bluuebunny/crossref_metadata_2025_split huggingface dataset:
PU.1 regulates chromatin modifications of the Il9 gene in Th9 cells (57.5)
Authors: Goswami Ritobrata , Kaplan Mark 
Published: January 2023

Abstract
IL-9-secreting Th9 cells are generated when naïve CD4+ T cells are cultured with IL-4 and TGF-β. The transcription factor, PU.1 is required for the development of Th9 cells. The expression of PU.1, which is abundantly expressed in Th9 cells, is dependent on TGF-β dose. Dose dependent increase in TGF-β leads to a concomitant increase in PU.1 expression and IL-9 production. Ectopic expression of PU.1 can convert Th2 cells to Th9 phenotype and enhance IL-9 production from Th9 cells. The DNA binding domain and the transactivation domains of PU.1 are required for PU.1 to activate Il9, suggesting that as it binds Il9, it recruits other factors to mediate gene activation. We hypothesized that PU.1 recruits specific chromatin modifying enzymes to the Il9 locus. H3 acetylation is decreased in PU.1-deficient Th9 cells on both the Il9 promoter and a second conserved non-coding sequence immediately after 3’ of the Il9 gene. H3K9/18 acetylation is also diminished in PU.1-deficient Th9 cells while H4 acetylation is not altered by PU.1-deficiency demonstrating specific PU.1-mediated histone modifications correlating with Il9 transcription. Overall these results indicate that PU.1 promotes expression of IL-9 by modifying specific histones at the Il9 locus.
Interferon-alpha/beta inhibit immunity towards HBV in a mouse model of HBV persistence (59.8)
Authors: Huang Miao-tzu , Chiang Bor-Luen , James Cassandra , Chen Pei-Jer 
Published: January 2023

Abstract
In humans, most HBV infection in the adult resolves after the acute disease, however, around ninety percent of the infection in neonates and childhood leads to chronic HBV persistence. Until today, causes for the age-dependent infection outcome of HBV are still unclear. By using hydrodynamic injection of replication-competent HBV DNA plasmid, we established a mouse model of in vivo HBV transfection in which HBV persistence was generated in young C57BL/6 mice of 4-6 w/o, but not in mice older than 10 w/o. In this system, we found that there was higher hepatic IFN-alpha/beta expression in the young mice after HBV transfection compared to adult mice. We speculate that differential IFN-alpha/beta immune regulation during early HBV infection leads to the age-dependent HBV persistence outcome. To address this, the adult mice were overexpressed with IFN-beta in the liver. HBV persistence rate of these mice was increased compared to controls. In addition, blockage of IFN-alpha/beta signaling in the young mice accelerated HBV clearance. The young mice expressed more IFN-alpha/beta-associated immune suppressor genes, Axl/Twist, after HBV transfection than the adult mice, suggesting that type-I IFN executed active immune suppression towards HBV immunity in the young mice. Our findings suggest a role for IFN-alpha/beta in suppressing effective anti-HBV immunity in the young mice and shed light on our understanding of the age-dependent immune function during early HBV infection.
Functional non-coding ncRNA in immunity and tolerance: what can be learned from structures and functions of transfer factors of delayed-type[-IV] hypersensititvity on genetics, epigenetics and recognition repertoires (62.12)
Authors: Wissler Josef 
Published: January 2023

Abstract
AIM: Immunity and [self-]tolerance are usually considered orchestrated by protein repertoires upon genetic [Mendelian] and epigenetic [non-Mendelian] variation mechanisms. All is still not fully understood, as evident from transfer factor and LeDouarin phenomena, environmental influences, peptidome complexity and diversity [Adv.Immunol.11,195-266,1969; Int.J.Dev.Biol.49,131-136,2005]. Endogenous ncRNA incl. microRNA mostly escaped consideration. METHODS: Ann.N.Y.Acad.Sci.1137,316-342,2008. RESULTS: Landsteiner-Chase-Lawrence transfer factors showed up as paradigmatic guides in some terra incognita of adaptive immune memory. Original crude preparations were found as paucidisperse solute systems of numerous functional small ncRNA [&lt;200n] in interaction with proteins. Some environment-modified redox- and metalloregulated small hairpin shRNA [&lt;200 bases] were sequenced. By 5'-CUG-3’-hairpin loops, they may address conserved homologous helix-nucleating domains shared in self and foreign proteofactors of tolerated growth, metabolism, vascularization, cancer and epigenome indexing. CONCLUSIONS: Immune cells are not restricted to known protein recognition systems. They have further repertoires of environment-adapted ncRNA as earliest outputs in transcription and translation. These are superior in diversity/specificity [≥10E17] to immune proteins repertoires [~10E13]. All attributes make them competent to integrate information flow on possible molecular shapes into genomic mechanisms.
The role of 2B4 on the generation of OVA-induced effector and memory CD8+ T-cells. (63.1)
Authors: Lee Jung Eun , Kim Seok-Ho , Kim Tae Woo , Lee You Jeong , Jung Kyeong Cheon , Kim Jae-Hong , Lee Kyung-Mi 
Published: January 2023

Abstract
NK receptor 2B4 belongs to the signaling lymphocyte activation molecule (SLAM) family and has been shown to modulate NK cell responses. Previously, we and others have found that 2B4 became expressed on effector, not naive, CD8+ T cells and regulated their proliferation in vitro. However, the role of 2B4 in the Ag-specific CD8+ T cell responses in vivo remains elusive. To address this, we investigated the effector and memory CD8+ T cell generation using the 2B4-deficient mice. Upon primary OVA-Vaccinia virus infection of 2B4-/- mice, we observed significantly reduced numbers of OVA-specific effector and memory CD8+ T cells along with reduced IFN-γ, compared with WT controls. During secondary OVA-vaccinia challenge, 2B4-/- memory CD8+ T cells expanded to a much lesser extent than that seen in wild-type mice. These results demonstrate the participation of 2B4 signaling in the generation, expansion, and maintenance of Ag-specific CD8+ T cell during the course of OVA-vaccinia infection. Our data reveal previously unrecognized role of 2B4 on Ova-specific CD8+ T cells.
NF-κB-inducing kinase plays an essential T cell intrinsic role in graft-versus-host disease and OX40-mediated costimulation, and its overexpression causes lethal autoimmunity (63.3)
Authors: Murray Susan , Polesso Fanny , Rowe Alexander , Parker David 
Published: January 2023

Abstract
NF-κB-inducing kinase (NIK) is an essential upstream kinase in non-canonical, or alternative, NF-κB activation. TNF receptor family members such as BAFFR and LTβR depend on NIK for signaling, but little is known about the role of NIK downstream of TNF receptors in T cells. Here, we describe a T cell-intrinsic requirement for NIK in graft-versus-host disease (GvHD), wherein NIK-deficient alymphoplasia (aly) T cells transferred into MHC class II mismatched recipients fail to cause disease. We show that although NIK is not necessary for antigen receptor signaling, it is essential for costimulation through the TNF receptor family member OX40 (CD134). Notably, OX40 deficient T cells also fail to elicit GvHD. To assess whether NIK overexpression could recapitulate chronic OX40 activation, we conditionally overexpressed NIK in T cells in vivo using a Cre-inducible transgene. Mice with modest NIK overexpression limited to T cells suffered rapid fatal autoimmunity characterized by hyperactive effector T cells and poorly suppressive Foxp3+ regulatory T cells. Together, these data reveal a critical T cell-intrinsic role for NIK during immune responses, and suggest that tight regulation of the non-canonical NF-κB pathway is crucial to avoid autoimmunity.
Characterization of committed T cell progenitors within adult human bone marrow. (64.21)
Authors: Ramos Joseph , García-Ojeda Marcos 
Published: January 2023

Abstract
Hematopoietic stem cell transplantation (HSCT) remains the chief method for treating hematological and autoimmune disorders. However, HLA-matched donors are rare, leading to the use of allogeneic donors. Successful allo-HSCT relies on balancing the levels of donor T cells that facilitate engraftment and provide beneficial graft-versus-leukemia (GVL) effect without inducing graft-versus-host-disease (GVHD). A method for improving allo-HSCTs involves co-transplantation of hematopoietic stem cells (HSCs) with committed T cell progenitors (CTP). Mouse bone marrow contains a population of CTP that swiftly reconstitute T cells in allo-HSCT without inducing GVHD. We identified a CD34+CD38loCD7+CD10-Lin- population in human bone marrow using multi-color flow cytometry that we hypothesize is a human CTP. CD34+CD38loCD7+CD10-Lin- cells expresses CCR7, CXCR6, CCR9, and CD45RA. Using qPCR, we examined the gene expression profile of this population for the expression of T-, B-, and myeloid specific genes. We observed that CD34+CD38loCD7+CD10-Lin- cells have higher levels of lymphoid and T cell specific genes than CD34+CD38lo HSC or CD10+ BM cells. We examined myeloid development potential by methylcellulose cultures, and lymphoid potential using OP9 and OP9DL1 stroma. Our data indicates that the CD34+CD38loCD7+CD10-Lin- bone marrow population may be a true CTP. Future work would help us determine if this hCTP population can mitigate complications caused by allo-HSCT engraftments.
Transcription factor expression pattern differences are present in OP9 culture derived fetal liver origin early thymocytes when compared to fetal and adult thymocytes (64.22)
Authors: Scripture-Adams Deirdre , Georgescu Constantin , Rothenberg Ellen 
Published: January 2023

Abstract
The advent of the OP9 stromal culture system has tremendously improved our ability to replicate T cell development in vitro. While giving unprecedented access and numerical advantage, these cells may not mirror real thymocytes in their developmental capacity and transcription factor expression patterns. We have examined the pattern of expression of 65 developmentally regulated gene transcripts across the early thymocyte stages of DN1, DN2, DN3 and DN4, in fetal liver derived thymocytes (FLDN) derived from co-culture on OP9 DL-1 cells, and compared them to those found in fetal and adult thymocytes using real time quantitative PCR. Our assessment suggests an overall pattern of similarity between FLDN expression patterns and “real” freshly isolated thymocytes, but some classes of genes are not regulated similarly, and these may have important consequences for development and progression. We present a cluster analysis identifying transcription factors which are differentially regulated in FLDN relative to adult and fetal populations, and identify groups of factors which track with those differentially regulated transcripts. We additionally analyze the effect of long vs. short term culture on these changes in the transcription factor control network that drives T cell development.
The transcription factor PLZF controls the development of mouse and human innate T cells (64.6)
Authors: Sant'Angelo Derek 
Published: January 2023

Abstract
Natural killer T cells (NKT cells) have an innate immunity-like rapidity of response and the capacity to modulate effector functions of other cells. We have shown that NKT cells express the BTB-ZF transcriptional regulator PLZF. In the absence of PLZF, NKT cells developed, but lacked many innate T cell features. We have also shown that PLZF expression is not restricted to NKT cells, but is also expressed by a subset of NKT cell-like γδ T cells. Interestingly, TCR signal strength and expression of Id3 appear to control the frequency of PLZF-expressing γδ T cells. In human T cells PLZF is expressed in NKT cells, γδ T cells and, unexpectedly, in a population of CD8+ T cells. Analysis of T cells from the only known human with a biallelic loss of functional PLZF demonstrates that the development of invariant NKT cells and other PLZF-expressing T cell subsets is dependent upon expression of PLZF. The PLZF-expressing CD8+ T cells are functionally distinct from both conventional T cells and from invariant NKT cells. Furthermore, this subset of T cells is expanded in the peripheral blood of patients with metastatic melanoma; however it is greatly diminished in that of patients with autoimmune disease. Therefore, the expression of PLZF defines a new human T cell population that is differentially regulated in response to different types of immune stress. Furthermore, these data highlight important differences between the human and mouse immune system.
In vitro production of fully human monoclonal antibodies targeting therapeutic self-antigens (65.10)
Authors: Hoel Brian , Sun Wei , Halstead Lucinda , White David , Fernandes Daniel , Rubinchik Semyon , Sutkowski Natalie 
Published: January 2023

Abstract
Despite their role in autoimmune disease, not all autoreactive antibodies are harmful. Autoantibodies targeting tumor antigens, growth factors and their receptors are currently used therapeutically in cancer and autoimmunity. Ordinarily, healthy subjects do not exhibit strong secondary antibody responses to self-proteins, because most autoreactive B cells do not receive sufficient T cell help required for the germinal center reaction and for differentiation into IgG secreting cells. Our data demonstrate that rare, potentially therapeutic autoreactive B cells can be efficiently rescued from tonsil with EBV immortalization, and manipulated in vitro into secreting IgG, by supplying factors that mimic antigen stimulation and T cell help. Because this process is performed wholly in vitro, it constitutes a rapid and cost effective technology, resulting in the isolation of fully human antibodies. In addition, antibodies can be generated against highly toxic antigens, since immunization is unnecessary. We have developed two panels of human monoclonal antibodies targeting distinct self-antigens for use in cancer immunotherapy, one targeting the tumor antigen nucleolin and the other angiogenic placenta growth factor. We hypothesize that infection of B cells with the ubiquitous herpesvirus EBV might contribute to the persistance of autoreactive memory B cells in vivo, altering the B cell repertoire and resulting in the secretion of destructive and possibly of protective autoantibodies.
Obtain consistent and accurate PBMC cell counting results with Cellometer automatic cell counter (65.14)
Authors: Lin Bo , Chan Leo , Lai Ning , Pirani Alnoor , Smith Tim , Lyettefi Emily , Qiu Jean 
Published: January 2023

Abstract
Traditional methods for fluorescence-based PBMC analysis commonly employ manual hemacytometer and standard flow cytometry for concentration and viability measurement. Manual cell counting requires trained technicians, which is time-consuming and prone to human error. In addition, PBMC samples are usually contaminated with RBCs and platelets, which may increase manual counting difficulty. Standard flow cytometry remains expensive, large in size, and require considerable amount of maintenance, which may not be ideal for research laboratories that need a cost-effective method. In addition, traditional flow cytometers do not have imaging capabilities, which often generate some uncertainties in the fluorescence results obtained. Recently, an imaging cytometry platform has been developed by Nexcelom Bioscience. This system allows automated cell image acquisition and processing with a novel counting algorithm for accurate and consistent measurement of cell population and viability with 20 μl of PBMCs sample. In this work, we demonstrate a rapid and cost-effective method for concentration and viability measurement of PBMCs using the Cellometer imaging cytometry method. This method has the ability to resolve the issues caused by manual hemacytometer and flow cytometer. By using Cellometer imaging cytometry, the assay time for generating concentration and viability result is greatly reduced, which is significant for research development in the biomedical and clinical studies.
A novel ELISA for eosinophil peroxidase provides a sensitive high throughput assay for eosinophil degranulation in either mouse or human biological samples (65.29)
Authors: Ochkur Sergei , Kim John , Protheroe Cheryl , Nair Parameswaran , Furuta Glenn , Lacy Paige , Moqbel Redwan , Lee James , Lee Nancy 
Published: January 2023

Abstract
Eosinophils comprise only 1-3% of circulating leukocytes but are often a diagnostic feature associated with a variety of inflammatory and disease states, including parasitic and fungal infections, allergic diseases (e.g., asthma, rhinitis and sensitivities to specific foods), cancer, and transplant rejection. The accurate evaluations of eosinophilia as well as the release of stored eosinophil granule proteins are important for the monitoring disease progression and/or assessing the effectiveness of a given treatment strategy(ies). Despite the availability of detection methods for each of the eosinophil granule proteins logistical difficulties limiting either the assays specificity and/or sensitivity have prevented their extensive use. We have generated unique eosinophil peroxidase specific monoclonal antibodies (EPX-mAb) and a high throughput sandwich ELISA assay as a means of overcoming these difficulties. Our EPX-mAb based ELISA is ~10 times more sensitive than traditional OPD based activity assays and allows detection of EPX in mouse BAL fluid after an acute OVA protocol as well as EPX release from mouse eosinophils stimulated ex vivo. The assay is highly specific and gives no signal in samples from EPX deficient mice even with massive eosinophilia (e.g., EPX deficient IL-5 transgenic mice). More significantly, this assay detects EPX in human tissue extracts and biological fluids and thus represents novel diagnostic assay previously unavailable in clinical settings.
Optimiser™ microfluidics ELISA plates overcome confounding rheumatoid factor-like and HAMA-like false positive effects in immunoassay detection of IL-17A in serum matrices. (65.35)
Authors: Sehy David , Kai Junhai , Santiago Nelson , Puntambekar Aniruddha , Lee Se Hwan , Durnell Randy , Schultheis Ron , Han Jungyoup , Ahn Chong 
Published: January 2023

Abstract
The measurement of analytes in serum matrices by sandwich ELISA can be confounded by naturally-occurring interfering factors which can cross link capture and detection antibodies, yielding distinct false positives. Such naturally-occurring interfering activities are often attributed to rheumatoid factor or HAMA (Human Anti-Mouse Antibody)-like effects in the serum sample. Rh factor, an autoantibody reactive with the Fc portion of IgG, is often identified in patients suspected of having arthritis, but, notably, this activity is observed in 5-10% of healthy persons. Recently, studies of mouse sera from a panel of outbred mice analyzed by mouse IL-17A sandwich ELISA demonstrated strong false positives when conventional ELISA plates were used. In side-by-side testing, such aberrant false positives were not observed upon running the same samples using the microfluidics-based Optimiser™ ELISA microplate. The absence of false positives in the Optimiser™ ELISA microplate render it an ideal candidate for use in screening serum samples for analytes of interest when naturally-present HAMA-like activity can confound ELISA results and interpretation.
Brilliant Violet 421™ and Brilliant Violet 570™ antibody conjugates deliver consistent and superior performance on violet-laser equipped flow cytometers with varied specifications (65.4)
Authors: Perna Avi , Koh Carolyn , Lundsten Kelly , Nosworthy Lara , Wormsley Susan , Jiang Nan , Lay Gene 
Published: January 2023

Abstract
Brilliant Violet™ derived fluorophores are novel and highly sensitive polymeric molecules that fluoresce upon excitation by a 405 nm laser line. In this study, Brilliant Violet 421™ and Brilliant Violet 570™ antibody conjugates were evaluated for their performance on violet laser equipped flow cytometers with varying instrument configurations. Instrument specific variables included sheath pressure, laser power, PMT gain and position, optical configuration, and filter sets. Cross beam spectral overlap was also evaluated for 488nm and 561nm lasers. All instrument configurations revealed significantly increased signal to noise ratio with Brilliant Violet™ as compared to traditional violet laser dyes. Brilliant Violet 421™ yielded logarithmic improvements in signal to noise ratio, while maintaining manageable spectral compensation properties. Brilliant Violet 421™ antibody conjugates against high and low-density surface markers also increased resolution and accuracy, notably for human CD25, CD56, CD127 and mouse NK1.1 and CD4. The Brilliant Violet™ conjugates were also found to be effective for detection of intracellular cytokines. Overall, Brilliant Violet™ 421 and Brilliant Violet™ 570 were determined to outperform traditional violet-excitable organic dyes on flow cytometers with a variety of specifications and settings.
Tools for enhancement of diagnostic immunoassay applications (65.42)
Authors: Jentz Tim , Nelson Wendy , Opperman Gary 
Published: January 2023

Abstract
Optimization of immunoassay applications is often hampered by issues such as non-specific binding, matrix interferences, destabilization of antibody/antigen interactions, and limited sensitivity. SurModics offers tools to address these problems and provides the framework to develop sensitive, reproducible, and robust immunoassays. Stabilization of antibody-protein interactions is fundamental for achieving a robust and reproducible assay. Novel stabilizer formulations have been developed to provide protein stability in both the dried state as well as in solution. The data presented here show improved stability compared to both common in-house formulations as well as other competitor solutions. Problems with non-specific binding and matrix interferences can cause high background, loss of sensitivity and false positives in many diagnostic applications. These issues were mitigated by use of protein-free blocking solutions, or novel passivating surface chemistry for microarray applications. Data here suggest the TRIDIA™ surface chemistry provides significantly reduced non-specific binding in protein arrays. Shown here are data from a new, protein-free diluent designed to reduce matrix interferences and to be substituted with ease into your existing assay protocol. Whether it is in solution or on a surface, SurModics provides the tools necessary to develop and optimize immunoassays that are sensitive, reproducible, and robust.
Analysis of whole blood immune cell function using imaging flow cytometry. (65.8)
Authors: George Thaddeus , Hall Brian , Friend Sherree , Mordecai Scott , DeMarco Richard , Kong Raymond 
Published: January 2023

Abstract
Analysis of immune function directly in human whole blood samples has several advantages over analysis in processed samples. First, leucocytes are activated in conditions closely matching their natural environment in the bloodstream, complete with all cofactors and cell types necessary for normal function. Second, purification processes are time consuming, technically challenging, and can themselves be a source of stress (temperature, physical, pH, etc) that modulates immune cell function. Furthermore, whole blood is the most obtainable source of clinically-relevant material from patients and healthy controls. Whole blood imaging assays are challenging due to the need for simultaneous multispectral immunophenotyping and in many cases due to the rarity of the cell type of interest. However, recent advancements in high speed flow imaging uniquely enable the study of leukocyte function directly in whole blood samples in three image-based applications that we present here. These include measurement of: 1) chemokine-induced receptor internalization in whole blood T cells; 2) chemokine-induced shape change in whole blood monocytes; and 3) dose and time kinetic activation of NFkB translocation in monocytes and plasmacytoid dendritic cells, the latter of which represent less than 0.1% of whole blood leukocytes. These results uniquely demonstrate methods for statistically robust image-based measurement of rare immune cell function directly in whole blood samples.