bluuebunny/crossref_metadata_2025_split huggingface dataset:
Batf3-dependent dendritic cells impact T-cell responses differently between adult and neonatal mice in an intestinal viral infection.
Authors: Sun Tian , Philpott Dana J , Gommerman Jennifer L 
Published: January 2023

Abstract
The role of dendritic cells (DCs) in shaping the immunity against bacterial infections in the colon (e.g. Citrobacter rodentium) has been well investigated; however, what subset modulates the immune response against viral infections in the small bowel is less known. Rotavirus (RV) almost exclusively infects and replicates in the small intestinal villi resulting in both cellular and humoral adaptive immunity, and RV infection serves as a model to study the DC-elicited antiviral responses in adult and neonatal mice. Batf3−/− adult and neonatal mice lack CD103+CD11b− DCs in the small intestinal lamina propria (SILP) and displayed a delay in viral clearance. CD8+ T cells have a role in the resolution of primary RV infection, and indeed, we found that while no antigen-specific CD8+ T cell response was detected in the Batf3−/− neonatal mice, a residual CD8+ T cell response was observed in the Batf3−/− adult mice, suggesting compensatory antigen-presentation from other adult DC subsets in the SILP (such as CD103+CD11b+ DCs). In terms of the CD4+ T cell response, no Th1 response was found in adult Batf3-deficient or –sufficient mice, however, a robust Th1 response was present in neonatal mice which was dependent on Batf3, implying a requirement of CD103+CD11b−DCs for priming/maintaining a Th1 response only in the neonatal period. Both the local and systemic anti-RV IgA response was normal in adult Batf3−/− mice, however, neonatal Batf3−/− mice displayed a stronger systemic IgA response than littermate controls. Our results demonstrate a requirement for Batf3-dependent DCs in antiviral responses which differs between neonates and adults, and these results may shed light on vaccine design.
VDJML – tools for capturing the results of inferring immune receptor rearrangements
Authors: Toby Inimary , Breden Felix , Buntzman Adam , Christley Scott , Corrie Brian , Fonner John , Gupta Namita , Hershberg Uri , Jordan Chris , Kim Min S , Kleinstein Steven , Marthandan Nishanth , Mock Stephen , Monson Nancy , Rounds William H , Rojas Manual , Rosenfeld Aaron , Rubelt Florian , Scarborough Walter , Scheuermann Richard H , Scott Jamie , Uduman Mohamed , Heiden Jason Vander , Cowell Lindsay G 
Published: January 2023

Abstract
Despite the widespread use of immune repertoire profiling, there is currently no standardized format for output files from VDJ analysis. Researchers utilize software such as IgBlast and IMGT/High V-Quest to perform VDJ analysis and infer germline rearrangements. Each of these software tools produces results in a different file format, and can identify the same result using different labels. These differences make it challenging for users to perform additional analysis using the output file from one software to the next. We have addressed this problem by developing a standardized file format for representing results. The purpose of VDJML is to provide a common standardized format for different VDJ analysis applications and to facilitate downstream processing of the results in an application-agnostic manner. The VDJML file format is accompanied by a suite of analysis tools, which are accessible via command line and written in C++ and python. The VDJML suite will allow users to streamline their VDJ analysis and facilitate the sharing of scientific knowledge within the community. The VDJML suite and documentation are available from https://www.vdjserver.org/software. We welcome participation from others in developing the file format standard, as well as code contributions.
Characterization of monoclonal antibodies generated by in vitro immunization
Authors: Maier Natalia , Holzloehner Pamela , Hoenow Anja , Scheunemann Astrid , Weschke Daniel , Hanack Katja 
Published: January 2023

Abstract
Monoclonal antibodies are highly valuable tools in biomedicine but the generation by hybridoma technology is very time-consuming and elaborate. In order to circumvent the consisting drawbacks an in vitro immunization approach was established by which murine as well as human monoclonal antibodies against a viral coat protein could be developed. The in vitro immunization process was performed by isolation of murine hematopoietic stem cells or human monocytes and an in vitro differentiation into immature dendritic cells. After antigen loading the cells were co-cultivated with naive T and B lymphocytes for three days in order to obtain antigen-specific B lymphocytes in culture, followed by fusion with murine myeloma cells or human/murine heteromyeloma cells. Antigen-specific hybridomas were selected and the generated antibodies were purified and characterized in this study by ELISA, western blot, gene sequencing, affinity measurements. Further the characteristics were compared to a monoclonal antibody against the same target generated by conventional hybridoma technology. Isotype detection revealed a murine IgM and a human IgG4 antibody in comparison to an IgG1 for the conventionally generated antibody. The antibodies derived from in vitro immunization showed indeed a lower affinity for the antigen as compared to the conventionally generated one, which is probably based on the significantly shorter B cell maturation (3 days) during the immunization process. Nevertheless, they were suitable for building up a sandwich based detection system. Therefore, the in vitro immunization approach seems to be a good and particularly fast alternative to conventional hybridoma technology.
Immunomagnetic enrichment of human ILC2 cells from peripheral blood leukopak
Authors: Poon Grace FT , Kyei Stephen K , Valdez Yanet , Takei Fumio , Peters Carrie , Woodside Steven M , Eaves Allen C , Thomas Terry E 
Published: January 2023

Abstract
Group 2 innate lymphoid cells (ILC2s) are essential for airway tissue repair, protection against helminth infection, metabolic homeostasis, and the development of allergic airway diseases. They are widely distributed throughout the human body in lung, intestine, palatine tonsils, skin and peripheral blood, but are extremely rare within a given tissue. In healthy individuals, ILC2s comprise 0.01–0.04% of leukocytes in the peripheral blood. Currently, flow cytometric cell (FACS) sorting is the only method to purify ILC2s, which is time-consuming due to their low frequency. We have adapted EasySep™ to pre-enrich ILC2s from peripheral blood leukopaks, and thereby shorten subsequent FACS analysis and sorting times. Non-ILC2 cells in an unprocessed leukopak were immunomagnetically labeled using a cocktail of antibody complexes and magnetic particles. The sample was then placed in a magnet for 10 minutes, the labeled cells were retained, and the unlabeled cells, containing the ILC2 population, were recovered. ILC2s were enriched from 5 x108unprocessed cells in 30 minutes. Enriched cells were counted and evaluated by FACS. ILC2s, defined as lineage negative (CD1a− CD3− CD11c− CD14− CD19− CD34− CD123− TCRαβ− TCRγδ− BDCA2− FcɛR1−), CRTH2+ CD161+CD127+, were enriched 268±167 fold, with 74± 34% recovery (means ± SD, n=7). EasySep™ pre-enrichment of ILC2s reduced subsequent FACS analysis and sorting time compared to non-enriched samples. Importantly, ILC2s enriched with EasySep™ were functional, as shown by production of the type 2 cytokine IL-13 upon stimulation with IL-33 and IL-2. Overall, EasySep™ is a simple and rapid method to pre-enrich ILC2s from leukopak for subsequent FACS analysis or sorting and functional analyses.
MojoSort™ kit isolated cells maintain physical function in magnetic cell separator and column
Authors: Zhang Hong , Tam Miguel , Gohel Dhanesh , Koury Jeffrey , Shen Crystal , Chen David , Yang Xifeng , Lay Gene 
Published: January 2023

Abstract
Magnetic cell sorting has been widely used to isolate different cell types as it is a fast and reliable method to obtain discrete populations with high purity and yield. However, to maintain cell functionality with this approach has been concerned for different studies. To address this, the cells were isolated with our recently developed MojoSort™ isolation kit using commercially available magnetic cell separation column, and compared that with other commercial magnetic column related products. The stickiness of the magnetic particles of those isolated cells were then imaged with electron microscope, and the cellular functionality was tested by activation of MAPK/ERK pathway and cell proliferation assay. Our data show that MojoSort™ negative isolated cells with MojoSort™ separator or magnetic column do not display beads on cell surface, phosphorylation of ERK1/2 level did not increase as detected by western blot, and the isolated cells showed fully functional. In addition, both positively isolated cells with either MojoSort™ kit or magnetic separation column related kit preserved functionality. Furthermore, MojoSort™ isolated cells only have &lt;10% of particles covered on the cell surface. Finally, when analyzing positively selected cells using MojoSort™ kit with MojoSort™ magnet, we observed a higher number of beads on the cell surface as compared to cells isolated using separation columns, but the cells still maintain their functionality. Thus, our data demonstrates that cells isolated with MojoSort™ reagents are viable and functional, independently of the magnetic separator used, either column-based or handheld magnet.
Systems Biology Approach to Uncover Signaling Defects in Primary Immunodeficiency Diseases
Authors: Choi Jeff , Fernandez Rosemary , Maecker Holden T , Butte Manish J 
Published: January 2023

Abstract
To improve diagnoses and further our understanding of functional defects in subjects with primary immunodeficiency (PI) diseases, we developed a new screen to broadly study the signaling of defective human immune responses to infections. Using time-of-flight mass cytometry (CyTOF) and phospho-specific antibodies, we simultaneously examined the major signaling pathways of all circulating innate and adaptive immune cell types in response to cytokines and TLR agonists to identify signaling responses. We studied healthy controls and developed software tools to generate a systematic map of signaling responses. CyTOF successfully recapitulated established signaling responses, and further, elucidated new pathways that would not have been appreciated with traditional studies. Signaling map of controls was compared to maps generated by analyzing PI subjects with gain-of-function STAT1 and autosomal dominant STAT3 deficiency diseases. CyTOF allowed us to perform unbiased studies to uncover many ex-vivo signaling defects simultaneously to better understand how known genetic etiologies manifest functionally, and exactly which cell subtypes are affected. We identified more glaring defective signaling responses in these subjects aside from the canonical defects, elucidating the true breadth of cell subtypes and pathways affected. Broad, unbiased, functional analysis can complement whole exome sequencing to facilitate identification of novel or rare immune diseases. Comprehensive view of signaling across all immune cell subsets facilitates learning more about abnormal signaling patterns that confer susceptibility to infection or autoimmunity, improving our understanding of immune responses and can lead to new therapies.
Controlling role of Ly6Chigh Monocytes in breast cancer and C26 colon carcinoma
Authors: Zare Fatemeh 
Published: January 2023

Abstract
Tumor microenvironment encompasses a wide variety of immune cells, which macrophages comprise the most dominant portion of them and thus are the major players in the connection between inflammation and cancer. These tumor-associated macrophages (TAMs) are derived from blood monocyte precursors and subsequently acquire distinct characteristics as a result of tumor micro-environmental cues. Monocytes are a heterogeneous population in the blood with an enormous plasticity whose fate and functions are dictated by the microenvironment. Therefore, the roles of specific Monocytes subsets in tumor progression and the molecular mechanisms for their impacts need to be elucidated. Ly6Chigh and Ly6Clow are two main different types of murine monocytes subsets that have been defined by distinct phenotypes and immunoregulatory functions. Recent data demonstrates that Ly6Chigh monocytes can recruit to inflammation loci while Ly6Clow monocytes are patrolling cells. We have developed a method to produce large number of Ly6Chigh monocytes in vitro. In our study we observed that, injection of these cells affects tumor progression in breast cancer and C26 colon carcinoma animal models. Activation of Ly6Clow monocytes by pro- or anti-inflammatory cytokines, results in displaying a genetic expression profile, corresponding to pro- or anti-inflammatory genes, respectively. Injection of pre- activated Ly6Clow monocytes toward pro- or anti-inflammatory polarization in C26 colon carcinoma showed that anti-inflammatory activated monocytes are more beneficial in delaying cancer cachexia. Increased knowledge of monocytes improves the chances to find therapies against a broad spectrum of diseases including cancer.
Foxp3 controls oxidative phosphorylation in regulatory T cells
Authors: Beier Ulf H , Angelin Alessia , Jiao Jing , Xiao Haiyan , Wang Liqing , Dahiya Satinder , Wells Andrew D , Wallace Douglas C , Hancock Wayne W 
Published: January 2023

Abstract
Many T cell subsets have distinct metabolic requirements. Activated CD4 helper and cytotoxic CD8 T cells require glycolysis for optimal function, whereas Foxp3+ T-regulatory (Treg) cells are thought to be dependent on oxidative phosphorylation. We questioned if Foxp3 is involved with re-programming T cell metabolism. We retrovirally transduced murine T cells with Foxp3 or empty vector (EV), and also cultured CD4+Foxp3− T cells from Foxp3YFPcre mice under polarizing conditions with TGFβ to form induced Tregs, using YFP to track Foxp3 expression. Our analysis of FACS-sorted YFP+ iTreg and YFP− non-iTreg showed that both iTreg and Foxp3-transduced T cells had significantly higher basal oxygen consumption rates than non-iTreg or EV transduced T cell controls (44.1±49% and 76.1±76.5%, respectively, p&lt;0.05, n=4), despite equal mitochondrial mass. Using Foxp3 ChIP-seq and microarray studies, we identified multiple binding sites of Foxp3 and Foxp3-dependent transcripts among key genes involved in control of oxidative phosphorylation as well as nuclear encoded electron transport chain genes. FACS-sorted YFP+ iTreg showed increased protein expression of electron transport chain complexes, especially complex I, compared to YFP− non-iTreg. We found that mice deficient in ND6, a mitochondrial encoded gene of complex I, have deficient Treg function. Furthermore, 50 nM rotenone, a complex I inhibitor, could selectively inhibit Treg suppressive function without affecting Tconv cell proliferation. The effects of Foxp3 on Treg metabolism may be physiological important to enable Tregs operating in low glucose environments such as the tumor microenvironment, and could offer an opportunity for therapeutic immune modulation.
Staphylococcal enterotoxin G and I: augmenting the T cell response to murine melanoma.
Authors: Knopick Peter Leo , Benedict Katherine C , Alvine Travis D , Nilles Matthew L , Terman David S , Bradley David S 
Published: January 2023

Abstract
Staphylococcal enterotoxins (SEs) have been shown to be effectual proteins which demonstrate anti-tumor activity. SEG and SEI, produced from the enterotoxin gene cluster (egc) of Staphylococcal aureus, activate T cells with Vβ specificity to elicit robust T cell proliferation, T helper cell 1 (TH1) and TH2 cytokine secretion, and nitric oxide dependent tumor lysis. Our data highlight the effects of SE stimulated T cells and the subsequent consequence on aggressive, metastatic cancer progression using B16-F10 murine melanoma model. Specifically, we explore the differences between major histocompatibility complex (MHC) and human leukocyte antigen (HLA) SE presentation to the T cells via the T cell receptor (TCR). Our data demonstrates increased survival of B16-F10 tumor bearing mice, C57BL/6 and DQ8 (HLA-DQA1*0301, HLA-DQB1*0302) transgenic mice, after irradiated B16-F10 vaccination and SE stimulation. Interestingly, SEG and SEI induce strong T cell proliferation yet do not induce neutralizing antibodies to the extent of classical SEs, SEA and SEB, nor induce autoimmune pathology. Our findings demonstrate that superantigen administration enhances lymphocytic tumor killing and suggest a potential role for SEG and SEI as potent immunotherapeutics for human cancer.
Inhibition of Tumor-Derived Semaphorin7A Decreases Tumor Progression in a Murine Model of Metastatic by modulating production angiogenic chemokines and immune infiltration
Authors: Garcia-Areas Ramon Antonio , Libreros Stephania , Simoes Michael , Gazaniga Nathalia , Schilling Kathy , Iragavarapu-Charyulu Vijaya 
Published: January 2023

Abstract
It is estimated that one in eight women will be diagnosed with breast cancer. Developing an understanding of the tumor microenvironment is critical for developing treatments for breast cancer patients. Poorly differentiated blood vessels can fashion an oxygen-deprived microenvironment that triggers the expression of transcription factor Hypoxia Inducible Factor alpha (HIF-1alpha) that in turn can up regulate genes mediating a pro-tumor effect. Our laboratory has discovered that mammary tumors express Semaphorin7a (SEMA7A), a HIF-1alpha inducible protein. Tumor-derived SEMA7A induces monocytes to secrete proangiogenic chemokines to enhance tumor growth. Decreasing tumor-derived SEMA7A limits tumor growth and the production of angiogenic CXCL-2/MIP-2 and VEGF-A by monocytes. Immune cells also express elevated levels of SEMA7A in tumors, however the role of stromal-derived SEMA7A in tumorigenesis is largely unknown. We hypothesized that SEMA7A may be a hypoxia-inducible factor and that inhibition may deter the effects of hypoxia on tumor and immune cells. Following hypoxic stimuli, WT monocytes increased production of CXCL2, VEGF-A and Chitinase-3-like protein1. However, SEMA7A null monocytes failed to respond to hypoxia, which may be attributed to an impaired MAPK signaling response. Monocytes from SEMA KO tumor bearing mice showed a decreased production of angiogenic molecules. More importantly, we found that SEMA7A KO 4T1 mammary tumor bearing mice showed decreased tumor growth and metastasis compared to WT. Collectively, we show a role for not only a tumor-derived, but also stromal-derived SEMA7A in hypoxia-mediated mammary tumor progression.
Host-protective anti-tumor immune responses induce immunoediting of indolent but not quiescent dormant tumor cells
Authors: Manjili Masoud H , Payne Kyle K , Keim Rebecca , Graham Laura , Idowu Michael , Wan Wen , Toor Amir , Wang Xiang-Yang Shawn , Bear Harry D 
Published: January 2023

Abstract
Two major barriers to cancer immunotherapy include tumor-induced immune suppression mediated by myeloid-derived suppressor cells (MDSCs), and poor immunogenicity of the tumor expressing self-antigens. To overcome these barriers, we used adoptive immunotherapy (AIT) by means of tumor-sensitized T cells and CD25+ NKT cells combined with Decitabine (Dec). Dec enhanced immunogenicity of the tumor, and the presence of CD25+ NKT cells rendered T cells resistant to remaining MDSCs. This combinatorial therapy significantly prolonged survival of animals bearing metastatic tumor cells. However, AIT eventually induced tumor immunoediting and subsequent tumor escape and progression. We hypothesized that conventional cancer therapeutics result in residual dormant tumor cells with a heterogeneous sensitivity to immunoediting; we therefore sought to identify the characteristics of dormant tumor cells that are resistant to immunoediting. We used Adriamycin (ADR) chemotherapy or radiation therapy (RT) which simultaneously induces tumor cell death and tumor dormancy. Resultant dormant cells became refractory to additional doses of ADR or RT, but they remained sensitive to tumor-reactive immune cells. Importantly, we discovered that dormant tumor cells contained indolent cells that expressed low levels of Ki67 (Ki67+/low) and quiescent cells that were Ki67 negative (Ki67−). Whereas the former were prone to tumor immunoediting and escape, the latter did not demonstrate immunoediting. Our results suggest that administration of immunotherapy during quiescent tumor dormancy could overcome tumor relapse and prevent disease progression to advanced stage cancer.
‘PD-1 related effector functions rely on the presence/absence of CD28 co-stimulatory molecule in Ag-specific CD8+ T cell clones isolated from melanoma patients’
Authors: Palermo Belinda , Franzese Ornella , Di Donna Cosmo , Panetta Mariangela , Gualtieri Novella , Soriani Antonella , Foddai Maria Laura , Santoni Angela , Nisticò Paola 
Published: January 2023

Abstract
The relationship between PD-1 expression and T-cell effector functions is still unclear, although crucial in the new era of immunotherapy targeting the PD-1/PDL-1 pathway. We have recently reported that Melan-A-specific CD8+ T-cells isolated from melanoma patients treated with combined chemo-immunotherapy (dacarbazine before peptide Melan-A/gp100-vaccination), show an enlarged T-cell repertoire, CD28− PD-1+AKT+ phenotype with high anti-tumor polyfunctionality sustained by ICOS (Franzese et al, OncoImmunology, in press). Herein, we have analyzed the gp100-specific CD8+ T-cell clones isolated from the same patients. Cells have been characterized for gp-100 specificity, and TCR beta-chain sequencing analysis evidenced that they possess an oligoclonal repertoire. The relationship among inhibitory receptors (PD-1, TIM-3 and LAG-3), co-stimulatory molecules (CD27 and CD28) and effector functions of T cells has been studied. Taking advantage from a battery of Melan-A- and gp100-specific T-cell clones, here we show that gp100-CD8+ T cells with a CD28+ PD-1+AKT+ phenotype are unable to kill gp100-expressing melanoma cells, differently from data obtained with Melan-A-specific clones showing a CD28− PD-1+ AKT+ phenotype, and able to lyse tumor cells with high efficiency. Studies are in progress to identify the biochemical pathways involved in the control of functionality of PD-1-expressing CD8+ T cells.