bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sirt1 is a requisite for the antigen presentation by B cells
Authors: Park Seok-Rae , Han Younghwan , Shin Jongdae , Kang Jaeku 
Published: January 2023

Abstract
Sirt1 is a NAD+-dependent deacetylase that is well known to control aging and metabolism. Many reports show that Sirt1 regulates innate and adaptive immune responses. Among them, several studies have examined the role of Sirt1 in antigen processing and presentation in dendritic cells. The aim of the present study is to determine the role of Sirt1 in antigen presentation in B cells. First, we examined the expression of major components of the MHCII antigen presentation pathway (Ii, HLA-DM, HLA-DO, and MHCII) and maturation markers (CD40, CD80, and CD86) in Sirt1-deficient B cells using qRT-PCR and flow cytometric analysis. All the components and the markers expressions were lower in Sirt1-deficient B cells than wild-type (WT). To determine whether B cell APC function is dependent on Sirt1, we performed experiments regarding CD4+ OT-II T cell responses to OVA-pulsed Sirt1-deficient B cells or WT B cells in vitro co-culture. CD4+CD69+, CD4+TNF-α+, and CD4+IL-17+ T cells were decreased in Sirt1-deficient B cells compared with that of WT. In addition, T-bet/RORγt mRNA expression and TNF-α/IL-17 secretion were diminished in Sirt1-deficient B cells in the culture. Collectively, these results indicate that Sirt1 in B cells is required for expression of components of MHCII antigen presentation pathway and APC function to activate and functionally differentiate CD4+ T cells.
Proteogenomics and de novo sequencing based approach for neoantigen discovery from the immunopeptidomes of patient CRC liver metastases using Mass Spectrometry
Authors: shah Darshit , Rye-Weller Anna , Dhanik Ankur , Cygan Kamil , Olsen Olav , Olson William , Salzler Robert 
Published: January 2023

Abstract

Introduction
Using High-resolution Mass Spectrometry (MS), we developed a novel immunopeptidomics workflow using de novo sequencing. This method does not rely on a reference database to deduce full-length peptide sequences. As a consequence, peptide discovery is not limited to the reference database and allows for the discovery of novel peptides directly from MS.

Goal
Identify HLA-associated peptides that appear in high frequency in tumors through de novo sequencing and missed by reference database searches.

Method
We employed a highly selective anti-HLA Class I monoclonal antibody, W6/32, to enrich HLA-complexes from 21 CRC liver metastases and identified HLA associated peptides using a Thermo Orbitrap Fusion Lumos on-line with a nanoLC 1200. RNA-Seq was also performed on each tumor. MS raw spectra were analyzed by de novo assisted PEAKS-X (BSI)

Results
Approximately 1600 unique de novo sequenced HLA-associated peptides were identified in a single LC-MS analysis with high confidence (95% ALC cut-off) from each tumor. Approximately 45% of the 1600 unique de novo sequenced peptides matched to reference databases (e.g Uniprot.), leaving a large percentage of peptides with no match. Interestingly, some of these unmatched peptides have been validated as neoantigens that arise from gene mutation, spliced peptides generated by the proteasomes, and non-coding region derived peptides.

Conclusion
These de novo sequenced peptides without matches in reference databases may provide a unique source of disease-specific HLA class I-presented peptides and trigger specific immune responses. Some of the higher frequency unmatched de novo sequenced peptides may thus serve as tumor-specific targets for next-generation immunotherapies.
Destabilization of exotoxin A diminishes serum antibody titer and affinity maturation by reducing peptide-MHCII abundance
Authors: Moss Daniel L , Song Kejing , Wanek Alanna G , Shu Qingbo , Hu Tony , Kolls Jay K , Mettu Ramgopal R , Landry Samuel J 
Published: January 2023

Abstract
Potent antibody responses depend on the proteolytic processing of protein antigens and the presentation of MHC Class II bound peptides to CD4+ T cells. We have previously reported a single amino acid substitution (R494A) made to pseudomonas exotoxin A domain III (PE-III) that alters processing and antibody responses with only minor changes to CD4+ T-cell priming. These findings could not explain how the R494A substitution causes a substantial reduction in antibody titer. Previous work by our laboratory and others has shown that the stability of protein antigens affects T-cell priming through effects on antigen processing. However, there is no direct mechanism for how antigen processing alters antibody immunogenicity. We hypothesized that destabilization of PE-III by the R494A substitution reduces the abundance of PE-III peptide-containing MHCII complexes on B cells and thereby reduces their capacity to solicit T cell help for affinity maturation. Here we have observed that antibodies raised against PE-III R494A exhibit lower avidity than those raised against wild type PE-III. Furthermore, R494A PE-III was a poorer source of T-cell epitopes when provided to splenocytes from mice immunized with either wild type or R494A. Currently, PE-III peptide abundance is being analyzed by mass spectrometry, and antigen specific B cells are being characterized by single cell RNA sequencing.
Molecular requirements for B cell receptor engagement and activation
Authors: Ferapontov Alexey , Omer Marjan , Nielsen Jesper , Thiel Steffen , Kjems Jørgen , Degn Søren Egedal 
Published: January 2023

Abstract
B cells are a central component of the adaptive branch of the immune system, responsible for humoral immunity through production of antibodies. Antigen engagement of the B cell receptor (BCR) is the first step in B cell activation; yet despite its recognized importance, the exact mechanism of BCR activation remains controversial. A central point of contention has been whether monovalent antigen is capable of activating the BCR or not. To address this question, we leveraged the B1-8hi knock-in BCR model, in which λ light-chain positive B cells display intermediate and high affinity binding to the haptens NP ((4-hydroxy-3-nitrophenyl)acetyl) and NIP ((4-hydroxy-3-iodo-5-nitrophenyl)acetyl), respectively, and combined this with a recently developed nucleic acid based scaffolding technology (Holliday junctions [HJs]) to prepare defined mono-, di- and trivalent displays of NP and NIP. Using confocal imaging, flow and imaging cytometry, as well as calcium-flux analyses, we find that HJs carrying 2 or 3 copies of either NP or NIP can bind and activate B1-8hi B cells across a wide range of concentrations, whereas HJs carrying a single NP require high concentrations for any measurable activity. Most interestingly, HJs carrying a single NIP are able to bind B1-8hi B cells at low concentrations, approaching equimolar stoichiometry, but despite measurable BCR engagement do not elicit activation. Our results may reconcile previous contradictory reports regarding monovalent antigen activation, by providing a framework for understanding complex interaction effects of antigen affinity, valency and concentration.
Pertussis toxin treatment promotes a B cell driven disease during TH17 EAE
Authors: Maria Zahra , Axtell Robert C. 
Published: January 2023

Abstract
Pertussis toxin (PTX) is an enigmatic co-adjuvant that is required for disease induction in active Experimental autoimmune encephalomyelitis (EAE), a model of multiple sclerosis. The objective of this study was to investigate the functional role of PTX during adoptive transfer TH17-EAE. TH17-EAE was induced by transferring myelin-specific TH17 cells, harvested and cultured from MOG35–55 immunized wild type (WT) donor mice, into WT or B cell deficient (μMT) recipient mice. Recipient mice were treated with PTX or PBS on days 0 and 2 and monitored for paralysis. In WT mice, PTX delayed disease onset but did not alter disease severity or incidence. We found that PTX reduced trafficking of myeloid cells and inflammatory T helper cells in the CNS. Importantly, PTX treatment increased the number of B cells in the brain with increased antigen presenting function, suggesting an altered disease toward a B cell-dependent pathology. When disease progression was compared between WT and μMT mice treated with PTX or PBS, there was no significant difference in TH17-EAE in the PBS treated groups. However, PTX treatment significantly delayed disease onset, severity and incidence in the μMT mice vs. WT. In conclusion, our current data suggests that during TH17-EAE, PTX restricts the trafficking of pathogenic T helper cells and myeloid cells into the CNS and thereby delays the disease onset. However, not only PTX does not alter trafficking of B cells into the CNS it also stimulates a more inflammatory B cell phenotype and therefore promotes a B cell driven disease. This study provides novel insights to interactions between TH17 and B cells in mice and has defined a new model to study B cell activity during multiple sclerosis.
Expansion of polyreactive and autoreactive IgG B cells in NOD.H-2h4 mice, a model of Sjögren’s Syndrome
Authors: Engel Pablo , Gutiérrez-Cózar Rebeca , Puñet-Ortiz Joan , Carrillo Jorge , Blanco Julìa , Moya Manuel Sáez 
Published: January 2023

Abstract
In genetically prone individuals, chronic immune activation may lead to expansion of autoreactive lymphocyte clones that can induce organ damage developing autoimmune disorders. Sjögren’s Syndrome (SjS) is one of the most common systemic chronic autoimmune diseases that primarily affects exocrine glands with progressive dryness of mouth and eyes. Despite the accumulated evidences of profound B-cell alterations of humoral immunity, the repertoire and onset of B-cell autoreactivity in SjS remains to be determined. We hypothesize that SjS mice will have an increased frequency of self-reactive B cells with a progressive evolution to antigen-driven oligoclonality. Here, we study the B cell repertoire of NOD.H-2h4 mice, a mouse model of spontaneous autoimmunity mimicking SjS without developing diabetes. All female mice presented salivary gland infiltrates and autoantibodies such as anti-dsDNA and anti-Ro52, both characteristic of SjS, at the age of 24 weeks. A library of 456 hybridomas from NOD.H-2h4 mice splenocytes at three different ages: 28, 47 and 66 weeks old was created. The presence of mono or polyreactive autoantibodies against dsDNA, Ro52, LPS, insulin, histones and OVA was evaluated by ELISA, and their staining patterns and cellular reactivity were tested by IFA and FACS. We observed a high percentage of autoreactivity among B-cell clones from NOD.H-2h4 mice. IgM autoreactive B cells were maintained, while polyreactive and autoreactive IgG clones increased with mice age. Interestingly, all anti-Ro52 autoantibodies were polyreactive. Our results indicate that in the NOD.H-2h4 mouse model of SjS, IgG+ B cells are mainly polyreactive and might expand following an unknown antigen-driven positive selection process.
Single Cell RNA Sequencing of Human Liver Infiltrating B Cells in Primary Biliary Cholangitis (PBC)
Authors: Zhang Weici , Wu Xunyao , Sun Ying , Duan Weijia , Dhaliwal Sandeep , Leung Patrick S.C. , Bowlus Christopher , Zhang Xuan , Gershwin M Eric 
Published: January 2023

Abstract
Increasing evidence supports the concept that dysregulated B cell differentiation and activation are pivotal in the initiation and progression of autoimmune disorders, in both antibody (Ab)-dependent and Ab-independent mechanisms. Antimitochondrial antibodies (AMA), the serologic hallmark of PBC, are present in greater than 95% of patients with PBC, with a long latency period between the detection of autoantibodies and the onset of clinical disease. However, the mechanisms involved in the role of B cells in the pathogenesis of PBC have remained enigmatic. Herein, we have applied scRNA sequencing to simultaneously characterize B cell repertoire and transcriptome status in blood-liver paired samples from patients with PBC. Our data reveal that there is a dramatic increase in the heterogeneity of the blood CD27− B-cell population in PBC as compared to control. Strikingly, this overwhelmingly expanded naïve-like population were IgM+/IgD+, and encoded by germline sequences. In contrast with blood B cells, the dominant liver CD27− B-cell population is comprised of a high frequency of class-switched clonal B cells, which strongly express MHC class II genes. Upon stimulation with CpG (a surrogate TI-antigen), PBC CD27− B-cell populations markedly expanded and were accompanied by a significantly reduced expression of MARCKS, a newly identified molecule that suppresses active BCR signaling, as compared to healthy controls. Our data indicate that PBC CD27− B-cells exhibit abnormalities and heterogeneity, which may arise from a consistent exposure to TI-antigens. Our findings underscore the significance of B cells in PBC and suggest that more efforts should be placed on PBC B cell immunobiology and as potential therapeutic targets.
Defects in lysosome acidification are evident in active, but not inactive, systemic lupus erythematosus (SLE)
Authors: Kang SunAh , Rogers Jennifer L. , Clowse Megan E.B. , Sheikh Saira Z. , Vilen Barbara J. 
Published: January 2023

Abstract
Better strategies are needed in SLE to identify the receptors and molecular events that promote inflammation. We identified a defect in lysosomal acidification in multiple hematopoietic cell types in the MRL/lpr, NZM2410, and sle123 murine models of lupus. On myeloid cells, lysosome dysfunction is induced by chronic Fcgamma receptor (FcγR) signal transduction and results in the recycling of internalized IgG-immune complexes, and their accumulation on the cell surface. This perpetuates FcγR activation, promoting BAFF and IFNα/β secretion upstream of autoantibody production, lupus nephritis, and tertiary lymphoid organogenesis. Here, we define whether lysosomal defects and accumulation of nuclear antigens (Ags) are evident on human blood cells in SLE. Our data show that diminished lysosome function and the accumulation of nuclear Ags on patients’ blood cells are more evident in active, compared to inactive disease. On monocytes, 78% of active (n=18), but only 38% of inactive (n=16) patients showed diminished lysosomal acidification. On B cells, 47% of active, while only 9% of inactive patients, showed defects in lysosomal acidification. To assess whether lysosomal defects were coincident with the accumulation of nuclear Ags, we measured surface DNA levels (n = 57 active, 51 inactive patients, 109 HCs). In active patients, surface DNA levels were also elevated on blood B cells (7-fold; p = &lt;0.002), DCs (3.7 fold; p = 0.06), T cells (2.4-fold; p = 0.03), and monocytes (1.8-fold; p = 0.09). Because monocytes exhibited lysosome defects, the low levels of surface DNA on monocytes was unexpected. However, it raises the possibility that monocytes activated by lysosome dysfunction and chronic FcγR signaling leave the blood.
PU.1 mediates hematopoietic stem cell self-renewal during cellular stress by non-canonical Wnt signaling
Authors: Welner Robert S , Bararia Deepak , Levantini Elena , Camacho Virginia , Patel Sweta , Matkins Victoria R. , Tenen Daniel G 
Published: January 2023

Abstract
Hematopoietic stem cells (HSCs) reside in a dormant state during tissue homeostasis. However, secreted niche factors and cellular programs that maintain HSC dormancy following hematopoietic stress remain unknown. HSC are capable of re-entering quiescence following proliferation, suggesting local factors control HSC exhaustion. In the present study, we found that the myeloid-associated transcription factor PU.1 alters cell cycle activity and differentiation during cellular stress. PU.1 is typically associated with myeloid differentiation and lineage commitment, but during HSC perturbation, PU.1 regulates HSC maintenance and self-renewal potential. Taken together, PU.1 is required to limit HSC exhaustion; furthermore, limiting PU.1 expression during stress leads to impaired HSC function. Using cell-specific reporter models and reductionist culture assays, we find that a non-canonical Wnt-PU.1 axis constrains HSC differentiation and activation to maintain tissue homeostasis. Moreover, using scRNAseq and ChIPseq, we found unique cellular programs associated with PU.1 localization that mediate cell cycling and metabolism of proliferative HSC are mediated by Wnt. In the context of cellular stress, exposure to non-canonical Wnt signaling transitions HSCs into PU.1 expressing cells with increased engraftment potential and multilineage reconstitution. Our results suggest Wnt-induced PU.1 expression limit proliferation and differentiation programs to promote HSC function. Altogether, our data identify PU.1 as a key mediator of HSC maintenance in response to cellular stress.
Exploring the transcriptional impact of ERα in the B cell response of systemic lupus erythematosus
Authors: Richard Mara Lennard , Tsao Betty P. , Chung Dongjun , Gilkeson Gary S , Cunningham Melissa A 
Published: January 2023

Abstract
Systemic lupus erythematosus (SLE) is a heterogeneous, autoimmune disease. Being female is a significant, baseline risk factor for developing lupus. The mechanisms responsible for enhanced risk remain unknown. The nuclear hormone receptor and key transcription factor, estrogen receptor alpha (ERα), has a number of immune gene targets; yet, understanding of its regulation of the immune response is incomplete. Lupus prone mice, expressing a truncated functional ERα knockout, survived longer and had reduced renal disease. However, a complete knockout of ERα was not protective. Our goal is to identify the molecular mechanisms utilized by ERα in regulating the immune response in lupus B cells. We identified ERα associated genes and determined expression differences in B cells isolated from female African American (AA) lupus patients. RNA-seq analysis indicates that 60% of ERα target genes were deferentially expressed and 82% of these genes were upregulated in patients compared to controls. To understand ERα function, full-length ERα and an isoform, ERα46 (lacking the AF-1 activation domain), were transfected into an EBV transformed SLE B cell line and the expression of ERα gene targets, including inflammatory cytokines (IL1β and IL6) examined. Transfection results varied by gene and suggest the interaction between ERα isoforms is complex. The effect of epigenetic modifying agents on ERα protein expression in transfected SLE B cells was also studied. Evidence suggests that an increase in DNA methylation leads to increased protein expression of ERα isoforms. The regulatory role of ERα in lupus B cells is complex, involves epigenetic changes and interplay between isoforms. Results support a role for ERα in the pathogenesis of SLE.
TNIP1/ABIN1 mutation contributes to lupus nephritis via chemokine IP-10 induction
Authors: Powell David W , Brady Makayla P , Barati Michelle T , Caster Dawn J 
Published: January 2023

Abstract
Systemic lupus erythematosus (SLE) is a chronic autoimmune disease. Kidney inflammation or lupus nephritis (LN) is the most common and severe complication of SLE and mechanisms of pathogenesis are not clearly defined and current therapies are toxic and ineffective. We previously reported TNIP1 gene variants as risks for LN. TNIP1 encodes the protein ABIN1, which is a polyubiquitin binding protein that negatively regulates the prominent immune regulatory transcription factor NF-κB. We reported that transgenic mice with impaired ABIN1 ubiquitin binding function (ABIN1[D485N]) spontaneously develop SLE-like autoimmunity and LN and that ABIN1 determines the severity of LN via activation of kidney and immune cell inflammation. Interferon gamma-inducible protein -10 (IP-10) is a pro-inflammatory chemokine and NF-κB target that has been implicated in the pathogenesis and as a diagnostic marker of LN. The current project tested a hypothesis that LN development is mediated by induction of P-10 expression due to loss of cellular ABIN1 ubiquitin binding activity. We found that serum, urine, and kidney cell IP-10 expression is enhanced in ABIN1[D485N] mice. We also found that urinary IP-10 levels are higher in LN patients with TINIP1/ABIN1 variant rs4958881 when compare to LN patients without the TNIP1 variant and healthy controls. Our findings indicate that TNIIP/ABIN1 mutation contributes to the pathogenesis of LN via kidney and immune cell induction of IP-10 secretion and that serum and urinary IP-10 are promising diagnostic markers for LN especially in patients with TNIP1 variants. Further, successful Phase 2 clinical trials with IP-10 mAb for ulcerative colitis indicate its potential for effective LN treatment.
Role of 2B4 on dermal γδ T cells in the development of psoriasis-like skin inflammation
Authors: Kim Jiyoung , Kim Tae-Jin , Lee Kyung-mi 
Published: January 2023

Abstract
Psoriasis is a chronic inflammatory skin disease that has comorbid with systemic inflammatory disease, however, their precise pathologic mechanisms remain poorly understood. Transcriptome analysis of dermis in the psoriasis patient has revealed that the signaling lymphocyte activation molecule (SLAM) family receptor, 2B4 (CD244), was significantly down-regulated in the skin of psoriasis patients, suggesting that 2B4 might have served as an important regulator in the process of psoriatic inflammation. To test this hypothesis, we induced psoriatic skin inflammation with topical application of Imiquimod (IMQ), a toll-like receptor 7 ligand, on the back skin of WT or 2B4KO mice and examined their clinical disease score up to 6 days. As expected, IMQ-treated WT mice exhibited the signs of erythema, scales and skin thickness, however all these clinical manifestations were significantly worsened in 2B4KO mice. Furthermore, 2B4 deficiency caused elevated expression of antimicrobial peptides, along with increased IL-17A, a key cytokine driving the pathogenesis of psoriasis. Upon further analysis, we found that increased IL-17A production in the psoriatic skin of 2B4KO mice was attributed to the presence of dermal γδ T cells, not DCs or monocytes, within inflamed skin. Taken together, we present a previously unidentified role of 2B4 as a key coreceptor regulating the pathogenesis of psoriasis via controlling the dermal γδ T cells.
A novel mouse model of proteasome associated autoinflammatory syndromes
Authors: Brown Ivy Khristine , O’Brien Tommy , Jin Jingxiao , Jiang Simon , Reinhardt R. Lee 
Published: January 2023

Abstract
Proteasome associated autoinflammatory syndromes (PRAAS) represent a rare class of early-onset autoinflammatory diseases, including chronic atypical neutrophilic dermatosis with lipodystrophy and elevated temperature (CANDLE syndrome). CANDLE is an inherited autosomal recessive disease associated with recurrent fevers, skin lesions, lipodystrophy and other comorbidities. Point mutations in the proteasome subunit beta type-8 (psmb8) gene, which encodes the beta-5i (ß5i) catalytic subunit of the 20S immunoproteasome, have been linked to CANDLE. The immunoproteasome is induced in cells in response to interferon (IFN) signaling. In cells lacking functional immunoproteasomes, oxidant-damaged proteins aggregate and likely create a feed-forward loop resulting in greater cytokine-mediated stress. We have developed a novel mouse model via targeted mutation within the psmb8 gene, which harbors a specific point mutation (224C&gt;T) present in CANDLE patients. Our data shows that this mutation leads to marked differences in the expression of the immunoproteasome subunit ß5i within these mice. Thus, this mouse model is likely to exhibit changes in the immunoproteasome consistent with human disease upon interferon signaling. As mice with the targeted mutation do not directly yield a CANDLE-like phenotype at rest, it suggests that induction of disease-associated morbidity requires additional drivers. To test this, we are investigating interferons as initiators of disease pathogenesis. Future research will entail subjecting these mice to viral infection in order to identify if such triggers can initiate PRAAS-like symptoms in CANDLE patients. These mice may prove to an essential tool in understanding such disorders.