Protocol for detection of in vitro R-loop formation using dot blots

Dot-blot analysis is a technique that allows for fast and convenient detection and identification of nucleic acids and proteins. Here, we provide a guide for nucleic acid isolation from eukaryotic cells and sample processing to detect RNA/DNA hybrids. We then provide detailed steps to quantify dot signal intensity. This protocol can be adapted for screening conditions that result in the accumulation of R-loops. For complete details on the use and execution of this protocol, please refer to Smith et al.1.

MEF2A suppresses stress responses that trigger DDX41-dependent IFN production

Cellular stress in the form of disrupted transcription, loss of organelle integrity, or damage to nucleic acids can elicit inflammatory responses by activating signaling cascades canonically tasked with controlling pathogen infections. These stressors must be kept in check to prevent unscheduled activation of interferon, which contributes to autoinflammation. This study examines the role of the transcription factor myocyte enhancing factor 2A (MEF2A) in setting the threshold of transcriptional stress responses to prevent R-loop accumulation. Increases in R-loops lead to the induction of interferon and inflammatory responses in a DEAD-box helicase 41 (DDX41)-, cyclic GMP-AMP synthase (cGAS)-, and stimulator of interferon genes (STING)-dependent manner. The loss of MEF2A results in the activation of ATM and RAD3-related (ATR) kinase, which is also necessary for the activation of STING. This study identifies the role of MEF2A in sustaining transcriptional homeostasis and highlights the role of ATR in positively regulating R-loop-associated inflammatory responses.

Human IL-35 Inhibits the Bioactivity of IL-12 and Its Interaction with IL-12Rβ2

IL-35 is an immunosuppressive cytokine with roles in cancer, autoimmunity, and infectious disease. In the conventional model of IL-35 biology, the p35 and Ebi3 domains of this cytokine interact with IL-12Rβ2 and gp130, respectively, on the cell surface of regulatory T and regulatory B cells, triggering their suppression of Th cell activity. Here we use a human IL-12 bioactivity reporter cell line, protein binding assays, and primary human Th cells to demonstrate an additional mechanism by which IL-35 suppresses Th cell activity, wherein IL-35 directly inhibits the association of IL-12 with its surface receptor IL-12Rβ2 and downstream IL-12-dependent activities. IL-12 binding to the surface receptor IL-12Rβ1 was unaffected by IL-35. These data demonstrate that in addition to acting via regulatory T and regulatory B cells, human IL-35 can also directly suppress IL-12 bioactivity and its interaction with IL-12Rβ2.

MEF2A is a Regulator of Interferon-Mediated Inflammation

Interferons (IFN) are antiviral cytokines induced by recognition of viral nucleic acids or cellular replicative stress. In particular, the accumulation of cytosolic nucleic acids or the accumulation of DNA lesions has the potential to activate cGAS/STING-mediated IFN induction if not properly constrained. While these responses can be harnessed as tumor therapies, the excessive induction of IFNs and deleterious IFN-mediated inflammation is associated with tissue damage in non-malignant disease. We sought to identify non-canonical IFN-modulatory transcription factors (TF) by examining factors with known genetic alterations that associate with both malignant and inflammatory diseases. Here, we identify MEF2A as a negative regulator of the production of IFNs at homeostasis. The loss of MEF2A function results in the spontaneous induction of type I and III IFNs and downstream ISG expression. We demonstrate that IFN production following MEF2A depletion was dependent on DNA replication and cell cycle progression with CDK2 inhibition ablating this response. Furthermore, DNA lesions that induced DNA damage responses following MEF2A loss resulted in cGAS/STING pathway activation and genetic deletion of STING maintained homeostatic levels of type I IFN in the absence of this TF factor. Thus, our study is first to connect MEF2A with protection from maladaptive type I IFN responses due to genomic instability across various cell types. Overall, our study reveals that therapeutic modulation of MEF2A or other members of its family could be beneficial for the management of viral, malignant, and autoinflammatory diseases.

Beyond Good and Evil: Molecular Mechanisms of Type I and III IFN Functions

IFNs are comprised of three families of cytokines that confer protection against pathogen infection and uncontrolled cellular proliferation. The broad role IFNs play in innate and adaptive immune regulation has placed them under heavy scrutiny to position them as "friend" or "foe" across pathologies. Genetic lesions in genes involving IFN synthesis and signaling underscore the disparate outcomes of aberrant IFN signaling. Abrogation of the response leads to susceptibility to microbial infections whereas unabated IFN induction underlies a variety of inflammatory diseases and tumor immune evasion. Type I and III IFNs have overlapping roles in antiviral protection, yet the mechanisms by which they are induced and promote the expression of IFN-stimulated genes and inflammation can distinguish their biological functions. In this review, we examine the molecular factors that shape the shared and distinct roles of type I and III IFNs in immunity.