bluuebunny/crossref_metadata_2025_split huggingface dataset:
HLA-Inception: A structure-based deep learning framework for MHC-I binding motif prediction
Authors: Wilson Eric A , Cava John , Anderson Karen , Singharoy Abhishek 
Published: January 2023

Abstract
The ability to accurately identify peptide ligands for a given major histocompatibility complex class I (MHC-I) molecule has immense value for targeted anticancer and antiviral therapeutics. However, the highly polymorphic nature of the MHC-I protein makes universal prediction of peptide ligands challenging due to lack of experimental data describing most MHC-I variants, and the vast number of protein variants precludes comprehensive experimental determination. Therefore, there is a need for a framework to cluster MHC-I alleles to prioritize for experimental validation as well as identify alleles with potential disease associations.
To address this challenge, we have developed a deep convolutional neural network, HLA-Inception, capable of predicting MHC-I peptide binding motif using data derived from the structure of the MHC-I binding pocket. By approaching this problem from a 3-dimensional perspective, we can fully consider the impact of sidechain arrangement and topology of the MHC-I binding pocket on peptide binding motif, which is not inherently captured by the popular protein sequence-based approaches. Through a combination of homology modeling and biophysical simulations, we created protein structure models for all full-length HLA-ABC alleles. The topology and interaction forces within the MHC-I binding pocket were accounted for by solving the 3-dimensional electrostatic potential near the surface of the protein. HLA-Inception was then trained on all MHC-I alleles with known MHC-I binding motifs and applied to the full set of MHC-I models. We found that predicted peptide binding motifs fell into distinct and well-defined clusters which maintained known peptide binding and disease associations.
The monocyte cell surface as a novel site of autoantigen generation in Rheumatoid Arthritis
Authors: Thomas Mekha A , Naik Pooja , Wang Hong , Jang Yura , Johnson Tory P , Curran Ashley M , Crawford Jonathan D , Jahanbani Shaghayegh , Robinson William H , Na Chan Hyun , Darrah Erika 
Published: January 2023

Abstract
Citrullination is recognized as a key pathogenic process in rheumatoid arthritis (RA), as evidenced by the formation of anti-citrullinated protein antibodies (APCAs) in the majority of patients; however, the mechanisms that result in citrullinated autoantigen generation are not fully understood. Although the citrullinating enzyme peptidylarginine deiminase IV (PAD4) is predominantly expressed by neutrophils and monocytes, the contribution of monocytes to the citrullinated autoantigen pool has been underexplored. In this study, we utilized multiple complementary methods including flow cytometry, immunofluorescence, and transmission electron microscopy, which revealed a predominantly extranuclear localization of PAD4 in monocytes with a fraction present on the cell surface. Surface PAD4 was enzymatically active and citrullinated both extracellular fibrinogen and endogenous surface proteins in a calcium dose–dependent manner. In addition, human monoclonal ACPAs cloned from patients with RA recognized fibrinogen citrullinated by monocyte-surface PAD4. Mass spectrometry analysis of citrullinated proteins from the cell surface fraction revealed CD11b to be a novel PAD4 substrate. Citrullinated CD11b was recognized by autoantibodies in 60% of ACPA+ RA patients compared to 6% of healthy controls (p=0.0021) and 0% of ACPA− RA patients (p≤0.001). Taken together, our study demonstrates that PAD4 is expressed on the surface of monocytes in an enzymatically active state that renders the monocyte surface a novel site of citrullinated autoantigen generation in RA.
Supported by funds received from Bristol-Myers Squibb.
Plasma-derived exosomes as biomarkers for therapy monitoring in head and neck cancer patients treated with surgery and (chemo)radiotherapy
Authors: Theodorakis Marie-Nicole , Lotfi Ramin , Whiteside Theresa L , Laban Simon , Hofmann Linda 
Published: January 2023

Abstract

Background
Head and neck squamous cell carcinomas (HNSCC) are highly immunosuppressive and aggressive malignancies. Exosomes are small extracellular vesicles that mediate intercellular communication. HNSCC patients have a significantly higher exosome load compared to healthy donors. Here, we evaluated the potential of plasma-derived exosomes as biomarkers for therapy monitoring in advanced HNSCC treated with conventional therapy.

Methods
Plasma from 17 HNSCC patients was collected before, during, and after treatment by surgery with adjuvant (chemo)radiation and at time of recurrence. Total exosomal protein (TEP) of exosomes was measured to estimate exosome load. Flow cytometry was used to evaluate relative fluorescence intensity (RFI) of tumor-associated and immunoregulatory proteins on exosomes. Effects of exosomes on CD8+ T cells and adenosine production by CD39+ T cells was assessed by flow cytometry and mass spectrometry.

Results
TEP levels and tumor-derived exosomes varied during and after therapy with an overall decrease in the tumor-free follow up but with an increase at time of recurrence. RFI values of immune checkpoints on exosomes, their potential for T cell inhibition, and adenosine production changed during and after therapy. Recurrent patients showed a different immunoinhibitory profile compared to disease-free patients. Exosomal PD-L1 emerged as the earliest discriminator for treatment failure and disease-free survival.

Conclusions
Plasma-derived exosomes from HNSCC patients emerge as promising non-invasive biomarkers for early detection of treatment failure. These exosomes can accurately inform about changes in patients’ immune status and may alert of impeding recurrence.
Old mice and elderly humans make increased autoimmune antibodies, inflammation and SASP from aged-increased B cells (ABCs in mice and DN in humans) which are hypermetabolic
Authors: Blomberg Bonnie , Diaz Alain , Romero Maria , Frasca Daniela 
Published: January 2023

Abstract
Immune mechanisms of human and murine diseases of aging include generation of chronic inflammation and autoimmunity. We and others have associated aging in mice and humans with increased chronic inflammation, reduced vaccine response and an increase in a B lymphocyte subset referred to as Age-associated B cells (ABCs) in mice and DN (double negative) in humans. Immune cell function is dependent on metabolic pathways and to date understudied. A. In this work we sorted splenic ABCs (CD19+AA4.1-CD21-CD23−) from young (3–4 months) and old (18–22 months) C57BL/6 mice showing an increased percentage in old and increased RNA expression of SASP (senescence-associated secretory phenotype) pro-inflammatory cytokines (TNFa, IL-6), proinflammatory micro-RNAs (miRs 155 and 16) and cell cycle regulators p16INK4 and p21Waf1 in old ABCs. We also show here old B cells produce more autoimmune IgG antibodies (to MDA, malondialdehyde and ADA, adipocyte-derived antigens), ABCs more than FO (follicular), and ABCs from old more than those from young. Total B cells and ABCs from old mice also have a higher metabolic profile compared with those of young mice. B. The frequency of DN cells is increased in human elderly as well as those younger with obesity. Plasma of obese had more autoantibodies to dsDNA, MDA, and ADA and the DN B cells showed higher levels of IA (Immune activation) markers and transcription factors, e.g. tbx21 (TBET) associated with autoimmunity. We have recently found that elderly human B cells are, like murine, hypermetabolic and are discovering possible mechanisms, such as fatty acids.
Supported by grants from NIH (AG32576, AG059719, and AG023717)
CD8 T cell exhaustion is reduced in subjects with autoimmune-associated DR4 risk alleles
Authors: Long Sarah Alice , Jones Britta , Wall Valerie , Muir Virginia , Ylescupidez Alyssa , Uchtenhagen Hannes , Linsley Peter S , Buckner Jane H 
Published: January 2023

Abstract
Exhausted CD8 T cells (TEX) are associated with worse outcome in cancer and better outcome in autoimmunity. However, factors contributing to reduced TEX in the context of autoimmunity are not well understood. Here, we identify co-expression of TIGIT and KLRG1 as a broad identifier of human TEX: TIGIT+KLRG1+ CD8 memory T cells share EOMES signature genes in healthy controls (HC), T1D and Rheumatoid Arthritis (RA) subjects, are increased with age and in chronic viral-specific cells, and are hyporesponsive (reduced proliferation and cytokine production) in vitro. We applied this inclusive, sample sparing and high throughput measure of TEX to larger longitudinal and autoimmune cohorts. Consistent with a genetic determinant, TEX are stable within HC and T1D individuals (Interclass correlation coefficient=92.0 and 83.7%, respectively), but display high interindividual variation (range 0.37–28.47 of CD8). In a large cohort of HC and RA subjects (n&gt;100/cohort), lower levels of EOMES modules and TEX were associated with the HLA Class II DR4 autoimmune risk allele, regardless of disease status. While the DR4 locus is complex, these findings suggest that TEX may be indirectly influenced by APC or CD4 T cell help. Moreover, therapeutic modulation of TEX may differ in DR4 risk and non risk subjects, with implications for precision medicine.
Supported by grants from the NIH (R01 AI141952, R21 5R21AR073508-02) and JDRF.
Interrogation of STAT3 activation in patients with polyarticular juvenile arthritis
Authors: Wood Stephanie Leigh , Branch Justin , Vasquez Pricilla , DeGuzman Marietta M , Brown Amanda , Sagcal Gironella A Carmela , Singla Saimun , Ramirez Andrea , Vogel Tiphanie P 
Published: January 2023

Abstract
Juvenile idiopathic arthritis (JIA) can cause pain and disability, but early disease control improves outcomes. The polyarticular JIA (polyJIA) subset is clinically similar to adult rheumatoid arthritis (RA), yet its pathogenesis remains incompletely understood. A pathway of interest in polyJIA is STAT3 signaling. STAT3 is a transcription factor critical to development of inflammatory Th17 cells and modulation of regulatory T cells. Elevated Th17s and activated STAT3 have been shown in RA. We aimed to profile T cell subsets and STAT3 activation in polyJIA.
Blood from 13 patients with polyJIA was collected at initial diagnosis and serially until remission. Peripheral blood mononuclear cells were isolated and T cell subsets and STAT activation (phosphorylation) were evaluated using flow cytometry.
Regulatory T cells from patients with polyJIA were found at similar levels as pediatric controls. However, treatment naïve polyJIA patients had increased Th17s compared to pediatric controls (0.15% v 0.44%, p=0.037). We identified IL-17 and IFN-γ dual+ helper T cells (non-classical Th1s) appearing in post-treatment samples from polyJIA patients. After stimulation (IL-6, IL-27 or IFN-α), a subset of polyJIA patients had highly activated STAT3, but not STAT1 or STAT5, in CD3+CD4+ T cells.
A better understanding of the mechanisms underlying polyJIA is needed for more efficient and effective clinical care. Although multiple therapeutics to treat JIA exist, a biomarker-driven approach to treatment does not. Patients with polyJIA have increased Th17s and a subset have highly activated STAT3. These immunologic features may help identify patients that would benefit from upfront, tailored treatment with therapeutics targeting this pathway.
Blockade of dendritic cell glutaminolysis induces allergic asthma desensitization via suppression of Tfh13 polarization
Authors: Tharakan Anuj , Liu Jinze , Cowart Ashley , Martin Rebecca 
Published: January 2023

Abstract
Allergic asthma is a pulmonary disease characterized by airway hyperresponsiveness (AhR) in response to inhaled allergens. AhR is largely mediated by allergen-specific (Ag-specific) IgE induced mast cell (MC) degranulation which drives inflammation of the airways following allergen exposure. Ag-specific IgE production requires T follicular helper 13 cells (Tfh13s) which must first be polarized by dendritic cells (DCs). The mechanisms by which DCs polarize Tfh13s, however, are unclear. We hypothesized that the Tfh13 inducing allergen Alternaria would induce a unique metabolic response compared to non-Tfh13 inducing stimuli. We found, by untargeted metabolomic analysis, that Alternaria induced accumulation of the glutamine-derived TCA cycle metabolite α-ketoglutarate compared to LPS stimulated or unstimulated DCs. Glutamine is converted to α-ketoglutarate by glutaminase (Gls), so we predicted that inhibition of Gls may suppress Tfh13 polarization by DCs. Indeed, we found that treatment with the Gls inhibitor, CB-839, reduced Tfh13 polarization and increased T follicular regulatory cells following Alternaria exposure. This finding was recapitulated in a DC adoptive transfer model, indicating that this mechanism is DC intrinsic. We next tested if CB-839 causes allergen desensitization in a model of allergic asthma. Mice were intranasally sensitized and challenged with Alternaria and intranasally treated with CB-839 or vehicle control prior to challenge. CB-839 treated mice exhibited reduced AhR, Ag-specific IgE, and airway MC degranulation. These data demonstrate that DC glutaminolysis is required for Tfh13 polarization, and that Gls inhibitors may promote allergen desensitization in allergic asthma.
This work was funded by VCU’s National Center for Advancing Translational Sciences (UL1TR002649) and NIAID (R56AI139658).
E3 Ubiquitin Ligase Cbl-b Inhibits Type 2 Innate Lymphoid Cell Development by Targeting ST2 for Ubiquitination
Authors: Guo Hui , Huang Ling , Waldstein Kody , Varga Steven M , Zhang Jian 
Published: January 2023

Abstract
Type 2 innate lymphoid cells (ILC2) play a crucial role in driving allergic airway inflammation, but the regulation of ILC2 development is not fully understood. Previously we have shown that E3 ubiquitin ligase Cbl-b negatively regulates Th2 response, but whether Cbl-b also regulates ILC2-mediated type 2 immunity remains to be defined. In this study, we found that Rag1−/−Cblb−/− mice are hypersensitive to inhalation of A. Fumigatus, a fungus that causes allergic asthma, as revealed by heightened airway hyperresponsiveness (AHR), increased airway inflammation, and mucus production. This hypersensitivity is associated with increased frequencies of ILC2 and eosinophils, but reduced frequency of alveolar macrophages in the lungs. Consistent with this, type 2 cytokines are also increased in the lung homogenates of Rag1−/−Cblb−/− mice. At the molecular level, ST2 undergoes ubiquitination and proteasome-mediated degradation upon IL-33 stimulation, which is abrogated in cells expressing Cbl-b C373A mutant. Therefore, our data indicate that Cbl-b inhibits the development of ILC2 and ILC2-mediated airway inflammation by targeting ST2 for ubiquitination.
Supported by NIH R01 AI090901, AI121196, and AI123253
PD-1 agonist modulates ILC2 metabolism and ameliorates airway hyperreactivity
Authors: Helou Georges Doumet , Shafiei-Jahani Pedram , Lo Richard , Howard Emily Diane , Hurrell Benjamin P , Galle-Treger Lauriane , Painter Jacob Dean , Lewis Gavin , Soroosh Pejman , Sharpe Arlene H , Akbari Omid 
Published: January 2023

Abstract
Allergic asthma is a chronic inflammatory disease characterized by airway hyperreactivity (AHR) and type-2 immune response. Type-2 innate lymphoid cells (ILC2s) mimic T helper 2 (Th2) cells in cytokine secretion and are among the first pulmonary immune responders to the allergen-induced alarmins. Programmed cell death protein-1 (PD-1) is known as an immune checkpoint equipped with tyrosine-based inhibitory motifs in the cytoplasmic tail. Since PD-1 is associated with immune regulation in many inflammatory diseases, the objective of this study was to investigate the role of PD-1 in the initiation and development of AHR. Lung function tests, RNA sequencing, flow cytometry, targeted metabolomic assays, and adoptive transfer experiments were principally used to explore the role of PD-1 in AHR mouse models and in human ILC2s. Using IL-33 and Alternaria alternata models, we have demonstrated that PD-1 knockout mice develop a higher AHR and lung inflammation as compared to control wild-type mice. In particular, PD-1 is highly inducible on lung ILC2s and downregulates their effector functions. Moreover, PD-1 controls glycolysis and methionine catabolism, limiting, therefore, the proliferation of activated pulmonary ILC2s. In line with mice data, PD-1 is inducible and functional in human ILC2s in response to IL-33. To confirm the translational relevance of our findings, we tested a novel human PD-1 agonist in vitro and in a humanized mouse model of AHR. Interestingly, the PD-1 agonist decreases human ILC2 activation and is able to dampen AHR and lung inflammation. Altogether this study reveals the protective role of PD-1 as regulators of ILC2s and highlights for the first time the therapeutic potential of PD-1 agonists in allergic asthma.
Supported by grants from NIH: R01 ES025786, R01 ES021801, R01 HL144790, and R21 AI109059 (O.A.)
Immune determinants of cardiometabolic risk in pre-existing type-2 diabetes (T2D) severe COVID-19 patients
Authors: Gunasena Manuja Gayashan Bandara , Wijewantha Yasasvi , Bowman Emily , Kumar Amendra , Weragalaarachchi Krishanthi , Furay Jerra , Skladany Tatum , Liu Shan-lu , Vilgelm Anna , Bednash Joseph , Kasturiratna Dhanuja , Demberg Thorsten , Funderburg Nicholas , Liyanage Namal 
Published: January 2023

Abstract
COVID-19, the disease caused by SARS-CoV-2, has led to a global public health emergency. Severity of disease course may be related to a dysregulated immune response and pre-existing health conditions. Recent studies have demonstrated that SARS-CoV-2 infection may directly or indirectly lead to an increase in cardiometabolic complications in patients with pre-existing type-2 diabetes mellites (T2DM) when compare to non-DM patients. A lack of mechanistic and systematic studies on how SARS-CoV-2 infection related immune responses may contribute to increase risk of cardiometabolic complications in pre-existing T2DM patients, hinder early risk identification and therapeutic interventions. Thus, in this study we investigate the biomarkers of cardiometabolic risk in non-DM and T2DM, severe COVID-19 patients admitted to the Intensive care unit.
Using high-dimensional flowcytometry and immune biomarker assays, we investigated functional and phenotypic changes in immune subsets in whole blood and plasma biomarkers of cardiovascular disease in healthy donors (n=17), T2DM severe-COVID-19 patients (n=10), non-diabetic severe-COVID-19 patients (n=10) admitted to the OSU medical center’s intensive care unit.
We found neutrophils and Intermediate monocytes (ITM) were significantly higher in the T2DM group compared to non T2DM patients. However, activated (HLA-DR+) NKT-like cells and NKG2A+ CD56 Dim CD16+ NK cells, were significantly lower in the T2DM-COVID-19+ group. Interestingly, LBP, FABP4, sCD14, IL-1b, RANTES and MIP-1a were significantly higher in the COVID-19 T2DM patients.
In this study, we identify core immune signatures that may predict increased cardiovascular disease risk in T2DM patients who had severe COVID-19.
Supported by PI’s startup funding
Selective IRAK4 degradation, not kinase inhibition, blocks TLR-activated NF-Kb and p38 Signaling leading to broad cytokine inhibition
Authors: Skouras Stephanie M , Massa Virginia , Lurier Emily , Hubeau Cedric , Wang Amy , Zheng Xiaozhang , Sharma Kirti , Walter Dirk , Browne Chris , Mayo Michele , Fitzgerald Michael , McDonald Alice , Gollob Jared , Mainolfi Nello , Slavin Anthony , Campbell Veronica 
Published: January 2023

Abstract
IL-1R/TLR activation plays a central role in the pathophysiology of multiple autoimmune and inflammatory diseases via the Myddosome that is dependent on both the kinase and scaffolding functions of Interleukin-1 receptor associated kinase 4 (IRAK4). Therefore, hetero-bifunctional molecules that selectively target IRAK4 for degradation and elimination by the ubiquitin proteasome pathway have the greatest potential to block IL-1R/TLR signaling, including NF-kb activation and cytokine production. To interrogate downstream signaling, phosphorylation events were monitored in monocytes and B cells following TLR7/8 or TLR9 activation, respectively. IRAK4 degradation, but not kinase inhibition, inhibited NF-kb p65 activation and phosphorylation of p38 pathway members by TLR agonists in both cell types. PBMCs pretreated with an IRAK4 degrader and then stimulated with the TLR7/8 agonist, R848, exhibited significantly broader inhibition of cytokines (IL-6, TNFa, IL-8 and IL-1b) compared to those pretreated with a selective IRAK4 kinase inhibitor. Compound washout experiments demonstrated a sustained effect of IRAK4 degrader on both target pharmacodynamics and cytokine inhibition that was differentiated from IRAK4 kinase inhibition. Overall, through removal of both scaffolding and kinase functions, IRAK4 degradation demonstrated greater activity compared to kinase inhibition across multiple TLR stimuli and cell types. These data highlight the potential for IRAK4 degraders to block multiple TLR signaling pathways across different immune cell types and thereby impact TLR/IL-1R-driven inflammatory and autoimmune diseases.
Dynamic changes in human single-cell transcriptional signatures during fatal sepsis
Authors: Qiu Xinru , Li Jiang , Bonenfant Jeff , Jaroszewski Lukasz , Mittal Aarti , Klein Walter , Godzik Adam , Li Jiang G 
Published: January 2023

Abstract
Systemic infections, especially in patients with chronic diseases, may result in sepsis: an explosive immune response that can lead to multisystem organ failure with a high mortality rate. Patients with similar clinical phenotypes or sepsis biomarker expression upon diagnosis may have different outcomes, suggesting that the dynamics of sepsis is critical in disease progression. A within-subject study of patients with Gram-negative bacterial sepsis with surviving and fatal outcomes was designed and single-cell transcriptomic analyses of peripheral blood mononuclear cells (PBMC) collected during the critical period between sepsis diagnosis and 6 h were performed. The single-cell observations in the study are consistent with trends from public datasets but also identify dynamic effects in individual cell subsets that change within hours. It is shown that platelet and erythroid precursor responses are drivers of fatal sepsis, with transcriptional signatures that are shared with severe COVID-19 disease. It is also shown that hypoxic stress is a driving factor in immune and metabolic dysfunction of monocytes and erythroid precursors. Last, the data support CD52 as a prognostic biomarker and therapeutic target for sepsis as its expression dynamically increases in lymphocytes and correlates with improved sepsis outcomes. In conclusion, this study describes the first single-cell study that analyzed short-term temporal changes in the immune cell populations and their characteristics in surviving or fatal sepsis. Tracking temporal expression changes in specific cell types could lead to more accurate predictions of sepsis outcomes and identify molecular biomarkers and pathways that could be therapeutically controlled.
This research was supported by the UCR School of Medicine (to A.G. and M.G.N.), the Dean Innovation Fund (to J.B. and M.G.N.), and the National Institutes of Health (NIAID, R21AI37830, and R01AI153195 to M.G.N.). The data from this study were generated at the UC San Diego IGM Genomics Center utilizing an Illumina NovaSeq 6000 that was purchased with funding from a National Institutes of Health SIG grant (#S10 OD026929).