The role of interferon in the thymus

Impaired Aire-dependent IFN signaling in the thymus precedes the protective autoantibodies to IFNα

Recent studies have highlighted the role of the thymus in maintaining immune tolerance to type 1 interferons (T1 IFNs). Individuals with thymic abnormalities, such as autoimmune regulator (AIRE) gene mutations, frequently develop neutralizing autoantibodies to interferon-alpha (IFNα). Unlike mice, Aire-deficient rats develop robust autoantibodies to IFNα. Using this rat model, we show that Aire regulates the thymic expression of interferon-stimulated genes (ISGs), which occurs before developing anti-IFNα autoantibodies. In the periphery, we observed a widespread downregulation of ISGs across immune cells and reduced activation of natural killer (NK) cells. Furthermore, the presence of anti-IFNα autoantibodies correlated with reduced peripheral tissue inflammation, suggesting their role in dampening T1 IFN signaling and minimizing tissue infiltration. Our findings reveal that Aire-mediated regulation of thymic T1 IFN signaling is linked to the production of protective anti-IFNα autoantibodies, which inversely correlate with autoimmune pathology in peripheral tissues.

Distinct type I and II interferon responses direct cortical and medullary thymic epithelial cell development

Advances in genomics have redefined our understanding of thymic epithelial heterogeneity and architecture, yet signals driving thymic epithelial differentiation remain incompletely understood. Here, we elucidated pathways instructing human thymic epithelial cell development in the context of other anterior foregut-derived organs. Activation of interferon response gene regulatory networks distinguished epithelial cells of the thymus from those of other anterior foregut-derived organs. Thymic cortex and medulla epithelia displayed distinctive interferon-responsive signatures defined by lineage-specific chromatin accessibility. We explored the effects of type I and II interferons on thymic epithelial progenitor differentiation from induced pluripotent stem cells. Type II interferon was essential for expressing proteasome and antigen-presenting molecules, whereas type I or II interferons were essential for inducing different cytokines in thymic epithelial progenitor cells. Our findings suggest that interferons are critical to cortical and medullary thymic epithelial cell differentiation.

Establishment of a microwell-array-based miniaturized thymic organoid model suitable for high-throughput applications

T cell development depends critically on the thymic stroma-in particular, the diverse array of functionally distinct thymic epithelial cell (TEC) types. However, a robust in vitro thymus model mimicking the native thymus and compatible with medium-/high-throughput analyses is currently lacking. Here, we demonstrate a high-density microwell-array-based miniaturized thymus organoid (mTO) model that supports T cell commitment and development, possesses key organizational characteristics of the native thymus, and is compatible with live imaging and medium-/high-throughput applications. We establish the minimum cellular input required for a functional mTO and show that mTO TEC phenotype and complexity closely mirror those of the native thymus. Finally, we use an mTO to probe the role of fetal thymic mesenchyme, revealing a requirement beyond maintenance of Foxn1 in differentiation/maintenance of mature TEC sub-populations. Collectively, mTOs present an invitro model of the native thymus adaptable to medium-/high-throughput applications and validated for exploration of thymus and thymus organoid biology.

Sterile production of interferons in the thymus

T-cell central tolerance is controlled by thymocyte TCR recognition of self-peptides presented by thymic APCs. While thymic epithelial cells are essential for T-cell central tolerance, a variety of other traditional APCs also play critical roles in T-cell selection. Similar to how peripheral APCs require activation to become effective, thymic APCs also require activation to become tolerogenic. Recent studies have identified IFNs as an essential factor for the activation and generation of an optimally tolerogenic thymic environment. In this review, we focus on interferon (IFN) production within the thymus and its effects on thymic APCs and developing thymocytes. We also examine the importance of T-cell tolerance to IFN itself as well as to interferon-stimulated proteins generated during peripheral immune responses.

Thymus ad astra, or spaceflight-induced thymic involution

Spaceflight imposes a constellation of physiological challenges-cosmic radiation, microgravity, disrupted circadian rhythms, and psychosocial stress-that critically compromise astronaut health. Among the most vulnerable organs is the thymus, a cornerstone of immune system functionality, tasked with generating naive T cells essential for adaptive immunity. The thymus is particularly sensitive to spaceflight conditions, as its role in maintaining immune homeostasis is tightly regulated by a balance of systemic and local factors easily disrupted in space. Cosmic radiation, an omnipresent hazard beyond Earth's magnetosphere, accelerates DNA damage and cellular senescence in thymic epithelial cells, impairing thymopoiesis and increasing the risk of immune dysregulation. Microgravity and circadian rhythm disruption exacerbate this by altering immune cell migration patterns and stromal support, critical for T-cell development. Psychosocial stressors, including prolonged isolation and mission-induced anxiety, further compound thymic atrophy by elevating systemic glucocorticoid levels. Ground-based analogs simulating cosmic radiation and microgravity have been instrumental in elucidating mechanisms of thymic involution and its downstream effects on immunity. These models reveal that long-duration missions result in diminished naive T-cell output, leaving astronauts vulnerable to infections and possibly at high risk for developing neoplasia. Advances in countermeasures, such as pharmacological interventions targeting thymic regeneration and bioengineering approaches to protect thymic architecture, are emerging as vital strategies to preserve immune resilience during prolonged space exploration. Focusing on the thymus as a central hub of immune vulnerability underscores its pivotal role in spaceflight-induced health risks. Understanding these dynamics will not only enhance the safety of human space missions but also provide critical insights into thymus biology under extreme conditions.

Antigen presentation for central tolerance induction

The extent of central T cell tolerance is determined by the diversity of self-antigens that developing thymocytes 'see' on thymic antigen-presenting cells (APCs). Here, focusing on insights from the past decade, we review the functional adaptations of medullary thymic epithelial cells, thymic dendritic cells and thymic B cells for the purpose of tolerance induction. Their distinct cellular characteristics range from unconventional phenomena, such as promiscuous gene expression or mimicry of peripheral cell types, to strategic positioning in distinct microenvironments and divergent propensities to preferentially access endogenous or exogenous antigen pools. We also discuss how 'tonic' inflammatory signals in the thymic microenvironment may extend the intrathymically visible 'self' to include autoantigens that are otherwise associated with highly immunogenic peripheral environments.

Sterile production of interferons in the thymus affects T cell repertoire selection

Type I and III interferons (IFNs) are robustly induced during infections and protect cells against viral infection. Both type I and III IFNs are also produced at low levels in the thymus at steady state; however, their role in T cell development and immune tolerance is unclear. Here, we found that both type I and III IFNs were constitutively produced by a very small number of AIRE+ murine thymic epithelial cells, independent of microbial stimulation. Antigen-presenting cells were highly responsive to thymic IFNs, and IFNs were required for the activation and maturation of thymic type 1 conventional dendritic cells, macrophages, and B cells. Loss of IFN sensing led to reduced regulatory T cell selection, reduced T cell receptor (TCR) repertoire diversity, and enhanced autoreactive T cell responses to self-antigens expressed during peripheral IFN signaling. Thus, constitutive exposure to IFNs in the thymus is required for generating a tolerant and diverse TCR repertoire.

Systemic inflammatory Th1 cytokines during Trypanosoma cruzi infection disrupt the typical anatomical cell distribution and phenotypic/functional characteristics of various cell subsets within the thymus

The thymus plays a crucial role in T cell differentiation, a complex process influenced by various factors such as antigens, the microenvironment and thymic architecture. The way the thymus resolves infections is critical, as chronic persistence of microbes or inflammatory mediators can obstruct the differentiation. Here, we illustrate that following inflammatory T helper 1 infectious processes like those caused by Candida albicans or Trypanosoma cruzi, single positive thymocytes adopt a mature phenotype. Further investigations focused on T. cruzi infection, reveal a substantial existence of CD44+ cells in both the cortical and medullary areas of the thymus at the onset of infection. This disturbance coincides with heightened interferon gamma (IFNγ) production by thymocytes and an increased cytotoxic capacity against T. cruzi-infected macrophages. Additionally, we observe a reduced exportation capacity in T. cruzi-infected mice. Some alterations can be reversed in IFNγ knockout mice (KO). Notably, the majority of these effects can be replicated by systemic expression of interleukin (IL)-12+IL-18, underlining the predominantly inflammatory rather than pathogen-specific nature of these phenomena. Understanding the mechanisms through which systemic inflammation disrupts normal T cell development, as well as subsequent T cell exportation to secondary lymphoid organs (SLO) is pivotal for comprehending susceptibility to diseases in different pathological scenarios.

Transcriptomic profiling of thymic dysregulation and viral tropism after neonatal roseolovirus infection

Introduction

Herpesviruses, including the roseoloviruses, have been linked to autoimmune disease. The ubiquitous and chronic nature of these infections have made it difficult to establish a causal relationship between acute infection and subsequent development of autoimmunity. We have shown that murine roseolovirus (MRV), which is highly related to human roseoloviruses, induces thymic atrophy and disruption of central tolerance after neonatal infection. Moreover, neonatal MRV infection results in development of autoimmunity in adult mice, long after resolution of acute infection. This suggests that MRV induces durable immune dysregulation.

Methods

In the current studies, we utilized single-cell RNA sequencing (scRNAseq) to study the tropism of MRV in the thymus and determine cellular processes in the thymus that were disrupted by neonatal MRV infection. We then utilized tropism data to establish a cell culture system.

Results

Herein, we describe how MRV alters the thymic transcriptome during acute neonatal infection. We found that MRV infection resulted in major shifts in inflammatory, differentiation and cell cycle pathways in the infected thymus. We also observed shifts in the relative number of specific cell populations. Moreover, utilizing expression of late viral transcripts as a proxy of viral replication, we identified the cellular tropism of MRV in the thymus. This approach demonstrated that double negative, double positive, and CD4 single positive thymocytes, as well as medullary thymic epithelial cells were infected by MRV in vivo. Finally, by applying pseudotime analysis to viral transcripts, which we refer to as "pseudokinetics," we identified viral gene transcription patterns associated with specific cell types and infection status. We utilized this information to establish the first cell culture systems susceptible to MRV infection in vitro.

Conclusion

Our research provides the first complete picture of roseolovirus tropism in the thymus after neonatal infection. Additionally, we identified major transcriptomic alterations in cell populations in the thymus during acute neonatal MRV infection. These studies offer important insight into the early events that occur after neonatal MRV infection that disrupt central tolerance and promote autoimmune disease.

Interferon autoantibodies as signals of a sick thymus

Type I interferons (IFN-I) are key immune messenger molecules that play an important role in viral defense. They act as a bridge between microbe sensing, immune function magnitude, and adaptive immunity to fight infections, and they must therefore be tightly regulated. It has become increasingly evident that thymic irregularities and mutations in immune genes affecting thymic tolerance can lead to the production of IFN-I autoantibodies (autoAbs). Whether these biomarkers affect the immune system or tissue integrity of the host is still controversial, but new data show that IFN-I autoAbs may increase susceptibility to severe disease caused by certain viruses, including SARS-CoV-2, herpes zoster, and varicella pneumonia. In this article, we will elaborate on disorders that have been identified with IFN-I autoAbs, discuss models of how tolerance to IFN-Is is lost, and explain the consequences for the host.