bluuebunny/crossref_metadata_2025_split huggingface dataset:
Select mucosa-associated intestinal commensal bacteria promote gut barrier repair by inducing IL-1b production
Authors: Wu Wan-Jung , Kim Myunghoo , Chang Lin-Chun , Assie Adrien , Saldana-Morales Fatima B , Ruiz Daniel Fernando Zegarra , Norwood Kendra , Samuel Buck , Diehl Gretchen E 
Published: January 2023

Abstract
Microbiota interactions with host tissue support proper intestinal functions. In diseases such as inflammatory bowel disease, microbial shift along with epithelial dysfunctions are found. Understanding how intestinal epithelial functions are regulated by distinct commensal bacteria is key to improving outcomes in such diseases. Here, we identified a mouse commensal E. coli isolate, GDAR2-2, that promotes intestinal barrier repair in mouse colitis models including Citrobacter rodentium infection and dextran sulfate sodium-induced colitis. In mice, protection after GDAR2-2 colonization depends on CX3CR1+ mononuclear phagocytes (MNPs), which induce expansion of IL-22-secreting type 3 innate lymphoid cells. We detect upregulation of markers of transit amplifying cells, proliferation of which is downstream of IL-22 signaling. Protection is lost if IL-22 is blocked, indicating IL-22 driven epithelial regeneration is downstream of GDAR2-2 colonization. By co-culturing bone marrow derived macrophages with live GDAR2-2, we found GDAR2-2 promotes IL-1b production and the in vivo protection was lost after blockade of IL-1b. We further identified a subset of human commensal E. coli isolates that similarly induce CX3CR1+ MNP expansion and IL-1b mediated protection from C. rodentium infection in mice. This study reveals an unexpected role for IL-1b that promotes intestinal barrier repair and is induced by select commensal bacteria.
Supported by NIH (AI125264, P30DK056338)
Crosstalk between skin homing innate T cells and epithelial cells via cholesterol byproduct messengers is required for tissue immunity
Authors: Frascoli Michela , Ferraj Enxhi , Miu Bing , Esposito Kelsey , Spidale Nicholas , Malin Justin , Cowan Jennifer , Bhandoola Avinash , Kang Joonsoo , Reboldi Andrea 
Published: January 2023

Abstract
Innate T cells and innate lymphoid cells in barrier tissues are essential for both tissue fitness and immunity against pathogens. γδTCR+ lymphocytes that secrete IL-17 (Tγδ17) localize to dermis and are critical regulators of skin immune responses. Despite their functional importance, how Tγδ17 cells mediate their unique function in the skin is largely unknown. Tγδ17 cells express the two prototypic G-protein coupled receptors (GPCRs) CCR6 and GPR183 (EBI2): mice lacking both receptors had significantly diminished dermal Tγδ17 cells and were resistant to psoriasis induction. This was due to a block in Tγδ17 cell maturation in the thymus of Ccr6−/− Gpr183−/− double knock-out mice. EBI2 recognizes oxysterols generated by the cholesterol hydroxylase CH25H and functional oxysterols were detected in both the thymus and skin. Analysis of Ch25h-reporter mice showed that interfollicular epithelial cells (IFEs) and a subset of medullary thymic epithelial cells (mTEC) are the depot for oxysterols in skin and thymus respectively. Ch25h+ TECs were also identified by unbiased single cell transcriptome analyses. These results demonstrate that developing Tγδ17 cells must be conditioned by sensing cholesterol byproducts synthesized by a discrete subset of mTECs to position in specific oxysterol rich niches in the skin. Moreover, in the skin, dietary cholesterol increased tissue oxysterol concentration and modulated homeostatic and pathogenic effector function of Tγδ17 cells in a EBI2 dependent fashion. Given that oxysterols can be regulated by infection and inflammation, this sensory circuit directed by cholesterol is predicted to program skin innate T cells’ ability to rapidly survey for perturbations in the skin.
Supported by grant from NIH R21AI143225.
The transcription factor LRF promotes Integrin β7 expression by and gut homing of CD8αα intraepithelial lymphocyte precursors
Authors: Nie Jia , Bohrer Andrea , Chopp Laura , Chen Ting , Balmaceno-Criss Mariah , Ciucci Thomas , Xiao Qi , Kelly Michael , McGavern Dorian , Belkaid Yasmine , Bosselut Remy 
Published: January 2023

Abstract
TCRαβ+ CD8α+ CD8β− intraepithelial lymphocytes (CD8αα IEL) differentiate from thymic IEL precursors (IELp) and contribute to gut homeostasis. However, their development remains poorly understood. Here we show that the zinc finger transcription factor LRF, encoded by Zbtb7a, is highly expressed in both CD8αα+ IELs and in IELp and serves in a cell-intrinsic manner to promote IEL differentiation. Mice genetically deficient for LRF (Cd4-Cre Zbtb7afl/fl) lack CD8αα+ IELs, contrasting with largely conserved numbers of conventional CD8αβ+ T cells in the thymus and the secondary lymphoid organs. Unlike their wild-type counterparts, LRF-deficient IELp failed to prevent colitis caused by adoptive transfer of CD4+ T cells in T cell-deficient mice. LRF disruption affects neither the development of thymic IELp, nor their in vitro expansion or differentiation in response to IL-15. However, Cd4-Cre Zbtb7afl/fl mice accumulate CD8αα+ T cells in the spleen, unlike wild-type controls, suggesting impaired migration of IELp to the gut. Single-cell RNA sequencing found LRF necessary for the expression of genes characteristic of the most mature IELp, including Itgb7, encoding the β7 subunit of α4β7. Chromatin immunoprecipitation and gene regulatory network analyses both defined Itgb7 as an LRF target. Our study identifies LRF as an essential transcriptional regulator of IELp maturation in the thymus and subsequent migration to the intestinal epithelium.
Potential Clinical Applicability of The PHENotype SIMulator for In Silico Viral Co-Infection Studies in COVID-19
Authors: Maria Naomi I , Rapicavoli Rosaria Valentina , Alaimo Salvatore , Bischof Evelyne , Pulvirenti Alfredo , Mishra Bud , Duits Ashley John , Ferro Alfredo 
Published: January 2023

Abstract
The PHENotype SIMulator, is a systems biology tool, which leverages available transcriptomic and proteomic databases to model of SARS-CoV-2 host-infection in silico. PHENSIM can determine the viral effects on cellular host-immune responses, which we recently applied to in silico drug repurposing for COVID-19. There is a clear importance of previously imprinted viral infections on the host-immune response against SARS-CoV2. In this study we explore the potential clinical applicability of PHENSIM in addressing co-infection of SARS-CoV2 (SCoV2) and human rhinovirus (HRV), or SCoV2 and Influenza A Virus (IAV).
We leveraged PHENSIM to simulate HRV-infection of A549 lung alveolar cells at 24hours in silico, yielding comparable cellular transcriptomic signatures as previously published for in vitro HRV-infection, including antiviral and inflammatory gene transcriptomics. Next, we simulated viral co-infection of HRV/SCoV2 or IAV/SCoV2 using PHENSIM, and assessed co-infection effects in silico.
Similar to recent in vitro studies, our in silico results indicated HRV-infection prior to SCoV2 exposure induced ISG responses and downregulated SCoV2 transcriptomic activity. Further analysis revealed several key SCoV2 affected pathways, including IFN Type-I & -III and MHC-II pathways, to be negatively affected by HRV-infection. In contrast, co-infection with IAV and SCoV2 resulted in overall increased SCoV2 transcriptomic activity.
Our PHENSIM results confirm HRV-imprinted downmodulation of SARS-CoV2 activity and the importance of timely IFN pathway activation for effective immune response and viral clearance. Identified anti-correlating pathways are of interest for therapeutic targeting and effective drug development.
N.I.M. was funded in part by a fellowship award from the Netherlands-Caribbean Foundation for Clinical Higher Education (NASKHO). S.A., A.F. and A.P. have been partially supported by the MIUR PON research project BILIGeCT “Liquid Biopsies for Cancer Clinical Management”. National Cancer Institute Physical Sciences-Oncology Center Grant U54 CA193313-01 (to B.M.), and US Army grant W911NF1810427 (to B.M.)
Semi and fully automated immunostaining sample preparation platforms improve live leukocyte recovery, reproducibility, and flow cytometry data quality
Authors: Feld Geoffrey K , Lye Melvin , Eberle Christoph , Wang Ann , Ke Chyan Ying 
Published: January 2023

Abstract
Limited innovation in automated cell and organelle sample preparation methodology limits the effectiveness of modern analytical methods, such as single-cell ‘omics, flow and mass cytometry. These techniques traditionally rely on manual centrifugation-based protocols for cell washing and suspension preparation, hampering researchers’ access to the reproducibility and scalability benefits of automation. We have developed a suite of cell suspension preparation systems that enable semi and full automation of cell washing protocols. These Laminar Wash™ technologies robustly, gently, and efficiently remove debris, dead cells, and unbound reagent using laminar flow and liquid handling robotics, rather than turbulent and harsh pelleting-plus-pipetting methods. Adaptation of standard protocols to Laminar Wash automation typically improves repetitive immunostaining processes and workflows, in terms of reduced hands-on time and inter- and intra-operator variability. We demonstrate the superior live cell retention and reproducibility of Laminar Wash over centrifugation in processing murine and humanized mouse peripheral blood mononuclear cells (PBMCs) and tumor infiltrating lymphocytes (TILs) for flow cytometry. Furthermore, we show how Laminar Wash improves flow cytometry data quality, in terms of debris removal and separation of immune cell subsets for both PBMCs and TILs. Overall, these results show how Laminar Wash methodology assists in standardizing sample preparation for cytometric analysis, an important and unmet need in cancer immunotherapy discovery and manufacturing workflows.
Barcode Enabled Antigen Mapping (BEAM) enables next-generation systems immunology analysis of the post-COVID-19 immune landscape
Authors: Stubbington Michael J T , Adams Bruce , Reyes Daniel , Royall Ariel , Song Maengseok , Marrache Sean , Shahi Payam , Tsai FuNien , Finnegan Peter , Vollbrecht Thomas , Khadilkar Tanmayee , Jaffe David , Ramenani Ravi , McDonnell Wyatt 
Published: January 2023

Abstract
A more complete understanding of immune responses to disease requires consideration of multiple different cell types across both the innate and adaptive branches of the immune system along with the detection of many different analytes.
We used Barcode Enabled Antigen Mapping (BEAM) and Immune Profiling technology to perform simultaneous multimodal profiling at single cell resolution in hundreds of thousands of peripheral blood mononuclear cells (PBMCs) from a human donor following recovery from COVID-19. In addition to measuring gene and protein expression, we generated full-length, paired sequences of the rearranged T- and B-cell receptors while also screening their specificity for a wide range of antigens from SARS-CoV-2 and other viral pathogens.
These data provide insights into the entirety of the immune landscape after recovery from acute viral disease. The scale and throughput of our experiments gave us high-resolution data from all cell types from the innate and adaptive immune systems.
We identified antigen-specific clones of both B and T lymphocytes, with the high cellular throughput enabling detection of rare clones. Analysis of all PBMC cell types allowed us to place these antigen-specific clones within the overall transcriptional landscape of the post-viral immune system.
Experiments such as these will underpin new systems immunology approaches and will continue to reveal the complex interplay between the components of the immune system. We envisage that these methods will be valuable in the analysis of the immune response to vaccination, infectious disease, cancer, allergy, autoimmune conditions, and ageing that can potentially lead to the development of novel diagnostic and therapeutic approaches.
Development of a point-of-care immunoassay for Ebola Virus Disease through the detection of Ebola virus soluble glycoprotein
Authors: Green Heather R , Hau Derrick , Pandit Sujata , Arias-Umana Jose , DeMers Haley , Chung Chelsea , Foster Abigail , Carrasco Lesly , Gates-Hollingsworth Marcellene A , AuCoin David 
Published: January 2023

Abstract
Ebola Virus Disease (EVD) is a deadly infectious disease that is caused by an infection with Ebola virus (EBOV). EVD is one of the deadliest viral diseases with a human case fatality rate of up to 90%. The largest outbreak to date was the 2013–2016 West African outbreak in which Zaire ebolavirus (ZEBOV) was responsible for over 11,000 deaths. Transmission of the virus can occur through contact with an infected animal or human. Early detection is imperative to prevent the spread of disease and reduce the risk of a potential epidemic by isolating known infected patients. The current gold standard for diagnosing EVD is polymerase chain reaction assays which requires complex laboratory equipment and highly trained personnel that is not easily accessible in resource-limited areas. There is a great need for an EBOV rapid diagnostic test that can be implemented at the point-of-care (POC). Multiple lateral flow immunoassays (LFIs) have been developed for this need and have received emergency use authorization. Many of these tests rely on the detection of Ebola virus VP40 antigen, however, soluble glycoprotein (sGP) has the potential to be a better biomarker for EVD rapid detection as it is abundant in the blood during an infection. The goal of this study was to produce an EBOV sGP LFI prototype. A library of seventeen monoclonal antibodies reactive to EBOV sGP were produced and characterized via enzyme-linked immunosorbent assay, surface plasmon resonance, and Western immunoblotting. From this mAb library, LFI prototypes were developed and assessed for the potential use as a rapid POC diagnostic for EVD.
Supports by the National Institute of Allergy and Infectious Diseases under grant 1R41AI149940
Precision killing of T cells via targeting of T cell receptors using two novel chimeric antigen receptor designs
Authors: Francis Prashanth , Yarnell Michael , Burchill Matthew , Fry Terry 
Published: January 2023

Abstract
Pathologic T cells drive T cell leukemia, solid organ transplant rejection, and many autoimmune diseases. Currently approved treatments have limited ability to target pathogenic vs non-pathogenic T cells. While pan-T cell treatments can be effective, they have significant risks such as infection and malignancy. Chimeric antigen receptors (CAR) are synthetic constructs that retarget T cells to a specific antigen of interest; we hypothesized that we could use this technology for targeted killing of T cells.
We developed two novel CAR designs which target T cells via their T cell receptor (TCR). We opted to target OT1 T cells, a model system with a known antigenic epitope. The anti-Vβ5 CAR is a second-generation CAR with a traditional extracellular scFv domain that targets Vβ5 of the OT1 TCR. The H2Kb bait CAR instead has an extracellular H2Kb complex loaded with the SIINFEKL cognate epitope. Both anti-Vβ5 and H2Kb bait CAR T cells demonstrate degranulation, activation, and proliferation upon binding OT1 T cells. In vitro co-culture with OT1 T cells results in internalization of the OT1 TCR and specific killing of OT1 T cells. Interestingly, the changes induced by the H2Kb bait CAR were delayed relative to the anti-Vβ5 CAR. In vivo experiments show both CAR designs kill adoptively transferred OT1 T cells without significant effect on the other T cell populations.
In conclusion, we report the development of two novel CAR designs which allow for the targeted killing of T cells via their T cell receptor. While the anti-Vβ5 CAR T cells generated a more rapid response, the H2Kb bait CAR offers the promise of more precisely targeting T cells. This work has the potential to transform the treatment of conditions where removal of pathogenic T cells is critical for cure.
Supported by NIH HL152756
The role of autophagy in thymic stromal cell maintenance with age
Authors: Emtage Simon Nicholas Bruce , Semwal Manpreet , Wedemeyer Sarah , Xiao Yangming , Griffith Ann 
Published: January 2023

Abstract
T lymphocytes develop in the thymus, where mutually inductive signaling between lymphoid progenitors and thymic stromal cells (TSCs) directs the progenitors along a well-characterized program of differentiation. However, the biology of the TSCs comprising the lymphopoietic thymic microenvironment remains relatively under-characterized because stromal cells are rare and difficult to isolate. TSCs exhibit high basal levels of autophagy at the steady state, which is critical for self-antigen presentation and T cell selection. The mechanisms governing high basal autophagy in TSCs are unknown, however autophagy is induced by many stressors, including high H202 levels. Using a deconvolution technique to study gene expression essentially in situ, we previously identified a deficiency in the H202 quenching enzyme catalase (CAT) in TSCs, and found that CAT deficiency results in high H202 levels in this population, eventually leading to thymic atrophy. Our current studies address the possibility that, in addition to a role in self-antigen presentation, autophagy may also mitigate thymic atrophy through its role in removing organelle damaged by H202. Our preliminary studies suggest that increased basal autophagy in Beclin 1 knock-in (Becn1F121A/F121A) mice promotes thymus function during aging. Supported by N.I.H. grant R01AI121367
Augmenting oxidation of branched-chain amino acids (BCAAs) treats murine chronic Graft-Versus-Host Disease (cGVHD)
Authors: Jin Sujeong , Wagers Sara Bolivar , Walker Kirsti L , Mirek Emily T , Sage Peter T , Arany Zoltan , Anthony Tracy G , Blazar Bruce R 
Published: January 2023

Abstract
Aberrant immune responses, such as high Tfollicular helper (Tfh) and germinal center B cells (GCB) in cGVHD inducing antibody (Ab) secretion with tissue deposition and fibrosis, require distinct metabolic reprogramming to sustain pathogenesis. Leucine, isoleucine, and valine are essential BCAAs that signal via mTORC1 to support glycolysis and protein synthesis. Alternatively, BCAAs can be oxidized to metabolites that directly enter the tricarboxylic acid cycle or become substrates for gluconeogenesis and ketogenesis. Branched chain ketoacid dehydrogenase kinase (BDK) is a negative regulator of BCAA metabolism, decreasing downstream oxidation and increasing mTORC1 and glycolysis. We sought to determine whether increasing BCAA oxidation could be exploited to inhibit cGVHD. BDK is inhibitable by 3,6-Dichlorobenzo[β] thiophene-2-carboxylic acid (BT2), increasing BCAA oxidation and decreasing T effector (Teff) activation. In a multiorgan cGVHD model with bronchiolitis obliterans, mice that received BDK knockout vs wildtype donor T cells had improved survival and pulmonary function with decreased GCB frequencies (p-value 0.005) and a trend toward decreased Tfh/Tfollicular regulatory ratios. An in vitro assay measuring Tfh-mediated B cell Ab production showed that BT2 downregulates IgG class switching, which is key for cGVHD pathogenesis. BT2-treated T effectors but not T regulatory cells (Treg) exhibited increased oxidative phosphorylation (OXPHOS). Therefore, limiting BCAAs inhibits Teff switch from a highly glycolytic state to OXPHOS. In contrast, BCAAs are not required for Treg energy production or survival. These data suggest that augmenting BCAA oxidation could be a new therapeutic approach for treating cGVHD.
Supported by NIH P01 AI056299
Leveraging CAR T cells to Achieve Desensitization and Enable Transplantation
Authors: Markmann Caroline Anna , Zheng Zheng , Yu Ming , Rostami Susan , Wang Wei , Ochoa Trini , Parvathaneni Kalpana , Xu Xiaoming , Scholler John , Zhang Qian , Posey Avery , Allman David , Milone Michael , Arruda Valder , Jones Ben Samelson , Naji Ali , Bhoj Vijay 
Published: January 2023

Abstract
Pre-existing allo-antibodies (allo-Abs), that preclude transplant due to the risk of hyperacute rejection, lead to prolonged wait times and high mortality rates. Current desensitization approaches are ineffective as they do not adequately deplete allo-specific B cells and plasma cells (PCs). We hypothesize that stringent depletion of these cells is required to eliminate pre-existing allo-Abs. We leverage the exquisite ability of CAR T cells to eliminate target cells to desensitize transplant candidates. We constructed CARs targeting murine CD19 or BCMA, which cover the entire B cell-PC continuum. We first evaluated the function of CAR T cells against B cells and PCs in vitro. C57BL/6 mice were sensitized with BALB/c skin grafts. After skin rejection, sensitized mice received total body irradiation followed by treatment with either control T cells, CART-19 T cells, or a combination of CART-19 and CART-BCMA T cells (combo-CART). Allo-Abs, total Ig, and B cells were measured over 13 weeks. Functional desensitization was then assessed by induction of diabetes followed by BALB/c-derived islet cell transplant and glucose were measured to assess graft survival. CD19- and BCMA-targeted CARs effectively depleted primary B cells and PCs in vitro and in vivo. Control and CART-19 T cells were ineffective at desensitizing mice, but combo-CART treatment resulted in significant decrease of allo-Abs. Islet cell grafts succumbed to hyperacute rejection in 80% of control and CART-19 treated mice. However, combo-CART treatment resulted in prolonged graft survival in all mice (mean 35 days, range 16–60). Thus, CAR T cells targeting B cell and PC antigens represent a promising approach to desensitization and could enable lifesaving transplantation.
Class Switching is Required for Antigen-Dependent B cell Anti-Tumor Activity
Authors: Guo Zihan , Claudio Natalie , Ziglari Tahereh , Pucci Ferdinando 
Published: January 2023

Abstract
Recent clinical studies demonstrated a positive correlation between B cell parameters and response to immune checkpoint blockade therapy. However, the potential mechanisms underlying B cell anti-tumor activities are still unclear. A better understanding of B cell-mediated immune responses in cancer will highlight novel vantage points to exploit therapeutically. To this end, we engineered tumor cells to express the B cell model antigen hen egg lysozyme (HEL). Adoptive transfer of CD45.1+ HEL-specific B cells (SWHEL B cells) into wild-type mice bearing HEL+ tumors significantly delayed tumor growth. SWHEL B cells from tumor-draining lymph nodes showed higher levels of MHCII expression, germinal center (GC) formation and class switch rate than non-tumor specific B cells. Of note, MD4 B cells, which recognize HEL but cannot class switch, were unable to control tumor growth, suggesting that immunoglobulin class M are not required for B cell anti-tumor activities. Accordingly, depletion of CD4 T cells (which are required for class switch) in mice bearing HEL+ tumors reverted the anti-tumor activity of SWHEL B cells. GC SWHEL B cells class switched to immunoglobulin G1 with a frequency between 20 and 80%, and resulted in a 10-fold increase of plasmablast (CD19+CD138+) and memory B cell (CD19+IgD-CD38+CCR6+) generation, as compared to non-tumor specific B cells. Collectively, these data point to a role for class-switched B cells and CD4 T cells in tumor immunosurveillance. Future studies will assess the ability of tumor antigen-specific B cells in priming naïve CD4 T cells and the role of other immunoglobulin classes in tumor control and escape.
Supported by V Foundation for Cancer Research V2019-012