Plasmacytoid dendritic cells (pDCs) are best known for their outstanding ability to rapidly produce large amounts of type I interferons (IFN-I), which are key antiviral mediators. However, after their initial IFN-I burst, the pDC lineage undergoes a number of adaptations that converge on the attenuation of pDC-derived interferons, ensuring their production remains short-lived regardless of whether the pathogen is cleared or persists. The convergence of multiple host adaptations that result in reduced pDC numbers and/or function after infection highlights the double-edged sword nature of pDCs: while they can be beneficial for antiviral defense, they can also drive tissue pathology. In this review, we summarize selected pDC-lineage adaptations that arise after their initial IFN-I peak following a viral infection, including compromised pDC development from bone marrow progenitors, fate plasticity that enables pDC conversion into conventional dendritic cells type 2 (cDC2)-like cells, and loss of the pDCs' hallmark capacity to produce IFN-I. We also provide an overview of the underlying molecular mechanisms contributing to the aforementioned adaptations, discuss potential evolutionary advantages, and highlight future avenues to dissect the fundamental biology of pDC reprogramming with the ultimate goal of leveraging these insights to therapeutically target pDCs in infections and beyond.

Plasmacytoid Dendritic cells (pDCs) are the most potent producers of interferons, which are critical antiviral cytokines. pDC development is, however, compromised following a viral infection, and this phenomenon, as well as its relationship to conventional (c)DC development is still incompletely understood. By using lymphocytic choriomeningitis virus (LCMV) infection in mice as a model system, we observed that DC progenitors skewed away from pDC and toward cDC development during in vivo viral infection. Subsequent characterization of the transcriptional and epigenetic landscape of fms-like tyrosine kinase 3 + (Flt3 + ) DC progenitors and follow-up studies revealed increased apoptosis and reduced proliferation in different individual DC-progenitors as well as a profound type I interferon (IFN-I)-dependent ablation of pre-pDCs, but not pre-DC precursors, after both acute and chronic LCMV infections. In addition, integrated genomic analysis identified altered activity of 34 transcription factors in Flt3 + DC progenitors from infected mice, including two regulators of Glucocorticoid (GC) responses. Subsequent studies demonstrated that addition of GCs to DC progenitors led to downregulated pDC-primed-genes while upregulating cDC-primed-genes, and that endogenous GCs selectively decreased pDC, but not cDC, numbers upon in vivo LCMV infection. These findings demonstrate a significant ablation of pre-pDCs in infected mice and identify GCs as suppressors of pDC generation from early progenitors. This provides a potential explanation for the impaired pDC development following viral infection and links pDC numbers to the hypothalamic–pituitary–adrenal axis.

While differential antibody responses SARS-CoV-2 in patients with inflammatory bowel disease (IBD) receiving infliximab and vedolizumab are well-characterized, the immune pathways underlying these differences remain unknown. Prior to COVID-19 vaccine development, we screened 235 patients with IBD receiving biological therapy for antibodies to SARS-CoV-2 and measured serum cytokines. In seropositive patients, we prospectively collected clinical data. We found a cytokine signature in patients receiving vedolizumab who are seropositive compared with seronegative for SARS-CoV-2 antibodies that may be linked to repeated SARS-CoV-2 infections. However, there were no differences between seropositive and seronegative patients receiving infliximab. In this single-center cohort of patients with IBD with anti-SARS-CoV-2 antibodies at the onset of the COVID-19 pandemic, and therefore without influence of vaccination, there is a cytokine signature in patients receiving vedolizumab but not infliximab. These findings lay the groundwork for further studies on immune consequences of viral infection in patients with IBD, which is postulated to evolve from aberrant host-microbe responses.

ABSTRACT Severe COVID-19 has been associated with coinfections with bacterial and fungal pathogens. Notably, patients with COVID-19 who develop Staphylococcus aureus bacteremia exhibit higher rates of mortality than those infected with either pathogen alone. To understand this clinical scenario, we collected and examined S. aureus blood and respiratory isolates from a hospital in New York City during the early phase of the pandemic from both SARS-CoV-2+ and SARS-CoV-2− patients. Whole genome sequencing of these S. aureus isolates revealed broad phylogenetic diversity in both patient groups, suggesting that SARS-CoV-2 coinfection was not associated with a particular S. aureus lineage. Phenotypic characterization of the contemporary collection of S. aureus isolates from SARS-CoV-2+ and SARS-CoV-2− patients revealed no notable differences in several virulence traits examined. However, we noted a trend toward overrepresentation of S. aureus bloodstream strains with low cytotoxicity in the SARS-CoV-2+ group. We observed that patients coinfected with SARS-CoV-2 and S. aureus were more likely to die during the acute phase of infection when the coinfecting S. aureus strain exhibited high or low cytotoxicity. To further investigate the relationship between SARS-CoV-2 and S. aureus infections, we developed a murine coinfection model. These studies revealed that infection with SARS-CoV-2 renders mice susceptible to subsequent superinfection with low cytotoxicity S. aureus . Thus, SARS-CoV-2 infection sensitizes the host to coinfections, including S. aureus isolates with low intrinsic virulence. IMPORTANCE The COVID-19 pandemic has had an enormous impact on healthcare across the globe. Patients who were severely infected with SARS-CoV-2, the virus causing COVID-19, sometimes became infected with other pathogens, which is termed coinfection. If the coinfecting pathogen is the bacterium Staphylococcus aureus , there is an increased risk of patient death. We collected S. aureus strains that coinfected patients with SARS-CoV-2 to study the disease outcome caused by the interaction of these two important pathogens. We found that both in patients and in mice, coinfection with an S. aureus strain lacking toxicity resulted in more severe disease during the early phase of infection, compared with infection with either pathogen alone. Thus, SARS-CoV-2 infection can directly increase the severity of S. aureus infection.

Gastrointestinal effects associated with Coronavirus Disease 2019 (COVID-19) are highly variable for reasons that are not understood. In this study, we used intestinal organoid-derived cultures differentiated from primary human specimens as a model to examine interindividual variability. Infection of intestinal organoids derived from different donors with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) resulted in orders of magnitude differences in virus replication in small intestinal and colonic organoid-derived monolayers. Susceptibility to infection correlated with angiotensin I converting enzyme 2 (ACE2) expression level and was independent of donor demographic or clinical features. ACE2 transcript levels in cell culture matched the amount of ACE2 in primary tissue, indicating that this feature of the intestinal epithelium is retained in the organoids. Longitudinal transcriptomics of organoid-derived monolayers identified a delayed yet robust interferon signature, the magnitude of which corresponded to the degree of SARS-CoV-2 infection. Interestingly, virus with the Omicron variant spike (S) protein infected the organoids with the highest infectivity, suggesting increased tropism of the virus for intestinal tissue. These results suggest that heterogeneity in SARS-CoV-2 replication in intestinal tissues results from differences in ACE2 levels, which may underlie variable patient outcomes.

29 Gastrointestinal effects associated with COVID-19 are highly variable for reasons that are not 30 understood. In this study, we used intestinal organoid-derived cultures differentiated from 31 primary human specimens as a model to examine inter-individual variability. Infection of 32 intestinal organoids derived from different donors with SARS-CoV-2 resulted in orders of 33 magnitude differences in virus replication in small intestinal and colonic organoid-derived 34 monolayers. Susceptibility to infection correlated with ACE2 expression level and was 35 independent of donor demographic or clinical features. ACE2 transcript levels in cell culture 36 matched the amount of ACE2 in primary tissue indicating this feature of the intestinal epithelium 37 is retained in the organoids. Longitudinal transcriptomics of organoid-derived monolayers 38 identified a delayed yet robust interferon signature, the magnitude of which corresponded to the 39 degree of SARS-CoV-2 infection. Interestingly, virus with the Omicron variant spike protein 40 infected the organoids with the highest infectivity, suggesting increased tropism of the virus for 41 intestinal tissue. These results suggest that heterogeneity in SARS-CoV-2 replication in 42 intestinal tissues results from differences in ACE2 levels, which may underlie variable patient 43 outcomes. 44 45 46

The contributions of the viral component of the microbiome-the virome-to the development of innate and adaptive immunity are largely unknown. Here, we systematically defined the host response in mice to a panel of eukaryotic enteric viruses representing six different families. Infections with most of these viruses were asymptomatic in the mice, the magnitude and duration of which was dependent on the microbiota. Flow cytometric and transcriptional profiling of mice mono-associated with these viruses unveiled general adaptations by the host, such as lymphocyte differentiation and IL-22 signatures in the intestine, as well as numerous viral-strain-specific responses that persisted. Comparison with a dataset derived from analogous bacterial mono-association in mice identified bacterial species that evoke an immune response comparable with the viruses we examined. These results expand an understanding of the immune space occupied by the enteric virome and underscore the importance of viral exposure events.

The enteric virome includes viruses that infect eukaryotic cells in the gut and is one constituent of the mammalian microbiome. Although best known for causing acute diarrheal disease, many of these viruses cause subclinical infections, and indeed are often detected in asymptomatic individuals. The consequences of harboring these viruses are unclear. We recently demonstrated that norovirus mono-colonization promotes the development of the intestinal architecture and the mucosal immune system of germ-free mice in a manner similar to symbiotic bacteria and can protect against models of chemical and microbial injury. It is unclear whether this symbiotic virus-host relationship is a unique feature of murine norovirus strain CR6 colonization. Here, we examined the extent to which members of the eukaryotic enteric virome contribute to the state of the host health. Examination of 10 enteric DNA and RNA viruses representing 6 viral families capable of spreading through the fecal-oral route revealed that many establish a prolonged infection, which often is not limited to the intestinal tissues, in the absence of visible disease after oral inoculation. Further histologic analysis of the small intestinal and colonic tissues confirmed no pathogenic effects on the intestinal tissues. To evaluate the direct impact of asymptomatic viral infections independently from the bacterial microbiome, we performed RNA-seq on intestinal tissues and a comprehensive flow cytometry analysis of intestinal and extraintestinal organs, assessing over 20 immune cell subsets and their cytokine production capacity, following viral mono-colonization of germ-free mice. We found profound effects exerted by the enteric viruses on the immune system in all the tissues tested. In addition to confirming anticipated consequences of viral infection such as expansions of Th1 cells and effector memory T cells, we identified novel virus-specific responses, such as norovirus-induced expansion of type 1 regulatory T cells and parvovirus-mediated induction of regulatory T cells. Interestingly, intestinal T cells and innate lymphoid cells from almost all the virome-colonized mice were more predisposed towards the production of proinflammatory Th1 cytokines, such as IFNγ, and of Il22. An increase in the IL22 signature was also detected in the intestinal transcriptome of virome-colonized mice, suggesting that the virome members support the production of this cytokine already at the steady-state level. Of note, only a few viruses were inducing a type I interferon signature in the tissues, suggesting that pathways other than type I interferon mediate the virome effects on the host. Taken together, these data demonstrate that multiple members of the enteric virome can contribute to the development and function of the mucosal immune system. This abstract is also being presented as Poster A13. Citation Format: Simone Dallari, Thomas Heaney, Adriana Rosas-Villegas, Ken Cadwell. Functional characterization of the enteric animal virome as mediator of host health [abstract]. In: Proceedings of the AACR Special Conference on the Microbiome, Viruses, and Cancer; 2020 Feb 21-24; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2020;80(8 Suppl):Abstract nr PR03.

The enteric virome includes viruses that infect eukaryotic cells in the gut and is one constituent of the mammalian microbiome. Although best known for causing acute diarrheal disease, many of these viruses are detected in asymptomatic individuals. The immune consequence of harboring these viruses is unclear. We recently demonstrated that norovirus infection promotes the development of the mucosal immune system in mice in a manner similar to symbiotic bacteria, and can protect against models of chemical and microbial injury. These results are reminiscent of findings from the microbiome field demonstrating that intestinal colonization by individual bacterial species directs the differentiation of the immune system. Here, we examined the extent to which the eukaryotic enteric virome contributes to the state of the host immune system. Examination of 10 enteric DNA and RNA viruses, representing 6 viral families, revealed that many establish prolonged infection in the absence of disease. To evaluate the immunological impact of these viral infections that occurs independently of other members of the microbiome, we performed a comprehensive flow cytometry analysis of several organs following infection of germ-free mice that assessed over 20 immune cell subsets and their capacity for cytokine production. We found profound effects of enteric viral infection in all the tissues tested, showing strain-specific responses, such as norovirus-induced expansion of type 1 regulatory T cells, and commonly shared ones, such as the increased potential of colonic T cells to produce Il-22. Taken together, these data demonstrate that enteric virome members contribute to the immune status of the host.

Products derived from bacterial members of the gut microbiota evoke immune signalling pathways of the host that promote immunity and barrier function in the intestine. How immune reactions to enteric viruses support intestinal homeostasis is unknown. We recently demonstrated that infection by murine norovirus (MNV) reverses intestinal abnormalities following depletion of bacteria, indicating that an intestinal animal virus can provide cues to the host that are typically attributed to the microbiota. Here, we elucidate mechanisms by which MNV evokes protective responses from the host. We identify an important role for the viral protein NS1/2 in establishing local replication and a type I interferon (IFN-I) response in the colon. We further show that IFN-I acts on intestinal epithelial cells to increase the proportion of CCR2-dependent macrophages and interleukin (IL)-22-producing innate lymphoid cells, which in turn promote pSTAT3 signalling in intestinal epithelial cells and protection from intestinal injury. In addition, we demonstrate that MNV provides a striking IL-22-dependent protection against early-life lethal infection by Citrobacter rodentium. These findings demonstrate novel ways in which a viral member of the microbiota fortifies the intestinal barrier during chemical injury and infectious challenges.

ABSTRACT Chronic viral infections represent a major challenge to the host immune response, and a unique network of immunological elements, including cytokines, are required for their containment. By using a model persistent infection with the natural murine pathogen lymphocytic choriomeningitis virus clone 13 (LCMV Cl13) we investigated the role of one such cytokine, interleukin-27 (IL-27), in the control of chronic infection. We found that IL-27 receptor (IL-27R) signaling promoted control of LCMV Cl13 as early as days 1 and 5 after infection and that il27p28 transcripts were rapidly elevated in multiple subsets of dendritic cells (DCs) and myeloid cells. In particular, plasmacytoid DCs (pDCs), the most potent type 1 interferon (IFN-I)-producing cells, significantly increased il27p28 in a Toll-like receptor 7 (TLR7)-dependent fashion. Notably, mice deficient in an IL-27-specific receptor, WSX-1, exhibited a pleiotropy of innate and adaptive immune alterations after chronic lymphocytic choriomeningitis virus (LCMV) infection, including compromised NK cell cytotoxicity and antibody responses. While, the majority of these immune alterations appeared to be cell extrinsic, cell-intrinsic IL-27R was necessary to maintain early pDC numbers, which, alongside lower IFN-I transcription in CD11b + DCs and myeloid cells, may explain the compromised IFN-I elevation that we observed early after LCMV Cl13 infection in IL-27R-deficient mice. Together, these data highlight the critical role of IL-27 in enabling optimal antiviral immunity early and late after infection with a systemic persistent virus and suggest that a previously unrecognized positive-feedback loop mediated by IL-27 in pDCs might be involved in this process. IMPORTANCE Persistently replicating pathogens, such as human immunodeficiency virus, hepatitis B virus, and hepatitis C virus, represent major health problems worldwide. These infections impose a long-term challenge on the host immune system, which must be heavily and continuously regulated to keep pathogen replication in check without causing fatal immunopathology. Using a persistently replicating rodent pathogen, LCMV, in its natural host, we identified the cellular sources and effects of one important regulatory pathway, interleukin-27 receptor WSX-1 signaling, that is required for both very early and late restriction of chronic (but not acute) infection. We found that WSX-1 was necessary to promote innate immunity and the development of aberrant adaptive immune responses. This not only highlights the role of IL-27 receptor signaling in regulating distinct host responses that are known to be necessary to control chronic infections, but also positions IL-27 as a potential therapeutic target for their modulation.

Although characterization of T cell exhaustion has unlocked powerful immunotherapies, the mechanisms sustaining adaptations of short-lived innate cells to chronic inflammatory settings remain unknown. During murine chronic viral infection, we found that concerted events in bone marrow and spleen mediated by type I interferon (IFN-I) and Toll-like receptor 7 (TLR7) maintained a pool of functionally exhausted plasmacytoid dendritic cells (pDCs). In the bone marrow, IFN-I compromised the number and the developmental capacity of pDC progenitors, which generated dysfunctional pDCs. Concurrently, exhausted pDCs in the periphery were maintained by self-renewal via IFN-I-and TLR7-induced proliferation of CD4(-) subsets. On the other hand, pDC functional loss was mediated by TLR7, leading to compromised IFN-I production and resistance to secondary infection. These findings unveil the mechanisms sustaining a self-perpetuating pool of functionally exhausted pDCs and provide a framework for deciphering long-term exhaustion of other short-lived innate cells during chronic inflammation.

Several arenaviruses cause hemorrhagic fever (HF) diseases that are associated with high morbidity and mortality in humans. Accordingly, HF arenaviruses have been listed as top-priority emerging diseases for which countermeasures are urgently needed. Because arenavirus nucleoprotein (NP) plays critical roles in both virus multiplication and immune-evasion, we used an unbiased proteomic approach to identify NP-interacting proteins in human cells. DDX3, a DEAD-box ATP-dependent-RNA-helicase, interacted with NP in both NP-transfected and virus-infected cells. Importantly, DDX3 deficiency compromised the propagation of both Old and New World arenaviruses, including the HF arenaviruses Lassa and Junin viruses. The DDX3 role in promoting arenavirus multiplication associated with both a previously un-recognized DDX3 inhibitory role in type I interferon production in arenavirus infected cells and a positive DDX3 effect on arenavirus RNA synthesis that was dependent on its ATPase and Helicase activities. Our results uncover novel mechanisms used by arenaviruses to exploit the host machinery and subvert immunity, singling out DDX3 as a potential host target for developing new therapies against highly pathogenic arenaviruses.

Several arenaviruses cause hemorrhagic fever (HF) diseases that are associated with high morbidity and mortality in humans. Accordingly, HF arenaviruses have been listed as top-priority emerging diseases for which countermeasures are urgently needed. Because arenavirus nucleoprotein (NP) plays critical roles in both virus multiplication and immune-evasion, we used an unbiased proteomic approach to identify NP-interacting proteins in human cells. DDX3, a DEAD-box ATP-dependent-RNA-helicase, interacted with NP in both NP-transfected and virus-infected cells. Importantly, DDX3 deficiency compromised the propagation of both Old and New World arenaviruses, including the HF arenaviruses Lassa and Junin viruses. The DDX3 role in promoting arenavirus multiplication correlated with both a previously un-recognized DDX3 contribution to type I interferon suppression in arenavirus infected cells and a positive effect of DDX3 on viral RNA synthesis. Our results uncover novel mechanisms used by arenavirus to exploit the host machinery and subvert immunity, singling out DDX3 as a potential host target for developing new therapies against highly pathogenic arenaviruses.AUTHOR SUMMARY Arenaviruses include severe clinical pathogens causing hemorrhagic fevers and have been recently incorporated by the World Health Organization in a list of critical emerging diseases for which additional research and identification of clinical targets is urgently required. A better understanding of how viral proteins interact with host cellular factors to favor arenavirus multiplication can illuminate novel pipelines on therapeutic strategies. Here we demonstrated that the ATP-dependent RNA helicase DDX3 interacted with the arenavirus nucleoprotein, which displays fundamental functions in different steps of the viral-cycle. Our work also revealed an unexpected new biology on the role that DDX3 might play during viral infections. In sharp contrast to previous studies showing DDX3 enhancement of IFN-I induction, we demonstrated that DDX3 suppressed IFN-I production at late time points after arenavirus infection, contributing to a DDX3 pro-viral effect. We also showed that early after infection, DDX3 pro-viral role was IFN-I independent and was mediated by DDX3 facilitation of viral RNA synthesis without affecting RNA translation. Altogether, our study established DDX3 as a critical host interacting partner of the arenavirus nucleoprotein and demonstrated two previously unrecognized DDX3-dependent strategies by which these deadly viruses exploit the host cellular machinery and suppress immunity.

During chronic infections, sustained cell adaptation via functional exhaustion has been mostly studied in the adaptive immune compartment but much less is known on how innate immune cells adjust to a persistently infectious milieu. Thus, to understand how innate cells adapt to persistent infections, we studied plasmacytoid dendritic cells (pDCs), which specialize in Type I Interferon (IFN-I) production and often become functionally exhausted in chronic settings. Using a murine chronic viral infection model we demonstrated that pDC IFN-I exhaustion is caused by concerted events at central (bone marrow) and local (spleen) compartments. On one hand, undifferentiated bone marrow pDC progenitors exhibited quantitative and qualitative defects and failed to generate functional pDCs ex vivo. Analysis of transcription and chromatin landscapes via RNA-seq and ATAC-seq revealed that IFN-I signaling pathway was enhanced in bone marrow pDC progenitors. Consistently, IFN-I receptor blockade restored the quantitative (albeit not the qualitative) defects of bone marrow pDC progenitors, which was accompanied by restoration of E2-2, a transcription factor critical for pDC development. On the other hand, splenic pDCs received sustained TLR7 signaling, which promoted their maturation but also rendered them unable to produce IFN-I upon ex vivo TLR re-stimulation or in vivo secondary infection. RNA-seq and ATAC-seq analysis in splenic pDCs revealed significant alterations in multiple pathways and transcriptional regulators that are currently being studied. Our work provides an anatomical, cellular and molecular framework to understand how innate immune exhaustion can be triggered and sustained during a chronic viral infection.

Plasmacytoid dendritic cells (pDC) are type I interferon-producing cells with critical functions in a number of human illnesses; however, their molecular regulation is incompletely understood. Here we show the role of Src family kinases (SFK) in mouse and human pDCs. pDCs express Fyn and Lyn and their activating residues are phosphorylated both before and after Toll-like receptor (TLR) stimulation. Fyn or Lyn genetic ablation as well as treatment with SFK inhibitors ablate pDC (but not conventional DC) responses both in vitro and in vivo. Inhibition of SFK activity not only alters TLR-ligand localization and inhibits downstream signalling events, but, independent of ex-vivo TLR stimulation, also affects constitutive phosphorylation of BCAP, an adaptor protein bridging PI3K and TLR pathways. Our data identify Fyn and Lyn as important factors that promote pDC responses, describe the mechanisms involved and highlight a tonic SFK-mediated signalling that precedes pathogen encounter, raising the possibility that small molecules targeting SFKs could modulate pDC responses in human diseases.

JC virus (JCV) is a widespread member of the Polyomaviridae family. Following primary infection, which occurs asymptomatically during childhood, JCV establishes latency in the host. JCV seroprevalence can reach 80 % in healthy adults, but the age of viral exposure has not been yet characterized. This study was conducted to define JCV seroprevalence in Italian infants and to estimate the date of primary infection. A JCV viral protein 1 (VP1)–GST fusion protein was used in conjunction with a homemade indirect enzyme-linked immunosorbent assay (ELISA) to test for the presence of IgG antibodies to JCV in 981 serum samples collected from 644 Italian infants of different ages (1 day to 3 years old) and in 102 breast milk samples. IgM antibody presence was also evaluated in longitudinally collected samples from 17 selected children. JCV antibody prevalence and normalized optical density (nOD) were calculated. For the longitudinal analysis, generalized estimating equation techniques and spline functions were used to estimate the possible non-linear effects of time on antibody production kinetics. JCV IgG was detected in 71.8 % of the sera. Prevalence increased over time from 46.1 % (1 month old) to 80.7 % (12 months old), 85.9 % (24 months old), and 85.5 % (36 months old). As determined by nOD, the longitudinal analysis of serum IgG amounts in children of this study (ages 1 day to 3 years old) illustrated IgG kinetic changes with statistically significant trends (p = 0.001). One-month-old children were largely negative for JCV IgM (82.4 %), and 58.8 % of children produced JCV IgM within the second and sixth months of life. JCV IgG was detected in 27.3 % of breast milk samples. JCV primary infection likely occurs before 6 months of age, and a sizeable percentage of Italian infants will become JCV seropositive within 2 years of age. This study can be used to determine the optimal age for potential future JCV vaccination in infants.

Natalizumab is a humanized monoclonal antibody against the α4 subunit of VLA-4 integrin that is used to treat conditions such as multiple sclerosis (MS). Although its effects on lymphocytes have been widely described, little is known about its effects on monocytes. Here we described the effects of natalizumab treatment on peripheral blood monocytes from a small cohort of MS patients in terms of relative frequencies and surface integrin (CD49d and CD18) expression. We showed that natalizumab treatment altered the surface integrin expression on monocyte subsets in the peripheral compartment, suggesting a role for them as mediators of natalizumab effects.