bluuebunny/crossref_metadata_2025_split huggingface dataset:
MicroRNA-9 fine tunes dendritic cell function by suppressing negative regulators
Authors: Cordeiro Brendan , Jeon Peter , Boukhaled Giselle , Corrado Mario , Lapohos Orsolya , Roy Dominic G , Williams Kelsey , Jones Russell G , Gruenheid Samantha , Sagan Selena M. , Krawczyk Connie M. 
Published: January 2023

Abstract
MicroRNAs (miRNA) are emerging as important regulators of immune function due to their fast action and ability to regulate programs of gene expression. Dendritic cell (DC) responses to stimuli involves a rapid transition from steady-state an activated state, leading to numerous phenotypic changes underpinned by changes in gene expression. We have found that microRNA-9 (miR-9) expression is rapidly increased upon LPS stimulation. Pathway analysis on predicted miR-9 targets show a significant enrichment of negative regulators of gene expression. We investigated whether miR-9 promotes DC activation through targeting negative regulators. We found that DCs overexpressing miR-9 showed an increased activation phenotype whereas DCs sequestering miR-9 showed blunted activation. Co-culture of miR-9 sequestering DCs with T cells led to decreased T-cell activation, whereas miR-9 overexpressing DCs promoted T cell activation. Mice immunized with miR-9 overexpressing DCs following injection with B16-OVA melanoma cells displayed decreased tumour volume compared to controls. This work demonstrates that miR-9 promotes the activation and function of DCs, adding to the growing evidence that miRNAs are involved in the regulation of immune responses.
Identification of splice isoforms in T helper cells using Nanopore-based cDNA sequencing
Authors: Mir Quoseena , Srivastava Rajneesh , Ulrich Benjamin J , Kaplan Mark H , Janga Sarath Chandra 
Published: January 2023

Abstract
The T helper (Th) cell compartment of the adaptive immune response provides a central mechanism of balance between inflammation and immune tolerance. The differentiation of naïve Th cells into both regulatory and effector Th subsets is regulated through complex gene regulatory networks that lead to distinct transcriptomes. Alternative RNA splicing is a major component of cellular differentiation that allows protein heterogeneity and mechanistic diversity across cell types. However, our understanding of alternative splicing control is still limited. Here we show differential expression of RNA binding Proteins (RBP) genes among Th cell subsets suggesting a regulatory role of RBPs in RNA splicing and Th differentiation. In order to interrogate the regulatory gene network, we utilized innovative Nanopore-based sequencing to generate a single molecule transcriptome map of naïve CD4 T cells, and differentiated Treg and Th1 cells to characterize full-length cDNA transcripts and alternatively spliced isoforms. Gene expression was compared across four major gene categories; RBPs, Transcription Factors (TFs), Other Protein Coding (OPC) and LncRNA. Our study revealed that RBPs exhibited high splicing potential while LncRNA exhibited relatively less splicing potential in comparison to other gene categories in all cell types. Overall, we identify RBPs that are both differentially expressed in Th subsets and differentially spliced themselves. This might represent an important control mechanism of functional protein diversity in regulating immune responses.
How do CD8+ T cells complete DNA replication in less than 4 hours?
Authors: Sugitani Norie , Moiseeva Tatiana , Wang Yiyan , Palmer Drake , Ford Rhodes , Schamus Sandra , Singh Ankita , Lemon Kathryn , Kammula Udai , Vendetti Frank P , Poholek Amanda , Osmanbeyoglu Hatice , Delgoffe Greg M. , Bakkenist Christopher J 
Published: January 2023

Abstract
We demonstrate that activated CD8+ T cells from Pmel mice replicate their genome within 4 hours which is significantly faster than most cancer cells. Many genotoxic chemotherapeutic agents target the rapid proliferation of cancer cells. However, activated T cells also expand rapidly and this can lead to lymphopenia in patients receiving these chemotherapeutic agents. Understanding how CD8+ T cells complete DNA replication in less than 4 hours could lead to the development of treatment schedules that spare CD8+ T cells.
Three possible mechanisms may underlie the rapid DNA replication in CD8+ T cells: 1) faster replication fork velocity, 2) higher density of origin firing, or 3) modified replication timing program, allowing for simultaneous replication of early- and late-replicating regions of the genome. Using DNA combing, we show that the replication fork velocity and inter-origin distance is similar in unperturbed CD8+ T cells and B16 cancer cells. Repli-seq analysis, a NGS genome-wide replication timing analysis, suggest that regions of the genome replicated late in S phase in fibroblasts are replicated earlier in CD8+ T cells, suggesting that the rapid DNA replication in CD8+ T cells is a consequence of a modified, truncated replication timing program. We also show for the first time that actively replicating CD8+ T cells have dormant origins suggesting that this mechanism of genome stability is maintained in activated CD8+ T cells.
Dissecting the mechanisms responsible for the generation of regulatory versus pathogenic human CD4+ T cells by TLR9-activated plasmacytoid dendritic cells
Authors: Caielli Simone , Banchereau Jacques , Pascual Virginia 
Published: January 2023

Abstract
Understanding the mechanisms underlying how regulatory and pathogenic CD4+ T cells are generated will accelerate therapeutic target identification in autoimmune diseases such as Systemic Lupus Erythematosus (SLE), where this balance is altered. We recently described that in vitro priming of naïve CD4+ T cells with plasmacytoid DCs (pDCs) activated with either CpGA or Oxidized mitochondrial DNA (Ox mtDNA) leads to the generation of Type 1 regulatory T cells (Tr1) or of a novel T helper subset (Th10 cells), respectively. Th10 cells are expanded in the blood of SLE patients and accumulate within the tubuloinsterstitial areas of proliferative nephritis (PLN) lesions. These cells produce IL10 and mitochondrial ROS (mtROS) as the result of reverse electron transport (RET) fueled by the tricarboxylic acid (TCA) cycle intermediate succinate. Functionally, Th10 cells are not suppressive, but they provide B cell help through the synergistic effect of IL10 and succinate. The mechanisms responsible for the acquisition of a regulatory versus a helper phenotype remain elusive. We now show that naïve CD4+ T cells require the activation of the Delta Like Canonical Notch Ligand 4 (Dll4)-Notch pathway in order to acquire a TH10 phenotype. Conversely, the TLR7-IRF7 pathway is necessary for the generation of Tr1 cells. These pathways might be exploited for therapeutic intervention in human autoimmune diseases.
High-affinity tonic TCR:self-pMHC interactions inhibit T follicular helper cell development
Authors: Bartleson Juliet M , Viehmann Milam Ashley A , Donermeyer David L , Horvath Stephen , Allen Paul M 
Published: January 2023

Abstract
T cells receive tonic signals before encountering their immunogenic antigen, but whether or not peripheral, tonic TCR:self-pMHC interactions can affect a T cell’s response to foreign antigen remains relatively unexplored. We interrogated potential T effector functions controlled by tonic signaling with the use of a transgenic TCR system composed of two distinct CD4+ T cells that recognize the same Listerolysin O epitope but lie at opposite ends of the TCR:self-pMHC affinity spectrum. Remarkably, studies revealed differences in the ability of these two cells to produce Tfh cells during a primary immune response. The cells with lower-affinity tonic TCR:self-pMHC interactions generated a significantly greater frequency and total number of Tfh cells when compared to the high-affinity cells, which directly impacted the humoral immune response. To test whether affinity for self-pMHC controls Tfh development through tonic signaling, we generated two mouse lines: Scn5a/CD4-creERT2 and H2-DMf/f/UBC-creERT2. These mouse lines allow us to temporally increase or decrease tonic signaling, respectively. Results showed decreasing tonic self-pMHC availability did not allow for the survival of cells accustomed to high-affinity tonic TCR:self-pMHC interactions; however, increasing tonic signaling in cells that normally experience low-affinity TCR:self-pMHC interactions did indeed inhibit Tfh development. Furthermore, the H2-DMf/f mouse line was additionally crossed to various cre-strains to reveal that the CD11c+ antigen presenting cell subset is responsible for tonic signaling maintenance through presentation of self-pMHC. These studies reveal critical roles tonic signaling plays in Tfh development and CD4+ T cell survival.
T cell receptor repertoire features display universal rules for selection and plasticity in the functional CD4 T cell subsets
Authors: Kasatskaya Sofya A , Ladell Kristin , Egorov Evgeny S. , Price David A. , Chudakov Dmitriy 
Published: January 2023

Abstract
Helper T cell choice of functional subset may depend on the mode and strength of T cell receptor interaction with peptide-MHC complex on antigen presenting cells. However, the extent, complexity, and homogeneity of this influence of TCR structure on the selection into a functional subset, as well as further stability of acquired clonal programs remain poorly studied. Here we present the first analysis of deep sequenced T-cell receptor repertoires of the eight effector CD4 T cell subsets (Th1, Th2, Th2a, Th17, Th1-17, Th22, Treg, and Tfh) from peripheral blood of 5 healthy donors, revealing unexpectedly prominent, multivariate subset-specific differences that are highly reproducible across unrelated donors. Similar analysis performed for the sorted naive CD4 T cell subsets showed that specific TCR features of Tregs (short and strongly interacting CDR3 region) are rooted in thymic selection, while differences between other subsets accumulate later upon T cell functional engagement. We next provide the first deep analysis of the plasticity of human effector CD4 subsets ex vivo. We demonstrate high plasticity within Th17 and Th22 functional subsets and prominent clonal exchange of both Th17 and Th22 with Th2. Th1-17 subset shares clones with Th1 but not with the Th17 subset. Finally, we investigate relative publicity of effector CD4 subset repertoires across donors. We reveal high publicity of Treg and Tfh, and high privacy of Th22 and Th2a repertoires, which corresponds to the number of added N-nucleotides for these subsets, suggesting their earlier fetal and evolutionary origin. Altogether, we provide the first detailed picture of distinct repertoire features, plasticity, and publicity of helper CD4 T cell subsets.
Gut microbial composition and expression of host immune-related genes are tightly linked in the model teleost system, Gasterosteus aculeatus (three-spined stickleback)
Authors: Fuess Lauren E , Ling Fei , Steinel Natalie C , Weber Jesse , Bolnick Daniel I 
Published: January 2023

Abstract
Associations between eukaryotic organisms and microbial symbionts contribute to a diversity of host functions, including growth and immune system development. Despite these broad effects of the microbiome on host function, the mechanisms linking host processes and microbiome composition are still being elucidated. Using a model teleost species, Gasterosteus aculeatus (three-spined stickleback), we investigated patterns of co-variation between gut microbiome composition and host gene expression, focusing specifically on immune-related processes. First, we tested hypotheses of co-variation between microbiome diversity and expression of immune-related genes, and found strong positive associations between microbial alpha diversity and immune gene expression. Next we examined correlations between abundance of specific microbial taxa and gene expression. We identified 15 microbial families that were highly correlated with approximately 1200 host genes. These 15 families fell into three categories: those positively correlated, negatively correlated, and neutrally related to immune processes. Positively immune-correlated families included unclassified Firmicutes, while negatively immune-correlated families included many families within the phylum Proteobacteria. Increased functional understanding of these specific families will help disentangle mechanisms of correlation between microbial families and host immune processes. This is, to our knowledge, the first comprehensive study of co-variation between gut microbiome composition and host gene expression. Our data supports predominate hypotheses of an intimate link between gut microbial composition and host immune function.
Memory-like innate immunity following infection with Pneumocystis murina
Authors: Samet Shelly , Bishop Lisa , Kovacs Joseph 
Published: January 2023

Abstract
Pneumocystis pneumonia (PCP) continues to be a life-threatening infection in HIV-infected patients, renal transplant patients, and other immunocompromised individuals. Dendritic cells are key antigen presenters to CD4+ T cells, which are critical to controlling Pneumocystis infection. β-1,3 glucans are found in the cell wall of the cyst form of Pneumocystis and are a known activator of innate immune cells via the dectin-1 receptor. β-glucans derived from other fungi have been shown to induce an enhanced “memory-like” immune response, termed trained immunity, in innate cells, including monocytes, macrophages, and dendritic cells. Therefore, we explored if Pneumocystis infection can induce an enhanced innate immune response in mice following exposure via a natural route of infection. We conducted mixing experiments using purified CD4+ T cells and dendritic cells from unexposed C57BL/6 mice and mice that spontaneously cleared infection. We found that CD4+ T cells from naïve mice exhibited a significantly greater proliferation after 5-day cultures when a crude Pneumocystis antigen was presented by CD11c+ dendritic cells from exposed mice compared to unexposed mice. In support of this, CD4+ T cells from C57BL/6 mice that were immunized with Freund’s adjuvant alone exhibited significantly greater proliferation when a crude Pneumocystis antigen was presented by either CD11c+ dendritic cells or CD11b+ macrophages from mice immunized with Pneumocystis antigen mixed with Freund’s adjuvant vs. adjuvant alone. These results suggest that Pneumocystis infection stimulates a memory-like innate immune response which may be important in controlling subsequent exposure to Pneumocystis, as well as exposure to other pulmonary pathogens.
Developmental immaturity of sialic acid recognition mediates neonatal susceptibility to GBS pneumonia
Authors: Lund Sean J , Patras Kathryn A , Kimmey Jacqueline M , Yamamura Asami , Butcher Lindsay D , Del Rosario Pamela G B , Hernandez Gilberto E , McCoy Alyssa M , Lakhdari Omar , Nizet Victor , Prince Lawrence S 
Published: January 2023

Abstract
Group B Streptococcus (GBS) is a major neonatal pathogen but rarely causes disease in adults. We previously showed in mice that GBS escapes killing in the neonatal lung via its heavily sialylated capsule. Immune cells detect sialic acid moieties via expression of a repertoire of Siglec receptors. Combinatory expression of proinflammatory and anti-inflammatory Siglec receptors allows differentiation between host and pathogenic microbial sialic acid modifications. We test here the hypothesis that neonatal alveolar macrophages (AMs) fail to detect and kill GBS due to developmental immaturity of Siglec receptor expression. Adult AMs express the proinflammatory sialic acid receptor Sialoadhesin (Sn, Siglec-1) and the anti-inflammatory receptors Siglec-E and Siglec-F. However, real time PCR, immunofluorescence, and FACS detected only Siglec-E in neonatal lung macrophage populations. Sn expression increased soon after birth and was restricted to AMs. The timing of increased Sn expression in newborn mice correlated with susceptibility to GBS. Mice infected with GBS on day 1 suffered early onset mortality, while mice infected on day 2 displayed late onset disease. Mice infected on day 3 survived GBS infection. Further implicating AM immaturity, Csf2−/− mice, which have defects in AM differentiation, lacked Sn expression and had reduced GBS clearance following infection. The presence of Siglec-E but absence of Sn in newborn AMs appeared to promote tolerance to GBS. Newborn SigE−/− mice had increased GBS phagocytosis and killing compared to WT controls. We therefore conclude that GBS exploits developmental immaturity of Siglec expression in AMs via its sialic acid capsule in causing neonatal disease.
Initial phospholipid recognition on Toxoplasma vacuoles elicits IFN-inducible GTPase-mediated host defense
Authors: Yamamoto Masahiro , Lee Youngae 
Published: January 2023

Abstract
Toxoplasma gondii is an obligate intracellular protozoan parasite capable of infecting warm-blooded animals by ingestion. The organism enters host cells and resides in the cytoplasm in a membrane-bound parasitophorous vacuole (PV). Inducing an interferon response enables IFN-γ-inducible immunity-related GTPase (IRG protein) to accumulate on the PV and to restrict parasite growth. However, little is known about the mechanisms by which IRG proteins recognize and destroy T. gondii PV. We characterized the role of IRG protein Irgb6 in the cell-autonomous response against T. gondii, which involves vacuole ubiquitination and breakdown. We show that Irgb6 is capable of binding a specific phospholipid on the PV membrane. Furthermore, the absence of Irgb6 causes reduced targeting of other effector IRG proteins to the PV. This suggests that Irgb6 has a role as a pioneer in the process by which multiple IRG proteins access the PV. Irgb6-deficient mice are highly susceptible to infection by a strain of T. gondii avirulent in wild-type mice.
Identification and characterization of Escherichia coli genes associated with grazing resistance to the social amoeba Dictyostelium discoideum
Authors: Perez Vazquez Marta G , Snyder Michelle , Johnson De’Sha , Rasko David 
Published: January 2023

Abstract
Pathogenic Escherichia coli strains remain a significant health challenge, particularly in developing countries. The social amoeba, Dictyostelium discoideum, which phagocytizes bacteria for nutritional purposes, serves as a host model for several pathogenic bacteria, including E. coli. Here we have characterized the interactions of D. discoideum with 35 representative E. coli strains and identified strains sensitive and resistant to D. discoideum grazing in each E. coli pathotype. Whole genome phylogenomic analysis revealed that grazing resistance is distributed among the phylotypes, although resistant strains are enriched in the B2 phylogenomic group. Comparative genomic analysis identified genes more prevalent among strains resistant to D. discoideum grazing, including genes associated with adhesion, carbohydrate modification, iron transport, signaling and metabolism. Interestingly, the gipA (growth in Peyer’s Patches) gene, which has been found associated with microbiota in patients with Crohn’s disease, was widely present in E. coli strains resistant for D. discoideum grazing. We are currently working to characterize the role of E. coli genes associated with resistance to phagocytosis and killing by D. discoideum, through creation and analysis of E. coli strains manipulated for expression of the identified genes. Such characterization is aimed at providing insight into potentially novel E. coli virulence factors.
Anti-Vibrio cholerae responses in the human periphery and intestine following a live-attenuated vaccine
Authors: Nyhoff Lindsay E , Adekunle Oluwaseyi , Kauffman Robert C , Keilin Steven , Rouphael Nadine , Wrammert Jens 
Published: January 2023

Abstract
Vibrio cholerae is a prototypical mucosal pathogen that causes cholera, a severe diarrheal disease. Cholera affects an estimated 3 to 5 million people annually, resulting in over 100,000 deaths. Infection leads to serotype-specific immunity that can last for up to ten years. Immunity is likely mediated by intestinal antibodies, which primarily target the immunodominant antigens lipopolysaccharide (LPS) and cholera toxin (CT). However, how immunity is generated and maintained is not well understood. Here we have used the live-attenuated cholera vaccine, Vaxchora, to characterize the primary immune response in both the periphery and the human duodenum. Previously, this vaccine showed 80% protective efficacy 90 days after vaccination of naïve volunteers, and induced early antibody responses in levels similar to infection. We developed new technology to identify and characterize V. cholerae-specific plasmablasts and plasma cells by flow cytometry, and found that antigen-specific plasmablasts in peripheral blood quickly expand and upregulate mucosal trafficking markers CCR9 and CCR10. These B cells either develop locally or home to the small intestine, where anti-LPS and anti-CT antibody-secreting cells are present by day 28. Surprisingly, our preliminary data shows that vaccinees may exhibit robust anti-CT responses in the duodenum even when peripheral anti-CT antibody secreting cells are not detected, which provides novel insight into the generation of sustained protection. These data will help us understand not only protective immunity to V. cholerae, but also how the human mucosal plasma cell compartment is developed and maintained.
Lymph Node Priming Licenses Intestinal CD103+ CD8 Tissue-Resident Memory T Cell Development
Authors: Qiu Zhijuan , Khairallah Camille , Imperato Jessica Nancy , Chu Timothy H , Xu Daqi , Romanov Galina , Puddington Lynn , Sheridan Brian S 
Published: January 2023

Abstract
CD8 tissue-resident memory T (TRM) cells provide front-line protective immunity at barrier tissues. Understanding TRM cell development will provide significant insights for vaccine design targeting infections and cancers at barrier tissues. Here, we demonstrate that pathogen-induced inflammation and pathogen-derived cognate antigen had minimal impact on intestinal CD103+ TRM cell differentiation. Instead, T cell priming in the mesenteric lymph nodes (MLN) was the principal determinant of CD103+ TRM cell differentiation in the intestine. In contrast, T cells primed in the spleen were incapable of differentiating into intestinal CD103+ TRM cells. Foodborne rechallenge of spleen-primed memory T cells was unable to induce intestinal CD103+ TRM cell differentiation, suggesting initial priming promoted a lasting fate. Moreover, both CD103− and CD103+ naïve T cells were highly efficient in differentiating into CD103+ TRM cells in the intestine after priming in the MLN, suggesting preconditioning of naïve T cells by TGF-b during homeostasis had little impact on intestinal CD103+ TRM cell differentiation. We further demonstrate that MLN priming initiated a CD103+ TRM cell program before effector T cell migration to the intestine and promoted CD103+ TRM cell differentiation in situ in part by promoting CCR9 expression and the ability to respond to TGF-b in a cell-extrinsic manner. Thus, mesenteric lymph node priming is specialized to license intestinal CD103+ CD8 TRM cell development.