Adriana Forero

The host defense against emerging respiratory pathogens begins with the induction of cell-intrinsic, interferon-mediated antiviral responses. The interferon response induces innate effector and adaptive cellular responses crucial for viral clearance and the establishment of long-lasting immune memory. Although these antiviral processes are primarily characterized at the transcriptional level, the epigenetic mechanisms that orchestrate the cellular transcriptional output during infection remain understudied. Technological advances in systems immunology and virology have revealed dynamic changes in the cellular epigenetic landscape following infection, and their contextual roles in the fine-tuning of antiviral defense. This minireview covers our current understanding of how DNA methylation, post-translational modifications of histones, and chromatin remodelers are dynamically reprogrammed during respiratory virus infections, and the distinct strategies that respiratory viruses employ to subvert epigenetic control. We place further emphasis on cell-type-specific programs and the biological factors that alter the epigenetic landscape and regulate the balance between protective or pathogenic immune responses to infection.

Targeting cell death pathways, including pyroptosis and necroptosis, has been shown to mitigate influenza virus infection severity. Here, we examined whether pyroptosis specifically driven by the pore-forming protein gasdermin E (GSDME) is involved in regulating influenza virus infection outcomes. We found that Gsdme ^-/- mice showed similar weight loss and survival in severe A/PR/8/34 (H1N1) virus infections compared to WT counterparts. Likewise, lung dysfunction, histopathological damage, viral titers, and inflammatory cytokine levels were similar in the two groups. Global transcriptomic analysis also revealed similar inflammatory and antiviral gene expression programs in WT versus Gsdme ^-/- mouse lungs at baseline and in response to infection. To confirm the generality of these findings, we infected mice with minimally mouse-adapted 2009 pandemic H1N1 virus and again observed similar weight loss, lung dysfunction, and mortality in WT and Gsdme ^-/- mice. Our results overall demonstrate that GSDME contributes negligibly to the host response against H1N1 influenza virus, refining our understanding of cell death pathways in influenza pathogenesis. IMPORTANCE: Influenza virus infection activates multiple cell death pathways that shape disease outcomes. Here, we demonstrate that gasdermin E (GSDME)-mediated pyroptotic cell death does not significantly affect lung pathology or survival during severe H1N1 influenza virus infection. This finding contrasts with prior reports showing that GSDME worsens disease caused by H3N2 or H7N9 strains, as well as studies implicating gasdermin D in exacerbating H1N1 pathology. Thus, our data clarify that gasdermin family members contribute to influenza pathogenesis in a context-specific manner, underscoring the importance of considering viral diversity when evaluating the therapeutic potential of targeting cell death pathways.

SARS-CoV-2 can infect and adapt to multiple animal species, yet the host determinants that control interspecies viral adaptation remain poorly defined. Here we investigate whether interferon-induced transmembrane protein 3 (IFITM3), a key antiviral protein deficient in certain human populations, affects interspecies adaptation of SARS-CoV-2. We find that SARS-CoV-2 Beta and Omicron BA.4 variants passaged through IFITM3-deficient versus wild type mice exhibit enhanced replication and pathogenesis in this new host species. These enhancements are associated with amino acid substitutions in the viral genome, suggesting that IFITM3 limits accumulation of adaptive mutations. Mouse-adapted viruses enable comparative studies of variants in mice. Beta causes lung dysfunction and alters cilia-associated gene programs, consistent with broad viral antigen distribution in the lungs. Omicron, which shows mild pathogenicity and upper respiratory tract preference in humans, replicates to high nasal titers while exhibiting limited lung spread and reduced inflammatory responses compared to Beta. Our findings demonstrate that IFITM3 deficiency accelerates SARS-CoV-2 adaptation while preserving pre-existing variant-specific properties, highlighting that host adaptation enhances viral fitness without necessarily overriding intrinsic viral characteristics.

CD8⁺ virtual memory T (T_VM) cells rapidly respond to infection via antigen-independent bystander effector functions. While it is recognized that T_VM cells arise independently of foreign antigen encounter, the mechanisms governing their development are not fully understood. Here, we identify the Ikaros transcription factor Aiolos as a negative regulator of T_VM cell programming. We observe enhanced frequencies and numbers of T_VM in the spleen, liver, and blood of unchallenged Aiolos-deficient (Ikzf3^-/-) mice and in the lungs 1-day post-infection with influenza A virus (IAV). Furthermore, Ikzf3^-/- T_VM cells produce elevated IFN-γ and granzyme B in response to cytokine stimulation. Importantly, Aiolos-deficient mice control IAV more rapidly and exhibit reduced morbidity, indicating enhanced T_VM cell functionality. Mechanistically, Aiolos represses the expression of the transcription factor Eomes and the IL-15R subunit CD122, known positive regulators of T_VM gene program. Collectively, these findings establish Aiolos as a molecular repressor of T_VM programming and responses.

Ozone (O3) is an air pollutant that induces pulmonary inflammation and injury, leading to increased susceptibility and exacerbation of chronic lung diseases. Furthermore, ambient O3 concentrations are expected to rise with increasing global temperatures. Docosahexaenoic acid (DHA) is an omega-3 polyunsaturated fatty acid found primarily in oily fish that reduces inflammation and enhances the resolution of inflammation. This is attributed partially to DHA-derived oxylipins termed specialized proresolving mediators that have antiinflammatory and/or proresolving properties. However, whether dietary DHA protects the lungs from O3-induced inflammation and injury is unclear. We hypothesized that dietary DHA supplementation increases pulmonary specialized proresolving mediators and thereby decreases O3-induced pulmonary inflammation. To test this, C57BL/6J mice were fed a control diet or a DHA-enriched diet (2% kcal from DHA) for 6 weeks, exposed to filtered air or 1 ppm O3 for 3 hours (comparable with an O3 action day for humans), and necropsied 24 or 48 hours after exposure. DHA supplementation reduced airspace neutrophilia, decreased cytokine production, and promoted transcriptomic signatures for leukocyte chemotaxis and fatty acid oxidation. Furthermore, dietary DHA increased pulmonary DHA and its oxylipins while decreasing proinflammatory omega-6 polyunsaturated fatty acids and their oxylipins. Oropharyngeal aspiration of DHA oxylipins monohydroxylated 14-hydroxy-DHA and maresin 1 decreased O3-induced airspace neutrophilia and reduced bone marrow–derived macrophage production of neutrophil chemokines Cxcl1 and Cxcl2. These findings reveal that dietary DHA protects the lungs from O3 exposure by driving monohydroxylated 14-hydroxy-DHA and maresin 1 production, which reduces neutrophil-recruiting chemokine production by macrophages. This pathway highlights a potential therapeutic dietary approach for mitigating air pollution–induced pulmonary inflammation.

Cardiac complications are among the most common and severe extrapulmonary manifestations of influenza virus infection, yet they are rarely recapitulated in mouse models without immunodeficiency. We found that influenza virus A/California/04/2009 (H1N1) carrying a mouse-adaptive amino acid substitution in the PB2 protein (E158A) disseminates to the heart in WT C57BL/6 mice, where it induces inflammation, electrical dysfunction, and fibrotic remodeling. Influenza virus-infected heart tissue was significantly altered in mitochondrial metabolism, extracellular matrix, circadian rhythm, and immunity pathways. Particularly striking was activation of gene expression downstream of the mitochondrial biogenesis-promoting AMPK/PGC-1α axis, which occurred late in infection but failed to reverse the repression of mitochondria-associated genes, suggesting an insufficient or delayed compensatory response. Accordingly, we administered AMPK activator 5-aminoimidazole-4-carboxamide ribonucleoside (AICAR) early in infection and observed restoration of mitochondria-associated gene levels, amelioration of cardiac electrical dysfunction and fibrosis, and improvement in survival without overt effects on lung function. Overall, the advent of an immunocompetent model for severe influenza-associated cardiac dysfunction revealed activation of AMPK signaling as a host-targeted metabolic intervention for mitigating virus-induced heart pathologies

Targeting cell death pathways, including pyroptosis and necroptosis, has been shown to mitigate influenza virus infection severity. Here, we examined whether pyroptosis specifically driven by the pore-forming protein gasdermin E (GSDME) is involved in regulating influenza virus infection outcomes. We found that Gsdme ^−/− mice showed similar weight loss and survival in severe A/PR/8/34 (H1N1) virus infections compared to WT counterparts. Likewise, lung dysfunction, histopathological damage, viral titers, and inflammatory cytokine levels were similar in the two groups. Global transcriptomic analysis also revealed similar inflammatory and antiviral gene expression programs in WT versus Gsdme ^−/− mouse lungs at baseline and in response to infection. To confirm the generality of these findings, we infected mice with 2009 pandemic H1N1 virus and again observed similar weight loss, mortality, and lung dysfunction in WT and Gsdme ^−/− mice. Our results overall demonstrate that GSDME contributes negligibly to the host response against H1N1 influenza virus, refining our understanding of cell death pathways in influenza pathogenesis.

CD8 ⁺ virtual memory T (T _VM ) cells are memory-like cells that rapidly respond to infection via antigen-independent bystander effector functions. While it is recognized that T _VM cells arise independently of foreign antigen encounter, the mechanisms governing their development are not fully understood. Here, we identify the transcription factor Aiolos as a negative regulator of T _VM cells. We observed higher quantities of T _VM cells in the spleens of uninfected Aiolos-deficient ( Ikzf3 ^-/- ) mice relative to wild-type (WT). Furthermore, Ikzf3 ^-/- T _VM cells produced higher levels of IFN-γ and granzyme B. In addition, we found that Ikzf3 ^-/- T _VM cells accumulated to higher quantities in the lungs within 24 hours of influenza virus infection. In line with enhanced T _VM functional capacity and lung trafficking, Aiolos-deficient mice cleared virus more rapidly and exhibited reduced morbidity relative to WT animals. Mechanistically, we observed that Aiolos represses the T _VM transcriptional regulator Eomes and the IL-15R subunit CD122 (IL-15Rβ/IL-2Rβ), known contributors of T _VM cell generation. Collectively, these findings establish Aiolos as a novel molecular repressor of T _VM generation and function.

Here we investigated whether interferon induced transmembrane protein 3 (IFITM3), a key antiviral protein deficient in certain human populations, affects interspecies adaptation of SARS-CoV-2. We found that SARS-CoV-2 Beta and Omicron variants passaged through IFITM3-deficient versus wild type mice exhibit enhanced replication and pathogenesis in this new host species. Enhancements associated with amino acid substitutions in the viral genome, suggesting that IFITM3 limits accumulation of adaptive mutations. Mouse-adapted viruses enabled comparative studies of variants in mice. Beta caused lung dysfunction and altered cilia-associated gene programs, consistent with broad viral antigen distribution in lungs. Omicron, which shows low pathogenicity and upper respiratory tract preference in humans, replicated to high nasal titers while showing restrained spatial distribution in lungs and diminished lung inflammatory responses compared to Beta. Our findings demonstrate that IFITM3 deficiency accelerates coronavirus adaptation and reveal that intrinsic SARS-CoV-2 variant traits shape tropism, immunity, and pathogenesis across hosts. HIGHLIGHTS IFITM3 is a critical barrier to SARS-CoV-2 adaptation in new host species Mouse-adapted SARS-CoV-2 strains enable comparative pathology Omicron favors nose and large airways, leading to mild lung pathology Beta exhibits broad lung replication, driving severe inflammation and dysfunction