bluuebunny/crossref_metadata_2025_split huggingface dataset:
Investigating the MHC class-II processing and presentation “network” via high-throughput small molecule screening.
Authors: Wold Erik D. , Schultz David , Cherry Sara , Eisenlohr Laurence Crane 
Published: January 2023

Abstract
CD4+ T cells, activated by peptides presented in complex with MHCII, are key players in adaptive immune responses against most pathogens and cancers. Classically, MHCII presentation involves uptake of exogenous antigen, digestion in the endocytic compartment, and loading onto nascent MHCII in the late endosome. However, recent studies show viral pathogens do not exclusively adhere to the classical model. Two notable examples of non-classical MHC-II presentation are: 1) “Recycling” presentation (internalized MHCII molecules capture proteolytically unstable epitopes in the early endosome) and 2) endogenous presentation (the source of antigen is nascent viral protein). We have constructed a model in which these three MHCII processing and presentation pathways are mechanistically distinct and largely non-overlapping. To test this model, we have employed high throughput screening (HTS) using a 2240 member “known target” small molecule library with the goal of differentiating which cellular components are involved in the generation of influenza epitopes produced via the classical, recycling, and endogenous pathways. The preliminary HTS data strongly support our hypothesis, clearly identifying distinct pathways that are exclusively involved with either classical or endogenous antigen presentation. Among the 21 validated hit compounds, the screen identified 3 inhibitors of the proteasome (previously shown to figure prominently in endogenous processing). The remaining 18 compounds target pathways not previously known to contribute to MHCII antigen presentation. Compounds of particular interest are being investigated in vivo to assess their ability to bias the TCD4+ response in the context of an influenza infection.
A role for apoptotic and scavenger receptors in mediating antigen exchange between lymphatic endothelial cells and migratory dendritic cells
Authors: Caffrey Alayna Katherine , Tamburini Beth , Kedl Ross 
Published: January 2023

Abstract
Antigen persistence following viral infection or vaccination occurs for several weeks after resolution of the inflammatory response. Lymphatic endothelial cells (LECs) capture and archive antigen, which is then transferred to migratory dendritic cells (DCs) and ultimately cross-presented to circulating memory T cells. Following vaccination, both BatF3-dependent and BatF3-independent DCs are needed for antigen exchange, while virus-associated antigen exchange is mediated only by BatF3-dependent DCs. Here, we explore the role of apoptotic and scavenger receptors in mediating this antigen capture and exchange between LECs and DCs. Cross-presentation of the DC-associated antigen to circulating T cells results in a memory pool with increased effector function and enhanced protective capacity. Overall, this work furthers our understanding of how persisting antigen impacts the CD8+ memory T cell response in both vaccine and infectious settings.
An Unbiased Determination of pMHC Repertoires for Improved Antigen Prediction
Authors: Rappazzo C. Garrett , Birnbaum Michael 
Published: January 2023

Abstract
Successful understanding and treatment of immune diseases spanning autoimmunity, cancer, and infectious disease relies upon understanding what is seen by the immune system. For T cell responses, this is controlled by MHCs, specialized polymorphic proteins that present a snapshot of the proteome of their parent cell or surroundings. Importantly, MHC polymorphisms cluster at their peptide-binding surface, where even single substitutions can greatly alter the peptide-MHC (pMHC) repertoire seen by T cells. Due to extreme person-to-person variability in MHC usage, data for peptide MHC specificity is largely limited to a handful of the most prevalent alleles. While algorithms that predict pMHC interactions perform well for these alleles, they can suffer from inaccuracy for less-studied alleles, due in part to biases and limited diversity in their training data.
We present a platform that provides large unbiased data sets to improve pMHC repertoire definitions and predictions. Using yeast-displayed MHC molecules displaying a random peptide library, we identified hundreds of thousands of unique peptide binders for both well- and poorly-studied human MHC alleles. Our data demonstrates strong amino acid preferences at defined “anchor” positions for each allele, but also finds preferences at auxiliary sites that are not considered by most prediction software. We also find noncanonical amino acid preferences at defined anchor positions that confound current software, suggesting alternative peptide conformations. These data show the importance of unbiased pMHC repertoires to improve existing antigen prediction software, and suggest our approach can be used to define presently under-studied MHC alleles.
The unfolded protein response alters MHC class I antigen presentation in a mouse cell line
Authors: Nagamine Brandy S. , Dolan Brian P. 
Published: January 2023

Abstract
Direct MHC class I antigen presentation is a necessary step to identify cells for elimination by cytotoxic CD8+ T cells. Antigenic peptides may originate from host-derived unnecessary or “retired” proteins as well as defective ribosomal products (DRiPs). DRiPs are newly synthesized polypeptides incapable of attaining a stable configuration and are thus rapidly degraded. The balance between protein synthesis and degradation, key processes to antigenic peptide generation, are likely influenced by the unfolded protein response (UPR). The UPR is a cellular response designed to alleviate the toxic accumulation of unfolded proteins in the endoplasmic reticulum. Several disease conditions requiring CD8+ T cell responses such as viral infection and tumorigenesis are known to influence the UPR. In this study, we utilized small inhibitory molecules targeting individual branches of the UPR to investigate the effect on both global MHC class I levels and the presentation of peptides from both DRiP and non-DRiP sources. Inhibition of the IRE1α signaling pathway but not the PERK pathway reduced total MHC class I levels. Presentation of peptides derived from DRiPs was unaffected by inhibiting either branch of the UPR. These data suggest that specific perturbations to the UPR has the capacity to alter host antigen presentation of peptides from particular peptide sources.
IL-23 is essential for the switching between Tfh-IFN-γ and Tfh-IL-17 in lupus
Authors: Hong Huixian , Wu Qi , Yang PingAr , Luo Bao , Li Jun , Li Hao , Cua Daniel J , Hsu Hui-Chen , Mountz John D 
Published: January 2023

Abstract
The role of IL-23 in promoting pathogenic autoantibody development in autoimmune disease is unclear. The purposes of this study are to use the IL-23p19 knockout in the BXD2, a lupus mouse strain, to determine: (i) if IL-23 is required for germinal center (GC) and pathogenic autoantibody development; and (ii) if IL-23 acts through follicular T-helper cells (Tfh) lineage switching to induce autoantibody formation. Sera autoantibodies were measured by ELISA. GC development and the expression of AID were determined by confocal imaging. IL-17 and IFN-γ producing Tfh cells were detected by intracellular staining. The expression of GC program genes and T cell program genes was measured by qRT-PCR. Exogenous IL-23 was administered to B6 mice using an IL-23 expressing adenovirus (AdIL-23). There was significantly increased IgM but decreased IgG autoantibodies in BXD2-p19−/− mice compared to BXD2 mice. The expression of AID was decreased in BXD2-p19−/− mice. Surprisingly, the size and number of GC were increased in BXD2-p19−/− mice. There was also similar percentage of PD1+CXCR5+Tfh cells in BXD2 and BXD2-p19−/− mice. However, the percentage of IL-17A expressing Tfh cells was suppressed but the IFN-γ producing Tfh was increased in BXD2-p19−/− mice. Consistent with this, AdIL-23 administration suppressed the expression of Tbet, Ifng, Bcl6, Il21, Gata3, and Il4 but enhanced the expression Il17a, Il17f in Tfh cells. Our data suggest Tfh-IFN-γ and Tfh-IL-17 each plays an important role to determine the development of autoantibody producing B cells. While IL-23-mediated Tfh-IL-17 does not promote the size of autoreactive GCs, it regulates the induction of AID and thereby plays an important role to determine autoantibody affinity maturation.
NKG2D signaling within the pancreas decreases NOD diabetes by enhancing CD8+ central memory T cell formation
Authors: Markiewicz Mary A , Trembath Andrew P , Sharma Neekun , Mathews Clayton E 
Published: January 2023

Abstract
The main drivers of type 1 diabetes are islet-specific T cells. These cells must escape a myriad of tolerance mechanisms that control their activation in healthy individuals. One pathway implicated in this process is signaling through Natural Killer Group 2 member D (NKG2D). We demonstrate that the mRNAs encoding both NKG2D and NKG2D ligands are increased in the islets of patients with type 1 diabetes, making discerning the role of NKG2D-ligand interaction in the pancreas during diabetes development of significant interest. To this end, we developed a novel mouse model to determine the role of NKG2D specifically within the pancreas. This is a NOD mouse that expresses a transgene driving expression of the NKG2D ligand RAE1ɛ in islets (RIP-RAE1ɛ NOD mice). Spontaneous diabetes development was significantly decreased in RIP-RAE1ɛ-NOD mice compared with control NOD mice, and RIP-RAE1ɛ mice contained decreased numbers of CD44hiCD62Llo(effector/effector memory, Tem, phenotype) CD8+ T cells in both the pancreas and spleen. This decrease correlated with increased numbers of CD44hiCD62Lhi(central memory T cell, Tcm, phenotype) CD8+ T cells, which is a cell population previously demonstrated to contain cells that inhibit the CD8+ Teff response. Further, we found that NKG2D signaling in both NOD and human CD8+ T cells increased CD8+ Tcm differentiation in vitro. Together, these novel results suggest that the NKG2D pathway in CD8+ T cells could be utilized to inhibit type 1 diabetes progression.
The pathogenic role of stem cell-like memory T cells in rheumatoid arthritis
Authors: Lee Ye Ji , Kim Miriam , Lee Eun Bong 
Published: January 2023

Abstract
Stem cell-like memory T (Tscm) cells are known as the least differentiated T cells that have ability to self-renew and differentiate into subsets of T cells. Recently, Tscm cells have been studied in various autoimmune diseases including systemic lupus erythematosus (SLE), aplastic anemia. However, the association between Tscm cells and rheumatoid arthritis (RA) remains unexplored. So, we measured the proportion of Tscm cells in peripheral blood mononuclear cells (PBMCs) of RA patients by flow cytometry using pertinent Tscm-associated fluorescent markers (CD3+ CD4+/CD8+ CCR7+ CD45RO− CD45RA+ CD62L+ CD27+ CD28+ CD127+ CD122+ CD95hi). The proportion of Tscm cells among CD4+ T cells as well as CD8+ T cells were significantly increased in RA patients than healthy controls (HCs). Tscm cells from RA patients could replicate themselves and differentiate into other T cell subsets in response to anti-CD3/CD28 stimulation. When FACS-sorted Tscm cells were stimulated with IL-6 or TNF which are key inflammatory cytokines in RA and expression of activation markers (CD69, CD25 (IL-2Rα), CD154 (CD40 ligand)) and secretion of cytokines (IFN-γ, IL-4 and IL-17A) were measured, Tscm cells from RA patients were more easily stimulated than those from HCs. In addition, RA patients in remission showed low proportion of Tscm cells among the CD4+/CD8+ T cells and responded less against cytokines than active RA patients.
Our study suggests that Tscm cells from RA patients may perpetuate RA by providing the patients with pathogenic T cells constantly.
Pathogenic follicular CD8 T cells acquire diverse function during autoimmune disease
Authors: Valentine Kristen M , Mullins Genevieve N , Lawrence Travis J , Hoyer Katrina K 
Published: January 2023

Abstract
CXCR5+ CD8 T cells identified within the germinal center have the capacity for diverse function in response to chronic antigen including chronic viral infection and cancer. CXCR5+ CD8 T cell pathogenic or protective function likely depends on the immunological setting. We have identified CXCR5+PD-1+ CD8 effector T cells (CD8 T follicular; Tfc) that resemble CD4 T follicular helper cells (Tfh) in multiple models of spontaneous autoantibody-mediated disease, including IL-2 deficient (IL-2-KO), scurfy and MRL/MpJ-FASlpr mice. Autoimmune CD8 T cells induce antibody class switching, and plasma cell differentiation synergistically with CD4 T cells in support of a novel function for CD8 Tfc cells during germinal center reactions. RNA-sequencing identified 478 differentially expressed genes unique to IL-2-KO CD8 Tfc compared to IL-2-KO CD4 Tfh including il21, Ifnγ, prf1. CD8 Tfc are polyfunctional and co-produce significant amounts of IL-21 and IL-4. Yet, only IL-21 produced by CD4 Tfh and not CD8 Tfc promotes total IgG class switching in in vitro cultures of activated T cell supernatant incubated with naïve B cells. CD8 Tfc supernatant deficient in IFNγ does not change antibody production. In addition to the helper profile, CD8 Tfc cells maintain the capacity to produce granzyme B, perforin, and CD107a when stimulated suggesting the possibility of direct cytolytic function within the germinal center. Our results indicate that CD8 Tfc cells contribute to autoimmune disease with CD4 Tfh cells to induce B cell responses and antibody class-switch. We will continue to investigate pathogenic CD8 Tfc cells in helper-like and cytotoxic roles during autoimmune disease.
Funding from NIH R15 and the UC President’s Dissertation Year Fellowship
Antigen-presenting cells from naive mice constitutively present the T cell epitope of SERCA2a and induce inflammatory cytokine production in antigen-specific T cells
Authors: Arumugam Rajkumar , Yalaka Bharathi , Massilamany Chandirasegaran , Ali Shihabudeen , Riethoven Jean-Jack , Sun Xinghui , Reddy Jay 
Published: January 2023

Abstract
We recently reported that sarcoplasmic/endoplasmic reticulum (SR) calcium-ATPase2a (SERCA2a) 971–990 induces atrial myocarditis by generating autoreactive T cells in A/J mice. However, it was unknown as to how the antigen-sensitized T cells could recognize SERCA2a 971–990, since SERCA2a-expression is confined to SR. Here, we present evidence that antigen-presenting cells (APCs) from naïve animals constitutively present SERCA2a 971–990 and stimulate T cells antigen-specifically. By using major histocompatibility complex (MHC) class IIdextramers for SERCA2a 971–990, we created a panel of antigen-specific T cell hybridomas and demonstrated that splenocytes from naïve A/J mice stimulated the hybridoma cells without exogenous supplementation of SERCA2a 971–990, and such an effect was pronounced with unirradiated cells as compared to irradiated cells. We recapitulated this phenomenon by using SERCA2a 971–990-specific, primary T cells, and the T cell responses were verified to be MHC-restricted. While T cells exposed to mononuclear cells obtained from heart and liver responded similar to splenocytes, endothelial cells (ECs) generated from the corresponding organs displayed opposing effects in that the T cell responses were suppressed with the heart-ECs, but not from liver. Finally, SERCA2a 971–990-reactive T cells exposed to APCs were found to produce inflammatory cytokines namely, interferon-γ, granulocyte macrophage colony stimulating factor and interleukin-17. Our data suggest that the constitutive expression of SERCA2a 971–990 by APCs can trigger pathogenic responses under the conditions of autoimmunity that may have implications on endothelial dysfunction.
Biomarker discovery in pre-Type 1 Diabetes; Th40 cells as a predictive risk factor
Authors: Vaitaitis Gisela , Waid Dan , Wagner David H 
Published: January 2023

Abstract
The incidence of Type 1 Diabetes (T1D) is on the rise. Quests to understand T1D etiology as well as how to predict onset are ongoing and, in many ways, those goals intertwine. CD4+CD40+ T cell (Th40) percentages are expanded in T1D subjects compared to controls. Antibodies to β-cell antigens are considered risk factors for T1D development but risk of seroconversion to antibody-positivity declines after age 10. While genetic components associate with T1D, not all T1D subjects have those components and not all subjects with those components develop T1D. Therefore, more robust methods for prediction of T1D are needed. Can high Th40 cell percentages be a biomarker in addition to other markers?
We assessed Th40 cell percentages, along with other parameters, in blood collected from TrialNet preT1D subjects and stratified them according to their percentages. Th40-low versus Th40-high preT1D subjects demonstrate patterns of CD4 T cell levels that parallel those seen between control and T1D. Cytokine patterns are significantly different between the Th40 groups and a CD4+CD8+ population, described previously in Rheumatoid Arthritis, is more common in Th40-high subjects. Subjects experiencing impaired glucose tolerance have significantly higher Th40 cell percentages than controls. PreT1Ds expressing T1D associated HLA DR4/DR4 or DQ8/DQ8 are more likely found among Th40-high subjects. Interestingly, DR4/DR4 subjects were significantly older compared to all other preT1Ds, suggesting that this haplotype together with a high Th40 cell percentage may represent someone who will onset after age 30, which is reported for 42% of T1D cases. It will be important to determine if preT1D subjects with high Th40 cell percentages will develop overt T1D.
Agonist-induced 4-1BB activation ameliorates the pathogenesis of Sjögren’s syndrome-like sialadenitis in non-obese diabetic mice
Authors: Zhou Jing , Yoo Bora , Yu Qing 
Published: January 2023

Abstract
4-1BB is a member of the tumor-necrosis factor receptor (TNFR) superfamily. As a potent costimulatory molecule, it is critically involved in both enhancement and suppression of immune responses in a disease context-dependent manner. The role of 4-1BB in the development and onset of Sjögren’s syndrome (SS), an autoimmune disease as a result of immune system attacking self-exocrine glands with dryness of mouth and eyes as major clinical symptoms, still remains unknown. To elucidate the precise function of 4-1BB in the pathogenesis of SS, we intraperitoneally administered an agonistic anti-4-1BB monoclonal antibody to female non-obese diabetic (NOD) mice, a well-defined mouse model of this disorder, during the stage prior to SS disease onset. We observed that anti-4-1BB treatment significantly increased the salivary flow rate, indicating an effective amelioration of SS clinical manifestation. Administration of anti-4-1BB antibody markedly suppressed the leukocyte infiltration of the submandibular glands (SMGs) and reduced the percentage of CD4 T cells among total infiltrating leukocytes, without altering that of CD8 T cells and B cells with statistical significance. The decrease in the frequency of CD4 T cells was accompanied by a reduced expression of T-bet but not IL-4 in the SMGs, suggesting an inhibitory effect of 4-1BB activation on type 1 T helper cells. In addition, treatment with this agonistic anti-4-1BB also caused a significant reduction in the level of serum antinuclear antibodies. Taken together, our findings imply that 4-1BB plays a protective role against the pathogenesis of SS-like sialadenitis and its agonists could serve as promising therapeutic agents for controlling this autoimmune disorder.
Type 1 alveolar epithelial cell-derived chemokine CCL19 promotes airway inflammation
Authors: Nakano Hideki , Lyons-Cohen Miranda , Nakano Keiko , Karcz Tadeusz , Thomas Seddon Y , Whitehead Gregory , Cook Donald N 
Published: January 2023

Abstract
Allergic asthma is largely driven by the actions of allergen-specific CD4+T helper cells. Following allergen inhalation, these cells are induced by the interaction of naïve CD4+ T cells with antigen-bearing dendritic cells (DCs) in lung-draining lymph nodes. The molecular mechanisms underlying the induction of T helper cells have been well studied, and include the migration of allergen-bearing DCs to lung-draining lymph nodes in a manner dependent on the chemokine receptor, CCR7. However, comparatively little is known regarding how these effector T cells become activated following their subsequent encounter with allergen in the lung. This knowledge would be useful in the design of novel therapies for asthma, especially for neutrophilic asthma, which is refractory to inhaled glucocorticoids. We recently noticed that lung DCs migrating to lymph nodes originate from the large airways, whereas DCs associated with small airways, parenchyma and subpleural areas are non-migratory. Video confocal analysis of precision cut lung slices revealed that these non-migratory DCs form tight interactions with OVA-specific T cells and stimulate T cell receptor signaling, as measured by activation of a Nur77-gfpreporter gene. Furthermore, Ccl19, which encodes a CCR7-ligand, is highly expressed by type 1 alveolar epithelial cells, and in mouse model of asthma, airway inflammation was significantly diminished in CCL19-deficient mice compared with WT mice. Together, our findings suggest that CCL19 produced by type I epithelial cells acts to position lung DCs in the distal area of the lung where they interact with effector T cells, thereby promoting allergic airway inflammation.
β-catenin negatively regulates IL-6 and IL-8 expression at transcriptional level and induces reactivity in human astrocytes
Authors: Robinson KaReisha , Narasipura Srinivas , Al-Harthi Lena 
Published: January 2023

Abstract
HIV invades the brain during acute infection, setting the stage for persistent neuroinflammation despite combined antiretroviral therapy (cART) and leads to HIV-Associated Neurocognitive Disorders (HAND), which occurs in ~50% of HIV-infected individuals. Our lab is focused on understanding the role of Wnt/β-catenin signaling in HAND. Here, we evaluated the impact of β-catenin on inflammatory mediators associated with neuroinflammation, chemotactic molecules, and regulation of A1 (proinflammatory)/A2 (protective/repair) phenotypes of astrocytes. We demonstrate that knockdown (KD) of β-catenin in normal human astrocytes (NHAs) significantly induced IL-6 and IL-8 at the transcription and protein levels and conversely, induction of β-catenin significantly downregulated these two molecules. These findings are intriguing given that no role for β-catenin to date is associated with IL-6 and IL-8 regulation. Further, KD of β-catenin induced three genes associated with A1 phenotype by 2.4–6.4 fold. These findings indicate that β-catenin expression in astrocytes is a critical regulator of anti-inflammatory responses and its disruption can potentially mediate persistent neuroinflammation.