bluuebunny/crossref_metadata_2025_split huggingface dataset:
The enteric microbiome stimulates localized interferon responses and provides preemptive antiviral protection of intestinal epithelial cells through IFNLR1 signaling
Authors: Van Winkle Jacob , Peterson Stefan , Kennedy Elizabeth , Wheadon Michael , Ingle Harshad , Desai Chandi , Artyomov Maxim , Lee Sanghyun , Baldridge Megan , Nice Timothy 
Published: February 2023

Abstract
Specialized immune responses have evolved to eliminate pathogens in the gastrointestinal tract. In particular, intestinal epithelial cells (IECs) are uniquely responsive to interferon lambda (IFN-λ) and depend on IFN-λ for antiviral defense to a greater extent than other types of IFN. IFN-λ signaling protects IECs by inducing expression of antiviral IFN-stimulated genes (ISGs), but it is unclear if the intestinal microbiome interacts with the IFN-λ pathway. We find that commensal microbes stimulate a steady-state ISG signal in the gastrointestinal tract that is depleted with broad-spectrum antibiotics, as assessed by whole-tissue RNA sequencing. Steady-state ISG expression is also significantly reduced in mice lacking IFN-λ receptor (IFNLR) specifically in IECs. These data suggest that enteric bacteria stimulate expression of IFN-λ and, subsequently, epithelial ISGs at homeostasis. Strikingly, imaging data reveals that these steady-state ISGs are present in distinct pockets throughout the small intestinal epithelium and are concentrated in IECs at the tips of individual villi. Furthermore, we find that IFNLR protects IECs during initiation of murine rotavirus infection at early time-points post-infection, suggesting that steady-state ISGs are protective against viral infection. Lastly, we find that steady-state ISGs are expressed in a subpopulation of human IECs when we re-analyze publicly available single-cell RNA sequencing datasets. These novel observations indicate that commensal microbes stimulate ISGs in localized regions of the intestinal epithelium at homeostasis and may preemptively activate antiviral defenses in vulnerable IECs to improve host fitness against enteric viruses.
CD4+ Foxp3+ T-regulatory cells support fecal microbiota transplantation engraftment and resolution of Clostridioides difficile infection
Authors: Abt Michael C , Alam Zahidul , Littmann Eric R , Denny Joshua E , Lee Jung-Jin , Bittinger Kyle 
Published: February 2023

Abstract
Clostridioides difficile is an opportunistic pathogen that infects the large intestine following perturbation of the intestinal microbiota causing epithelial damage and debilitating, potentially fatal, colitis. Fecal microbiota transplantation (FMT) is a successful therapeutic strategy for treating recurrent C. difficile infection. Despite remarkable efficacy, implementation of FMT therapy is limited and the mechanism of action remains poorly understood. Here, we demonstrate a critical role for Foxp3+ CD4+T-regulatory cells in supporting FMT therapy using a murine C. difficile infection system. Following FMT, chronically infected wild-type mice resolve C. difficile. In contrast, cohoused Rag1−/− or CD4+ T cell deficient mice fail to clear the infection. Genetic deletion of TH1 or TH17 effector cytokines does not impact efficacy of FMT, however, C. difficile infected Il10−/− mice are non-responsive to FMT therapy. Further, targeted ablation of CD4+ Foxp3+T-regulatory cells in C. difficile infected Foxp3-DTR mice prior to FMT reveal a necessary role for this CD4+T cell subset in FMT-mediated resolution of C. difficile infection. FMT non-responsive mice exhibit impaired engraftment of the FMT bacterial consortia and failed restoration of commensal bacteria-derived secondary bile acids in the large intestine, metabolites associated with limiting C. difficile disease in FMT recipient patients. These data demonstrate that the host’s inflammatory immune status can limit the efficacy of microbiota-based therapeutics to treat C. difficile infection.
Oral administration of a peptide antigen with the cholera toxin adjuvant induces Th17 rather than Th2 cells
Authors: Hong Sung-Wook , Jenkins Marc K 
Published: February 2023

Abstract
Cholera toxin (CT) is widely used an as adjuvant to elicit mucosal immune responses to co-administered antigens. The observation that antigens given orally with CT induce IL-4-producing T cells and antigen-specific IgE has led to the concept that CT is a Th2 adjuvant. We revisited this issue by using a peptide:MHCII tetramer-based approach to follow the fate of polyclonal CD4+ T cells specific for an MHCII-bound peptide from Toxoplasma gondii CD4Ag28m in mice fed with this peptide and CT. We found that this regimen induced the clonal expansion of CD4Ag28m peptide-specific CD4+ T cells in the secondary lymphoid organs. Surprisingly, the expanded tetramer-binding population consisted of 20 percent RORgt+ Th17 cells but only 3 percent Th2 cells. Th17 cell generation induced by oral peptide plus CT immunization was lost in mice lacking IL-6 or the microbe sensor MyD88. The latter result raised the possibility that the adjuvanticity of CT depended on gut microbes. Treatment of B6 mice with antibiotics to eradicate commensal bacteria, however, only slightly reduced Th17 cell formation in response to oral administration of the peptide plus CT, raising the possibility that viral or fungal microbes are required. Collectively, our data demonstrate that CT induces a Th17 immune response via a pathway that depends on MyD88.
Function of circulating myeloid cells in healthy donors and patients with metastatic solid tumors
Authors: Contreras Cristina F , Kaczanowska Sabina , Kaplan Rosandra N 
Published: February 2023

Abstract
Monocytes are a heterogeneous group of mononuclear innate immune cells that have diverse inflammatory responses. In the context of cancer, monocytes and monocyte-derived cells have been evaluated for their pro- and anti-tumoral effects in the tumor microenvironment. These functions range from induction of tumor cell death to suppression of T cells, promotion of angiogenesis and remodeling of the extracellular matrix. Outside of the primary tumor, monocytes in circulation maintain their dichotomous role in cancer immunosurveillance. Specifically, patrolling non-classical CD14−CD16+ monocytes have been found to play a role in the prevention of metastasis. In contrast, CD14+ monocyte-derived cells from patients with solid tumors have been shown to promote tumor progression. Therefore, understanding this monocytic heterogeneity as well as other unexplored roles (i.e. monocyte-mediated phagocytosis of tumor cells) is crucially important for malignancies with high rates of metastasis. Yet, the phenotypic and functional diversity of circulating monocytes in patients with metastatic solid malignancies is still largely unknown. In this study, we sought to characterize and compare peripheral blood monocytes obtained from healthy donors and patients with advanced stage solid tumors. Through flow cytometric analysis and functional assays, we determined the subpopulation distributions as well as the phagocytic and suppressive activities of the monocytic compartment in patients with advanced cancer and healthy controls. Providing new insights into their cancer-related functions, we highlight the need for consideration of circulating monocytes into immune-targeting approaches in metastatic solid malignancies.
Impact of constitutive FLT3 signaling on dendritic cell development and function in a genetically engineered mouse model of Acute Myeloid Leukemia
Authors: Flynn Patrick A , Lind Evan 
Published: February 2023

Abstract
Acute myeloid leukemia (AML) is a hematological cancer with a very poor prognosis. FLT3-ITD mutations, which result in constitutive FLT3 signaling, are the most common mutation. Our lab and others have shown that many AML patient samples exhibit hallmarks of immune exhaustion such as T cell dysfunction, increased MDSCs, and increased T regulatory cells (Tregs). Understanding mechanisms that drive immune dysfunction in AML can improve patient outcomes. FLT3 signaling is critical for dendritic cell (DC) development, but little is known about the effects of FLT3-ITD has on DC development and function in AML. We found that FLT3-ITD driven AML mice have significantly expanded DC and Treg populations compared to healthy controls, which is reported in patients with AML. Analysis of serum cytokines identified significantly increased levels of IL-10, IL-17a, and IL-27 in leukemia mice compared to healthy controls, suggesting that the expansion of DCs in our leukemia mice may be driving expansion of CD4+ T cells. We hypothesize that FLT3-ITD DCs are a significant driver of the systemic expansion of Tregs and T cell exhaustion in AML. Understanding the mechanisms by which FLT3-ITD DCs contribute to AML immune dysfunction is critical to understanding leukemia etiology and the development of potential immune based therapies such as immune checkpoint blockade or vaccines.
Divergent immune impacts elicited by chemically dissimilar agonists of the STING protein
Authors: Boehm Dylan T , Mizuno Nobuyo , Pryke Kara , DeFilippis Victor 
Published: February 2023

Abstract
Vaccines comprised of inert antigen are very safe, yet they are typically only weakly immunogenic and thus require co-administration of factors such as adjuvants that enhance immunostimulation. Unfortunately, very few adjuvants are approved for clinical use and the mechanistic bases of their function are poorly understood. Stimulator of Interferon Genes (STING) is the PRR that senses intracellular cyclic dinucleotides (CDN) synthesized by the enzyme cGAS following its sensing of cytosolic DNA. Numerous molecules have been identified and developed that directly induce STING-mediated activity and can enhance establishment of the adaptive immune response. However, a significant barrier to clinical utilization of STING-based adjuvants exist including an understanding of their mechanisms of action and the unexpected diversity in molecular and cellular responses that correlate with chemical nature of the agonists. We utilized a mouse model of vaccination with the model antigen ovalbumin, in combination with chemically distinct STING agonists. While all CDNs and small molecules directly bind to and activate STING, we determined that downstream immune reactivity to antigens varied significantly. We have identified key dissimilarities including agonist-specific gene transcription patterns, cytokine induction, APC maturation, TFH enhancement, and T helper polarization biases. Furthermore, we observed these differences using two clinically relevant VLP-based vaccine antigens against Chikungunya and Zika viruses. Our findings provide new insights into STING-initiated immune responses, which can direct future research toward an optimization of adjuvants directed toward this and other innate immune pathways.
Antigen archiving promotes secondary CD8+ T cell memory responses during an unrelated infection
Authors: Doan Thu A. , Schafer Johnathon , Lucas Erin D. , Tamburini Beth 
Published: February 2023

Abstract
Numerous studies have shown viral antigens can persist in lymph nodes after resolution of the infection. We showed that lymphatic endothelial cells (LECs), which comprise the lymphatic vasculature necessary for antigen drainage from the tissue, is the predominant cell type required for the persistence of antigen within the lymph node. We termed this process antigen archiving due the ability of LECs to actively archive antigens to which an immune response has occurred. This process involves antigen acquisition, retention, and exchange of the antigen between LECs and dendritic cells (DC), resulting in presentation of the archived antigens to CD8+ memory T cells and improving effector function. In more recent data, we demonstrated that LEC death causes the release of archived antigens during LN contraction. The objective of this study was to determine if during a secondary unrelated infection whether LEC death would occur and cause archived antigens to be released. As expected, we found that a second and unrelated viral infection causes LEC death within two to three weeks following infection. Within the same time frame that we observed LEC death, we observed a significant increase in archived antigen-specific endogenous memory T cells. This increase only occurred in mice that received an unrelated viral infection and not in those mice that did not receive the unrelated viral infection. In conclusion, archived antigen release during a secondary unrelated infection potentially boosts the archived antigen specific memory CD8+ T cell population. Understanding the mechanism of antigen release during multiple infections could ultimately lead to better strategies for vaccination and improve our understanding of how LECs influence immunity.
Restoring CD8+ T cell anti-HIV activity using combinatorial immune checkpoint blockade
Authors: Jones Amber D , Van Duyne Rachel , Khakhina Svetlana , Smith Stephen M , Klase Zachary A 
Published: February 2023

Abstract
Antiretroviral therapy (ART) effectively reduces viral load and improves life expectancy but does not fully restore host immune function. During chronic infection, T cells upregulate multiple inhibitory immune checkpoint receptors (ICR) which results in the loss of T cell functionality; a state called T cell exhaustion. In this study, we utilized HIV-1 controllers (HC) who have an inherent ability to control viral replication in the absence of ART but eventually gain viral susceptibility due to unknown mechanisms. We hypothesize that efficient control of viral replication becomes compromised by CD8+ T cell exhaustion. Using our cohort, we demonstrate that CD8+ T cells of ART naïve HCs are both necessary and sufficient to suppress viral replication. We also demonstrate that during times of clinical viral control, ART naïve HCs have low expression of exhaustion markers and sustain in vitro viral control. Upon loss of control, our HCs upregulate exhaustion markers and are susceptible to in vitro infection. This study evaluates the synergistic effects of immune checkpoint blockade (ICB) to determine if blockade of ICRs can restore anti-viral functionality of exhausted CD8+ T cells. Using our in vitro spreading infection assay, we demonstrate that treatment with single ICB results in a modest improvement of anti-viral functionality in CD8+ T cells from HCs who have lost viral control. However, former HCs who support in vitro viral replication demonstrate restored suppression of viral replication in tissue culture in the presence of combinatorial anti-PD1 and anti-TIM3 ICB. Our data suggests that combinatorial ICB can restore CD8+ T cells anti-viral functionality and has the potential to be a novel HIV therapeutic intervention.
A single immunization with CAF08 provides newborns with Th1-mediated protection against Respiratory Syncytial Virus infection
Authors: van Haren Simon D. , Pedersen Gabriel , Kumar Azad , Ruckwardt Tracy , Moin Syed , Moore Ian , Minai Mahnaz , Liu Mark , Pak Jensen , Borriello Francesco , Ahmed Saima , Helmel Michaela , Andersen Peter , Graham Barney S , Steen Hanno , Christensen Dennis , Levy Ofer 
Published: February 2023

Abstract
Respiratory Syncytial Virus (RSV) is a leading cause of morbidity and mortality in children, due in part to their distinct immune system, characterized by impaired induction of T-helper 1 (Th1)□immunity. Here we describe cationic adjuvant formulation (CAF)-08, a liposomal vaccine formulation tailored to induce Th1 immunity in early life via synergistic engagement of Toll-like Receptor 7/8 and the C-type lectin receptor Mincle. Quantitative phosphoproteomics applied to human dendritic cells revealed a key role for Protein Kinase C-d for enhanced Th1 cytokine production in neonatal dendritic cells and identified signaling events resulting in antigen cross-presentation. In vivo, a single immunization at birth with CAF08-adjuvanted RSV pre-fusion antigen protected newborn mice from RSV infection through induction of antigen-specific CD8+ and Th1 cells. Overall, we describe a novel pediatric adjuvant formulation and characterize its mechanism of action providing a promising avenue for development of early life vaccines against RSV and other intracellular pathogens.
Influence of vaccine adjuvant physical properties on antigen processing and presentation in the lymph node
Authors: Ball Alexander , Pompano Rebecca R 
Published: February 2023

Abstract
Despite the efficacy of vaccines, there is a growing need for novel vaccine adjuvants that can drive type-1 immunity, a response governed by antigen presenting cells (APCs). Current methods used to evaluate efficacy of novel adjuvants fail to consider the spatiotemporal events of antigen presentation that dictate the development of cellular immunity. Understanding how adjuvants affect the initial development of type-1 immunity would result in the design of more effective adjuvants. We hypothesized that adjuvants induce unique spatiotemporal patterns within lymph nodes that differ based on the extent to which an adjuvant drains to the LN. These patterns are then responsible for shaping the adaptive immune response. We tested this hypothesis by converting alum, a depot-forming adjuvant that remained at the site of inoculation, into nanoparticles (np) that enter the lymphatics and drained to the LN after vaccination. The size and charge of the np alum was measured through dynamic light scattering and zeta potential. The immunostimulatory effects of both alum and np alum were measured through inflammasome activation of bone marrow-derived macrophages. The two adjuvant formulations were then used to examine the influence of depot-forming alum versus lymph-node (LN) draining alum on skin-resident dendritic cell migration to the LN. The number of migratory DCs in the LN after vaccination was measured by flow cytometry. Next, we made use of live ex vivo lymph node slices to measure chemokine secretion in the LN by ELISA and to observe patterns of DC migration through widefield microscopy. This study illustrates the impact of the physical properties of an adjuvant in shaping the early stages of the adaptive immune response.
Pre-existing cellular immunity to SARS-CoV-2 through an immunodominant epitope
Authors: Grant Emma J , Lineburg Katie E , Swaminathan Srividhya , Chatzileontiadou Demetra S.M. , Szeto Christopher , Sloane Hannah , Panikkar Archana , Raju Jyothy , Crooks Pauline , Rehan Sweera , Nguyen Andrea T , Lekieffre Lea , Neller Michelle , Tong Zhen Wei Marcus , Jayasinghe Dhilshan , Chew Keng Yih , Lobos Christian A , Halim Hanim , Burrows Jacqueline M , Riboldi-Tunnicliffe Alan , Chen Weisan , D’Orsogna Lloyd , Khanna Rajiv , Short Kirsty R , Smith Corey , Gras Stephanie 
Published: February 2023

Abstract
Significant efforts are being made worldwide to understand the immune response to SARS-CoV-2, responsible for the COVID-19 pandemic, including the role of preexisting T cell immunity. Understanding the mechanisms that promote crossrecognition by T cells induced by seasonal coronaviruses will be critical for future predictions on the role of pre-existing immunity in protection against severe disease. We demonstrate that the SARS-CoV-2 nucleocapsid (N) protein induces an immunodominant response in HLA-B7+ COVID-19-recovered individuals that is also readily detectable in unexposed donors. This immunodominant response is driven by a single N-encoded epitope that displays a high degree of conservation with the homologous region in circulating coronaviruses. We show that T cell-mediated crossreactivity can be detected towards the circulating OC43/HKU-1 coronaviruses, but not the 229E or NL63 coronaviruses, due to different peptide conformations. This cross-reactivity is driven by private T cell receptor repertoires with a bias for TRBV27 and a long CDR3b loop in unexposed and COVID-19-recovered individuals. Together, our findings demonstrate the basis of pre-existing immunity to a conserved and highly immunogenic SARS-CoV-2 epitope driven by cross-reactive memory T cells, suggesting long-lived protective immunity.
Immunodominant, Qa-1-restricted CD8 T cell response elicited against a non-canonical translation product in influenza A virus
Authors: Hogan Michael J , Maheshwari Nikita , Nicastri Annalisa , Ternette Nicola , Eisenlohr Laurence C. 
Published: February 2023

Abstract
The extent to which non-canonical translation products drive antiviral T cell responses is incompletely understood. We explored this question using an immunopeptidomic approach in an influenza virus model. C57Bl/6 mouse-derived cells were infected with influenza virus A/Puerto Rico/8/1934 (PR8), and MHC-bound peptides were eluted and analyzed by tandem mass spectrometry. Mass spectra were searched against a database of all viral gene segments translated in all possible reading frames, irrespective of the presence of start codons. We identified a 9-mer peptide, here termed M-SL9, that maps to an alternative reading frame of the sequence encoding matrix protein 1 (M1). To validate M-SL9 as a T cell epitope, we infected C57Bl/6 mice with PR8, collected tissues, and measured T cell reactivation by synthetic M-SL9 peptide. Remarkably, 10% of all CD8 T cells in the lung were specifically reactivated by M-SL9 peptide, and the vast majority of these were polyfunctional, producing two or more Th1 cytokines. An analysis of M-SL9 processing and presentation revealed that M-SL9 is restricted to the non-classical MHC class Ib molecule, Qa-1, and that presentation is dependent on the second 5′-proximal AUG codon within the M1-coding sequence, suggesting that its translation results from leaky ribosomal scanning. These data contribute to a growing body of work showing the importance of non-canonical MHC presentation in protective immune responses.
T cell insufficiency enables emergence of polyomavirus antibody escape variants
Authors: Lauver Matthew D , Goetschius Daniel J , Hafenstein Susan L , Lukacher Aron E 
Published: February 2023

Abstract
Deficient adaptive immunity underlies CNS diseases caused by JC polyomavirus (JCPyV), a ubiquitous member of the human virome. The best characterized of these is progressive multifocal leukoencephalopathy (PML), a frequently fatal brain demyelinating disease. Risk factors for PML are poorly defined but mainly involve conditions of T cell insufficiency or dysfunction, including AIDS and particular immunomodulatory therapies (natalizumab, rituximab). JCPyV isolates from PML patients’ brains frequently contain point mutations in the major capsid protein, VP1. However, these variants are not present in the patients’ kidneys, the major site of JCPyV persistence. How/if these mutations confer neurovirulence is actively debated. Mapping a common JCPyV-PML VP1 mutation into mouse polyomavirus (MuPyV), we found that this variant virus was resistant to a neutralizing monoclonal antibody (mAb) and poorly replicated in the kidney. Cryo EM analysis unambiguously defined the antibody epitope and identified the mechanism of antibody escape. Passaging MuPyV in the presence of VP1 mAb allowed emergence of antibody escape variants in vitro. To investigate the connection between T cell impairment and antibody escape in vivo, we infected antibody-deficient μMT mice with MuPyV, treated them with VP1 mAb, then subjected them to CD4 and CD8 antibody-mediated T cell depletion during persistent infection. In contrast to non-T cell depleted mice, which maintained long term control over MuPyV infection, T cell depletion led to lethal MuPyV disease resulting from the outgrowth of antibody-escape variants. These data show that a narrow PyV antibody response compounded by T cell insufficiency promotes emergence of nAb escape neurotropic variants.