CD8+ T-cell exhaustion limits the immune response to tumors because of ineffective T-cell effector functions. Thus, therapies that inhibit T-cell exhaustion are critical for optimizing cancer treatment. Recent studies have implicated epigenetic proteins in T-cell exhaustion. In this study, we identified activating transcription factor 7-interacting protein (ATF7ip) as an epigenetic protein critical for inducing T-cell exhaustion. Loss of Atf7ip in CD8+ T cells resulted in decreased terminal exhaustion and increased numbers of progenitor-exhausted cells in both chronic viral infections and cancer. Given the decreased T-cell terminal exhaustion observed with Atf7ip deficiency in CD8+ T cells, this may be one mechanism that leads to decreased tumor burden. Mechanistically, ATF7ip functions to stimulate the deposition of repressive H3K9me3 at critical immune-effector gene loci, such as Il7r and Il2, leading to enhanced exhaustion. Our data suggest that ATF7ip may be a rational target for deletion in adoptive T-cell therapies to reduce CD8+ T-cell exhaustion.

Most breast cancers arise from luminal epithelial cells and 25–30% of these tumours overexpress the ErbB-2 receptor. Herein, a non-transformed, immortalized cell system was used to investigate the effects of ErbB-2 overexpression in luminal epithelial cells. The phenotypic consequence of ErbB-2 overexpression is a shortening of the G1 phase of the cell cycle and early S phase entry, which leads to hyperproliferation. We show that this effect was mediated through the up-regulation of cdk6 and cyclins D1 and E, and enhanced degradation and relocalization of p27Kip1. These changes were effected predominantly through enhanced MAPK signalling, resulting in cdk2 hyperactivation. PI3K signalling also participated in cell cycle progression, since PI3K and MAPK coordinately regulated changes in cyclin D1 and cdk6 expression. Cdk4 activity was not required for cell cycle progression in these cells, and was constitutively inhibited through its association with p16INK4A. MAPK-dependent induction of p21Cip1 was also necessary for G1 phase progression, although its degradation by the proteasome was required for S phase entry. These data provide new insights into the complex molecular mechanisms underlying mitogenic cell cycle control in luminal epithelial cells, the cell type relevant to primary breast cancer, and show how ErbB-2 overexpression subverts this normal control.

The AIRE protein drives the expression of tissue-restricted self-antigens, required to induce immune tolerance for self-proteins. New work shows the importance of an external interaction between AIRE and the transcriptional activator CBP/p300, and an internal competition for nuclear-condensate formation.

The role of the autoimmune regulator (Aire) in central immune tolerance and thymic self-representation was first described more than 20 years ago, but fascinating new insights into its biology continue to emerge, particularly in the era of advanced single-cell genomics. We briefly describe the role of human genetics in the discovery of Aire, as well as insights into its function gained from genotype-phenotype correlations and the spectrum of Aire-associated autoimmunity-including insights from patients with Aire mutations with broad and diverse implications for human health. We then highlight emerging trends in Aire biology, focusing on three topic areas. First, we discuss medullary thymic epithelial diversity and the role of Aire in thymic epithelial development. Second, we highlight recent developments regarding the molecular mechanisms of Aire and its binding partners. Finally, we describe the rapidly evolving biology of the identity and function of extrathymic Aire-expressing cells (eTACs), and a novel eTAC subset called Janus cells, as well as their potential roles in immune homeostasis.

Mutations in the gene encoding the zinc-finger transcription factor Ikaros (IKZF1) are found in patients with immunodeficiency, leukemia, and autoimmunity. Although Ikaros has a well-established function in modulating gene expression programs important for hematopoietic development, its role in other cell types is less well defined. Here, we uncover functions for Ikaros in thymic epithelial lineage development in mice and show that Ikzf1 expression in medullary thymic epithelial cells (mTECs) is required for both autoimmune regulator-positive (Aire+) mTEC development and tissue-specific antigen (TSA) gene expression. Accordingly, TEC-specific deletion of Ikzf1 in mice results in a profound decrease in Aire+ mTECs, a global loss of TSA gene expression, and the development of autoimmunity. Moreover, Ikaros shapes thymic mimetic cell diversity, and its deletion results in a marked expansion of thymic tuft cells and muscle-like mTECs and a loss of other Aire-dependent mimetic populations. Single-cell analysis reveals that Ikaros modulates core transcriptional programs in TECs that correlate with the observed cellular changes. Our findings highlight a previously undescribed role for Ikaros in regulating epithelial lineage development and function and suggest that failed thymic central tolerance could contribute to the autoimmunity seen in humans with IKZF1 mutations.

Supplementary Figure 1 from Gene and Protein Expression Profiling of Human Ovarian Cancer Cells Treated with the Heat Shock Protein 90 Inhibitor 17-Allylamino-17-Demethoxygeldanamycin

BACKGROUND:Eight human catalytic phosphoinositide 3-kinase (PI3K) isoforms exist which are subdivided into three classes. While class I isoforms have been well-studied in cancer, little is known about the functions of class II PI3Ks.MATERIALS AND METHODS:The expression pattern and functions of the class II PI3KC2β isoform were investigated in a panel of tumour samples and cell lines.RESULTS:Overexpression of PI3KC2β was found in subsets of tumours and cell lines from acute myeloid leukemia (AML), glioblastoma multiforme (GBM), medulloblastoma (MB), neuroblastoma (NB), and small cell lung cancer (SCLC). Specific pharmacological inhibitors of PI3KC2β or RNA interference impaired proliferation of a panel of human cancer cell lines and primary cultures. Inhibition of PI3KC2β also induced apoptosis and sensitised the cancer cells to chemotherapeutic agents.CONCLUSION:Together, these data show that PI3KC2β contributes to proliferation and survival in AML, brain tumours and neuroendocrine tumours, and may represent a novel target in these malignancies.

CD8+ T cells are critical for the immune response to pathogens and tumors, and CD8+ T cell memory protects against repeat infections. In this study, we identify the activating transcription factor 7 interacting protein (ATF7ip) as a critical regulator of CD8+ T cell immune responses. Mice with a T cell-specific deletion of ATF7ip have a CD8+ T cell-intrinsic enhancement of Il7r expression and Il2 expression leading to enhanced effector and memory responses. Chromatin immunoprecipitation sequencing studies identified ATF7ip as a repressor of Il7r and Il2 gene expression through the deposition of the repressive histone mark H3K9me3 at the Il7r gene and Il2-Il21 intergenic region. Interestingly, ATF7ip targeted transposable elements for H3K9me3 deposition at both the IL7r locus and the Il2-Il21 intergenic region, indicating that ATF7ip silencing of transposable elements is important for regulating CD8+ T cell function. These results demonstrate a new epigenetic pathway by which IL-7R and IL-2 production are constrained in CD8+ T cells, and this may open up new avenues for modulating their production.

We have identified a novel function for a zinc finger transcription factor in medullary thymic epithelial cell (mTEC) development and central tolerance. Previous studies have shown that the transcription factor has critical functions in immune cell development, however our study is one of the first to describe a role for the transcription factor in the epithelial lineage. Probing publicly available gene expression databases, we found that the transcription factor is highly expressed in mTECs. Recent studies on mTECs have shown considerable cellular heterogeneity within mTECs with at least five mTEC subtypes including a transient amplifying population (TAC-TECs), autoimmune regulator (Aire+) mTECs, Late/Post Aire mTECs, Ccl21a mTECS, and tuft cells. Using a conditional knockout mouse line, we deleted the transcription factor in mTECs which resulted in drastic changes in the cellular composition of mTECs with substantial increase in Ccl21a mTECs and tuft cells and a dramatic decrease in Aire+ mTECs and Late Aire mTECs. Furthermore, the remaining Aire+ mTECs have a significant decrease in tissue-specific antigen gene expression resulting in autoimmunity in mice. To gain mechanistic understanding of the developmental changes we observed, we performed scRNA-seq and scATAC-seq, which showed significant changes in gene expression and the chromatin landscape in mTECs and helps to explain the critical function for this transcription factor in mTEC development.

T helper 17 cells (Th17) are critical for fighting infections at mucosal surfaces; however, they have also been found to contribute to the pathogenesis of multiple autoimmune diseases and have been targeted therapeutically. Due to the role of Th17 cells in autoimmune pathogenesis, it is important to understand the factors that control Th17 development. Here we identify the activating transcription factor 7 interacting protein (ATF7ip) as a critical regulator of Th17 differentiation. Mice with T cell-specific deletion of Atf7ip have impaired Th17 differentiation secondary to the aberrant overproduction of IL-2 with T cell receptor (TCR) stimulation and are resistant to colitis in vivo. ChIP-seq studies identified ATF7ip as an inhibitor of Il2 gene expression through the deposition of the repressive histone mark H3K9me3 in the Il2-Il21 intergenic region. These results demonstrate a new epigenetic pathway by which IL-2 production is constrained, and this may open up new avenues for modulating its production.

We conducted a comprehensive gene expression meta-analysis in dermatomyositis (DM) muscle and skin tissues to identify shared disease-relevant genes and pathways across tissues. Six publicly available data sets from DM muscle and two from skin were identified. Meta-analysis was performed by first processing data sets individually then cross-study normalization and merging creating tissue-specific gene expression matrices for subsequent analysis. Complementary single-gene and network analyses using Significance Analysis of Microarrays (SAM) and Weighted Gene Co-expression Network Analysis (WGCNA) were conducted to identify genes significantly associated with DM. Cell-type enrichment was performed using xCell. There were 544 differentially expressed genes (FC ≥ 1.3, q < 0.05) in muscle and 300 in skin. There were 94 shared upregulated genes across tissues enriched in type I and II interferon (IFN) signaling and major histocompatibility complex (MHC) class I antigen-processing pathways. In a network analysis, we identified eight significant gene modules in muscle and seven in skin. The most highly correlated modules were enriched in pathways consistent with the single-gene analysis. Additional pathways uncovered by WGCNA included T-cell activation and T-cell receptor signaling. In the cell-type enrichment analysis, both tissues were highly enriched in activated dendritic cells and M1 macrophages. There is striking similarity in gene expression across DM target tissues with enrichment of type I and II IFN pathways, MHC class I antigen-processing, T-cell activation, and antigen-presenting cells. These results suggest IFN-γ may contribute to the global IFN signature in DM, and altered auto-antigen presentation through the class I MHC pathway may be important in disease pathogenesis.

The COPA syndrome is a monogenic, autoimmune lung and joint disorder first identified in 2015. This study sought to define the main pulmonary features of the COPA syndrome in an international cohort of patients, analyse patient responses to treatment and highlight when genetic testing should be considered. We established a cohort of subjects (N=14) with COPA syndrome seen at multiple centres including the University of California, San Francisco, CA, USA. All subjects had one of the previously established mutations in the COPA gene, and had clinically apparent lung disease and arthritis. We analysed cohort characteristics using descriptive statistics. All subjects manifested symptoms before the age of 12 years, had a family history of disease, and developed diffuse parenchymal lung disease and arthritis. 50% had diffuse alveolar haemorrhage. The most common pulmonary findings included cysts on chest computed tomography and evidence of follicular bronchiolitis on lung biopsy. All subjects were positive for anti-neutrophil cytoplasmic antibody, anti-nuclear antibody or both and 71% of subjects had rheumatoid factor positivity. All subjects received immunosuppressive therapy. COPA syndrome is an autoimmune disorder defined by diffuse parenchymal lung disease and arthritis. We analysed an international cohort of subjects with genetically confirmed COPA syndrome and found that common pulmonary features included cysts, follicular bronchiolitis and diffuse alveolar haemorrhage. Common extrapulmonary features included early age of onset, family history of disease, autoantibody positivity and arthritis. Longitudinal data demonstrated improvement on chest radiology but an overall decline in pulmonary function despite chronic treatment.

Central tolerance is critical to prevent autoimmunity, but limits T cell responses to tumor antigens (Ags) that are self Ags. Previously, we identified that gamma-interferon-inducible lysosomal thiol reductase (GILT) is required for thymic deletion of CD4+ T cells specific for self and melanoma Ag, tyrosinase-related protein 1 (TRP1). Here, we show that GILT expression is enriched in thymic Ag presenting cells (APCs) capable of mediating deletion, medullary thymic epithelial cells (mTECs) and dendritic cells (DCs). TRP1 expression is restricted to mTECs, consistent with Aire-mediated transcriptional regulation. GILT facilitates MHC class II-restricted presentation of endogenous TRP1 by pooled thymic APCs. Bone marrow chimeras demonstrate that GILT expression in TECs is necessary and sufficient for efficient deletion of TRP1-specific thymocytes. Diminished MHC class II expression on Aire+ mTECs has no effect on thymic deletion or the percentage or activation of peripheral TRP1-specific T cells, suggesting that TRP1 is processed by GILT in mTECs and transferred to DCs to mediate deletion. In chimeras that express GILT in TECs TRP1-specific thymocytes undergo deletion, and chimeras are not protected from melanoma. Although an intermediate level of TRP1-specific T cells develop in chimeras in which GILT expression is limited to bone marrow-derived cells, only chimeras lacking GILT in both populations are protected from melanoma. Chimeras that express GILT in TECs or in which GILT is limited to bone marrow-derived cells have a substantially higher percentage of TRP1-specific regulatory T (Treg) cells and lower effector:Treg cell ratio. These findings suggest that GILT operates in mTECs to facilitate the processing of tissue-restricted Ags and promote thymic deletion and development of Treg cells, resulting in diminished T cell-mediated protection from melanoma.

Abstract Central tolerance is critical to prevent autoimmunity, but limits T cell responses to tumor Ag that are self Ag. We have identified that gamma-interferon-inducible lysosomal thiol reductase (GILT) is required for thymic deletion of CD4+ T cells specific for the self and melanoma Ag, tyrosinase-related protein 1 (TRP1). To define GILT’s role in central tolerance, we show that GILT expression is enriched in thymic APC capable of mediating deletion, medullary thymic epithelial cells (mTEC) and dendritic cells. TRP1 expression is restricted to mTEC. GILT facilitates MHC class II-restricted presentation of endogenous TRP1 by pooled thymic APC. Bone marrow (BM) chimeras demonstrate that GILT expression in TEC is necessary and sufficient for efficient deletion of TRP1-specific thymocytes. In chimeras that express GILT in TEC, TRP1-specific T cells undergo deletion, and chimeras are not protected from melanoma challenge. Although an intermediate level of TRP1-specific T cells develop in chimeras with GILT expression limited to BM-derived cells, only chimeras lacking GILT in both populations are protected from melanoma challenge. Chimeras that express GILT in TECs or in which GILT is limited to BM-derived cells have a substantially higher percentage of TRP1-specific regulatory T (Treg) cells and lower effector:Treg cell ratio. These findings suggest that GILT operates in mTEC to facilitate the presentation of tissue-specific self Ag and promote deletion and development of Treg cells.

Unbiased genetic studies have uncovered surprising molecular mechanisms in human cellular immunity and autoimmunity. We performed whole-exome sequencing and targeted sequencing in five families with an apparent mendelian syndrome of autoimmunity characterized by high-titer autoantibodies, inflammatory arthritis and interstitial lung disease. We identified four unique deleterious variants in the COPA gene (encoding coatomer subunit α) affecting the same functional domain. Hypothesizing that mutant COPA leads to defective intracellular transport via coat protein complex I (COPI), we show that COPA variants impair binding to proteins targeted for retrograde Golgi-to-ER transport. Additionally, expression of mutant COPA results in ER stress and the upregulation of cytokines priming for a T helper type 17 (TH17) response. Patient-derived CD4(+) T cells also demonstrate significant skewing toward a TH17 phenotype that is implicated in autoimmunity. Our findings uncover an unexpected molecular link between a vesicular transport protein and a syndrome of autoimmunity manifested by lung and joint disease.

Thymic central tolerance is essential to preventing autoimmunity. In medullary thymic epithelial cells (mTECs), the Autoimmune regulator (Aire) gene plays an essential role in this process by driving the expression of a diverse set of tissue-specific antigens (TSAs), which are presented and help tolerize self-reactive thymocytes. Interestingly, Aire has a highly tissue-restricted pattern of expression, with only mTECs and peripheral extrathymic Aire-expressing cells (eTACs) known to express detectable levels in adults. Despite this high level of tissue specificity, the cis-regulatory elements that control Aire expression have remained obscure. Here, we identify a highly conserved noncoding DNA element that is essential for Aire expression. This element shows enrichment of enhancer-associated histone marks in mTECs and also has characteristics of being an NF-κB-responsive element. Finally, we find that this element is essential for Aire expression in vivo and necessary to prevent spontaneous autoimmunity, reflecting the importance of this regulatory DNA element in promoting immune tolerance.

Nat. Immunol. 15, 258–265 (2014); published online 26 January 2014; corrected after print 24 February 2014 In the version of this article initially published, the blot in the third row on the right in Figure 1c (Flag-Aire, 3% input) was incorrect. The error has been corrected in the HTML and PDF versions of the article.