bluuebunny/crossref_metadata_2025_split huggingface dataset:
CD300c is a negative regulator of T cell immunity
Authors: Lai Laijun , Cui Cheng , Su Min , Lin Yujun 
Published: January 2023

Abstract
Immune responses are tightly controlled by T cell regulators in which B7 family members are of central importance. The importance of the B7 family molecules has been highlighted by the FDA approval of several drugs for the treatment of cancer and autoimmune disease by targeting the ligands or their receptors. The unprecedented success has attracted considerable interest in identifying additional T cell regulators. In this study, we identify CD300c as a novel T cell co-inhibitory molecule that shares significant sequence homology with existing B7 family members. CD300c protein is expressed on professional antigen-presenting cells, including B cells, monocytes, macrophages and dendritic cells. The putative CD300c receptor is expressed on CD4 and CD8 T cells, and the expression levels are upregulated upon activation. Soluble human and mouse CD300c-Fc fusion proteins significantly inhibit the proliferation, activation, and cytokine production by CD4 and CD8 T cells in vitro. Administration of CD300c-Fc protein attenuates graft-versus-host disease (GVHD) and experimental autoimmune encephalomyelitis (EAE) in mice. Our results suggest that therapeutic interaction with the CD300c inhibitory pathway may represent a new strategy to modulate T cell-mediated immunity for the treatment of GVHD and autoimmune disease. [This work was supported by grants from NIH (1R01AI123131), and Connecticut Regenerative Medicine Research Fund (16-RMB-UCONN-02)].
Peripherally induced tissue resident memory CD8 T cells in the brain mediate protection against CNS infections
Authors: Urban Stina Lisa , Jensen Isaac J , Pewe Lecia L. , Badovinac Vladimir P , Harty John T 
Published: January 2023

Abstract
The central nervous system (CNS) is classically viewed as an immune privileged site; however recent advances in the field highlight the importance between the interaction of the peripheral immune system and the CNS in maintaining tissue homeostasis. Tissue resident memory (Trm) CD8 T cells have been described in almost every organ and are shown to provide a first line of defense against secondary invading pathogens. Trm cell generation generally involves active infection at the site of tissue residence. Using multicolor flow cytometry, we describe an increased representation of antigen-specific (Ag) CD8 T cells in the CNS after peripheral systemic immunizations or infections. Utilizing unbiased SPADE analysis, the intravascular (IV) stain negative Ag-specific tissue residing cells isolated from the CNS were phenotypically distinct from the IV stain positive cells in the vasculature. Further characterization indicated peripherally-induced CD8 T cells residing in the brain adopted a Trm phenotype and were resistant to systemic antibody-mediated depletion. The increased representation and phenotype of CD8 T cells in the brain after systemic immunization was similarly found in the meninges but not in peripheral organs including liver or lungs. 2-photon microscopy revealed peripherally-induced Trm are highly dynamic in the brain. CD8 T cells surveyed the tissue with multiple mechanisms including moving along the blood vessels, traveling long distances in apparently random fashion or remaining stationary. Most importantly, systemically-induced Trm cells in the CNS provided protection against neurotropic challenges by reducing bacterial and viral loads and limiting morbidity and mortality associated with the infections.
BAFF and VCAM-1 cooperate on the Interaction between B lymphocytes and fibroblast-like synoviocytes
Authors: Moon Eun Yi , Yoon Sung Sik 
Published: January 2023

Abstract
Synovium and joint in rheumatoid arthritis (RA) is expanded and destructed by chronic and systemic inflammatory disorders. Fibroblast-like synoviocytes (FLSs) play a key role in the pathogenesis of RA by producing inflammatory cytokines leading to cartilage destruction. RA-FLSs develop a unique aggressive phenotype that increases invasiveness into the extracellular matrix and further exacerbates joint damage. Tumor necrosis factor-α(TNF-α), a major pro-inflammatory cytokine triggers the expression of inflammatory molecules such as B cell activating factor(BAFF) and cell adhesion molecules such as vascular cell adhesion molecule-1(VCAM-1). Here, we investigated whether cell-cell contact between B cells and FLSs may be significant in the patho-physiology of RA through BAFF and VCAM-1 using WIL-2NS and MH7A synovial cells. TNF-α treatment increased the number of B cells bound FLSs as judged by MTT assay, cell count, cell staining and flow cytometry analysis. TNF-α treatment enhanced the expression of BAFF and VCAM-1 as measured by RT-PCR, promoter assay and western blot analysis. Small interference (si) RNA of BAFF or VCAM-1 inhibited the number of B cells bound FLSs. TNF-α induced JNK phosphorylation, which might mediate the interaction between e B cells and FLSs. Taken altogether, data suggest that TNF-α-induced BAFF and VCAM-1 could be related with the interactions between MH7A cell and WIL-2NS leading to the aggravation of RA.
This work was supported by the R&D program for Society of the National Research Foundation (NRF) funded by the Ministry of Science, ICT & Future Planning (Grant from Mid-career Researcher Program : #2016R1A2B4007446 and # 2018R1A2A3075602), Republic of Korea.
Sclerostin depletion may induce inflammation in the bone marrow
Authors: Donham Cristine , Loots Gabriela , Manilay Jennifer 
Published: January 2023

Abstract
The interactions between long-term hematopoietic stem cells (LT-HSCs) and cells in the bone microenvironment result in changes in stem cell behavior that are incompletely understood. Our goal is to define the molecular mechanisms that guide the behavior of LT-HSCs after exposure to an irregular bone marrow (BM) niche. Sclerostin (Sost) is a secreted Wnt antagonist that is important for bone homeostasis. We hypothesized that that loss of Sost would influence LT-HSC differentiation and migration. To test this, we performed hematopoietic progenitor transplantation assays to track donor-derived hematopoiesis in wild-type (WT) and Sost-knockout (KO) recipients. We observed increased frequencies of donor-derived myelopoiesis as well as decreased lymphopoiesis in WT to KO chimeras possibly due to an inflammatory microenvironment. We are currently investigating LT-HSC inflammatory response genes, such as C/EBP-beta and PU.1, as well as BM serum inflammatory cytokine levels. As the SostKO mice age, we observe extramedullary hematopoiesis (EMH) in the spleen compared to age matched controls. We hypothesize that changes in the BM microenvironment as well as cytokine levels in the spleen induce LT-HSC migration to the spleen. We are characterizing the EMH LT-HSC splenic niche by investigating LT-HSC localization as well as examining cytokines, such as CXCL12, known to induce LT-HSC migration to the spleen. Taken together, our data indicates that depletion of Sost in the bone regulates LT-HSC differentiation and migration. Our results could have significant impact on the tracking of hematopoietic function in human patients treated with SOST-depleting antibodies for bone diseases such as osteoporosis.
Metabolic pathways that mediate expansion and homeostasis of hematopoietic lineages
Authors: Pizzato Hannah A , Lam Wing Y , Finck Brian N , Wolfgang Michael J , Bhattacharya Deepta 
Published: January 2023

Abstract
Due to the rarity of hematopoietic stem cells, their differentiation into progenitors then on to mature cells must occur with proliferation, leading to an expansion of each downstream population. This process, called transit amplification, is required to produce a sufficient mature cell population and must be balanced with survival to maintain homeostasis and prevent hematological malignancies. How transit amplification and subsequent homeostasis is controlled is not well understood but may involve metabolic switches. Various groups have demonstrated that hematopoietic expansion requires a switch from glycolysis to oxidative phosphorylation, but what induces this switch and the specific carbon sources that fuel it remain unclear. To address these questions, we employed mice conditionally deficient in mitochondrial pyruvate import, fatty acid oxidation, or glutamine hydrolysis and examined the requirements of these pathways in hematopoietic homeostasis. Ablation of carnitine palmitoyltransferase II (Cpt2) or glutaminase (Gls) had no effect on lineages examined, suggesting fatty acid oxidation and glutaminolysis are not required for the production or survival of various immune cells. In contrast, upon deletion of mitochondrial pyruvate carrier 2 (Mpc2), peripheral myeloid and lymphoid cell numbers declined dramatically. Over time after MPC2 ablation, a progressive recovery of mature cells was observed. This recovery was associated with increased proliferation seen in Mpc2−/− progenitors relative to their wild type counterparts immediately following genetic deletion. Further studies will seek to elucidate if cells switch to another metabolic pathway to recover from mitochondrial pyruvate ablation.
Inhibiting host DNA release prevents mixed neutrophilic/eosinophilic airway inflammation in severe asthma phenotype
Authors: Chung Sangwoon , Karpurapu Manjula , Christman John W. 
Published: January 2023

Abstract
Asthma pathophysiology and treatment strategies are predicted by inflammatory phenotypes. Unlike the relatively well-defined mechanisms that result in eosinophilia, those leading to noneosinophilic asthma, particularly non-type 2 neutrophilic/eosinophilic asthma, remain relatively poorly understood.
We recently discovered that leukocytes released extracellular traps (ETs) comprising DNA fibers and granule proteins in the BAL fluid of patients with mild asthma who were experimentally challenged with allergen according to the subsegmental bronchoprovocation to allergen (SBP-AG) protocol. Key aspects of ETs in the immune response are sufficient to recapitulate many features of asthma pathophysiology which results in mucus hypersecretion and airway remodeling in the airways of asthmatics.
To test hypothesize that inhibiting ET-associated host dsDNA release prevents neutrophilic/eosinophilic airway inflammation in severe asthma (SA) phenotype, we set up the SA mouse model, that mirrors the complex immune response identified in human SA. We showed that host dsDNA and neutrophil elastase were greatly increased in the airways and short noncoding miR-155 contributes to the release of host dsDNA, which exacerbates many features of allergic inflammation. In accordance with what we observed in high miR-155 expression in alveolar macrophages, we also noted that there was markedly less ETs formation in the airways of miR-155fl/flLysMcre mice subjected to the SA model compared with their WT counterparts. In sum, miR-155 engages in the release of host dsDNA that contributes to airway damage and thus promotes mixed granulocytic inflammation.
Effect of different adjuvants on various immune cells and cytokines in allergic asthma mouse model
Authors: Shin Hyun soo , Chun Hye Rin , Na Hye Young , Sohn Moah , Ryu Seul Hye , Choi Wanho , In Hyunju , Park Ji Soo , Park Chae Gyu 
Published: January 2023

Abstract
Allergic asthma is a complex chronic disease which displays combined traits referred to as Th2 mediated eosinophilic allergy, ILC2 mediated allergy, and Th17 cell mediated neutrophilic allergy. In our current study of allergic asthma model, the populations of immune cells related to as well as outside of the Th2 immune response were analyzed for the ratio of cytokines in IL-4, IL5, IL17A and IFN-γ expressing CD4+ T cells utilizing of BALB/c mice sensitized with ovalbumin and a different adjuvant such as Alhydrogel (alum), papain, lipopolysaccharide (LPS), and CpG. In lung and bronchoalveolar lavage fluid, the percentage of eosinophils was lower in groups injected with LPS and papain than those with no adjuvant. In contrast, the injection of LPS and papain increased the percentage of neutrophils when compared to the no adjuvant group. The number of B cells in alum-injected group was higher than those of other groups. Although the percentage of innate lymphoid cells (ILCs) increased slightly for ILC1 and ILC2 in the group injected with papain, the other adjuvants did not cause any differences. After PMA/ionomycin stimulation, the ratio of IL-4 expressing CD4+ T cells in the papain-injected group increased significantly while the other adjuvant groups showed little or no changes. The production of IL-17A in CD4+ T cells increased in LPS-injected group and that of IFN-gamma also increased in CpG-injected group. Our results suggest that many distinct allergic asthma mouse models can be established by specific sensitization protocols exploiting different adjuvants, thus representing the complexity of clinical symptoms.
Role of Ets Transcription factors in the development of TH9 cells
Authors: Kharwadkar Rakshin P , Ulrich Benjamin J. , Fu Yongyao , Kaplan Mark H 
Published: January 2023

Abstract
T cells are critical regulators of inflammatory diseases and immunity. CD4+ T helper cells develop into various subsets that are specialized in the secretion of particular cytokines and mediate restricted types of inflammation. One of these subsets recently identified to play an important role in development of allergic inflammatory response, is the IL-9 producing TH9 subset. TH9 cells differentiate in the presence of IL-4 and TGFβ, which activate a network of transcription factors downstream of STAT6 and SMAD signaling pathways to regulate IL-9 secretion. Previous studies showed that PU.1, an Ets transcription factor, can bind at the Il9 promoter region to regulate TH9 function during pro-allergic inflammation. Furthermore, members of the Ets family of transcription factors Etv5 and PU.1 appear to share overlapping functions to promote IL-9 production and TH9 development. We screened for additional ETS factors that might play a role in IL-9 regulation. Jabeen et. al. showed the Ets transcription factor termed Erg (Ets-related gene) is expressed preferentially in TH9 subset. Accordingly, we determined that siRNA knock down of Erg in TH9 cells decreased IL-9 production in vitro. Moreover, chromatin immunoprecipitation assay demonstrated that Erg binding at the Il9 promoter and enhancer region is enriched in TH9 cells. Furthermore, ectopic expression of Erg induced IL-9 secretion in TH2 cells. In addition to Erg, we identified Fli-1, another Ets transcription factor, that can enhance IL-9 secretion in TH2 subset and whose expression is altered by Erg-deficiency. Thus, multiple Ets transcription factors regulate Il9 expression in TH9 cells, suggesting that Erg and other Ets transcription factors may cooperate to promote TH9 function.
Highly multiplexed single-cell spatial analysis of tissue specimens using CODEX
Authors: Mistry Sejal , Dakshinamoorthy Gajalakshmi , Singh Jaskirat , Nikulina Nadya , Kim Joseph , Bashier Roya , Gallina Maria Elena , Kennedy-Darling Julia 
Published: January 2023

Abstract
Characterizing the complexities of the tumor microenvironment is elemental to understanding disease mechanisms. The spatial relationships between infiltrating immune cells and the remodeling of the cellular matrix is widely recognized as a key component to defining tumor heterogeneity. Here, we present a novel multiplexed imaging technology, termed CODEX, (CO-Detection by indEXing) that combines the high parameter capabilities of single-cell methodologies with the associated spatial dimension. Over 50 parameters are measured within a single tissue through fully-automated, iterative cycles of adding and removing dye-conjugated Reporters to corresponding nucleic acid based Barcodes. The CODEX technology, developed by Akoya, is comprised of a fluidics instrument that interfaces with existing microscope hardware, a suite of reagents and associated control and analysis software. Over 100 antibody clones have been validated for this platform with more than ten tissue types analyzed, including both FFPE and fresh-frozen from human and mouse samples. The CODEX technology can be used to ascertain complex cellular niches and spatial associations between multiple cell types based on their staining pattern. CODEX data from various normal and cancer tissue types are shown here with corresponding single-cell analysis of key tissue features. Overall, the CODEX platform is an accessible and versatile technology for high parameter, spatial profiling of tissue specimens.
Generation of a B-1 lymphocyte-specific conditional knockout mouse model Bhlhe41tdTomato-Cre
Authors: Wang Hui , Hong Li , Tang Yangyang , Xu Meizhen , Pan Shuai , Wang Qingling , He Cheng 
Published: January 2023

Abstract
B-1 lymphocytes play indispensable roles in defensing a wide range of pathogens prior to adaptive immune response arising. Although several transgenic mouse models targeting different stages of B lymphocytes have been established e.g. Cd19-Cre and Mb1-Cre, a B-1 lymphocyte specific conditional knockout mouse model for illuminating the role of a gene of interest in B-1 lymphocytes is still missing. In this study, we aimed to generate a B-1 lymphocyte-specific knockout mouse model by expression of Cre recombinase under the control of the promoter of Bhlhe41, which is preferentially expressed in B-1 lymphocyte and microglia in immune system. A tdTomato-2A-Cre-polyA cassette was inserted to the locus of Bhlhe41 by CRISPR-CAS9 technology. Bhlhe41tdTomato-Cre/+Rosa26EYFP/+ mice were generated for determining Cre-mediated recombination efficiency. The accuracy of insertion of tdTomato-2A-Cre-polyA cassette to Bhlhe41 locus was confirmed by significantly reduced peritoneal B-1a lymphocytes in Bhlhe41tdTomato-Cre/tdTomato-Cre mice. Flow cytometric analysis of tdTomato in immune cells from Bhlhe41tdTomato-Cre/+confirmed the specific expression of BHLHE41 in B-1 lymphocytes rather than other B subsets. Further analysis of EYFP in immune cells from Bhlhe41tdTomato-Cre/+Rosa26EYFP/+ mice revealed larger than 90% recombination in splenic and peritoneal B-1 lymphocytes while less than 10% recombination in other B subsets. Hence, we generated a B-1 lymphocyte-specific conditional knockout mouse model Bhlhe41tdTomato-Cre, which can be used for studying the function of a specific gene in B-1 lymphocyte-mediated immune responses.
Integration of multi-omics data from re-wilded laboratory mice to identify key parameters that determine immune heterogeneity and activation
Authors: Lin Jian-Da , Yeung Frank , Devlin Cooper , Chen Ying-Han , Mccauley Caroline , Cronkite Alex , Leung Jacqueline M. , Graham Andrea L. , Cadwell Ken H. , Loke P’ng 
Published: January 2023

Abstract
Current research on immunology are largely based on clean laboratory mice kept in specific pathogen free (SPF) environments. They have the advantage of being inbred, genetically homogeneous and can be manipulated genetically in disease models. However, humans as with all free-living mammals face a more complex environment and are exposed to various food resources, microbial experiences, thermogenic changes, and must constantly respond to environmental challenges. We have established a unique experimental system in which laboratory mice are “re-wilded” through release into an outdoor enclosure facility. Here, we use multi-parameter assays including 16S/Metagenomic sequencing, intestinal RNA-sequencing, and 34 parameters of flow cytometry to explain heterogeneity of immune responses from exposure to the wild environment. Increased immune activation of re-wilded mice occur in the absence of viral, bacterial or parasitic pathogen exposure in this enclosure, including increase of CD4+ and CD8+ memory T cells, effector T cells, innate lymphoid cells (ILCs), circulating neutrophils, reduction in naïve T cells, and increased expression of costimulatory molecules on antigen presenting cells. When we examined cytokine production in response to ex vivo stimulation of mesenteric lymph node cells with 8 bacterial and fungal stimuli, the mesenteric lymph node cells from re-wilded mice are poised for different responses via robust induction of cytokines than laboratory mice. By using machine learning models, we are integrating these multi-omic datasets to better predict the association between environmental and host genetic factors on driving heterogeneity of immune responses in the re-wilded mice.
Scalable and comprehensive characterization of antigen-specific CD8 T cells using multi-omics single cell analysis
Authors: Boutet Stephane C , Walter Dagmar , Stubbington Michael J T , Pfeiffer Katherine A , Lee Josephine Y , Taylor Sarah E B , Montesclaros Luz , Lau Julia K , Riordan Daniel P , Barrio Alvaro Martinez , Brix Liselotte , Jacobsen Kivin , Yeung Bertrand , Zhao Xinfang , Mikkelsen Tarjei S 
Published: January 2023

Abstract
Understanding the antigen binding specificities of lymphocytes is key to the development of effective therapeutics for cancers and infectious diseases. Recent technological advancements have enabled the integration of simultaneous cell-surface protein, transcriptome, immune repertoire and antigen specificity measurements at single cell resolution, providing comprehensive, scalable, high-throughput characterization of immune cells.
Using the 10x Genomics Single Cell Immune Profiling Solution with Feature Barcoding technology with 14 oligo-conjugated antibodies and 50 Immudex peptide-MHC I Dextramer reagents (pMHC) panels spanning different CMV, EBV, Influenza, HIV and Cancer antigens, we performed multi-omic characterization of ~100,000 CD8+ T cells from four MHC-matched donors. The multi-omic combination of gene expression, paired alpha/beta T cell receptor (TCR) repertoire, cell surface proteins and pMHC binding specificity allowed the identification of CD8+ T cell subpopulations with specificity for pMHCs within our panel. We observed multiple TCRs that bound the same pMHC and identified enriched amino acid motifs within TCR sequences that shared specificities. We compared the CDR3 amino acid sequences of the pMHC-specific TCR clonotypes with previously reported sequences with the same binding specificities to show that we could identify new and known CDR3 sequences. This analytical framework provides a systematic and scalable method for deciphering TCR–pMHC specificity combined with cellular phenotype identity which is critical for developing a better understanding of the adaptive immune response to cancer and infectious diseases and will be key in the development of successful immunotherapies.