bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structure of a TAPBPR/nanobody complex reveals dynamic plasticity of unbound regions of TAPBPR
Authors: Jiang Jiansheng , Natarajan Kannan , Ingram Jessica , Margulies David H. 
Published: January 2023

Abstract
Recently determined structures of the tapasin homolog, TAPBPR, complexed with peptide-receptive MHC-I molecules, revealed interaction of TAPBPR with the a2-1 helix of MHC-I, and displacement of the C-terminal region of the peptide binding groove, resulting in a conformation amenable to peptide loading. These structures were based on X-ray data at ~3.4 Å resolution and a number of regions of the electron density map were ill-defined. In an effort to obtain a higher resolution structure of TAPBPR, we isolated TAPBPR-specific nanobodies (camelid-derived single domain antibody fragments), from phage display libraries generated from peripheral blood lymphocyte mRNA of an alpaca immunized with TAPBPR. E. coli-expressed and purified nanobodies were complexed with TAPBPR. Crystal structures of a TAPBPR/nanobody complex and of nanobody alone were determined at 2.8 Å and 1.55 Å resolution respectively. In the structure of the complex the nanobody binds to the C-terminal Ig domain of TAPBPR, rigidifying the region of contact and thus permitting modeling of TAPBPR residues that were not visible in the reported TAPBPR/MHC-I structures. Unliganded surfaces of TAPBPR were more disordered than in the MHC-I liganded form. These data are consistent with the view that the luminal domains of TAPBPR, in solution, are structurally dynamic, and rigidify on ligand (i.e. MHC-I) interaction. Such structural plasticity may explain the ability of TAPBPR to interact with a variety of MHC-I allelomorphs.
Systematic profiling of HLA-C epitopes
Authors: Keskin Derin B. , Sarkizova Siranush , Klaeger Suzan Klaeger , Li Letitia , Le Phuong M. , Keshishian Hasmik , Hartigan Christina R. R. , Zhang Guang Lan , Clauser Karl , Carr Steven A. , Hacohen Nir , Wu Catherine J. 
Published: January 2023

Abstract
Accurate predictive algorithms have required elucidation of HLA-peptide binding motifs from extensive HLA binding peptide ligand databases. Historically, however, little attention has been paid to HLA-C because of its perceived lower surface expression, even as newer studies have identified important HLA-C restricted viral epitopes. Robust predictive algorithms for HLA-C are thus lacking and yet, if improved, could markedly expand the spectrum of immune targets contributing to protective immune responses. We generated 21 distinct single HLA-C allele-expressing cell lines and subjected them to immunoaffinity purification and MS-based sequencing. From 33851 peptides identified from the 21 HLA-C expressing cell lines, we discovered novel anchor motifs. These data were used to train machine-learning algorithms to generate an accurate and novel HLA-C epitope prediction tool. Finally, we used our novel algorithm to predict HLA-C restricted neo-epitopes out of tumor biopsies.
DO:DM tunes antigen presentation in a BCR affinity-dependent manner
Authors: Jiang Wei , Adler Lital N. , Macmillan Henriette , Mellins Elizabeth 
Published: January 2023

Abstract
HLA-DO, a non-classical class II major histocompatibility complex (MHCII), competitively inhibits HLA-DM in B cells. B cells lower DO levels during antigen-mediated activation in germinal centers, implying a regulatory function of DO in resting B cells. We transfected T2 (T/B hybrid) DR4.DM cells with DO and used index FACS to measure single cell variation in DO:DM ratios. High DO:DM ratios allowed groove occupancy by class II-associated Ii peptides (CLIP), and low DO:DM ratios enabled CLIP removal. 3D structured illumination microscopy revealed DMDO concentrated in LAMP1+ endosomes. Both DM+DO+ and DM−DO− cells express CLIP/DR complexes, but a larger fraction of CLIP/DR localizes to LAMP1+ endosomes in DM+DO+ cells. Using memory and naïve human tonsillar B cells, we saw significant downregulation of DO after cell activation. CLIP/MHCII density relative to free DM (estimated by 1-DO/DM) was generally higher in resting vs. activated B cells, especially in memory cells. This memory B cell phenotype primarily reflected higher intracellular CLIP/MHCII; upon BCR-mediated stimulation, total CLIP/MHCII fell to levels in activated naïve cells. We hypothesized that higher CLIP/MHCII and DO in resting memory B cells sets a threshold for the activation needed to efficiently recruit Tfh and selects for cells with higher affinity BCR. Using antigen stimulation of 2 clonal B cell lines expressing BCRs with different affinities for GAD65, we confirmed that, in this system, BCR affinity correlates with the amount of reduction in total CLIP/MHCII after activation. A positive correlation between BCR affinity and the extent of peptide exchange on MHCII is likely mediated by the effects of BCR affinity on signaling and antigen delivery.
Investigating a role for the MHC class II accessory molecule HLA-DO in autoimmune disease
Authors: Welsh Robin A. , Song Nianbin , Boronina Tatiana , Cole Robert , Foss Catherine , Sadegh-Nasseri Scheherazade 
Published: January 2023

Abstract
HLA-DO (DO), H2-O in mice, is a non-classical, non-polymorphic MHC Class II accessory molecule. Expressed primarily in the thymic medulla and B cells little is known about its physiological role in vivo. To gain insight into what role DO might have in CD4 T cell selection, our lab previously used in vitro biochemical assays to show that DO itself enhances the binding of DM insensitive peptides to the HLA-DR1 molecule, while inhibiting the binding of DM sensitive peptides. This led us to hypothesize that in vivo, DO might be important for ensuring proper presentation of immunodominant epitopes in the thymic medulla; thereby ensuring proper negative selection occurs. Lack of DO then could lead to a larger precursor pool of autoreactive CD4+ T cells in the periphery due to faulty negative selection. To test this, we utilized H2-O knock-out (KO) mice and the autoimmune model experimental autoimmune encephalomyelitis (EAE). With this model, we have found that KO mice have a faster onset of disease when compared to C57BL/6 wild-type mice. This increase in onset correlated with the recovery of more MOG specific cells from the CNS of KO mice at all stages of disease. Moreover, naïve mouse data also supports our hypothesis with naïve KO mice having a larger number of MOG specific CD4+ T cells. More recently, we found that KO mice also harbor increased percentages of regulatory T cells (Tregs) in both the naïve and diseased states. Correlating this finding with disease onset, we saw that KO Tregs appear to have impaired upregulating of the inhibitory molecule CTLA-4 in early disease. As a whole, our data suggests that KO mice not only have an increased precursor pool of autoreactive CD4 T cells but might also have impaired Treg function; all leading to faster disease onset.
One size doesn’t fit all: SLAM-Associated Protein is dispensable for type 1 diabetes but required for autoantibody-mediated arthritis
Authors: Bonami Rachel , Nyhoff Lindsay , Hulbert Chrys , Felton Jamie , Kendall Peggy L. , Thomas James W 
Published: January 2023

Abstract
Signaling lymphocytic activation molecule-associated protein (SAP), a critical intracellular signaling molecule for T-B interactions, drives Tfh development in germinal centers (GC) in the setting of protective immune responses. SAP promotes long-lived T cell-B cell interactions necessary to sustain germinal center reactions that lead to antibody production. High-affinity islet autoantibodies predict type 1 diabetes (T1D) but do not cause beta cell destruction. This paradox intimates T follicular helper cells (Tfh) as key pathologic effectors. To understand Tfh contribution to autoimmune processes, we investigated the role of SAP in T1D and autoantibody-mediated arthritis. Whereas spontaneous autoimmune arthritis depended on SAP, organized insulitis and diabetes onset were unabated, despite a blocked anti-insulin vaccine response. SAP-deficient T cell function was therefore investigated in the non-obese diabetic (NOD) T1D model. B lymphocyte antigen presentation drove SAP-deficient NOD T cell proliferation. Although germinal center B cell formation was markedly reduced, GC-Tfh were found at sites of autoimmune attack in SAP-deficient NOD mice. Thus, Tfh induced in germinal center reactions are dispensable for T1D and suggest that the autoimmune process in NOD retains pathogenic Tfh in the absence of prolonged B cell interactions. These findings demonstrate that SAP is essential for Tfh formation and autoimmunity when autoantibodies play a central role in autoimmune arthritis but not in cell-mediated T1D. SAP inhibition is thus a compelling strategy for autoantibody-mediated disease treatment, but additional cognate cellular interaction molecules must be targeted to treat cell-mediated autoimmune diseases.
Tryptamine treatment results in the amelioration of EAE by inducing an anti-inflammatory shift in the Th17/Treg balance mediated by regulation of miRNA expression profile
Authors: Dopkins Nicholas , Nagarkatti Prakash , Nagarkatti Mitzi 
Published: January 2023

Abstract
In this study we focus on understanding the novel immunotherapeutic potential of tryptamine, a bioactive indole compound derived from microorganisms and various botanicals, in the context of ameliorating symptoms of Experimental Autoimmune Encephalomyelitis (EAE). EAE is used in the laboratory setting to replicate the etiology as well as pathology of Multiple Sclerosis (MS) in murine organisms for research purposes. Globally MS, an incurable autoimmune disorder, is experiencing increases in incidence and treatment costs which places emphasis on the discovery of novel immunosuppressents with limited toxicity. In this study we show that tryptamine poses potent immunosuppressive activity and ameliorates the clinical parameters of EAE by shifting the balance of CD4+ T cells from a pro-inflammatory T helper 17 cell (Th17) towards an anti-inflammatory T regulatory cell (Treg) dominated landscape in chronic progressive EAE. Based on preliminary miRNA array data, we have found that the observed shift in the Th17/Treg balance following tryptamine treatment is due to an anti-inflammatory miRNA expression profile within the lymphocytes of treated mice. MiR-3473g and miR-140-3p, putative targets of the enzyme SIRT1, were found to be upregulated within the lymphocytes of tryptamine treated mice. SIRT1 in the context of inflammatory disorders works as a marker of pro-inflammatory responses in lymphocytes due to SIRT1’s activation of the master transcription factor of Th17 cells known as RORγt. This epigenetic regulation of gene expression provides a clearly linkable mechanism explaining the shift in the Th17/Treg balance as well as the amelioration of symptoms observed following tryptamine treatment in EAE mice.
Lymphocytes populations in murine models of Systemic Lupus Erythematosus exhibit different responses to treatment with metabolic modulators
Authors: Cornaby Caleb , Zeumer-Spataro Leilani , Choi Seung-Chul , Li Wei , Morel Laurence 
Published: January 2023

Abstract
An often debilitating autoimmune disease involving multiple immune cell types and tissues, Systemic Lupus Erythematosus (SLE) afflicts nearly 3 in a 1000 people, an estimated 9.7 million in the United States. Murine models of lupus are essential for the study of disease progression, prevention, and treatment of SLE, with B6.Sle1.Sle2.Sle3 triple congenic (TC) and NZB X NZW F1 hybrid (NZB/W) being two murine models commonly used for these purposes. While these murine models show similar disease symptomology, they exhibit immune cell subsets that differ metabolically. CD4+ T cells from TC mice show increased glycolysis and phosphorylation (OXPHOS) function, however CD4+ T cells from NZB/W mice demonstrate similar activity of OXPHOS and glycolysis compared to control B6 mice. B cells from both strains present similar elevated metabolism. Further, CD4+ T cell and B cell populations from these two strains display differential metabolic modulation during treatment with the same metabolic inhibitors. This contrasts with a similar therapeutic efficiency of a treatment inhibiting glycolysis with 2DG and mitochondrial respiration with metformin in both murine models of lupus. This implies metabolic inhibitors may have therapeutic efficiency across cell-specific differences in metabolic defects.
Evaluating cooperative roles for STAT3 and Aiolos in lymphocyte mimicry associated with metastatic disease
Authors: Sandhu Simran , Read Kaitlin , Jones Devin , Dickerson Sam , Oestreich Kenneth J 
Published: January 2023

Abstract
Inappropriate expression and function of cytokine and chemokine receptors by both hematopoietic and non-hematopoietic cell populations have been linked to human disease. One example of this is the expression of lymphocytic genes by metastatic cancers, termed lymphocyte mimicry. Specifically, the aberrant expression of chemokine receptors by cancer cells allows for inappropriate responses to immune signals, migration, and increased ability to survive in circulation. The mechanisms that regulate lymphocyte mimicry are currently incompletely understood. Our laboratory recently identified a novel transcriptional complex composed of the Ikaros Zinc Finger transcription factor Aiolos and STAT3 that regulates gene expression in CD4+ T cells, including that of chemokine receptors. Interestingly, Aiolos and STAT3 have been independently implicated in multiple cancers, including metastatic breast cancer. We hypothesized that Aiolos and STAT3 may cooperate to induce chemokine receptor expression in metastatic breast cancer cells. Our study observed increased Aiolos expression and STAT3 activation in metastatic breast cancer cells as compared to non-tumorgenic and non-metastatic controls. This correlated with increased expression of the chemokine receptor CXCR4, which has been previously linked to metastatic cancer. Importantly, shRNA knockdown of Aiolos in metastatic cells resulted in decreased expression of CXCR4. Collectively, these data support a role for Aiolos, possibly in collaboration with STAT3, in the induction of a metastatic gene signature in human breast cancer.
Neuroinflammation functionally regulates CNS lymphatic vasculature and drainage
Authors: Hsu Martin , Rayasam Aditya , Kijak Julie A. , Choi Yun Hwa , Harding Jeffrey S. , Marcus Sarah A. , Karpus William J , Sandor Matyas , Fabry Zsuzsanna 
Published: January 2023

Abstract
There are no conventional lymphatic vessels within the CNS parenchyma, although it has been hypothesized that lymphatics near the cribriform plate or dura maintain fluid homeostasis and immune surveillance during steady-state conditions. However, the role of these lymphatic vessels during neuroinflammation is not well understood. We report that lymphatic vessels near the cribriform plate undergo lymphangiogenesis in a VEGFC – VEGFR3 dependent manner during experimental autoimmune encephalomyelitis (EAE) and drain both CSF and cells that were once in the CNS parenchyma. Lymphangiogenesis also contributes to the drainage of CNS derived antigens that leads to antigen specific T cell proliferation in the draining lymph nodes during EAE. In contrast, meningeal lymphatics do not undergo lymphangiogenesis during EAE, suggesting heterogeneity in CNS lymphatics. We conclude that increased lymphangiogenesis near the cribriform plate can contribute to the management of neuroinflammation-induced fluid accumulation and immune surveillance.
Analysis of leukocyte populations and nerves in developing murine corneas
Authors: Abou-Slaybi Abdo , Jamali Arsia , Harris Deshea L , Seyed-Razavi Yashar , Hamrah Pedram 
Published: January 2023

Abstract
The avascular cornea is the most densely innervated tissue in the body and is endowed with resident bone marrow-derived cells. We have identified a novel subset of resident corneal plasmacytoid dendritic cells (pDCs). We have shown pDCs support corneal nerves through release of nerve growth factor (NGF).
This study was to examine the presence of pDCs in the developing cornea. We examined corneas from E17, P2, and 8 week adult C57BL/6 mice. Corneas were stained for the pan-leukocyte marker CD45, the pDC marker plasmacytoid dendritic cell antigen-1 (PDCA-1), the pan-neuronal marker bIII-tubulin. Corneal CD45+ and PDCA-1+ cells and nerves were quantified. Significance was assigned by ANOVA and post-hoc Tukey test. All data is reported as mean ± standard deviation.
Corneal CD45+ leukocyte density increased from E17 (65.4±14 cells/mm2) to P2 pups (301.9±19 cells/mm2, p&lt;0.05). Both E17 and P2 corneas had lower CD45+ density when compared to adults (345±34 cells/mm2, p&lt;0.05). We observed pDCs in the anterior stroma proximal to corneal nerves in E17, P2, and adult corneas. In E17, few pDCs were present in the peripheral cornea (1.5±2.6 cells/mm2), with none in the central cornea. In P2, pDCs were found in the periphery (68.19±8.99 cells/mm2), but not central corneas. The density of pDCs in adult peripheral (82.2±5.1 cells/mm2) and central (51.6±4.9 cells/mm2) corneas was greater than E17 (p&lt;0.001) and P2 (p&lt;0.05) corneas. Nerve density increased from E17 (45.43±6.75 mm/mm2) when compared to P2 (83.15±.21.6 mm/mm2 p&lt;0.05) and to adult (151.6±3.25 mm/mm2 p&lt;0.05) corneas.
Our data show pDC density increased from embryonic, to neonatal, and adult corneas. Concurrently corneal nerve density increased during development from embryonic to adult mice.
Systemic Lupus Erythematosus (SLE) patients’ Peripheral Blood Mononuclear Cells (PBMCs) display an altered transcript isoform repertoire
Authors: Singh Prashant , Veiga Diogo Troggian , Rossi Robert , Marches Radu , Belaid Djamel Nehar , Pascual Virginia , Banchereau Jacques 
Published: January 2023

Abstract
Alternative splicing (AS) is a key mechanism of biological diversity in eukaryotes allowing a single gene to generate multiple mRNA transcript isoforms, yielding unique proteins that may have distinct or opposing functions. Alterations in AS have been associated with numerous diseases. SLE patients display autoantibodies to components of the spliceosome, chiefly anti-Sm/RNP, anti-Ro/La, and anti-dsDNA. We performed Long-Read sequencing using Pacific Biosciences equipment (LR-Seq), as well as short read RNA-Seq, from adolescent SLE patients’ and healthy controls’ PBMCs, to discover and quantitate splice junctions. A computational pipeline was built to differentially quantify splice junctions in the LR-Seq sequenced isoforms, both known and novel using rMATS (Multivariate Analysis of Transcript Splicing). Compared to Gencode, LR-Seq revealed ~9000 novel transcript isoforms. 55% of all transcripts were expressed in 2 or more samples. A majority of these transcripts belonged to genes associated with cell cycle, metabolism, and inflammation. Additionally, we interrogated our SLE LR-Seq generated transcriptome with publicly available RNA-Seq data from adult SLE and healthy donors. We observed 250 differential expression of exon skipping (ES) splice junctions in transcript isoforms of genes, a majority of which did not exhibit any significant change in gene expression. Of the 250 ES transcript isoforms, 160 exon inclusion events were observed in SLE PBMCs. Fifty percent of the exon inclusion events were found to be in novel transcript isoforms. Thus LR-Seq, besides revealing novel transcripts, allows us to study changes in transcript isoform expression.
The impact of the TRPM2 ion channel on inflammation and macrophage metabolism in gastrointestinal models
Authors: Algood Holly Marie Scott , Dixon Beverly R.E.A. , Olivares-Villagomez Danyvid , Serezani Carlos Henrique , Washington M. Kay , Rathmell Jeffrey C. , Coburn Lori A. 
Published: January 2023

Abstract
Macrophages can play a vital role in regulating pro-inflammatory pathways that drive chronic inflammation and impact carcinogenesis. We previously published that TRPM2 regulates ROS production and the pro-inflammatory cytokine profile of macrophages in vivo and in vitro in H. pylori infection models. Since macrophage function and activation profiles can be regulated by metabolism, the impact of the TRPM2 channel on macrophage metabolism was assessed using bone marrow derived macrophages in Seahorse Extracellular Flux Assays and Mitotracker assays. The data demonstrated an unfavorable shift in mitochondrial content in Trpm2−/− macrophages after M1 activation. Consistent with this shift, the oxygen consumption rate was reduced in Trpm2−/− macrophages compared to WT macrophages, and the extracellular acidification rate at baseline and glycolytic reserve were higher in Trpm2−/− macrophages following classical activation. To investigate the role of TRPM2 in controlling other gastrointestinal pathologies, including acute colitis and carcinogenesis, the dextran sulfate sodium (DSS) colitis model and the azoxymethane (AOM)/DSS colitis-associated cancer (CAC) model were used. Trpm2−/− mice were not protected against acute DSS-induced colitis. Our endpoint analysis in the CAC model demonstrated that Trpm2−/− mice developed more numerous but smaller tumors than WT mice and immunohistological analysis suggests a shift in numbers of innate cells in the Trpm2−/− tumors compared to WT tumors. In the non-tumor areas, the histological injury score was reduced in the Trpm2−/− mice compared to WT mice. These data suggest that TRPM2 regulates Mϕ metabolism and impacts inflammation in the gastrointestinal tract.
Comparing docosahexaenoic acid as a prophylactic treatment for acute and chronic particle-exposed Balb/c mice
Authors: Fletcher Paige , Hamilton Ray F , Buford Mary , Postma Britten , Pestka James J , Holian Andrij 
Published: January 2023

Abstract

Rationale
There is a rising trend in the use of nanomaterials in various consumer products; increasing the risk of human exposures. Inflammation is a vital contributing factor to pulmonary diseases which can be triggered by exposure to airborne toxicants such as nanomaterials. However there are no effective treatments. One potential treatment shown to have anti-inflammatory effects is the dietary supplement docosahexaenoic acid (DHA); an omega-3 polyunsaturated fatty acid found in fish oil. This study compares DHA as a prophylactic treatment for acute and chronic particle-induced inflammation.

Method
Balb/c mice were fed a control or 1% DHA-containing diet for 5 weeks (acute) or 18 weeks (chronic). At week 4 (acute) or weeks 2, 3, 4, and 5 (chronic) the mice were anesthetized and oropharyngeal instilled with dispersion media (50 μl) or a highly inflammatory multi-walled carbon nanotube (50 μg). One week (acute) or 13 weeks (chronic) after instillation, macrophage NLRP3 inflammasome activation and lung lavage fluid (LLF) levels of lactate dehydrogenase (LDH) and protein levels were evaluated. Inflammatory cytokines were evaluated in LLF and plasma of the mice. DHA’s impact on macrophage phenotype was also examined.

Result for both exposures
Macrophage production of IL-1β and LLF levels of LDH, protein, and pro-inflammatory cytokines, such as IL-33 and TNF-α, decreased in mice fed the DHA diet. DHA appears to be altering macrophage phenotype within the lung and spleen tissues; specifically the M2 phenotype.

Conclusion
DHA could potentially be used as a prophylactic treatment for acute and chronic particle exposures since it was demonstrated to have a number of anti-inflammatory effects on Balb/c mice exposed to a common nanomaterial.