2B, which was previously demonstrated to be an essential factor that mediates the activation of innate immunity induced by dsDNA. Knockdown of histone H2B using specific small interfering RNA abolished cell injury-induced innate immune activation and increased sodium/iodide symporter expression. These results indicate that genomic DNA fragments released by cell injury are recognized by extrachromosomal histone H2B, which results in the activation of genes involved in both innate and acquired immune responses in thyroid cells and suppression of thyroid function. These results suggest that sterile thyroid injury, in the absence of infection, may be sufficient to trigger autoimmune reaction and to induce thyroid dysfunction.

The effect of class II transactivator mutations on bleomycin-induced lung inflammation and fibrosis

IFN-γ expression increases during the inflammatory response after bleomycin injury in mice. IFN-γ deficiency attenuates lung inflammation and fibrosis. Because IFN-γ stimulates class II transactivator (CIITA) expression, which activates major histocompatibility class (MHC) II and represses collagen expression, it was hypothesized that CIITA mediates IFN-γ action after bleomycin injury. To test this hypothesis, two CIITA mouse lines, one carrying a mutation of the leucine-rich region of CIITA (CIITA C-/-) and one with a deletion extending into the GTP-binding domain (CIITA G-/-), were used. IFN-γ treatment of lung cells isolated from both strains of mice induced mutant CIITA expression, which did not activate MHC II transcription. Collagen expression was similar in both mutant mouse strains and comparable to C57BL/6 (wild-type) mice. When mice were exposed to intratracheal bleomycin, both strains of CIITA mutant mice retained body weight and altered inflammation at 14 days after bleomycin injury compared with bleomycin-treated wild-type mice. However, there was no difference in fibrosis as judged by histology, mRNA, and protein expression of lungs. Bronchoalveolar lavage cells from CIITA C-/- and C57BL/6 lungs were examined at 3, 7, and 14 days after bleomycin injury. CD4 mRNA expression in bronchoalveolar lavage cells was down-regulated, whereas IL-4 and IL-10 expression was up-regulated, in CIITA C-/- mice, indicating a diminished, skewed Th2 response. The expression of IFN-γ was the same in all mice tested. Combined, our data suggest that CIITA mutations altered the immune response without affecting fibrosis.

Excess iodide decreases transcription of NIS and VEGF genes in rat FRTL-5 thyroid cells

Although it is well known that an excess of iodide suppresses thyroid function and blood flow in vivo, the underlying molecular mechanisms are not fully known. The functional effect of iodide occurs at multiple steps, which include inhibition of sodium/iodide symporter (NIS) expression, transient block of organification, and inhibition of hormonal release. The vascular effect likely involves suppression of the vascular endothelial growth factor (VEGF) gene. In this report, we show that excess iodide coordinately suppresses the expression of the NIS and VEGF genes in FRTL-5 thyroid cells. We also demonstrate that the mechanism of iodide suppression of NIS gene expression is transcriptional, which is synergized by the addition of thyroglobulin. Based on the findings of reporter gene assays and electrophoretic gel mobility shift analysis, we also report two novel DNA binding proteins that responded specifically to iodide and modulated NIS promoter activity. The results suggest that excess iodide affects thyroid vascular function in addition to iodide uptake. This study provides additional insights into the mechanism of action of excess iodide on thyroid function.

Thyroglobulin (Tg) induces thyroid cell growth in a concentration-specific manner by a mechanism other than thyrotropin/cAMP stimulation

Thyroglobulin (Tg), a major product of the thyroid gland, serves as a macromolecular precursor of thyroid hormone biosynthesis. In addition, Tg stored in the thyroid follicles is a potent regulator of thyroid-specific gene expression. In conjunction with thyroid stimulating hormone (TSH) and iodide, Tg regulates thyroid follicle function, which is the minimal functional unit of the thyroid gland. In the present study, we show that Tg stimulates growth of FRTL-5 thyroid cells in the absence of TSH, insulin and serum. Unlike TSH, Tg did not increase cellular cyclic AMP (cAMP) levels; rather, the TSH signal counteracted Tg-induced cell growth. A specific inhibitor of A-kinase, H-89, did not modulate the effect of Tg. Tg increased kinase activity of Akt to the same level as TSH, insulin and 5% serum, while LY294002 abolished Tg-induced growth. Interestingly, low Tg concentrations maximized growth-promotion activity and induction of the apical iodide transporter (PDS; SLC26A4), whereas high Tg concentrations suppressed both cell growth and the expression of thyroid-specific genes. These results suggest that a low levels of Tg in the follicular lumen might stimulates cell growth and iodide transport to accelerate the iodide organification process; however, elevated Tg levels in the follicle might then shut down all of these functions.

Regulating the activity of class II transactivator by posttranslational modifications: exploring the possibilities

First identified as the master regulator of major histocompatibility complex II transcription, class II transactivator (CIITA) has since been implicated in a host of pathologies by modulating the transcription of multiple different genes. How CIITA caters to cell- and tissue-specific transcriptional needs is hotly debated and investigated. One of the possible mechanisms underlying spatiotemporal control of CIITA transcriptional activity is the posttranslational modification (PTM) machinery that refines certain amino acid residues of CIITA and hence alters its activity in response to specific cellular and environmental cues. This review discusses our current understanding of the PTM map of CIITA, how these modifications fine-tune its activity, and how the study of this area may lead to potential therapeutic strategies.

CIITA mediates interferon-gamma repression of collagen transcription through phosphorylation-dependent interactions with co-repressor molecules

Previously, we have demonstrated that major histocompatibility class II trans-activator (CIITA) is crucial in mediating interferon-gamma (IFN-gamma)-induced repression of collagen type I gene transcription. Here we report that CIITA represses collagen transcription through a phosphorylation-dependent interaction between its proline/serine/threonine domain and co-repressor molecules such as histone deacetylase (HDAC2) and Sin3B. Mutation of a serine (S373A) in CIITA, within a glycogen synthase kinase 3 (GSK3) consensus site, decreases repression of collagen transcription by blocking interaction with Sin3B. In vitro phosphorylation of CIITA by GSK3 relies on a casein kinase I site three amino acids C-terminal to the GSK3 site in CIITA. Both GSK3 and casein kinase I inhibitors alleviate collagen repression and disrupt IFN-gamma-mediated recruitment of Sin3B and HDAC2 to the collagen start site. Therefore, we have identified the region within CIITA responsible for mediating IFN-gamma-induced inhibition of collagen synthesis.

Class II major histocompatibility complex transactivator (CIITA) inhibits matrix metalloproteinase-9 gene expression

Matrix metalloproteinases (MMPs) are a family of structurally related proteins with the collective capability to degrade all components of the extracellular matrix. Although MMP-mediated degradation of the extracellular matrix occurs physiologically, numerous pathological conditions exhibit increased MMP levels and excessive matrix degradation. Previous work from our laboratory has shown that interferon-gamma inhibits MMP-9 expression in a manner dependent upon STAT-1alpha. Here we extend our previous observations and show that the class II major histocompatibility complex transactivator (CIITA), a transcriptional target of STAT-1alpha, is also capable of inhibiting MMP-9 expression. By using stable cell lines that inducibly express CIITA or various mutant forms of CIITA, we show that CIITA requires the ability to bind the CREB-binding protein (CBP) to effectively inhibit MMP-9 expression. Furthermore, we show that CIITA-mediated inhibition of the MMP-9 gene does not rely on the transcriptional capability of CIITA. These findings support a model wherein CIITA inhibits MMP-9 expression by binding to and sequestering CBP, which reduces the levels of CBP at the MMP-9 promoter, inhibits levels of acetylated histone 3 at the MMP-9 promoter, and subsequently inhibits MMP-9 expression.

The RFX family interacts at the collagen (COL1A2) start site and represses transcription

The transcription start site of the collagen alpha2(1) gene (COL1A2) has a sequence-specific binding site for a DNA methylation-responsive binding protein called regulatory factor for X-box 1 (RFX1) (Sengupta, P. K., Erhlich, M., and Smith, B. D. (1999) J. Biol. Chem. 274, 36649-36655). In this report, we demonstrate that RFX1 forms homodimers as well as heterodimers with RFX2 spanning the collagen transcription start site. Methylation at +7 on the coding strand increases RFX1 complex formation in gel shift assays. Methylation on the template strand, however, does not increase RFX1 complex formation. DNA from human fibroblasts contains minimal methylation on the coding strand (<4%) with variable methylation on the template strand. RFX1 acts as a repressor of collagen transcription as judged by in vitro transcription and co-transfection assays with an unmethylated collagen promoter-reporter construct. In addition, an RFX5 complex present in human fibroblasts interacts with the collagen RFX site, which is not sensitive to methylation. This is the first demonstration of RFX5 complex formation on a gene other than major histocompatibility complex (MHC) promoters. Also, RFX5 represses transcription of a collagen promoter-reporter construct in rat fibroblasts that have no detectable RFX5 complex formation or protein. RFX5 complex activates MHC II transcription by interacting with an interferon-gamma (IFN-gamma)-inducible protein, major histocompatibility class II trans-activator (CIITA). Collagen transcription is repressed by IFN-gamma in a dose-dependent manner in human but not in rat fibroblasts. IFN-gamma enhances RFX5 binding activity, and CIITA is present in the RFX5 complex of IFN-gamma-treated human fibroblasts. CIITA repressed collagen gene transcription more effectively in human fibroblasts than in rat fibroblasts, suggesting that the RFX5 complex may, in part, recruit CIITA protein to the collagen transcription start site. Thus the RFX family may be important repressors of collagen gene transcription through a RFX binding site spanning the transcription start site.